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Zhang W, Young JI, Gomez L, Schmidt MA, Lukacsovich D, Varma A, Chen XS, Kunkle B, Martin ER, Wang L. Critical evaluation of the reliability of DNA methylation probes on the Illumina MethylationEPIC v1.0 BeadChip microarrays. Epigenetics 2024; 19:2333660. [PMID: 38564759 PMCID: PMC10989698 DOI: 10.1080/15592294.2024.2333660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 03/18/2024] [Indexed: 04/04/2024] Open
Abstract
DNA methylation (DNAm) plays a crucial role in a number of complex diseases. However, the reliability of DNAm levels measured using Illumina arrays varies across different probes. Previous research primarily assessed probe reliability by comparing duplicate samples between the 450k-450k or 450k-EPIC platforms, with limited investigations on Illumina EPIC v1.0 arrays. We conducted a comprehensive assessment of the EPIC v1.0 array probe reliability using 69 blood DNA samples, each measured twice, generated by the Alzheimer's Disease Neuroimaging Initiative study. We observed higher reliability in probes with average methylation beta values of 0.2 to 0.8, and lower reliability in type I probes or those within the promoter and CpG island regions. Importantly, we found that probe reliability has significant implications in the analyses of Epigenome-wide Association Studies (EWAS). Higher reliability is associated with more consistent effect sizes in different studies, the identification of differentially methylated regions (DMRs) and methylation quantitative trait locus (mQTLs), and significant correlations with downstream gene expression. Moreover, blood DNAm measurements obtained from probes with higher reliability are more likely to show concordance with brain DNAm measurements. Our findings, which provide crucial reliability information for probes on the EPIC v1.0 array, will serve as a valuable resource for future DNAm studies.
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Affiliation(s)
- Wei Zhang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Juan I Young
- Dr. John T MacDonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
| | - Lissette Gomez
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
| | - Michael A Schmidt
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
| | - David Lukacsovich
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Achintya Varma
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
| | - X Steven Chen
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Brian Kunkle
- Dr. John T MacDonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
| | - Eden R Martin
- Dr. John T MacDonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
| | - Lily Wang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, USA
- Dr. John T MacDonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL, USA
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Huang JJ, Rodriguez DA, Slifer SH, Martin ER, Levitt RC, Galor A. Genome Wide Association Study of Neuropathic Ocular Pain. Ophthalmol Sci 2024; 4:100384. [PMID: 37868788 PMCID: PMC10587615 DOI: 10.1016/j.xops.2023.100384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/02/2023] [Accepted: 08/07/2023] [Indexed: 10/24/2023]
Abstract
Purpose To conduct a genome-wide association study (GWAS) of individuals with neuropathic ocular pain (NOP) symptoms to identify genomic variants that may predispose to NOP development. Design Prospective study of individuals with NOP. Participants Three hundred twenty-nine patients recruited from the Miami Veterans Affairs eye clinic. Methods The Neuropathic Pain Symptom Inventory modified for the eye (NPSI-Eye) was completed to calculate a NPSI-Eye-Sub-Score (summed ratings of burning and wind sensitivity) as an indicator of NOP severity. A GWAS was performed for the NPSI-Eye-Sub-Score with a significance threshold of P < 5 × 10-8. A gene-based analysis was performed using the multimarker analysis of genomic annotation software (in the functional mapping and annotation of GWAS online platform). The 13 865 778 single nucleotide polymorphisms (SNPs) from our GWAS analysis were mapped to 10 834 protein coding genes, and significant genes were run through gene set enrichment analysis. Main Outcome Measures Identification of SNPs and protein products that may be associated with the development of NOP. Results One hundred seventy-one SNPs reached a threshold of P < 10-5, of which 10 SNPs reached the suggestive level of significance of P < 5 × 10-7 and 1 SNP met our genome-wide significance threshold of P < 5 × 10-8. This lead SNP, rs140293404 (P = 1.23 × 10-8), is an intronic variant found within gene ENSG00000287251 coding for transcript ENST00000662732.1. Rs140293404 is in linkage disequilibrium with exon variant rs7926353 (r2 > 0.8) within ENSG00000279046 coding for transcript ENST00000624288.1. The most significant genes from gene-based tests were matrix metalloproteinase-19 (MMP19) (P = 1.12 × 10-5), zinc finger RNA-binding motif and serine/arginine rich-1 (ZRSR1) (P = 1.48 × 10-4), CTC-487M23.8 (P = 1.79 × 10-4), receptor expression-enhancing protein-5 (REEP5) (P = 2.36 × 10-4), and signal recognition particle-19 (SRP19) (P = 2.56 × 10-4). From gene set enrichment analysis, the sensory perception (false discovery rate = 6.57 × 10-3) and olfactory signaling (false discovery rate = 1.63 × 10-2) pathways were enriched with the most significant genes. Conclusions Our GWAS revealed genes with protein products that may impact sensory perception, lending biological plausibility to a role for SNPs identified by our GWAS in the development of NOP. A better understanding of the biological relevance of these genes and pathways in the pathophysiology associated with NOP may facilitate future novel mechanism-based treatments. Financial Disclosures Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.
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Affiliation(s)
- Jaxon J. Huang
- Bascom Palmer Eye Institute, University of Miami, Miami, Florida
- Surgical and Research Services, Miami Veterans Administration Medical Center, Miami, Florida
| | | | - Susan H. Slifer
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
| | - Eden R. Martin
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
- John T. MacDonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida
| | - Roy C. Levitt
- Bascom Palmer Eye Institute, University of Miami, Miami, Florida
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
- John T. MacDonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida
- Department of Anesthesiology, Perioperative Medicine and Pain Management, University of Miami Miller School of Medicine, Miami, Florida
| | - Anat Galor
- Bascom Palmer Eye Institute, University of Miami, Miami, Florida
- Surgical and Research Services, Miami Veterans Administration Medical Center, Miami, Florida
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Eissman JM, Archer DB, Mukherjee S, Lee ML, Choi S, Scollard P, Trittschuh EH, Mez JB, Bush WS, Kunkle BW, Naj AC, Gifford KA, Cuccaro ML, Cruchaga C, Pericak‐Vance MA, Farrer LA, Wang L, Schellenberg GD, Mayeux RP, Haines JL, Jefferson AL, Kukull WA, Keene CD, Saykin AJ, Thompson PM, Martin ER, Bennett DA, Barnes LL, Schneider JA, Crane PK, Hohman TJ, Dumitrescu L. Sex-specific genetic architecture of late-life memory performance. Alzheimers Dement 2024; 20:1250-1267. [PMID: 37984853 PMCID: PMC10917043 DOI: 10.1002/alz.13507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 08/08/2023] [Accepted: 09/07/2023] [Indexed: 11/22/2023]
Abstract
BACKGROUND Women demonstrate a memory advantage when cognitively healthy yet lose this advantage to men in Alzheimer's disease. However, the genetic underpinnings of this sex difference in memory performance remain unclear. METHODS We conducted the largest sex-aware genetic study on late-life memory to date (Nmales = 11,942; Nfemales = 15,641). Leveraging harmonized memory composite scores from four cohorts of cognitive aging and AD, we performed sex-stratified and sex-interaction genome-wide association studies in 24,216 non-Hispanic White and 3367 non-Hispanic Black participants. RESULTS We identified three sex-specific loci (rs67099044-CBLN2, rs719070-SCHIP1/IQCJ-SCHIP), including an X-chromosome locus (rs5935633-EGL6/TCEANC/OFD1), that associated with memory. Additionally, we identified heparan sulfate signaling as a sex-specific pathway and found sex-specific genetic correlations between memory and cardiovascular, immune, and education traits. DISCUSSION This study showed memory is highly and comparably heritable across sexes, as well as highlighted novel sex-specific genes, pathways, and genetic correlations that related to late-life memory. HIGHLIGHTS Demonstrated the heritable component of late-life memory is similar across sexes. Identified two genetic loci with a sex-interaction with baseline memory. Identified an X-chromosome locus associated with memory decline in females. Highlighted sex-specific candidate genes and pathways associated with memory. Revealed sex-specific shared genetic architecture between memory and complex traits.
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Archer DB, Eissman JM, Mukherjee S, Lee ML, Choi S, Scollard P, Trittschuh EH, Mez JB, Bush WS, Kunkle BW, Naj AC, Gifford KA, Cuccaro ML, Pericak‐Vance MA, Farrer LA, Wang L, Schellenberg GD, Mayeux RP, Haines JL, Jefferson AL, Kukull WA, Keene CD, Saykin AJ, Thompson PM, Martin ER, Bennett DA, Barnes LL, Schneider JA, Crane PK, Dumitrescu L, Hohman TJ. Longitudinal change in memory performance as a strong endophenotype for Alzheimer's disease. Alzheimers Dement 2024; 20:1268-1283. [PMID: 37985223 PMCID: PMC10896586 DOI: 10.1002/alz.13508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 11/22/2023]
Abstract
INTRODUCTION Although large-scale genome-wide association studies (GWAS) have been conducted on AD, few have been conducted on continuous measures of memory performance and memory decline. METHODS We conducted a cross-ancestry GWAS on memory performance (in 27,633 participants) and memory decline (in 22,365 participants; 129,201 observations) by leveraging harmonized cognitive data from four aging cohorts. RESULTS We found high heritability for two ancestry backgrounds. Further, we found a novel ancestry locus for memory decline on chromosome 4 (rs6848524) and three loci in the non-Hispanic Black ancestry group for memory performance on chromosomes 2 (rs111471504), 7 (rs4142249), and 15 (rs74381744). In our gene-level analysis, we found novel genes for memory decline on chromosomes 1 (SLC25A44), 11 (BSX), and 15 (DPP8). Memory performance and memory decline shared genetic architecture with AD-related traits, neuropsychiatric traits, and autoimmune traits. DISCUSSION We discovered several novel loci, genes, and genetic correlations associated with late-life memory performance and decline. HIGHLIGHTS Late-life memory has high heritability that is similar across ancestries. We discovered four novel variants associated with late-life memory. We identified four novel genes associated with late-life memory. Late-life memory shares genetic architecture with psychiatric/autoimmune traits.
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Zhang X, Gomez L, Below JE, Naj AC, Martin ER, Kunkle BW, Bush WS. An X Chromosome Transcriptome Wide Association Study Implicates ARMCX6 in Alzheimer's Disease. J Alzheimers Dis 2024; 98:1053-1067. [PMID: 38489177 DOI: 10.3233/jad-231075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2024]
Abstract
Background The X chromosome is often omitted in disease association studies despite containing thousands of genes that may provide insight into well-known sex differences in the risk of Alzheimer's disease (AD). Objective To model the expression of X chromosome genes and evaluate their impact on AD risk in a sex-stratified manner. Methods Using elastic net, we evaluated multiple modeling strategies in a set of 175 whole blood samples and 126 brain cortex samples, with whole genome sequencing and RNA-seq data. SNPs (MAF > 0.05) within the cis-regulatory window were used to train tissue-specific models of each gene. We apply the best models in both tissues to sex-stratified summary statistics from a meta-analysis of Alzheimer's Disease Genetics Consortium (ADGC) studies to identify AD-related genes on the X chromosome. Results Across different model parameters, sample sex, and tissue types, we modeled the expression of 217 genes (95 genes in blood and 135 genes in brain cortex). The average model R2 was 0.12 (range from 0.03 to 0.34). We also compared sex-stratified and sex-combined models on the X chromosome. We further investigated genes that escaped X chromosome inactivation (XCI) to determine if their genetic regulation patterns were distinct. We found ten genes associated with AD at p < 0.05, with only ARMCX6 in female brain cortex (p = 0.008) nearing the significance threshold after adjusting for multiple testing (α = 0.002). Conclusions We optimized the expression prediction of X chromosome genes, applied these models to sex-stratified AD GWAS summary statistics, and identified one putative AD risk gene, ARMCX6.
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Affiliation(s)
- Xueyi Zhang
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Lissette Gomez
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Jennifer E Below
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Adam C Naj
- Department of Biostatistics, Epidemiology, and Informatics, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Eden R Martin
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Brian W Kunkle
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - William S Bush
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
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Tejeda M, Farrell J, Zhu C, Wetzler L, Lunetta KL, Bush WS, Martin ER, Wang L, Schellenberg GD, Pericak‐Vance MA, Haines JL, Farrer LA, Sherva R. DNA from multiple viral species is associated with Alzheimer's disease risk. Alzheimers Dement 2024; 20:253-265. [PMID: 37578203 PMCID: PMC10840621 DOI: 10.1002/alz.13414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 06/22/2023] [Accepted: 07/10/2023] [Indexed: 08/15/2023]
Abstract
INTRODUCTION Multiple infectious agents, including viruses, bacteria, fungi, and protozoa, have been linked to Alzheimer's disease (AD) risk by independent lines of evidence. We explored this association by comparing the frequencies of viral species identified in a large sample of AD cases and controls. METHODS DNA sequence reads that did not align to the human genome in sequences were mapped to viral reference sequences, quantified, and then were tested for association with AD in whole exome sequences (WES) and whole genome sequences (WGS) datasets. RESULTS Several viruses were significant predictors of AD according to the machine learning classifiers. Subsequent regression analyses showed that herpes simplex type 1 (HSV-1) (odds ratio [OR] = 3.71, p = 8.03 × 10-4) and human papillomavirus 71 (HPV-71; OR = 3.56, p = 0.02), were significantly associated with AD after Bonferroni correction. The phylogenetic-related cluster of Herpesviridae was significantly associated with AD in several strata of the data (p < 0.01). DISCUSSION Our results support the hypothesis that viral infection, especially HSV-1, is associated with AD risk.
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Affiliation(s)
- Marlene Tejeda
- Departments of Medicine Biomedical GeneticsBoston University Chobanian & Avedisian School of MedicineBostonMassachusettsUSA
| | - John Farrell
- Departments of Medicine Biomedical GeneticsBoston University Chobanian & Avedisian School of MedicineBostonMassachusettsUSA
| | - Congcong Zhu
- Departments of Medicine Biomedical GeneticsBoston University Chobanian & Avedisian School of MedicineBostonMassachusettsUSA
| | - Lee Wetzler
- Departments of Medicine Infectious DiseaseBoston University Chobanian & Avedisian School of MedicineBostonMassachusettsUSA
- Departments of Medicine MicrobiologyBoston University Chobanian & Avedisian School of MedicineBostonMassachusettsUSA
| | - Kathryn L. Lunetta
- Departments of BiostatisticsBoston University School of Public HealthBostonMassachusettsUSA
| | - William S. Bush
- Department of Population & Quantitative Health SciencesCleveland Institute for Computational BiologyCase Western Reserve University School of MedicineClevelandOhioUSA
| | - Eden R. Martin
- John P. Hussman Institute for Human Genomics and Dr John T. MacDonald Foundation Department of Human GeneticsMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
| | - Li‐San Wang
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory MedicineUniversity of Pennsylvania Perelman School of MedicinePhiladelphiaPennsylvaniaUSA
| | - Gerard D. Schellenberg
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory MedicineUniversity of Pennsylvania Perelman School of MedicinePhiladelphiaPennsylvaniaUSA
| | - Margaret A. Pericak‐Vance
- John P. Hussman Institute for Human Genomics and Dr John T. MacDonald Foundation Department of Human GeneticsMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
| | - Jonathan L. Haines
- Department of Population & Quantitative Health SciencesCleveland Institute for Computational BiologyCase Western Reserve University School of MedicineClevelandOhioUSA
| | - Lindsay A. Farrer
- Departments of Medicine Biomedical GeneticsBoston University Chobanian & Avedisian School of MedicineBostonMassachusettsUSA
- Departments of BiostatisticsBoston University School of Public HealthBostonMassachusettsUSA
- Departments of Medicine Neurologyand Boston University Chobanian & Avedisian School of MedicineBostonMassachusettsUSA
- OphthalmologyBoston University Chobanian & Avedisian School of MedicineBostonMassachusettsUSA
- Departments of EpidemiologyBoston University School of Public HealthBostonMassachusettsUSA
| | - Richard Sherva
- Departments of Medicine Biomedical GeneticsBoston University Chobanian & Avedisian School of MedicineBostonMassachusettsUSA
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Lukacsovich D, O’Shea D, Huang H, Zhang W, Young JI, Steven Chen X, Dietrich ST, Kunkle B, Martin ER, Wang L. MIAMI-AD (Methylation in Aging and Methylation in AD): an integrative knowledgebase that facilitates explorations of DNA methylation across sex, aging, and Alzheimer's disease. medRxiv 2023:2023.12.04.23299412. [PMID: 38105943 PMCID: PMC10723513 DOI: 10.1101/2023.12.04.23299412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Alzheimer's disease (AD) is a common neurodegenerative disorder with a significant impact on aging populations. DNA methylation (DNAm) alterations have been implicated in both the aging processes and the development of AD. Given that AD affects more women than men, it is also important to explore DNAm changes that occur specifically in each sex. We created MIAMI-AD, a comprehensive knowledge base containing manually curated summary statistics from 97 published tables in 37 studies, all of which included at least 100 participants. MIAMI-AD enables easy browsing, querying, and downloading DNAm associations at multiple levels - at individual CpG, gene, genomic regions, or genome-wide, in one or multiple studies. Moreover, it also offers tools to perform integrative analyses, such as comparing DNAm associations across different phenotypes or tissues, as well as interactive visualizations. Using several use case examples, we demonstrated that MIAMI-AD facilitates our understanding of age-associated CpGs in AD and the sex-specific roles of DNAm in AD. This open-access resource is freely available to the research community, and all the underlying data can be downloaded. MIAMI-AD (https://miami-ad.org/) facilitates integrative explorations to better understand the interplay between DNAm across aging, sex, and AD.
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Affiliation(s)
- David Lukacsovich
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Deirdre O’Shea
- Department of Neurology, Comprehensive Center for Brain Health, University of Miami Miller School of Medicine, Boca Raton, FL, 33433
| | - Hanchen Huang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Wei Zhang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Juan I. Young
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - X. Steven Chen
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Sven-Thorsten Dietrich
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Brian Kunkle
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Eden R. Martin
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Lily Wang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
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Li D, Farrell JJ, Mez J, Martin ER, Bush WS, Ruiz A, Boada M, de Rojas I, Mayeux R, Haines JL, Vance MAP, Wang LS, Schellenberg GD, Lunetta KL, Farrer LA. Novel loci for Alzheimer's disease identified by a genome-wide association study in Ashkenazi Jews. Alzheimers Dement 2023; 19:5550-5562. [PMID: 37260021 PMCID: PMC10689571 DOI: 10.1002/alz.13117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 03/29/2023] [Accepted: 04/11/2023] [Indexed: 06/02/2023]
Abstract
INTRODUCTION Most Alzheimer's disease (AD) loci have been discovered in individuals with European ancestry (EA). METHODS We applied principal component analysis using Gaussian mixture models and an Ashkenazi Jewish (AJ) reference genome-wide association study (GWAS) data set to identify Ashkenazi Jews ascertained in GWAS (n = 42,682), whole genome sequencing (WGS, n = 16,815), and whole exome sequencing (WES, n = 20,504) data sets. The association of AD was tested genome wide (GW) in the GWAS and WGS data sets and exome wide (EW) in all three data sets (EW). Gene-based analyses were performed using aggregated rare variants. RESULTS In addition to apolipoprotein E (APOE), GW analyses (1355 cases and 1661 controls) revealed associations with TREM2 R47H (p = 9.66 × 10-9 ), rs541586606 near RAB3B (p = 5.01 × 10-8 ), and rs760573036 between SPOCK3 and ANXA10 (p = 6.32 × 10-8 ). In EW analyses (1504 cases and 2047 controls), study-wide significant association was observed with rs1003710 near SMAP2 (p = 1.91 × 10-7 ). A significant gene-based association was identified with GIPR (p = 7.34 × 10-7 ). DISCUSSION Our results highlight the efficacy of founder populations for AD genetic studies.
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Affiliation(s)
- Donghe Li
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, 72 East Concord Street, Boston, MA 02118, USA
| | - John J Farrell
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, 72 East Concord Street, Boston, MA 02118, USA
| | - Jesse Mez
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, 72 East Concord Street, Boston, MA 02118, USA
| | - Eden R. Martin
- Dr. John T. Macdonald Foundation, University of Miami, Miami, FL 33136, USA
- Department of Human Genetics, University of Miami, Miami, FL 33136, USA
| | - William S. Bush
- Department of Population & Quantitative Health Science and Cleveland Institute for Computational Biology, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106, USA
| | - Agustin Ruiz
- Research Center and Memory Clinic, ACE Alzheimer Center Barcelona, Universitat Internacional de Catalunya, Barcelona, Spain
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Mercè Boada
- Research Center and Memory Clinic, ACE Alzheimer Center Barcelona, Universitat Internacional de Catalunya, Barcelona, Spain
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Itziar de Rojas
- Research Center and Memory Clinic, ACE Alzheimer Center Barcelona, Universitat Internacional de Catalunya, Barcelona, Spain
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Richard Mayeux
- Taub Institute on Alzheimer's Disease and the Aging Brain, Gertrude H. Sergievsky Center Department of Neurology, Columbia University, 710 West 168th Street, New York, NY 10032, USA
| | - Jonathan L. Haines
- Department of Population & Quantitative Health Science and Cleveland Institute for Computational Biology, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106, USA
| | - Margaret A. Pericak Vance
- Dr. John T. Macdonald Foundation, University of Miami, Miami, FL 33136, USA
- Department of Human Genetics, University of Miami, Miami, FL 33136, USA
- Department of Neurology, University of Miami, Miami, FL 33136, USA
| | - Li-San Wang
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania, 3400 Spruce Street, Philadelphia, PA 19104, USA
| | - Gerard D. Schellenberg
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania, 3400 Spruce Street, Philadelphia, PA 19104, USA
| | - Kathryn L. Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Lindsay A. Farrer
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, 72 East Concord Street, Boston, MA 02118, USA
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, 72 East Concord Street, Boston, MA 02118, USA
- Department of Ophthalmology, Boston University Chobanian & Avedisian School of Medicine, 72 East Concord Street, Boston, MA 02118, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA 02118, USA
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Bai H, Naj AC, Benchek P, Dumitrescu L, Hohman T, Hamilton-Nelson K, Kallianpur AR, Griswold AJ, Vardarajan B, Martin ER, Beecham GW, Below JE, Schellenberg G, Mayeux R, Farrer L, Pericak-Vance MA, Haines JL, Bush WS. A haptoglobin (HP) structural variant alters the effect of APOE alleles on Alzheimer's disease. Alzheimers Dement 2023; 19:4886-4895. [PMID: 37051669 DOI: 10.1002/alz.13050] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 04/14/2023]
Abstract
BACKGROUND Haptoglobin (HP) is an antioxidant of apolipoprotein E (APOE), and previous reports have shown HP binds with APOE and amyloid beta (Aβ) to aid its clearance. A common structural variant of the HP gene distinguishes it into two alleles: HP1 and HP2. METHODS HP genotypes were imputed in 29 cohorts from the Alzheimer's Disease Genetics Consortium (N = 20,512). Associations between the HP polymorphism and Alzheimer's disease (AD) risk and age of onset through APOE interactions were investigated using regression models. RESULTS The HP polymorphism significantly impacts AD risk in European-descent individuals (and in meta-analysis with African-descent individuals) by modifying both the protective effect of APOE ε2 and the detrimental effect of APOE ε4. The effect is particularly significant among APOE ε4 carriers. DISCUSSION The effect modification of APOE by HP suggests adjustment and/or stratification by HP genotype is warranted when APOE risk is considered. Our findings also provided directions for further investigations on potential mechanisms behind this association.
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Affiliation(s)
- Haimeng Bai
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, USA
- Systems Biology and Bioinformatics, Department of Nutrition, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Adam C Naj
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Penelope Benchek
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Population & Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Logan Dumitrescu
- Vanderbilt Memory & Alzheimer's Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Timothy Hohman
- Vanderbilt Memory & Alzheimer's Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kara Hamilton-Nelson
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA
| | - Asha R Kallianpur
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
- Department of Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Anthony J Griswold
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA
| | - Badri Vardarajan
- Department of Neurology, The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, New York, USA
| | - Eden R Martin
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA
| | - Gary W Beecham
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA
| | - Jennifer E Below
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Gerard Schellenberg
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Richard Mayeux
- Department of Neurology, The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, New York, USA
| | - Lindsay Farrer
- Departments of Medicine (Biomedical Genetics), Neurology, Ophthalmology, Biostatistics, and Epidemiology, Boston University Schools of Medicine and Public Health, Boston, Massachusetts, USA
| | | | - Jonathan L Haines
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Population & Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - William S Bush
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Population & Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
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10
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Zhang W, Young JI, Gomez L, Schmidt MA, Lukacsovich D, Varma A, Chen XS, Kunkle B, Martin ER, Wang L. Critical evaluation of the reliability of DNA methylation probes on the Illumina MethylationEPIC BeadChip microarrays. Res Sq 2023:rs.3.rs-3068938. [PMID: 37461726 PMCID: PMC10350239 DOI: 10.21203/rs.3.rs-3068938/v2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
DNA methylation (DNAm) plays a crucial role in a number of complex diseases. However, the reliability of DNAm levels measured using Illumina arrays varies across different probes. Previous research primarily assessed probe reliability by comparing duplicate samples between the 450k-450k or 450k-EPIC platforms, with limited investigations on Illumina EPIC arrays. We conducted a comprehensive assessment of the EPIC array probe reliability using 138 duplicated blood DNAm samples generated by the Alzheimer's Disease Neuroimaging Initiative study. We introduced a novel statistical measure, the modified intraclass correlation, to better account for the disagreement in duplicate measurements. We observed higher reliability in probes with average methylation beta values of 0.2 to 0.8, and lower reliability in type I probes or those within the promoter and CpG island regions. Importantly, we found that probe reliability has significant implications in the analyses of Epigenome-wide Association Studies (EWAS). Higher reliability is associated with more consistent effect sizes in different studies, the identification of differentially methylated regions (DMRs) and methylation quantitative trait locus (mQTLs), and significant correlations with downstream gene expression. Moreover, blood DNAm measurements obtained from probes with higher reliability are more likely to show concordance with brain DNAm measurements. Our findings, which provide crucial reliable information for probes on the EPIC array, will serve as a valuable resource for future DNAm studies.
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Affiliation(s)
- Wei Zhang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Juan I. Young
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Lissette Gomez
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Michael A. Schmidt
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - David Lukacsovich
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Achintya Varma
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - X. Steven Chen
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Brian Kunkle
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Eden R. Martin
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Lily Wang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
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11
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Zhang W, Young JI, Gomez L, Schmidt MA, Lukacsovich D, Varma A, Chen XS, Kunkle B, Martin ER, Wang L. Critical evaluation of the reliability of DNA methylation probes on the Illumina MethylationEPIC BeadChip microarrays. Res Sq 2023:rs.3.rs-3068938. [PMID: 37461726 PMCID: PMC10350239 DOI: 10.21203/rs.3.rs-3068938/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
DNA methylation (DNAm) plays a crucial role in a number of complex diseases. However, the reliability of DNAm levels measured using Illumina arrays varies across different probes. Previous research primarily assessed probe reliability by comparing duplicate samples between the 450k-450k or 450k-EPIC platforms, with limited investigations on Illumina EPIC arrays. We conducted a comprehensive assessment of the EPIC array probe reliability using 138 duplicated blood DNAm samples generated by the Alzheimer's Disease Neuroimaging Initiative study. We introduced a novel statistical measure, the modified intraclass correlation, to better account for the disagreement in duplicate measurements. We observed higher reliability in probes with average methylation beta values of 0.2 to 0.8, and lower reliability in type I probes or those within the promoter and CpG island regions. Importantly, we found that probe reliability has significant implications in the analyses of Epigenome-wide Association Studies (EWAS). Higher reliability is associated with more consistent effect sizes in different studies, the identification of differentially methylated regions (DMRs) and methylation quantitative trait locus (mQTLs), and significant correlations with downstream gene expression. Moreover, blood DNAm measurements obtained from probes with higher reliability are more likely to show concordance with brain DNAm measurements. Our findings, which provide crucial reliable information for probes on the EPIC array, will serve as a valuable resource for future DNAm studies.
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Affiliation(s)
- Wei Zhang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Juan I. Young
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Lissette Gomez
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Michael A. Schmidt
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - David Lukacsovich
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Achintya Varma
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - X. Steven Chen
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Brian Kunkle
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Eden R. Martin
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Lily Wang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
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12
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Walters S, Contreras AG, Eissman JM, Mukherjee S, Lee ML, Choi SE, Scollard P, Trittschuh EH, Mez JB, Bush WS, Kunkle BW, Naj AC, Peterson A, Gifford KA, Cuccaro ML, Cruchaga C, Pericak-Vance MA, Farrer LA, Wang LS, Haines JL, Jefferson AL, Kukull WA, Keene CD, Saykin AJ, Thompson PM, Martin ER, Bennett DA, Barnes LL, Schneider JA, Crane PK, Hohman TJ, Dumitrescu L. Associations of Sex, Race, and Apolipoprotein E Alleles With Multiple Domains of Cognition Among Older Adults. JAMA Neurol 2023; 80:929-939. [PMID: 37459083 PMCID: PMC10352930 DOI: 10.1001/jamaneurol.2023.2169] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 04/15/2023] [Indexed: 07/20/2023]
Abstract
Importance Sex differences are established in associations between apolipoprotein E (APOE) ε4 and cognitive impairment in Alzheimer disease (AD). However, it is unclear whether sex-specific cognitive consequences of APOE are consistent across races and extend to the APOE ε2 allele. Objective To investigate whether sex and race modify APOE ε4 and ε2 associations with cognition. Design, Setting, and Participants This genetic association study included longitudinal cognitive data from 4 AD and cognitive aging cohorts. Participants were older than 60 years and self-identified as non-Hispanic White or non-Hispanic Black (hereafter, White and Black). Data were previously collected across multiple US locations from 1994 to 2018. Secondary analyses began December 2021 and ended September 2022. Main Outcomes and Measures Harmonized composite scores for memory, executive function, and language were generated using psychometric approaches. Linear regression assessed interactions between APOE ε4 or APOE ε2 and sex on baseline cognitive scores, while linear mixed-effect models assessed interactions on cognitive trajectories. The intersectional effect of race was modeled using an APOE × sex × race interaction term, assessing whether APOE × sex interactions differed by race. Models were adjusted for age at baseline and corrected for multiple comparisons. Results Of 32 427 participants who met inclusion criteria, there were 19 007 females (59%), 4453 Black individuals (14%), and 27 974 White individuals (86%); the mean (SD) age at baseline was 74 years (7.9). At baseline, 6048 individuals (19%) had AD, 4398 (14%) were APOE ε2 carriers, and 12 538 (38%) were APOE ε4 carriers. Participants missing APOE status were excluded (n = 9266). For APOE ε4, a robust sex interaction was observed on baseline memory (β = -0.071, SE = 0.014; P = 9.6 × 10-7), whereby the APOE ε4 negative effect was stronger in females compared with males and did not significantly differ among races. Contrastingly, despite the large sample size, no APOE ε2 × sex interactions on cognition were observed among all participants. When testing for intersectional effects of sex, APOE ε2, and race, an interaction was revealed on baseline executive function among individuals who were cognitively unimpaired (β = -0.165, SE = 0.066; P = .01), whereby the APOE ε2 protective effect was female-specific among White individuals but male-specific among Black individuals. Conclusions and Relevance In this study, while race did not modify sex differences in APOE ε4, the APOE ε2 protective effect could vary by race and sex. Although female sex enhanced ε4-associated risk, there was no comparable sex difference in ε2, suggesting biological pathways underlying ε4-associated risk are distinct from ε2 and likely intersect with age-related changes in sex biology.
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Affiliation(s)
- Skylar Walters
- Vanderbilt Memory & Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Alex G. Contreras
- Vanderbilt Memory & Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jaclyn M. Eissman
- Vanderbilt Memory & Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | | | - Michael L. Lee
- Department of Medicine, University of Washington, Seattle
| | - Seo-Eun Choi
- Department of Medicine, University of Washington, Seattle
| | | | - Emily H. Trittschuh
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle
- Geriatric Research Education and Clinical Center (GRECC), VA Puget Sound Health Care System, Seattle, Washington
| | - Jesse B. Mez
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts
| | - William S. Bush
- Cleveland Institute for Computational Biology, Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Brian W. Kunkle
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
| | - Adam C. Naj
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Amalia Peterson
- Vanderbilt Memory & Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Katherine A. Gifford
- Vanderbilt Memory & Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Michael L. Cuccaro
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St Louis, Missouri
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St Louis, Missouri
| | - Margaret A. Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
| | - Lindsay A. Farrer
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts
| | - Li-San Wang
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Jonathan L. Haines
- Cleveland Institute for Computational Biology, Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Angela L. Jefferson
- Vanderbilt Memory & Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Walter A. Kukull
- Department of Epidemiology, School of Public Health, University of Washington, Seattle
| | - C. Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle
| | - Andrew J. Saykin
- Department of Radiology and Imaging Services, Indiana University School of Medicine, Indianapolis
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis
| | - Paul M. Thompson
- Keck School of Medicine, University of Southern California, Los Angeles
| | - Eden R. Martin
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois
| | - Lisa L. Barnes
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois
| | - Julie A. Schneider
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois
| | - Paul K. Crane
- Department of Medicine, University of Washington, Seattle
| | - Timothy J. Hohman
- Vanderbilt Memory & Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Logan Dumitrescu
- Vanderbilt Memory & Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, Tennessee
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
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Ray NR, Kunkle BW, Hamilton-Nelson K, Kurup JT, Rajabli F, Cosacak MI, Kizil C, Jean-Francois M, Cuccaro M, Reyes-Dumeyer D, Cantwell L, Kuzma A, Vance JM, Gao S, Hendrie HC, Baiyewu O, Ogunniyi A, Akinyemi RO, Lee WP, Martin ER, Wang LS, Beecham GW, Bush WS, Farrer LA, Haines JL, Byrd GS, Schellenberg GD, Mayeux R, Pericak-Vance MA, Reitz C. Extended genome-wide association study employing the African Genome Resources Panel identifies novel susceptibility loci for Alzheimer's Disease in individuals of African ancestry. medRxiv 2023:2023.08.29.23294774. [PMID: 37693582 PMCID: PMC10491365 DOI: 10.1101/2023.08.29.23294774] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
INTRODUCTION Despite a two-fold increased risk, individuals of African ancestry have been significantly underrepresented in Alzheimer's Disease (AD) genomics efforts. METHODS GWAS of 2,903 AD cases and 6,265 cognitive controls of African ancestry. Within-dataset results were meta-analyzed, followed by gene-based and pathway analyses, and analysis of RNAseq and whole-genome sequencing data. RESULTS A novel AD risk locus was identified in MPDZ on chromosome 9p23 (rs141610415, MAF=.002, P =3.68×10 -9 ). Two additional novel common and nine novel rare loci approached genome-wide significance at P <9×10 -7 . Comparison of association and LD patterns between datasets with higher and lower degrees of African ancestry showed differential association patterns at chr12q23.2 ( ASCL1 ), suggesting that the association is modulated by regional origin of local African ancestry. DISCUSSION Increased sample sizes and sample sets from Africa covering as much African genetic diversity as possible will be critical to identify additional disease-associated loci and improve deconvolution of local genetic ancestry effects.
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14
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Li YJ, Nuytemans K, La JO, Jiang R, Slifer SH, Sun S, Naj A, Gao XR, Martin ER. Identification of novel genes for age-at-onset of Alzheimer's disease by combining quantitative and survival trait analyses. Alzheimers Dement 2023; 19:3148-3157. [PMID: 36738287 DOI: 10.1002/alz.12927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 12/06/2022] [Accepted: 12/19/2022] [Indexed: 02/05/2023]
Abstract
INTRODUCTION Our understanding of the genetic predisposition for age-at-onset (AAO) of Alzheimer's disease (AD) is limited. Here, we sought to identify genes modifying AAO and examined whether any have sex-specific effects. METHODS Genome-wide association analysis were performed on imputed genetic data of 9219 AD cases and 10,345 controls from 20 cohorts of the Alzheimer's Disease Genetics Consortium. AAO was modeled from cases directly and as a survival outcome. RESULTS We identified 11 genome-wide significant loci (P < 5 × 10-8 ), including six known AD-risk genes and five novel loci, UMAD1, LUZP2, ARFGEF2, DSCAM, and 4q25, affecting AAO of AD. Additionally, 39 suggestive loci showed strong association. Twelve loci showed sex-specific effects on AAO including CD300LG and MLX/TUBG2 for females and MIR4445 for males. DISCUSSION Genes that influence AAO of AD are excellent therapeutic targets for delaying onset of AD. Several loci identified include genes with promising functional implications for AD.
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Affiliation(s)
- Yi-Ju Li
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Karen Nuytemans
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
- John T. MacDonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, Florida, USA
| | - Jong Ok La
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Rong Jiang
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Psychiatry and Behavior Science, Duke University School of Medicine, Durham, North Carolina, USA
| | - Susan H Slifer
- John T. MacDonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, Florida, USA
| | - Shuming Sun
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, North Carolina, USA
| | - Adam Naj
- Department of Biostatistics, Epidemiology, and Informatics, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Xiaoyi Raymond Gao
- Department of Ophthalmology and Visual Sciences, Division of Human Genetics, The Ohio State University, Columbus, Ohio, USA
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, USA
| | - Eden R Martin
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
- John T. MacDonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, Florida, USA
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15
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Rajabli F, Tosto G, Hamilton-Nelson KL, Kunkle BW, Vardarajan BN, Naj A, Whitehead PG, Gardner OK, Bush WS, Sariya S, Mayeux RP, Farrer LA, Cuccaro ML, Vance JM, Griswold AJ, Schellenberg GD, Haines JL, Byrd GS, Reitz C, Beecham GW, Pericak-Vance MA, Martin ER. Admixture mapping identifies novel Alzheimer's disease risk regions in African Americans. Alzheimers Dement 2023; 19:2538-2548. [PMID: 36539198 PMCID: PMC10272044 DOI: 10.1002/alz.12865] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 08/09/2022] [Accepted: 08/17/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND This study used admixture mapping to prioritize the genetic regions associated with Alzheimer's disease (AD) in African American (AA) individuals, followed by ancestry-aware regression analysis to fine-map the prioritized regions. METHODS We analyzed 10,271 individuals from 17 different AA datasets. We performed admixture mapping and meta-analyzed the results. We then used regression analysis, adjusting for local ancestry main effects and interactions with genotype, to refine the regions identified from admixture mapping. Finally, we leveraged in silico annotation and differential gene expression data to prioritize AD-related variants and genes. RESULTS Admixture mapping identified two genome-wide significant loci on chromosomes 17p13.2 (p = 2.2 × 10-5 ) and 18q21.33 (p = 1.2 × 10-5 ). Our fine mapping of the chromosome 17p13.2 and 18q21.33 regions revealed several interesting genes such as the MINK1, KIF1C, and BCL2. DISCUSSION Our ancestry-aware regression approach showed that AA individuals have a lower risk of AD if they inherited African ancestry admixture block at the 17p13.2 locus. HIGHLIGHTS We identified two genome-wide significant admixture mapping signals: on chromosomes 17p13.2 and 18q21.33, which are novel in African American (AA) populations. Our ancestry-aware regression approach showed that AA individuals have a lower risk of Alzheimer's disease (AD) if they inherited African ancestry admixture block at the 17p13.2 locus. We found that the overall proportion of African ancestry does not differ between the cases and controls that suggest African genetic ancestry alone is not likely to explain the AD prevalence difference between AA and non-Hispanic White populations.
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Affiliation(s)
- Farid Rajabli
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Giuseppe Tosto
- Gertrude H. Sergievsky Center, Taub Institute for Research on the Aging Brain, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Kara L. Hamilton-Nelson
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Brian W. Kunkle
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Badri N. Vardarajan
- Gertrude H. Sergievsky Center, Taub Institute for Research on the Aging Brain, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Adam Naj
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PE, USA
| | - Patrice G. Whitehead
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Olivia K. Gardner
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - William S. Bush
- Department of Population & Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Sanjeev Sariya
- Gertrude H. Sergievsky Center, Taub Institute for Research on the Aging Brain, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Richard P. Mayeux
- Gertrude H. Sergievsky Center, Taub Institute for Research on the Aging Brain, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Lindsay A. Farrer
- Departments of Medicine (Biomedical Genetics), Neurology, Ophthalmology, Epidemiology, and Biostatistics, Boston University Schools of Medicine and Public Health, Boston, MA, USA
| | - Michael L. Cuccaro
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
- Dr. John T. MacDonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Jeffrey M. Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
- Dr. John T. MacDonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Anthony J. Griswold
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
- Dr. John T. MacDonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Gerard D. Schellenberg
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PE, USA
| | - Jonathan L. Haines
- Department of Population & Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Goldie S. Byrd
- Maya Angelou Center for Health Equity, Wake Forest University, Winston-Salem, NC, USA
| | - Christiane Reitz
- Gertrude H. Sergievsky Center, Taub Institute for Research on the Aging Brain, Departments of Neurology, Psychiatry, and Epidemiology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Gary W. Beecham
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
- Dr. John T. MacDonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Margaret A. Pericak-Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
- Dr. John T. MacDonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Eden R. Martin
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
- Dr. John T. MacDonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
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16
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Zhang W, Young JI, Gomez L, Schmidt MA, Lukacsovich D, Varma A, Chen XS, Martin ER, Wang L. Distinct CSF biomarker-associated DNA methylation in Alzheimer's disease and cognitively normal subjects. Alzheimers Res Ther 2023; 15:78. [PMID: 37038196 PMCID: PMC10088180 DOI: 10.1186/s13195-023-01216-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 03/21/2023] [Indexed: 04/12/2023]
Abstract
BACKGROUND Growing evidence has demonstrated that DNA methylation (DNAm) plays an important role in Alzheimer's disease (AD) and that DNAm differences can be detected in the blood of AD subjects. Most studies have correlated blood DNAm with the clinical diagnosis of AD in living individuals. However, as the pathophysiological process of AD can begin many years before the onset of clinical symptoms, there is often disagreement between neuropathology in the brain and clinical phenotypes. Therefore, blood DNAm associated with AD neuropathology, rather than with clinical data, would provide more relevant information on AD pathogenesis. METHODS We performed a comprehensive analysis to identify blood DNAm associated with cerebrospinal fluid (CSF) pathological biomarkers for AD. Our study included matched samples of whole blood DNA methylation, CSF Aβ42, phosphorylated tau181 (pTau181), and total tau (tTau) biomarkers data, measured on the same subjects and at the same clinical visits from a total of 202 subjects (123 CN or cognitively normal, 79 AD) in the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort. To validate our findings, we also examined the association between premortem blood DNAm and postmortem brain neuropathology measured on a group of 69 subjects in the London dataset. RESULTS We identified a number of novel associations between blood DNAm and CSF biomarkers, demonstrating that changes in pathological processes in the CSF are reflected in the blood epigenome. Overall, the CSF biomarker-associated DNAm is relatively distinct in CN and AD subjects, highlighting the importance of analyzing omics data measured on cognitively normal subjects (which includes preclinical AD subjects) to identify diagnostic biomarkers, and considering disease stages in the development and testing of AD treatment strategies. Moreover, our analysis revealed biological processes associated with early brain impairment relevant to AD are marked by DNAm in the blood, and blood DNAm at several CpGs in the DMR on HOXA5 gene are associated with pTau181 in the CSF, as well as tau-pathology and DNAm in the brain, nominating DNAm at this locus as a promising candidate AD biomarker. CONCLUSIONS Our study provides a valuable resource for future mechanistic and biomarker studies of DNAm in AD.
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Affiliation(s)
- Wei Zhang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami Miller School of Medicine, 1120 NW 14Th Street, Miami, FL, 33136, USA
| | - Juan I Young
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Lissette Gomez
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Michael A Schmidt
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - David Lukacsovich
- Division of Biostatistics, Department of Public Health Sciences, University of Miami Miller School of Medicine, 1120 NW 14Th Street, Miami, FL, 33136, USA
| | - Achintya Varma
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - X Steven Chen
- Division of Biostatistics, Department of Public Health Sciences, University of Miami Miller School of Medicine, 1120 NW 14Th Street, Miami, FL, 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Eden R Martin
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Lily Wang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami Miller School of Medicine, 1120 NW 14Th Street, Miami, FL, 33136, USA.
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.
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17
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Zhang W, Young JI, Gomez L, Schmidt MA, Lukacsovich D, Varma A, Chen XS, Martin ER, Wang L. Distinct CSF biomarker-associated DNA methylation in Alzheimer's disease and cognitively normal subjects. Res Sq 2023:rs.3.rs-2391364. [PMID: 36865230 PMCID: PMC9980279 DOI: 10.21203/rs.3.rs-2391364/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Background Growing evidence has demonstrated that DNA methylation (DNAm) plays an important role in Alzheimer's disease (AD) and that DNAm differences can be detected in the blood of AD subjects. Most studies have correlated blood DNAm with the clinical diagnosis of AD in living individuals. However, as the pathophysiological process of AD can begin many years before the onset of clinical symptoms, there is often disagreement between neuropathology in the brain and clinical phenotypes. Therefore, blood DNAm associated with AD neuropathology, rather than with clinical data, would provide more relevant information on AD pathogenesis. Methods We performed a comprehensive analysis to identify blood DNAm associated with cerebrospinal fluid (CSF) pathological biomarkers for AD. Our study included matched samples of whole blood DNA methylation, CSF Aβ 42 , phosphorylated tau 181 (pTau 181 ), and total tau (tTau) biomarkers data, measured on the same subjects and at the same clinical visits from a total of 202 subjects (123 CN or cognitively normal, 79 AD) in the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort. To validate our findings, we also examined the association between premortem blood DNAm and postmortem brain neuropathology measured on a group of 69 subjects in the London dataset. Results We identified a number of novel associations between blood DNAm and CSF biomarkers, demonstrating that changes in pathological processes in the CSF are reflected in the blood epigenome. Overall, the CSF biomarker-associated DNAm is relatively distinct in CN and AD subjects, highlighting the importance of analyzing omics data measured on cognitively normal subjects (which includes preclinical AD subjects) to identify diagnostic biomarkers, and considering disease stages in the development and testing of AD treatment strategies. Moreover, our analysis revealed biological processes associated with early brain impairment relevant to AD are marked by DNAm in the blood, and blood DNAm at several CpGs in the DMR on HOXA5 gene are associated with pTau 181 in the CSF, as well as tau-pathology and DNAm in the brain, nominating DNAm at this locus as a promising candidate AD biomarker. Conclusions Our study provides a valuable resource for future mechanistic and biomarker studies of DNAm in AD.
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Affiliation(s)
- Wei Zhang
- University of Miami, Miller School of Medicine
| | - Juan I. Young
- Dr. John T Macdonald Foundation, University of Miami, Miller School of Medicine
| | | | - Michael A. Schmidt
- Dr. John T Macdonald Foundation, University of Miami, Miller School of Medicine
| | | | | | | | - Eden R. Martin
- Dr. John T Macdonald Foundation, University of Miami, Miller School of Medicine
| | - Lily Wang
- University of Miami, Miller School of Medicine
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18
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Gao XR, Chiariglione M, Qin K, Nuytemans K, Scharre DW, Li YJ, Martin ER. Explainable machine learning aggregates polygenic risk scores and electronic health records for Alzheimer's disease prediction. Sci Rep 2023; 13:450. [PMID: 36624143 PMCID: PMC9829871 DOI: 10.1038/s41598-023-27551-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Alzheimer's disease (AD) is the most common late-onset neurodegenerative disorder. Identifying individuals at increased risk of developing AD is important for early intervention. Using data from the Alzheimer Disease Genetics Consortium, we constructed polygenic risk scores (PRSs) for AD and age-at-onset (AAO) of AD for the UK Biobank participants. We then built machine learning (ML) models for predicting development of AD, and explored feature importance among PRSs, conventional risk factors, and ICD-10 codes from electronic health records, a total of > 11,000 features using the UK Biobank dataset. We used eXtreme Gradient Boosting (XGBoost) and SHapley Additive exPlanations (SHAP), which provided superior ML performance as well as aided ML model explanation. For participants age 40 and older, the area under the curve for AD was 0.88. For subjects of age 65 and older (late-onset AD), PRSs were the most important predictors. This is the first observation that PRSs constructed from the AD risk and AAO play more important roles than age in predicting AD. The ML model also identified important predictors from EHR, including urinary tract infection, syncope and collapse, chest pain, disorientation and hypercholesterolemia, for developing AD. Our ML model improved the accuracy of AD risk prediction by efficiently exploring numerous predictors and identified novel feature patterns.
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Affiliation(s)
- Xiaoyi Raymond Gao
- Department of Ophthalmology and Visual Sciences, The Ohio State University, Columbus, OH, USA.
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA.
- Division of Human Genetics, The Ohio State University, Columbus, OH, USA.
- Ohio State University Physicians Inc., Columbus, OH, USA.
| | - Marion Chiariglione
- Department of Ophthalmology and Visual Sciences, The Ohio State University, Columbus, OH, USA
| | - Ke Qin
- Department of Ophthalmology and Visual Sciences, The Ohio State University, Columbus, OH, USA
| | - Karen Nuytemans
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA
- Dr. John T. MacDonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Douglas W Scharre
- Department of Neurology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Yi-Ju Li
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
- Duke Molecular Physiology Institute, Durham, NC, USA
| | - Eden R Martin
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA
- Dr. John T. MacDonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, USA
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19
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Tejeda M, Farrell J, Zhu C, Wetzler L, Lunetta KL, Bush WS, Martin ER, Wang L, Schellenberg GD, Pericak‐Vance MA, Haines JL, Farrer LA, Sherva R. Multiple Viruses Detected in Human DNA are Associated with Alzheimer Disease Risk. Alzheimers Dement 2022. [DOI: 10.1002/alz.065753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | - John Farrell
- Boston University School of Medicine Boston MA USA
| | - Congcong Zhu
- Boston University School of Medicine Boston MA USA
| | - Lee Wetzler
- Boston University School of Medicine Boston MA USA
| | | | - William S. Bush
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Eden R Martin
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Li‐San Wang
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine Philadelphia PA USA
| | | | - Margaret A. Pericak‐Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | - Jonathan L. Haines
- Cleveland Institute for Computational Biology, Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Lindsay A. Farrer
- Boston University School of Medicine Boston MA USA
- Boston University School of Public Health Boston MA USA
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20
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Contreras AG, Walters S, Mukherjee S, Lee ML, Choi S, Scollard P, Trittschuh EH, Mez JB, Bush WS, Engelman CD, Lu Q, Fardo DW, Widaman KF, Buckley RF, Mormino EC, Kunkle BW, Naj AC, Clark LR, Gifford KA, Cuccaro ML, Cruchaga C, Pericak‐Vance MA, Farrer LA, Wang L, Schellenberg GD, Haines JL, Jefferson AL, Johnson SC, Kukull WA, Albert MS, Keene CD, Saykin AJ, Larson EB, Sperling RA, Mayeux R, Thompson PM, Martin ER, Bennett DA, Barnes LL, Schneider JA, Crane PK, Hohman TJ, Dumitrescu L. Sex differences in
APOE
effects on cognition are domain‐specific. Alzheimers Dement 2022. [DOI: 10.1002/alz.068262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Alex G Contreras
- Vanderbilt Memory and Alzheimer’s Center, Vanderbilt University Medical Center Nashville IN USA
| | - Skylar Walters
- Vanderbilt Memory and Alzheimer’s Center, Vanderbilt University Medical Center Nashville TN USA
| | | | | | | | | | | | - Jesse B. Mez
- Boston University School of Medicine Boston MA USA
| | - William S. Bush
- Case Western Reserve University School of Medicine Cleveland OH USA
| | - Corinne D. Engelman
- Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health Madison WI USA
| | - Qiongshi Lu
- University of Wisconsin School of Medicine and Public Health Madison WI USA
| | - David W. Fardo
- University of Kentucky / Sanders‐Brown Center on Aging Lexington KY USA
| | | | - Rachel F. Buckley
- Massachusetts General Hospital, Harvard Medical School Boston MA USA
| | | | - Brian W. Kunkle
- John P. Hussman Institute for Human Genomics, Miller School of Medicine Miami FL USA
| | - Adam C. Naj
- University of Pennsylvania, Perelman School of Medicine, Department of Biostatistics and Epidemiology/Center for Clinical Epidemiology and Biostatistics Philadelphia PA USA
| | - Lindsay R. Clark
- Wisconsin Alzheimer’s Institute, University of Wisconsin‐Madison School of Medicine and Public Health Madison WI USA
| | | | | | | | - Margaret A. Pericak‐Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | - Lindsay A. Farrer
- Boston University School of Medicine, Department of Medicine, Biomedical Genetics Boston MA USA
| | - Li‐San Wang
- University of Pennsylvania Philadelphia PA USA
| | - Gerard D. Schellenberg
- University of Pennsylvania, Perelman School of Medicine, Path & Lab Med, Stellar Chance Philadelphia PA USA
| | - Jonathan L. Haines
- Case Western Reserve University School of Medicine, Department of Population & Quantitative Health Sciences, Cleveland Institute for Computational Biology Cleveland OH USA
| | - Angela L. Jefferson
- Vanderbilt Memory & Alzheimer’s Center, Vanderbilt University Medical Center Nashville TN USA
| | - Sterling C. Johnson
- Wisconsin Alzheimer's Disease Research Center Madison WI USA
- University of Wisconsin‐Madison Madison WI USA
| | - Walter A. Kukull
- University of Washington Seattle WA USA
- National Alzheimer's Coordinating Center, University of Washington Seattle WA USA
| | | | | | | | | | - Reisa A. Sperling
- Massachusetts General Hospital, Harvard Medical SchoolDepartment of Neurology, Massachusetts General Hospital, Harvard Medical School Boston MA USA
| | | | - Paul M Thompson
- Keck School of Medicine, University of Southern California Los Angeles CA USA
| | - Eden R. Martin
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | - David A Bennett
- Rush Alzheimer’s Disease Center and Department of Neurological Sciences, Rush University Medical Center Chicago IL USA
| | - Lisa L. Barnes
- Rush Alzheimer's Disease Center, Rush University Medical Center Chicago IL USA
| | - Julie A Schneider
- Rush Alzheimer's Disease Center, Rush University Medical Center Chicago IL USA
| | - Paul K. Crane
- University of Washington Alzheimer’s Disease Research Center, University of Washington School of Medicine Seattle WA USA
| | - Timothy J. Hohman
- Vanderbilt Memory & Alzheimer’s Center, Vanderbilt University Medical Center Nashville TN USA
| | - Logan Dumitrescu
- Vanderbilt Memory and Alzheimer’s Center, Vanderbilt University Medical Center Nashville TN USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center Nashville TN USA
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21
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Kurup JT, Kunkle BW, Hamilton‐Nelson KL, Jean‐Francois M, Schmidt MA, Martin ER, Wang L, Beecham GW, Farrer LA, Haines JL, Byrd GS, Schellenberg GD, Mayeux R, Pericak‐Vance MA, Reitz C. Meta‐analysis employing the African Genome Resources panel identifies novel Alzheimer disease risk loci in African Americans. Alzheimers Dement 2022. [DOI: 10.1002/alz.063856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Jiji Thulaseedhara Kurup
- Columbia University, The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, The Gertrude H. Sergievsky Center and Departments of Neurology and Epidemiology New York NY USA
| | - Brian W. Kunkle
- John P. Hussman Institute for Human Genomics, Miller School of Medicine Miami FL USA
| | - Kara L. Hamilton‐Nelson
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | - Melissa Jean‐Francois
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Michael A. Schmidt
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Eden R Martin
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Li‐San Wang
- Perelman School of Medicine, University of Pennsylvania Philadelphia PA USA
| | - Gary W. Beecham
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | | | - Jonathan L. Haines
- Cleveland Institute for Computational Biology, Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
- Case Western Reserve University School of Medicine Cleveland OH USA
| | - Goldie S. Byrd
- Maya Angelou Center for Health Equity, Wake Forest School of Medicine, Winston‐Salem NC USA
| | | | - Richard Mayeux
- The Taub Institute for Research on Alzheimer’s Disease and The Aging Brain, Columbia University New York NY USA
| | - Margaret A. Pericak‐Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
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22
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Zhang X, Guo S, Naj AC, Below J, Kunkle BW, Dumitrescu L, Martin ER, Bush WS. Modeling gene expression on the X chromosome in the brain for transcriptome‐wide association studies. Alzheimers Dement 2022. [DOI: 10.1002/alz.063533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Xueyi Zhang
- Case Western Reserve University Cleveland OH USA
| | - Shengru Guo
- University of Miami Miller School of Medicine Miami FL USA
| | - Adam C. Naj
- University of Pennsylvania, Perelman School of Medicine, Department of Biostatistics and Epidemiology/Center for Clinical Epidemiology and Biostatistics Philadelphia PA USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine Philadelphia PA USA
| | | | - Brian W. Kunkle
- University of Miami, Miller School of Medicine, John P. Hussman Institute for Human Genomics Miami FL USA
| | - Logan Dumitrescu
- Vanderbilt Memory and Alzheimer’s Center, Vanderbilt University Medical Center Nashville TN USA
| | - Eden R. Martin
- University of Miami, Miller School of Medicine, John P. Hussman Institute for Human Genomics Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
| | - William S. Bush
- Case Western Reserve University School of Medicine Cleveland OH USA
- Cleveland Institute for Computational Biology, Case Western Reserve University Cleveland OH USA
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23
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Godrich D, Martin ER, Schellenberg G, Pericak‐Vance MA, Cuccaro M, Scott WK, Kukull W, Montine T, Beecham GW. Neuropathological lesions and their contribution to dementia and cognitive impairment in a heterogeneous clinical population. Alzheimers Dement 2022; 18:2403-2412. [PMID: 35142102 PMCID: PMC9360193 DOI: 10.1002/alz.12516] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 09/14/2021] [Accepted: 09/22/2021] [Indexed: 01/31/2023]
Abstract
INTRODUCTION Alzheimer disease (AD) and related dementias are characterized by damage caused by neuropathological lesions in the brain. These include AD lesions (plaques and tangles) and non-AD lesions such as vascular injury or Lewy bodies. We report here an assessment of lesion association to dementia in a large clinic-based population. METHODS We identified 5272 individuals with neuropathological data from the National Alzheimer's Coordinating Center. Individual lesions, as well as a neuropathological composite score (NPCS) were tested for association with dementia, and both functional and neurocognitive impairment using regression models. RESULTS Most individuals exhibited mixed pathologies, especially AD lesions in combination with non-AD lesions. All lesion types were associated with one or more clinical outcomes; most even while controlling for AD pathology. The NPCS was also associated with clinical outcomes. DISCUSSION These data suggest mixed-type pathologies are extremely common in a clinic-based population and may contribute to dementia and cognitive impairment.
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Affiliation(s)
- Dana Godrich
- Dr. John T MacDonald Foundation Department of Human GeneticsMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
| | - Eden R. Martin
- Dr. John T MacDonald Foundation Department of Human GeneticsMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
- John P. Hussman Institute for Human GenomicsMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
| | - Gerard Schellenberg
- Penn Neurodegeneration Genomics CenterDepartment of Pathology and Laboratory MedicineUniversity of Pennsylvania Perelman School of MedicinePhiladelphiaPennsylvaniaUSA
| | - Margaret A. Pericak‐Vance
- Dr. John T MacDonald Foundation Department of Human GeneticsMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
- John P. Hussman Institute for Human GenomicsMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
| | - Michael Cuccaro
- Dr. John T MacDonald Foundation Department of Human GeneticsMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
- John P. Hussman Institute for Human GenomicsMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
| | - William K. Scott
- Dr. John T MacDonald Foundation Department of Human GeneticsMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
- John P. Hussman Institute for Human GenomicsMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
| | - Walter Kukull
- Department of EpidemiologyUniversity of WashingtonSeattleWashingtonUSA
| | - Thomas Montine
- Department of PathologyStanford UniversityStanfordCaliforniaUSA
| | - Gary W. Beecham
- Dr. John T MacDonald Foundation Department of Human GeneticsMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
- John P. Hussman Institute for Human GenomicsMiller School of MedicineUniversity of MiamiMiamiFloridaUSA
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24
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Mena PR, Kunkle BW, Faber KM, Adams LD, Inciute JD, Whitehead PL, Foroud TM, Reyes‐Dumeyer D, Kuzma AB, Leung YY, Naj AC, Martin ER, Dalgard CL, Schellenberg GD, Wang L, Mayeux R, Vardarajan BN, Vance JM, Cuccaro ML, Pericak‐Vance MA. The Alzheimer’s Disease Sequencing Project Follow Up Study (ADSP‐FUS): increasing ethnic diversity in Alzheimer’s disease (AD) genetics research. Alzheimers Dement 2022. [DOI: 10.1002/alz.068083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Pedro Ramon Mena
- John P. Hussman Institute for Human Genomics, University of Miami Miami FL USA
| | - Brian W. Kunkle
- John P. Hussman Institute for Human Genomics, Miller School of Medicine Miami FL USA
| | - Kelley M. Faber
- Indiana University School of Medicine Indianapolis IN USA
- National Centralized Repository for Alzheimer's Disease and Related Dementias (NCRAD) Indianapolis IN USA
| | - Larry D. Adams
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Jovita D. Inciute
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Patrice L. Whitehead
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | - Tatiana M. Foroud
- Indiana University School of Medicine Indianapolis IN USA
- National Centralized Repository for Alzheimer's Disease and Related Dementias (NCRAD) Indianapolis IN USA
| | | | - Amanda B Kuzma
- University of Pennsylvania Perelman School of Medicine Philadelphia PA USA
| | - Yuk Yee Leung
- University of Pennsylvania Perelman School of Medicine Philadelphia PA USA
| | - Adam C. Naj
- University of Pennsylvania, Perelman School of Medicine, Department of Biostatistics and Epidemiology/Center for Clinical Epidemiology and Biostatistics Philadelphia PA USA
| | - Eden R. Martin
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | | | - Gerard D. Schellenberg
- University of Pennsylvania, Perelman School of Medicine, Path & Lab Med, Stellar Chance Philadelphia PA USA
| | - Li‐San Wang
- University of Pennsylvania Perelman School of Medicine Philadelphia PA USA
| | - Richard Mayeux
- Columbia University Irving Medical Center New York NY USA
| | - Badri N. Vardarajan
- G.H. Sergievsky Center, Vagelos College of Physicians and Surgeons, Columbia University New York NY USA
| | - Jeffery M. Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miami FL USA
| | - Michael L. Cuccaro
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Margaret A. Pericak‐Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
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25
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Holstege H, Hulsman M, Charbonnier C, Grenier-Boley B, Quenez O, Grozeva D, van Rooij JGJ, Sims R, Ahmad S, Amin N, Norsworthy PJ, Dols-Icardo O, Hummerich H, Kawalia A, Amouyel P, Beecham GW, Berr C, Bis JC, Boland A, Bossù P, Bouwman F, Bras J, Campion D, Cochran JN, Daniele A, Dartigues JF, Debette S, Deleuze JF, Denning N, DeStefano AL, Farrer LA, Fernández MV, Fox NC, Galimberti D, Genin E, Gille JJP, Le Guen Y, Guerreiro R, Haines JL, Holmes C, Ikram MA, Ikram MK, Jansen IE, Kraaij R, Lathrop M, Lemstra AW, Lleó A, Luckcuck L, Mannens MMAM, Marshall R, Martin ER, Masullo C, Mayeux R, Mecocci P, Meggy A, Mol MO, Morgan K, Myers RM, Nacmias B, Naj AC, Napolioni V, Pasquier F, Pastor P, Pericak-Vance MA, Raybould R, Redon R, Reinders MJT, Richard AC, Riedel-Heller SG, Rivadeneira F, Rousseau S, Ryan NS, Saad S, Sanchez-Juan P, Schellenberg GD, Scheltens P, Schott JM, Seripa D, Seshadri S, Sie D, Sistermans EA, Sorbi S, van Spaendonk R, Spalletta G, Tesi N, Tijms B, Uitterlinden AG, van der Lee SJ, Visser PJ, Wagner M, Wallon D, Wang LS, Zarea A, Clarimon J, van Swieten JC, Greicius MD, Yokoyama JS, Cruchaga C, Hardy J, Ramirez A, Mead S, van der Flier WM, van Duijn CM, Williams J, Nicolas G, Bellenguez C, Lambert JC. Exome sequencing identifies rare damaging variants in ATP8B4 and ABCA1 as risk factors for Alzheimer's disease. Nat Genet 2022; 54:1786-1794. [PMID: 36411364 PMCID: PMC9729101 DOI: 10.1038/s41588-022-01208-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 09/19/2022] [Indexed: 11/22/2022]
Abstract
Alzheimer's disease (AD), the leading cause of dementia, has an estimated heritability of approximately 70%1. The genetic component of AD has been mainly assessed using genome-wide association studies, which do not capture the risk contributed by rare variants2. Here, we compared the gene-based burden of rare damaging variants in exome sequencing data from 32,558 individuals-16,036 AD cases and 16,522 controls. Next to variants in TREM2, SORL1 and ABCA7, we observed a significant association of rare, predicted damaging variants in ATP8B4 and ABCA1 with AD risk, and a suggestive signal in ADAM10. Additionally, the rare-variant burden in RIN3, CLU, ZCWPW1 and ACE highlighted these genes as potential drivers of respective AD-genome-wide association study loci. Variants associated with the strongest effect on AD risk, in particular loss-of-function variants, are enriched in early-onset AD cases. Our results provide additional evidence for a major role for amyloid-β precursor protein processing, amyloid-β aggregation, lipid metabolism and microglial function in AD.
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Affiliation(s)
- Henne Holstege
- Genomics of Neurodegenerative Diseases and Aging, Human Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands.
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands.
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands.
- Delft Bioinformatics Lab, Delft University of Technology, Delft, the Netherlands.
| | - Marc Hulsman
- Genomics of Neurodegenerative Diseases and Aging, Human Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands.
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands.
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands.
- Delft Bioinformatics Lab, Delft University of Technology, Delft, the Netherlands.
| | - Camille Charbonnier
- Université Rouen Normandie, INSERM U1245 and CHU Rouen, Department of Genetics and CNRMAJ, Rouen, France
| | - Benjamin Grenier-Boley
- Université Lille, INSERM, Centre Hospitalier Universitaire Lille, Institut Pasteur de Lille, U1167-RID-AGE facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, Lille, France
| | - Olivier Quenez
- Université Rouen Normandie, INSERM U1245 and CHU Rouen, Department of Genetics and CNRMAJ, Rouen, France
| | - Detelina Grozeva
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics,, Division of Psychological Medicine and Clinical Neuroscience, School of Medicine, Cardiff University, Cardiff, UK
| | - Jeroen G J van Rooij
- Department of Neurology, Erasmus Medical Centre, Rotterdam, the Netherlands
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Rebecca Sims
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics,, Division of Psychological Medicine and Clinical Neuroscience, School of Medicine, Cardiff University, Cardiff, UK
| | - Shahzad Ahmad
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, the Netherlands
- Leiden Academic Centre for Drug Research, Leiden, the Netherlands
| | - Najaf Amin
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, the Netherlands
- Nuffield Department of Population Health Oxford University, Oxford, UK
| | - Penny J Norsworthy
- Medical Research Council Prion Unit at University College London, University College London Institute of Prion Diseases, London, UK
| | - Oriol Dols-Icardo
- Department of Neurology, II B Sant Pau, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
- Biomedical Research Networking Center on Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Holger Hummerich
- Medical Research Council Prion Unit at University College London, University College London Institute of Prion Diseases, London, UK
| | - Amit Kawalia
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Philippe Amouyel
- Université Lille, INSERM, Centre Hospitalier Universitaire Lille, Institut Pasteur de Lille, U1167-RID-AGE facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, Lille, France
| | - Gary W Beecham
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Claudine Berr
- Université Montpellier, INSERM, Institute for Neurosciences of Montpellier, Montpellier, France
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Anne Boland
- Université Paris-Saclay, Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Centre National de Recherche en Génomique Humaine Evry, Gif-sur-Yvette, France
| | - Paola Bossù
- Experimental Neuro-psychobiology Laboratory, Department of Clinical and Behavioral Neurology, Istituto di Ricovero e Cura a Carattere Scientifico Santa Lucia Foundation, Rome, Italy
| | - Femke Bouwman
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
| | - Jose Bras
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
- Division of Psychiatry and Behavioral Medicine, Michigan State University College of Human Medicine, Grand Rapids, MI, USA
| | - Dominique Campion
- Université Rouen Normandie, INSERM U1245 and CHU Rouen, Department of Genetics and CNRMAJ, Rouen, France
| | | | - Antonio Daniele
- Department of Neuroscience, Catholic University of Sacred Heart, Fondazione Policlinico Universitario A. Gemelli Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy
| | | | - Stéphanie Debette
- Université Bordeaux, INSERM, Bordeaux Population Health Research Center, Bordeaux, France
- Department of Neurology, Bordeaux University Hospital, Bordeaux, France
| | - Jean-François Deleuze
- Université Paris-Saclay, Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Centre National de Recherche en Génomique Humaine Evry, Gif-sur-Yvette, France
| | - Nicola Denning
- UKDRI Cardiff, School of Medicine, Cardiff University, Cardiff, UK
| | - Anita L DeStefano
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Lindsay A Farrer
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- Department of Epidemiology, Boston University, Boston, MA, USA
- Department of Medicine (Biomedical Genetics), Boston University, Boston, MA, USA
| | - Maria Victoria Fernández
- Neurogenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
- Psychiatry Department, Washington University School of Medicine, St Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA
| | - Nick C Fox
- Dementia Research Centre, University College London Queen Square Institute of Neurology, London, UK
| | - Daniela Galimberti
- Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Ca' Granda, Ospedale Policlinico, Milan, Italy
- University of Milan, Milan, Italy
| | - Emmanuelle Genin
- Université Brest, INSERM, Etablissement Français du Sang, Centre Hospitalier Universitaire Brest, Unité Mixte de Recherche 1078, GGB, Brest, France
| | - Johan J P Gille
- Genome Diagnostics, Department of Human Genetics, VU University, AmsterdamUMC (location VUmc), Amsterdam, the Netherlands
| | - Yann Le Guen
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Rita Guerreiro
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
- Division of Psychiatry and Behavioral Medicine, Michigan State University College of Human Medicine, Grand Rapids, MI, USA
| | - Jonathan L Haines
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA
| | - Clive Holmes
- Clinical and Experimental Science, Faculty of Medicine, University of Southampton, Southampton, UK
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - M Kamran Ikram
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Iris E Jansen
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije University, Amsterdam, the Netherlands
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Marc Lathrop
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Afina W Lemstra
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
| | - Alberto Lleó
- Department of Neurology, II B Sant Pau, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
- Biomedical Research Networking Center on Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Lauren Luckcuck
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics,, Division of Psychological Medicine and Clinical Neuroscience, School of Medicine, Cardiff University, Cardiff, UK
| | - Marcel M A M Mannens
- Department of Human Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam Reproduction and Development Research Institute, Amsterdam, the Netherlands
| | - Rachel Marshall
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics,, Division of Psychological Medicine and Clinical Neuroscience, School of Medicine, Cardiff University, Cardiff, UK
| | - Eden R Martin
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, USA
| | - Carlo Masullo
- Institute of Neurology, Catholic University of the Sacred Heart, Rome, Italy
| | - Richard Mayeux
- Taub Institute on Alzheimer's Disease and the Aging Brain, Department of Neurology, Columbia University, New York, NY, USA
- Gertrude H. Sergievsky Center, Columbia University, New York, NY, USA
| | - Patrizia Mecocci
- Institute of Gerontology and Geriatrics, Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Alun Meggy
- UKDRI Cardiff, School of Medicine, Cardiff University, Cardiff, UK
| | - Merel O Mol
- Department of Neurology, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Kevin Morgan
- Human Genetics, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Benedetta Nacmias
- Department of Neuroscience, Psychology, Drug Research and Child Health University of Florence, Florence, Italy
- IRCCS Fondazione Don Carlo Gnocchi, Florence, Italy
| | - Adam C Naj
- Penn Neurodegeneration Genomics Center, Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Valerio Napolioni
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Genomic and Molecular Epidemiology Laboratory, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Florence Pasquier
- Université Lille, INSERM, Centre Hospitalier Universitaire Lille, UMR1172, Resources and Research Memory Center (MRRC) of Distalz, Licend, Lille, France
| | - Pau Pastor
- Fundació Docència i Recerca MútuaTerrassa and Movement Disorders Unit, Department of Neurology, University Hospital MútuaTerrassa, Barcelona, Spain
- Memory Disorders Unit, Department of Neurology, Hospital Universitari Mutua de Terrassa, Barcelona, Spain
| | - Margaret A Pericak-Vance
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, USA
| | - Rachel Raybould
- UKDRI Cardiff, School of Medicine, Cardiff University, Cardiff, UK
| | - Richard Redon
- Université de Nantes, Centre Hospitalier Universitaire Nantes, Centre National de la Recherche Scientifique, INSERM, l'institut du Thorax, Nantes, France
| | - Marcel J T Reinders
- Delft Bioinformatics Lab, Delft University of Technology, Delft, the Netherlands
| | - Anne-Claire Richard
- Université Rouen Normandie, INSERM U1245 and CHU Rouen, Department of Genetics and CNRMAJ, Rouen, France
| | - Steffi G Riedel-Heller
- Institute of Social Medicine, Occupational Health and Public Health, University of Leipzig, Leipzig, Germany
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Stéphane Rousseau
- Université Rouen Normandie, INSERM U1245 and CHU Rouen, Department of Genetics and CNRMAJ, Rouen, France
| | - Natalie S Ryan
- Dementia Research Centre, University College London Queen Square Institute of Neurology, London, UK
| | - Salha Saad
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics,, Division of Psychological Medicine and Clinical Neuroscience, School of Medicine, Cardiff University, Cardiff, UK
| | - Pascual Sanchez-Juan
- Biomedical Research Networking Center on Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
- Neurology Service, Marqués de Valdecilla University Hospital (University of Cantabria and IDIVAL), Santander, Spain
| | - Gerard D Schellenberg
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Philip Scheltens
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
| | - Jonathan M Schott
- Dementia Research Centre, University College London Queen Square Institute of Neurology, London, UK
| | - Davide Seripa
- Laboratory for Advanced Hematological Diagnostics, Department of Hematology and Stem Cell Transplant, Lecce, Italy
| | - Sudha Seshadri
- Framingham Heart Study, Framingham, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- Department of Psychiatry and Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, San Antonio, TX, USA
| | - Daoud Sie
- Genome Diagnostics, Department of Human Genetics, VU University, AmsterdamUMC (location VUmc), Amsterdam, the Netherlands
| | - Erik A Sistermans
- Genome Diagnostics, Department of Human Genetics, VU University, AmsterdamUMC (location VUmc), Amsterdam, the Netherlands
| | - Sandro Sorbi
- Department of Neuroscience, Psychology, Drug Research and Child Health University of Florence, Florence, Italy
- IRCCS Fondazione Don Carlo Gnocchi, Florence, Italy
| | - Resie van Spaendonk
- Genome Diagnostics, Department of Human Genetics, VU University, AmsterdamUMC (location VUmc), Amsterdam, the Netherlands
| | - Gianfranco Spalletta
- Laboratory of Neuropsychiatry, Department of Clinical and Behavioral Neurology, Istituto di Ricovero e Cura a Carattere Scientifico Santa Lucia Foundation, Rome, Italy
| | - Niccolo' Tesi
- Genomics of Neurodegenerative Diseases and Aging, Human Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Delft, the Netherlands
| | - Betty Tijms
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Sven J van der Lee
- Genomics of Neurodegenerative Diseases and Aging, Human Genetics, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
- Delft Bioinformatics Lab, Delft University of Technology, Delft, the Netherlands
| | - Pieter Jelle Visser
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
| | - Michael Wagner
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, Medical Faculty, Bonn, Germany
- German Center for Neurodegenerative Diseases, Bonn, Germany
| | - David Wallon
- Université Rouen Normandie, INSERM U1245 and CHU Rouen, Department of Neurology and CNRMAJ, Rouen, France
| | - Li-San Wang
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Aline Zarea
- Université Rouen Normandie, INSERM U1245 and CHU Rouen, Department of Neurology and CNRMAJ, Rouen, France
| | - Jordi Clarimon
- Department of Neurology, II B Sant Pau, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
- Biomedical Research Networking Center on Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - John C van Swieten
- Department of Neurology, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Michael D Greicius
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Jennifer S Yokoyama
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, CA, USA
| | - Carlos Cruchaga
- Neurogenomics and Informatics Center, Washington University School of Medicine, St Louis, MO, USA
- Psychiatry Department, Washington University School of Medicine, St Louis, MO, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA
| | - John Hardy
- Reta Lila Weston Research Laboratories, Department of Molecular Neuroscience, University College London Institute of Neurology, London, UK
| | - Alfredo Ramirez
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Department of Psychiatry and Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, San Antonio, TX, USA
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, Medical Faculty, Bonn, Germany
- German Center for Neurodegenerative Diseases, Bonn, Germany
- Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Simon Mead
- Medical Research Council Prion Unit at University College London, University College London Institute of Prion Diseases, London, UK
| | - Wiesje M van der Flier
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit Amsterdam, Amsterdam UMC location VUmc, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, the Netherlands
- Nuffield Department of Population Health Oxford University, Oxford, UK
| | - Julie Williams
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics,, Division of Psychological Medicine and Clinical Neuroscience, School of Medicine, Cardiff University, Cardiff, UK
| | - Gaël Nicolas
- Université Rouen Normandie, INSERM U1245 and CHU Rouen, Department of Genetics and CNRMAJ, Rouen, France.
| | - Céline Bellenguez
- Université Lille, INSERM, Centre Hospitalier Universitaire Lille, Institut Pasteur de Lille, U1167-RID-AGE facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, Lille, France
| | - Jean-Charles Lambert
- Université Lille, INSERM, Centre Hospitalier Universitaire Lille, Institut Pasteur de Lille, U1167-RID-AGE facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, Lille, France.
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26
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Li Y, Nuytemans K, La JO, Jiang R, Slifer SH, Naj AC, Gao XR, Martin ER. Combining quantitative and survival trait analyses identifies novel general and sex‐specific genes for age‐at‐onset of Alzheimer’s disease. Alzheimers Dement 2022. [DOI: 10.1002/alz.069335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Yi‐Ju Li
- Duke Molecular Physiology Institute, Duke University School of Medicine Durham NC USA
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine Durham NC USA
| | - Karen Nuytemans
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Jong ok La
- Duke Molecular Physiology Institute, Duke University School of Medicine Durahm NC USA
| | - Rong Jiang
- Duke Moelcular Physiology Institute, Duke University School of Medicine Durham NC USA
| | - Susan H. Slifer
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Adam C. Naj
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine Philadelphia PA USA
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine Philadelphia PA USA
| | | | - Eden R. Martin
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
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27
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Eissman JM, Smith AN, Mukherjee S, Lee ML, Choi S, Scollard P, Trittschuh EH, Mez JB, Bush WS, Engelman CD, Lu Q, Fardo DW, Widaman KF, Buckley RF, Mormino EC, Kunkle BW, Naj AC, Clark LR, Gifford KA, Cuccaro ML, Cruchaga C, Pericak‐Vance MA, Farrer LA, Wang L, Schellenberg GD, Haines JL, Jefferson AL, Johnson SC, Kukull WA, Albert MS, Keene CD, Saykin AJ, Larson EB, Sperling RA, Mayeux R, Thompson PM, Martin ER, Bennett DA, Barnes LL, Schneider JA, Crane PK, Hohman TJ, Dumitrescu L. Sex‐specific genetic predictors of memory, executive function, and language performance. Alzheimers Dement 2022. [DOI: 10.1002/alz.067842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Jaclyn M. Eissman
- Vanderbilt Memory & Alzheimer’s Center, Vanderbilt University Medical Center Nashville TN USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center Nashville TN USA
| | - Alexandra N. Smith
- Vanderbilt Memory & Alzheimer’s Center, Vanderbilt University Medical Center Nashville TN USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center Nashville TN USA
| | | | | | | | | | | | - Jesse B. Mez
- Boston University School of Medicine Boston MA USA
| | - William S. Bush
- Cleveland Institute for Computational Biology, Case Western Reserve University Cleveland OH USA
| | | | - Qiongshi Lu
- University of Wisconsin School of Medicine and Public Health Madison WI USA
| | - David W. Fardo
- College of Public Health, University of Kentucky Lexington KY USA
- Sanders‐Brown Center on Aging, University of Kentucky Lexington KY USA
| | | | - Rachel F. Buckley
- Massachusetts General Hospital, Harvard Medical School Boston MA USA
- Melbourne School of Psychological Sciences, University of Melbourne Melbourne VIC Australia
- Center for Alzheimer’s Research and Treatment, Brigham and Women’s Hospital/Harvard Medical School Boston MA USA
| | | | - Brian W. Kunkle
- John P. Hussman Institute for Human Genomics, Miller School of Medicine Miami FL USA
| | - Adam C. Naj
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine Philadelphia PA USA
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine Philadelphia PA USA
| | - Lindsay R. Clark
- University of Wisconsin School of Medicine and Public Health Madison WI USA
| | - Katherine A. Gifford
- Vanderbilt Memory & Alzheimer’s Center, Vanderbilt University Medical Center Nashville TN USA
| | - Michael L. Cuccaro
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | | | - Margaret A. Pericak‐Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | - Lindsay A. Farrer
- Boston University School of Medicine Boston MA USA
- Boston University School of Public Health Boston MA USA
| | - Li‐San Wang
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine Philadelphia PA USA
| | - Gerard D. Schellenberg
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine Philadelphia PA USA
| | - Jonathan L. Haines
- Cleveland Institute for Computational Biology, Case Western Reserve University Cleveland OH USA
| | - Angela L. Jefferson
- Vanderbilt Memory & Alzheimer’s Center, Vanderbilt University Medical Center Nashville TN USA
| | | | | | - Marilyn S. Albert
- Department of Neurology, Johns Hopkins University School of Medicine Baltimore MD USA
| | | | - Andrew J. Saykin
- Indiana Alzheimer’s Disease Research Center, Indiana University School of Medicine Indianapolis IN USA
- Indiana University School of Medicine Indianapolis IN USA
| | - Eric B Larson
- University of Washington Seattle WA USA
- Kaiser Permanente Washington Health Research Institute Seattle WA USA
| | - Reisa A. Sperling
- Massachusetts General Hospital, Harvard Medical School Boston MA USA
- Center for Alzheimer’s Research and Treatment, Brigham and Women’s Hospital/Harvard Medical School Boston MA USA
| | - Richard Mayeux
- Columbia University New York NY USA
- The Taub Institute for Research on Alzheimer’s Disease and The Aging Brain, Columbia University New York NY USA
- The Institute for Genomic Medicine, Columbia University Medical Center and The New York Presbyterian Hospital New York NY USA
| | - Paul M Thompson
- Keck School of Medicine, University of Southern California Los Angeles CA USA
| | - Eden R Martin
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center Chicago IL USA
| | - Lisa L. Barnes
- Rush Alzheimer's Disease Center, Rush University Medical Center Chicago IL USA
| | - Julie A Schneider
- Rush Alzheimer's Disease Center, Rush University Medical Center Chicago IL USA
| | | | - Timothy J. Hohman
- Vanderbilt Memory & Alzheimer’s Center, Vanderbilt University Medical Center Nashville TN USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center Nashville TN USA
| | - Logan Dumitrescu
- Vanderbilt Memory & Alzheimer’s Center, Vanderbilt University Medical Center Nashville TN USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center Nashville TN USA
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Godrich D, Pasteris J, Martin ER, Schellenberg GD, Pericak‐Vance MA, Cuccaro ML, Scott WK, Kukull WA, Montine TJ, Beecham GW. Alzheimer Disease candidate variants are associated with cerebral amyloid angiopathy. Alzheimers Dement 2022. [DOI: 10.1002/alz.067799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Dana Godrich
- Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami Miami FL USA
| | - Jeremy Pasteris
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | - Eden R. Martin
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | - Gerard D. Schellenberg
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania Philadelphia PA USA
| | - Margaret A. Pericak‐Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | - Michael L. Cuccaro
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - William K. Scott
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | - Walter A. Kukull
- National Alzheimer's Coordinating Center, University of Washington Seattle WA USA
| | | | - Gary W. Beecham
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
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29
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Li D, Farrell J, Mez JB, Martin ER, Bush WS, Mayeux R, Haines JL, Pericak‐Vance MA, Wang L, Schellenberg GD, Lunetta KL, Farrer LA. Novel Loci for Alzheimer Disease Identified by Genome Wide Association Study in Ashkenazi Jews. Alzheimers Dement 2022. [DOI: 10.1002/alz.062075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Donghe Li
- Boston University School of Medicine Boston MA USA
| | - John Farrell
- Boston University School of Medicine Boston MA USA
| | - Jesse B. Mez
- Boston University School of Medicine Boston MA USA
| | - Eden R. Martin
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - William S. Bush
- Cleveland Institute for Computational Biology, Case Western Reserve University Cleveland OH USA
- Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
| | - Richard Mayeux
- The Taub Institute for Research on Alzheimer’s Disease and The Aging Brain, Columbia University New York NY USA
| | - Jonathan L. Haines
- Cleveland Institute for Computational Biology, Department of Population and Quantitative Health Sciences, Case Western Reserve University Cleveland OH USA
- Case Western Reserve University School of Medicine Cleveland OH USA
| | - Margaret A. Pericak‐Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
- Department of Neurology, University of Miami Miller School of Medicine Miami FL USA
| | - Li‐San Wang
- Perelman School of Medicine, University of Pennsylvania Philadelphia PA USA
| | | | | | - Lindsay A. Farrer
- Boston University School of Medicine Boston MA USA
- Boston University School of Public Health Boston MA USA
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Neupane A, da Fonseca EL, Kurup JT, Pericak‐Vance MA, Martin ER, Schellenberg GD, Reitz C, Beecham GW, Cruchaga C, Fernandez V. A large‐scale genome‐wide association study of early‐onset Alzheimer disease. Alzheimers Dement 2022. [DOI: 10.1002/alz.064268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Achal Neupane
- Washington University in St. Louis School of Medicine, St. Louis MO USA
- Hope Center for Neurological Disorders St. Louis MO USA
| | - Eder Lucio da Fonseca
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
| | - Jiji Thulaseedhara Kurup
- Columbia University, The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, The Gertrude H. Sergievsky Center and Departments of Neurology and Epidemiology New York NY USA
| | - Margaret A. Pericak‐Vance
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | - Eden R. Martin
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
| | | | - Christiane Reitz
- Columbia University, The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, The Gertrude H. Sergievsky Center and Departments of Neurology and Epidemiology New York NY USA
- Columbia University Medical Center New York NY USA
| | - Gary W. Beecham
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine Miami FL USA
| | - Carlos Cruchaga
- Hope Center for Neurological Disorders Saint Louis MO USA
- Washington University School of Medicine St Louis MO USA
| | - Victoria Fernandez
- Washington University in St. Louis School of Medicine, St. Louis MO USA
- Hope Center for Neurological Disorders St. Louis MO USA
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31
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C. Silva T, Zhang W, Young JI, Gomez L, Schmidt MA, Varma A, Chen XS, Martin ER, Wang L. Distinct sex-specific DNA methylation differences in Alzheimer's disease. Alzheimers Res Ther 2022; 14:133. [PMID: 36109771 PMCID: PMC9479371 DOI: 10.1186/s13195-022-01070-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 08/30/2022] [Indexed: 01/17/2023]
Abstract
BACKGROUND Sex is increasingly recognized as a significant factor contributing to the biological and clinical heterogeneity in AD. There is also growing evidence for the prominent role of DNA methylation (DNAm) in Alzheimer's disease (AD). METHODS We studied sex-specific DNA methylation differences in the blood samples of AD subjects compared to cognitively normal subjects, by performing sex-specific meta-analyses of two large blood-based epigenome-wide association studies (ADNI and AIBL), which included DNA methylation data for a total of 1284 whole blood samples (632 females and 652 males). Within each dataset, we used two complementary analytical strategies, a sex-stratified analysis that examined methylation to AD associations in male and female samples separately, and a methylation-by-sex interaction analysis that compared the magnitude of these associations between different sexes. After adjusting for age, estimated immune cell type proportions, batch effects, and correcting for inflation, the inverse-variance fixed-effects meta-analysis model was used to identify the most consistent DNAm differences across datasets. In addition, we also evaluated the performance of the sex-specific methylation-based risk prediction models for AD diagnosis using an independent external dataset. RESULTS In the sex-stratified analysis, we identified 2 CpGs, mapped to the PRRC2A and RPS8 genes, significantly associated with AD in females at a 5% false discovery rate, and an additional 25 significant CpGs (21 in females, 4 in males) at P-value < 1×10-5. In methylation-by-sex interaction analysis, we identified 5 significant CpGs at P-value < 10-5. Out-of-sample validations using the AddNeuroMed dataset showed in females, the best logistic prediction model included age, estimated immune cell-type proportions, and methylation risk scores (MRS) computed from 9 of the 23 CpGs identified in AD vs. CN analysis that are also available in AddNeuroMed dataset (AUC = 0.74, 95% CI: 0.65-0.83). In males, the best logistic prediction model included only age and MRS computed from 2 of the 5 CpGs identified in methylation-by-sex interaction analysis that are also available in the AddNeuroMed dataset (AUC = 0.70, 95% CI: 0.56-0.82). CONCLUSIONS Overall, our results show that the DNA methylation differences in AD are largely distinct between males and females. Our best-performing sex-specific methylation-based prediction model in females performed better than that for males and additionally included estimated cell-type proportions. The significant discriminatory classification of AD samples with our methylation-based prediction models demonstrates that sex-specific DNA methylation could be a predictive biomarker for AD. As sex is a strong factor underlying phenotypic variability in AD, the results of our study are particularly relevant for a better understanding of the epigenetic architecture that underlie AD and for promoting precision medicine in AD.
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Affiliation(s)
- Tiago C. Silva
- grid.26790.3a0000 0004 1936 8606Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, 1120 NW 14th Street, Miami, FL 33136 USA
| | - Wei Zhang
- grid.26790.3a0000 0004 1936 8606Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, 1120 NW 14th Street, Miami, FL 33136 USA
| | - Juan I. Young
- grid.26790.3a0000 0004 1936 8606Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Lissette Gomez
- grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Michael A. Schmidt
- grid.26790.3a0000 0004 1936 8606Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Achintya Varma
- grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - X. Steven Chen
- grid.26790.3a0000 0004 1936 8606Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, 1120 NW 14th Street, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
| | - Eden R. Martin
- grid.26790.3a0000 0004 1936 8606Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Lily Wang
- grid.26790.3a0000 0004 1936 8606Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, 1120 NW 14th Street, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
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Gardner OK, Van Booven D, Wang L, Gu T, Hofmann NK, Whitehead PL, Nuytemans K, Hamilton-Nelson KL, Adams LD, Starks TD, Cuccaro ML, Martin ER, Vance JM, Bush WS, Byrd GS, Haines JL, Beecham GW, Pericak-Vance MA, Griswold AJ. Genetic architecture of RNA editing regulation in Alzheimer's disease across diverse ancestral populations. Hum Mol Genet 2022; 31:2876-2886. [PMID: 35383839 PMCID: PMC9433728 DOI: 10.1093/hmg/ddac075] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 03/24/2022] [Accepted: 03/27/2022] [Indexed: 11/14/2022] Open
Abstract
Most Alzheimer's disease (AD)-associated genetic variants do not change protein coding sequence and thus likely exert their effects through regulatory mechanisms. RNA editing, the post-transcriptional modification of RNA bases, is a regulatory feature that is altered in AD patients that differs across ancestral backgrounds. Editing QTLs (edQTLs) are DNA variants that influence the level of RNA editing at a specific site. To study the relationship of DNA variants genome-wide, and particularly in AD-associated loci, with RNA editing, we performed edQTL analyses in self-reported individuals of African American (AF) or White (EU) race with corresponding global genetic ancestry averaging 82.2% African ancestry (AF) and 96.8% European global ancestry (EU) in the two groups, respectively. We used whole-genome genotyping array and RNA sequencing data from peripheral blood of 216 AD cases and 212 age-matched, cognitively intact controls. We identified 2144 edQTLs in AF and 3579 in EU, of which 1236 were found in both groups. Among these, edQTLs in linkage disequilibrium (r2 > 0.5) with AD-associated genetic variants in the SORL1, SPI1 and HLA-DRB1 loci were associated with sites that were differentially edited between AD cases and controls. While there is some shared RNA editing regulatory architecture, most edQTLs had distinct effects on the rate of RNA editing in different ancestral populations suggesting a complex architecture of RNA editing regulation. Altered RNA editing may be one possible mechanism for the functional effect of AD-associated variants and may contribute to observed differences in the genetic etiology of AD between ancestries.
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Affiliation(s)
- Olivia K Gardner
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Derek Van Booven
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Lily Wang
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Tianjie Gu
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Natalia K Hofmann
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Patrice L Whitehead
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Karen Nuytemans
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
- Maya Angelou Center for Health Equity, Wake Forest University, Winston-Salem, NC 27101, USA
| | - Kara L Hamilton-Nelson
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Larry D Adams
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Takiyah D Starks
- Maya Angelou Center for Health Equity, Wake Forest University, Winston-Salem, NC 27101, USA
| | - Michael L Cuccaro
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
- Department of Human Genetics, Dr. John T Macdonald Foundation, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Eden R Martin
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
- Department of Human Genetics, Dr. John T Macdonald Foundation, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Jeffery M Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
- Department of Human Genetics, Dr. John T Macdonald Foundation, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - William S Bush
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
- Cleveland Institute for Computational Biology, Cleveland, OH 44106, USA
| | - Goldie S Byrd
- Maya Angelou Center for Health Equity, Wake Forest University, Winston-Salem, NC 27101, USA
| | - Jonathan L Haines
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
- Cleveland Institute for Computational Biology, Cleveland, OH 44106, USA
| | - Gary W Beecham
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
- Department of Human Genetics, Dr. John T Macdonald Foundation, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
- Department of Human Genetics, Dr. John T Macdonald Foundation, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Anthony J Griswold
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
- Department of Human Genetics, Dr. John T Macdonald Foundation, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
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33
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C. Silva T, Young JI, Zhang L, Gomez L, Schmidt MA, Varma A, Chen XS, Martin ER, Wang L. Cross-tissue analysis of blood and brain epigenome-wide association studies in Alzheimer's disease. Nat Commun 2022; 13:4852. [PMID: 35982059 PMCID: PMC9388493 DOI: 10.1038/s41467-022-32475-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 08/01/2022] [Indexed: 01/17/2023] Open
Abstract
To better understand DNA methylation in Alzheimer's disease (AD) from both mechanistic and biomarker perspectives, we performed an epigenome-wide meta-analysis of blood DNA methylation in two large independent blood-based studies in AD, the ADNI and AIBL studies, and identified 5 CpGs, mapped to the SPIDR, CDH6 genes, and intergenic regions, that are significantly associated with AD diagnosis. A cross-tissue analysis that combined these blood DNA methylation datasets with four brain methylation datasets prioritized 97 CpGs and 10 genomic regions that are significantly associated with both AD neuropathology and AD diagnosis. An out-of-sample validation using the AddNeuroMed dataset showed the best performing logistic regression model includes age, sex, immune cell type proportions, and methylation risk score based on prioritized CpGs in cross-tissue analysis (AUC = 0.696, 95% CI: 0.616 - 0.770, P-value = 2.78 × 10-5). Our study offers new insights into epigenetics in AD and provides a valuable resource for future AD biomarker discovery.
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Affiliation(s)
- Tiago C. Silva
- grid.26790.3a0000 0004 1936 8606Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
| | - Juan I. Young
- grid.26790.3a0000 0004 1936 8606Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Lanyu Zhang
- grid.26790.3a0000 0004 1936 8606Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
| | - Lissette Gomez
- grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Michael A. Schmidt
- grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Achintya Varma
- grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - X. Steven Chen
- grid.26790.3a0000 0004 1936 8606Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
| | - Eden R. Martin
- grid.26790.3a0000 0004 1936 8606Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Lily Wang
- grid.26790.3a0000 0004 1936 8606Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
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34
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Chung J, Das A, Sun X, Sobreira DR, Leung YY, Igartua C, Mozaffari S, Chou YF, Thiagalingam S, Mez J, Zhang X, Jun GR, Stein TD, Kunkle BW, Martin ER, Pericak-Vance MA, Mayeux R, Haines JL, Schellenberg GD, Nobrega MA, Lunetta KL, Pinto JM, Wang LS, Ober C, Farrer LA. Genome-wide association and multi-omics studies identify MGMT as a novel risk gene for Alzheimer's disease among women. Alzheimers Dement 2022; 19:10.1002/alz.12719. [PMID: 35770850 PMCID: PMC9800643 DOI: 10.1002/alz.12719] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 01/18/2023]
Abstract
INTRODUCTION Variants in the tau gene (MAPT) region are associated with breast cancer in women and Alzheimer's disease (AD) among persons lacking apolipoprotein E ε4 (ε4-). METHODS To identify novel genes associated with tau-related pathology, we conducted two genome-wide association studies (GWAS) for AD, one among 10,340 ε4- women in the Alzheimer's Disease Genetics Consortium (ADGC) and another in 31 members (22 women) of a consanguineous Hutterite kindred. RESULTS We identified novel associations of AD with MGMT variants in the ADGC (rs12775171, odds ratio [OR] = 1.4, P = 4.9 × 10-8 ) and Hutterite (rs12256016 and rs2803456, OR = 2.0, P = 1.9 × 10-14 ) datasets. Multi-omics analyses showed that the most significant and largest number of associations among the single nucleotide polymorphisms (SNPs), DNA-methylated CpGs, MGMT expression, and AD-related neuropathological traits were observed among women. Furthermore, promoter capture Hi-C analyses revealed long-range interactions of the MGMT promoter with MGMT SNPs and CpG sites. DISCUSSION These findings suggest that epigenetically regulated MGMT expression is involved in AD pathogenesis, especially in women.
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Affiliation(s)
- Jaeyoon Chung
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts, USA
| | - Anjali Das
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, USA
| | - Xinyu Sun
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts, USA
| | - Débora R Sobreira
- Department of Surgery/Section of Otolaryngology-Head and Neck Surgery, The University of Chicago, Chicago, Illinois, USA
| | - Yuk Yee Leung
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Catherine Igartua
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, USA
| | - Sahar Mozaffari
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, USA
| | - Yi-Fan Chou
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Sam Thiagalingam
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts, USA
| | - Jesse Mez
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Xiaoling Zhang
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts, USA
| | - Gyungah R Jun
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts, USA
- Department of Ophthalmology, Boston University School of Medicine, Boston, Massachusetts, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Thor D Stein
- Department of Pathology & Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Brian W Kunkle
- Dr. John T. Macdonald Foundation of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Eden R Martin
- Dr. John T. Macdonald Foundation of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Margaret A Pericak-Vance
- Dr. John T. Macdonald Foundation of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Richard Mayeux
- Department of Neurology, Columbia University, New York City, New York, USA
| | - Jonathan L Haines
- Department of Population and Quantitative Health Sciences and Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Gerard D Schellenberg
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Marcelo A Nobrega
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, USA
| | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Jayant M Pinto
- Department of Surgery/Section of Otolaryngology-Head and Neck Surgery, The University of Chicago, Chicago, Illinois, USA
| | - Li-San Wang
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Carole Ober
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, USA
| | - Lindsay A Farrer
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts, USA
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, USA
- Department of Ophthalmology, Boston University School of Medicine, Boston, Massachusetts, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, Massachusetts, USA
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Jin B, Capra JA, Benchek P, Wheeler N, Naj AC, Hamilton-Nelson KL, Farrell JJ, Leung YY, Kunkle B, Vadarajan B, Schellenberg GD, Mayeux R, Wang LS, Farrer LA, Pericak-Vance MA, Martin ER, Haines JL, Crawford DC, Bush WS. Corrigendum: An association test of the spatial distribution of rare missense variants within protein structures identifies Alzheimer's disease–related patterns. Genome Res 2022. [PMCID: PMC9248876 DOI: 10.1101/gr.276900.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Silva TC, Young JI, Martin ER, Chen XS, Wang L. MethReg: estimating the regulatory potential of DNA methylation in gene transcription. Nucleic Acids Res 2022; 50:e51. [PMID: 35100398 PMCID: PMC9122535 DOI: 10.1093/nar/gkac030] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 12/17/2021] [Accepted: 01/11/2022] [Indexed: 01/02/2023] Open
Abstract
Epigenome-wide association studies often detect many differentially methylated sites, and many are located in distal regulatory regions. To further prioritize these significant sites, there is a critical need to better understand the functional impact of CpG methylation. Recent studies demonstrated that CpG methylation-dependent transcriptional regulation is a widespread phenomenon. Here, we present MethReg, an R/Bioconductor package that analyzes matched DNA methylation and gene expression data, along with external transcription factor (TF) binding information, to evaluate, prioritize and annotate CpG sites with high regulatory potential. At these CpG sites, TF-target gene associations are often only present in a subset of samples with high (or low) methylation levels, so they can be missed by analyses that use all samples. Using colorectal cancer and Alzheimer's disease datasets, we show MethReg significantly enhances our understanding of the regulatory roles of DNA methylation in complex diseases.
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Affiliation(s)
- Tiago C Silva
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Juan I Young
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Eden R Martin
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - X Steven Chen
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Lily Wang
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
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Heath L, Earls JC, Magis AT, Kornilov SA, Lovejoy JC, Funk CC, Rappaport N, Logsdon BA, Mangravite LM, Kunkle BW, Martin ER, Naj AC, Ertekin-Taner N, Golde TE, Hood L, Price ND. Manifestations of Alzheimer's disease genetic risk in the blood are evident in a multiomic analysis in healthy adults aged 18 to 90. Sci Rep 2022; 12:6117. [PMID: 35413975 PMCID: PMC9005657 DOI: 10.1038/s41598-022-09825-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/23/2022] [Indexed: 01/18/2023] Open
Abstract
Genetics play an important role in late-onset Alzheimer's Disease (AD) etiology and dozens of genetic variants have been implicated in AD risk through large-scale GWAS meta-analyses. However, the precise mechanistic effects of most of these variants have yet to be determined. Deeply phenotyped cohort data can reveal physiological changes associated with genetic risk for AD across an age spectrum that may provide clues to the biology of the disease. We utilized over 2000 high-quality quantitative measurements obtained from blood of 2831 cognitively normal adult clients of a consumer-based scientific wellness company, each with CLIA-certified whole-genome sequencing data. Measurements included: clinical laboratory blood tests, targeted chip-based proteomics, and metabolomics. We performed a phenome-wide association study utilizing this diverse blood marker data and 25 known AD genetic variants and an AD-specific polygenic risk score (PGRS), adjusting for sex, age, vendor (for clinical labs), and the first four genetic principal components; sex-SNP interactions were also assessed. We observed statistically significant SNP-analyte associations for five genetic variants after correction for multiple testing (for SNPs in or near NYAP1, ABCA7, INPP5D, and APOE), with effects detectable from early adulthood. The ABCA7 SNP and the APOE2 and APOE4 encoding alleles were associated with lipid variability, as seen in previous studies; in addition, six novel proteins were associated with the e2 allele. The most statistically significant finding was between the NYAP1 variant and PILRA and PILRB protein levels, supporting previous functional genomic studies in the identification of a putative causal variant within the PILRA gene. We did not observe associations between the PGRS and any analyte. Sex modified the effects of four genetic variants, with multiple interrelated immune-modulating effects associated with the PICALM variant. In post-hoc analysis, sex-stratified GWAS results from an independent AD case-control meta-analysis supported sex-specific disease effects of the PICALM variant, highlighting the importance of sex as a biological variable. Known AD genetic variation influenced lipid metabolism and immune response systems in a population of non-AD individuals, with associations observed from early adulthood onward. Further research is needed to determine whether and how these effects are implicated in early-stage biological pathways to AD. These analyses aim to complement ongoing work on the functional interpretation of AD-associated genetic variants.
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Affiliation(s)
- Laura Heath
- Institute for Systems Biology, Seattle, WA, USA.
- Sage Bionetworks, Seattle, WA, USA.
| | - John C Earls
- Institute for Systems Biology, Seattle, WA, USA
- Thorne HealthTech, New York, NY, USA
| | | | | | | | - Cory C Funk
- Institute for Systems Biology, Seattle, WA, USA
| | | | | | | | - Brian W Kunkle
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Eden R Martin
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Adam C Naj
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Nilüfer Ertekin-Taner
- Department of Neurology, Mayo Clinic, Jacksonville, FL, USA
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Todd E Golde
- Department of Neuroscience, College of Medicine, McKnight Brain Institute, Center for Translational Research in Neurodegenerative Disease University of Florida, Gainesville, FL, USA
| | - Leroy Hood
- Institute for Systems Biology, Seattle, WA, USA
- Providence St. Joseph Health, Renton, WA, USA
| | - Nathan D Price
- Institute for Systems Biology, Seattle, WA, USA.
- Thorne HealthTech, New York, NY, USA.
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38
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Bellenguez C, Küçükali F, Jansen IE, Kleineidam L, Moreno-Grau S, Amin N, Naj AC, Campos-Martin R, Grenier-Boley B, Andrade V, Holmans PA, Boland A, Damotte V, van der Lee SJ, Costa MR, Kuulasmaa T, Yang Q, de Rojas I, Bis JC, Yaqub A, Prokic I, Chapuis J, Ahmad S, Giedraitis V, Aarsland D, Garcia-Gonzalez P, Abdelnour C, Alarcón-Martín E, Alcolea D, Alegret M, Alvarez I, Álvarez V, Armstrong NJ, Tsolaki A, Antúnez C, Appollonio I, Arcaro M, Archetti S, Pastor AA, Arosio B, Athanasiu L, Bailly H, Banaj N, Baquero M, Barral S, Beiser A, Pastor AB, Below JE, Benchek P, Benussi L, Berr C, Besse C, Bessi V, Binetti G, Bizarro A, Blesa R, Boada M, Boerwinkle E, Borroni B, Boschi S, Bossù P, Bråthen G, Bressler J, Bresner C, Brodaty H, Brookes KJ, Brusco LI, Buiza-Rueda D, Bûrger K, Burholt V, Bush WS, Calero M, Cantwell LB, Chene G, Chung J, Cuccaro ML, Carracedo Á, Cecchetti R, Cervera-Carles L, Charbonnier C, Chen HH, Chillotti C, Ciccone S, Claassen JAHR, Clark C, Conti E, Corma-Gómez A, Costantini E, Custodero C, Daian D, Dalmasso MC, Daniele A, Dardiotis E, Dartigues JF, de Deyn PP, de Paiva Lopes K, de Witte LD, Debette S, Deckert J, Del Ser T, Denning N, DeStefano A, Dichgans M, Diehl-Schmid J, Diez-Fairen M, Rossi PD, Djurovic S, Duron E, Düzel E, Dufouil C, Eiriksdottir G, Engelborghs S, Escott-Price V, Espinosa A, Ewers M, Faber KM, Fabrizio T, Nielsen SF, Fardo DW, Farotti L, Fenoglio C, Fernández-Fuertes M, Ferrari R, Ferreira CB, Ferri E, Fin B, Fischer P, Fladby T, Fließbach K, Fongang B, Fornage M, Fortea J, Foroud TM, Fostinelli S, Fox NC, Franco-Macías E, Bullido MJ, Frank-García A, Froelich L, Fulton-Howard B, Galimberti D, García-Alberca JM, García-González P, Garcia-Madrona S, Garcia-Ribas G, Ghidoni R, Giegling I, Giorgio G, Goate AM, Goldhardt O, Gomez-Fonseca D, González-Pérez A, Graff C, Grande G, Green E, Grimmer T, Grünblatt E, Grunin M, Gudnason V, Guetta-Baranes T, Haapasalo A, Hadjigeorgiou G, Haines JL, Hamilton-Nelson KL, Hampel H, Hanon O, Hardy J, Hartmann AM, Hausner L, Harwood J, Heilmann-Heimbach S, Helisalmi S, Heneka MT, Hernández I, Herrmann MJ, Hoffmann P, Holmes C, Holstege H, Vilas RH, Hulsman M, Humphrey J, Biessels GJ, Jian X, Johansson C, Jun GR, Kastumata Y, Kauwe J, Kehoe PG, Kilander L, Ståhlbom AK, Kivipelto M, Koivisto A, Kornhuber J, Kosmidis MH, Kukull WA, Kuksa PP, Kunkle BW, Kuzma AB, Lage C, Laukka EJ, Launer L, Lauria A, Lee CY, Lehtisalo J, Lerch O, Lleó A, Longstreth W, Lopez O, de Munain AL, Love S, Löwemark M, Luckcuck L, Lunetta KL, Ma Y, Macías J, MacLeod CA, Maier W, Mangialasche F, Spallazzi M, Marquié M, Marshall R, Martin ER, Montes AM, Rodríguez CM, Masullo C, Mayeux R, Mead S, Mecocci P, Medina M, Meggy A, Mehrabian S, Mendoza S, Menéndez-González M, Mir P, Moebus S, Mol M, Molina-Porcel L, Montrreal L, Morelli L, Moreno F, Morgan K, Mosley T, Nöthen MM, Muchnik C, Mukherjee S, Nacmias B, Ngandu T, Nicolas G, Nordestgaard BG, Olaso R, Orellana A, Orsini M, Ortega G, Padovani A, Paolo C, Papenberg G, Parnetti L, Pasquier F, Pastor P, Peloso G, Pérez-Cordón A, Pérez-Tur J, Pericard P, Peters O, Pijnenburg YAL, Pineda JA, Piñol-Ripoll G, Pisanu C, Polak T, Popp J, Posthuma D, Priller J, Puerta R, Quenez O, Quintela I, Thomassen JQ, Rábano A, Rainero I, Rajabli F, Ramakers I, Real LM, Reinders MJT, Reitz C, Reyes-Dumeyer D, Ridge P, Riedel-Heller S, Riederer P, Roberto N, Rodriguez-Rodriguez E, Rongve A, Allende IR, Rosende-Roca M, Royo JL, Rubino E, Rujescu D, Sáez ME, Sakka P, Saltvedt I, Sanabria Á, Sánchez-Arjona MB, Sanchez-Garcia F, Juan PS, Sánchez-Valle R, Sando SB, Sarnowski C, Satizabal CL, Scamosci M, Scarmeas N, Scarpini E, Scheltens P, Scherbaum N, Scherer M, Schmid M, Schneider A, Schott JM, Selbæk G, Seripa D, Serrano M, Sha J, Shadrin AA, Skrobot O, Slifer S, Snijders GJL, Soininen H, Solfrizzi V, Solomon A, Song Y, Sorbi S, Sotolongo-Grau O, Spalletta G, Spottke A, Squassina A, Stordal E, Tartan JP, Tárraga L, Tesí N, Thalamuthu A, Thomas T, Tosto G, Traykov L, Tremolizzo L, Tybjærg-Hansen A, Uitterlinden A, Ullgren A, Ulstein I, Valero S, Valladares O, Broeckhoven CV, Vance J, Vardarajan BN, van der Lugt A, Dongen JV, van Rooij J, van Swieten J, Vandenberghe R, Verhey F, Vidal JS, Vogelgsang J, Vyhnalek M, Wagner M, Wallon D, Wang LS, Wang R, Weinhold L, Wiltfang J, Windle G, Woods B, Yannakoulia M, Zare H, Zhao Y, Zhang X, Zhu C, Zulaica M, Farrer LA, Psaty BM, Ghanbari M, Raj T, Sachdev P, Mather K, Jessen F, Ikram MA, de Mendonça A, Hort J, Tsolaki M, Pericak-Vance MA, Amouyel P, Williams J, Frikke-Schmidt R, Clarimon J, Deleuze JF, Rossi G, Seshadri S, Andreassen OA, Ingelsson M, Hiltunen M, Sleegers K, Schellenberg GD, van Duijn CM, Sims R, van der Flier WM, Ruiz A, Ramirez A, Lambert JC. New insights into the genetic etiology of Alzheimer's disease and related dementias. Nat Genet 2022; 54:412-436. [PMID: 35379992 PMCID: PMC9005347 DOI: 10.1038/s41588-022-01024-z] [Citation(s) in RCA: 582] [Impact Index Per Article: 291.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 01/27/2022] [Indexed: 02/08/2023]
Abstract
Characterization of the genetic landscape of Alzheimer's disease (AD) and related dementias (ADD) provides a unique opportunity for a better understanding of the associated pathophysiological processes. We performed a two-stage genome-wide association study totaling 111,326 clinically diagnosed/'proxy' AD cases and 677,663 controls. We found 75 risk loci, of which 42 were new at the time of analysis. Pathway enrichment analyses confirmed the involvement of amyloid/tau pathways and highlighted microglia implication. Gene prioritization in the new loci identified 31 genes that were suggestive of new genetically associated processes, including the tumor necrosis factor alpha pathway through the linear ubiquitin chain assembly complex. We also built a new genetic risk score associated with the risk of future AD/dementia or progression from mild cognitive impairment to AD/dementia. The improvement in prediction led to a 1.6- to 1.9-fold increase in AD risk from the lowest to the highest decile, in addition to effects of age and the APOE ε4 allele.
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Affiliation(s)
- Céline Bellenguez
- Université de Lille, INSERM, CHU Lille, Institut Pasteur Lille, U1167-RID-AGE, Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, Lille, France.
| | - Fahri Küçükali
- Complex Genetics of Alzheimer's Disease Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Laboratory of Neurogenetics, Institute Born - Bunge, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Iris E Jansen
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije University, Amsterdam, the Netherlands
| | - Luca Kleineidam
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, Bonn, Germany
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, University of Cologne, Medical Faculty, Cologne, Germany
- German Center for Neurodegenerative Diseases (DZNE Bonn), Bonn, Germany
| | - Sonia Moreno-Grau
- Research Center and Memory Clinic Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Najaf Amin
- Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands
- Nuffield Department of Population Health, Oxford University, Oxford, UK
| | - Adam C Naj
- Department of Biostatistics, Epidemiology, and Informatics, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Rafael Campos-Martin
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, University of Cologne, Medical Faculty, Cologne, Germany
| | - Benjamin Grenier-Boley
- Université de Lille, INSERM, CHU Lille, Institut Pasteur Lille, U1167-RID-AGE, Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, Lille, France
| | - Victor Andrade
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, Bonn, Germany
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, University of Cologne, Medical Faculty, Cologne, Germany
| | - Peter A Holmans
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neuroscience, School of Medicine, Cardiff University, Cardiff, UK
| | - Anne Boland
- CEA, Centre National de Recherche en Génomique Humaine, Université Paris-Saclay, Evry, France
| | - Vincent Damotte
- Université de Lille, INSERM, CHU Lille, Institut Pasteur Lille, U1167-RID-AGE, Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, Lille, France
| | - Sven J van der Lee
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
- Section Genomics of Neurodegenerative Diseases and Aging, Department of Human Genetics Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
| | - Marcos R Costa
- Université de Lille, INSERM, CHU Lille, Institut Pasteur Lille, U1167-RID-AGE, Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, Lille, France
- Brain Institute, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Teemu Kuulasmaa
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Qiong Yang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
| | - Itziar de Rojas
- Research Center and Memory Clinic Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Amber Yaqub
- Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands
| | - Ivana Prokic
- Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands
| | - Julien Chapuis
- Université de Lille, INSERM, CHU Lille, Institut Pasteur Lille, U1167-RID-AGE, Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, Lille, France
| | - Shahzad Ahmad
- Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands
- LACDR, Leiden, the Netherlands
| | - Vilmantas Giedraitis
- Department of Public Health and Carins Sciences/Geriatrics, Uppsala University, Uppsala, Sweden
| | - Dag Aarsland
- Centre of Age-Related Medicine, Stavanger University Hospital, Stavanger, Norway
- Institute of Psychiatry, Psychology & Neuroscience, London, UK
| | - Pablo Garcia-Gonzalez
- Research Center and Memory Clinic Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Carla Abdelnour
- Research Center and Memory Clinic Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Emilio Alarcón-Martín
- Research Center and Memory Clinic Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
- Department of Surgery, Biochemistry and Molecular Biology, School of Medicine, University of Málaga, Málaga, Spain
| | - Daniel Alcolea
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
- Department of Neurology, II B Sant Pau, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Montserrat Alegret
- Research Center and Memory Clinic Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Ignacio Alvarez
- Fundació Docència i Recerca MútuaTerrassa and Movement Disorders Unit, Department of Neurology, University Hospital MútuaTerrassa, Terrassa, Spain
- Memory Disorders Unit, Department of Neurology, Hospital Universitari Mutua de Terrassa, Terrassa, Spain
| | - Victoria Álvarez
- Laboratorio de Genética, Hospital Universitario Central de Asturias, Oviedo, Spain
- Servicio de Neurología, Hospital Universitario Central de Asturias- Oviedo and Instituto de Investigación Biosanitaria del Principado de Asturias, Oviedo, Spain
| | - Nicola J Armstrong
- Centre for Healthy Brain Ageing, School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Anthoula Tsolaki
- First Department of Neurology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Alzheimer Hellas, Thessaloniki, Greece
| | - Carmen Antúnez
- Unidad de Demencias, Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain
| | - Ildebrando Appollonio
- School of Medicine and Surgery, University of Milano-Bicocca, Milano, Italy
- Neurology Unit, San Gerardo Hospital, Monza, Italy
| | - Marina Arcaro
- Fondazione IRCCS Ca'Granda, Ospedale Policlinico, Milan, Italy
| | - Silvana Archetti
- Department of Laboratory Diagnostics, III Laboratory of Analysis, Brescia Hospital, Brescia, Italy
| | - Alfonso Arias Pastor
- Unitat Trastorns Cognitius, Hospital Universitari Santa Maria de Lleida, Lleida, Spain
- Institut de Recerca Biomedica de Lleida (IRBLLeida), Lleida, Spain
| | - Beatrice Arosio
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
- Geriatic Unit, Fondazione Cà Granda, IRCCS Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Henri Bailly
- EA 4468, Université de Paris, APHP, Hôpital Broca, Paris, France
| | - Nerisa Banaj
- Laboratory of Neuropsychiatry, Department of Clinical and Behavioral Neurology, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Miquel Baquero
- Servei de Neurologia, Hospital Universitari i Politècnic La Fe, Valencia, Spain
| | - Sandra Barral
- Taub Institute on Alzheimer's Disease and the Aging Brain, Department of Neurology, Columbia University, New York, NY, USA
- Unit of Neurology, University of Parma and AOU, Parma, Italy
- Clinic of Neurology, UH 'Alexandrovska', Medical University - Sofia, Sofia, Bulgaria
| | - Alexa Beiser
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
- Boston University and the NHLBI's Framingham Heart Study, Boston, MA, USA
| | - Ana Belén Pastor
- CIEN Foundation/Queen Sofia Foundation Alzheimer Center, Madrid, Spain
| | - Jennifer E Below
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA
| | - Penelope Benchek
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Luisa Benussi
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Claudine Berr
- Neuropsychiatry: Epidemiological and Clinical Research, PSNREC, Université de Montpellier, INSERM U1061, Montpellier, France
| | - Céline Besse
- CEA, Centre National de Recherche en Génomique Humaine, Université Paris-Saclay, Evry, France
| | - Valentina Bessi
- Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, Florence, Italy
- Azienda Ospedaliero-Universitaria Careggi, Florence, Italy
| | - Giuliano Binetti
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
- MAC - Memory Clinic, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | | | - Rafael Blesa
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
- Department of Neurology, II B Sant Pau, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Mercè Boada
- Research Center and Memory Clinic Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Eric Boerwinkle
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Barbara Borroni
- Centre for Neurodegenerative Disorders, Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
| | - Silvia Boschi
- Department of Neuroscience "Rita Levi Montalcini", University of Torino, Torino, Italy
| | - Paola Bossù
- Experimental Neuro-psychobiology Laboratory, Department of Clinical and Behavioral Neurology, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Geir Bråthen
- Department of Neurology and Clinical Neurophysiology, University Hospital of Trondheim, Trondheim, Norway
- Department of Neuromedicine and Movement Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jan Bressler
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Catherine Bresner
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neuroscience, School of Medicine, Cardiff University, Cardiff, UK
| | - Henry Brodaty
- Centre for Healthy Brain Ageing, School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
- Dementia Centre for Research Collaboration, School of Psychiatry, University of New South Wales, Sydney, New South Wales, Australia
| | - Keeley J Brookes
- Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Luis Ignacio Brusco
- Centro de Neuropsiquiatría y Neurología de la Conducta (CENECON), Facultad de Medicina, Universidad de Buenos Aires (UBA), C.A.B.A., Buenos Aires, Argentina
- Departamento Ciencias Fisiológicas UAII, Facultad de Medicina, UBA, C.A.B.A., Buenos Aires, Argentina
- Hospital Interzonal General de Agudos Eva Perón, San Martín, Buenos Aires, Argentina
| | - Dolores Buiza-Rueda
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
- Department of Neurology, Erasmus MC, Rotterdam, the Netherlands
| | - Katharina Bûrger
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig Maximilians Universität (LMU), Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE, Munich), Munich, Germany
| | - Vanessa Burholt
- Faculty of Medical & Health Sciences, University of Auckland, Auckland, New Zealand
- Wales Centre for Ageing & Dementia Research, Swansea University, Wales, New Zealand
| | - William S Bush
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Miguel Calero
- Research Center and Memory Clinic Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
- CIEN Foundation/Queen Sofia Foundation Alzheimer Center, Madrid, Spain
- UFIEC, Instituto de Salud Carlos III, Madrid, Spain
| | - Laura B Cantwell
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Geneviève Chene
- INSERM, Bordeaux Population Health Research Center, UMR 1219, ISPED, CIC 1401-EC, Université de Bordeaux, Bordeaux, France
- Pole Santé Publique, CHU de Bordeaux, Bordeaux, France
| | - Jaeyoon Chung
- Medicine Biomedical Genetics Boston University School of Medicine, Boston, MA, USA
| | - Michael L Cuccaro
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, USA
| | - Ángel Carracedo
- Grupo de Medicina Xenómica, Centro Nacional de Genotipado (CEGEN-PRB3-ISCIII), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Fundación Pública Galega de Medicina Xenómica- CIBERER-IDIS, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Roberta Cecchetti
- Institute of Gerontology and Geriatrics, Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Laura Cervera-Carles
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
- Department of Neurology, II B Sant Pau, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Camille Charbonnier
- Department of Genetics and CNR-MAJ, Normandie University, UNIROUEN, INSERM U1245, CHU Rouen, Rouen, France
| | - Hung-Hsin Chen
- Division of Genetic Medicine, Vanderbilt University, Nashville, TN, USA
| | - Caterina Chillotti
- Unit of Clinical Pharmacology, University Hospital of Cagliari, Cagliari, Italy
| | - Simona Ciccone
- Geriatic Unit, Fondazione Cà Granda, IRCCS Ospedale Maggiore Policlinico, Milan, Italy
| | - Jurgen A H R Claassen
- Radboudumc Alzheimer Center, Department of Geriatrics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Christopher Clark
- Institute for Regenerative Medicine, University of Zürich, Schlieren, Switzerland
| | - Elisa Conti
- School of Medicine and Surgery, University of Milano-Bicocca, Milano, Italy
| | - Anaïs Corma-Gómez
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario de Valme, Sevilla, Spain
| | - Emanuele Costantini
- Department of Neuroscience, Catholic University of Sacred Heart, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | | | - Delphine Daian
- CEA, Centre National de Recherche en Génomique Humaine, Université Paris-Saclay, Evry, France
| | - Maria Carolina Dalmasso
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, University of Cologne, Medical Faculty, Cologne, Germany
| | - Antonio Daniele
- Department of Neuroscience, Catholic University of Sacred Heart, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | | | | | - Peter Paul de Deyn
- Department of Neurology, University Medical Center Groningen, Groningen, the Netherlands
| | - Katia de Paiva Lopes
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lot D de Witte
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stéphanie Debette
- Bordeaux Population Health Research Center, University Bordeaux, INSERM, Bordeaux, France
| | - Jürgen Deckert
- Department of Psychiatry, Psychosomatics and Psychotherapy, Center of Mental Health, University Hospital, Wuerzburg, Germany
| | - Teodoro Del Ser
- CIEN Foundation/Queen Sofia Foundation Alzheimer Center, Madrid, Spain
| | - Nicola Denning
- UKDRI@ Cardiff, School of Medicine, Cardiff University, Cardiff, UK
| | - Anita DeStefano
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Martin Dichgans
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig Maximilians Universität (LMU), Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Janine Diehl-Schmid
- Klinikum rechts der Isar, Department of Psychiatry and Psychotherapy, Technical University of Munich, School of Medicine, Munich, Germany
| | - Mónica Diez-Fairen
- Fundació Docència i Recerca MútuaTerrassa and Movement Disorders Unit, Department of Neurology, University Hospital MútuaTerrassa, Terrassa, Spain
- Memory Disorders Unit, Department of Neurology, Hospital Universitari Mutua de Terrassa, Terrassa, Spain
| | - Paolo Dionigi Rossi
- Geriatic Unit, Fondazione Cà Granda, IRCCS Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Emmanuelle Duron
- EA 4468, Université de Paris, APHP, Hôpital Broca, Paris, France
| | - Emrah Düzel
- Institute of Cognitive Neurology and Dementia Research (IKND), Otto-Von-Guericke University, Magdeburg, Germany
- German Center for Neurodegenerative Diseases (DZNE), Magdeburg, Germany
| | - Carole Dufouil
- INSERM, Bordeaux Population Health Research Center, UMR 1219, ISPED, CIC 1401-EC, Université de Bordeaux, Bordeaux, France
- Pole Santé Publique, CHU de Bordeaux, Bordeaux, France
| | | | - Sebastiaan Engelborghs
- Center for Neurosciences, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- Reference Center for Biological Markers of Dementia (BIODEM), Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
- Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
- Department of Neurology, UZ Brussel, Brussels, Belgium
| | - Valentina Escott-Price
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- UKDRI@ Cardiff, School of Medicine, Cardiff University, Cardiff, UK
| | - Ana Espinosa
- Research Center and Memory Clinic Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Michael Ewers
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig Maximilians Universität (LMU), Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE, Munich), Munich, Germany
| | - Kelley M Faber
- Department of Medical and Molecular Genetics, Indiana University, Indianapolis, IN, USA
| | | | | | - David W Fardo
- Sanders-Brown Center on Aging, Department of Biostatistics, University of Kentucky, Lexington, KY, USA
| | - Lucia Farotti
- Centre for Memory Disturbances, Lab of Clinical Neurochemistry, Section of Neurology, University of Perugia, Perugia, Italy
| | | | - Marta Fernández-Fuertes
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario de Valme, Sevilla, Spain
| | - Raffaele Ferrari
- Laboratory of Neurogenetics, Department of Internal Medicine, Texas Tech University Health Science Center, Lubbock, TX, USA
- Reta Lila Weston Research Laboratories, Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | | | - Evelyn Ferri
- Geriatic Unit, Fondazione Cà Granda, IRCCS Ospedale Maggiore Policlinico, Milan, Italy
| | - Bertrand Fin
- CEA, Centre National de Recherche en Génomique Humaine, Université Paris-Saclay, Evry, France
| | - Peter Fischer
- Department of Psychiatry, Social Medicine Center East- Donauspital, Vienna, Austria
| | - Tormod Fladby
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Klaus Fließbach
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, University of Cologne, Medical Faculty, Cologne, Germany
- German Center for Neurodegenerative Diseases (DZNE Bonn), Bonn, Germany
| | - Bernard Fongang
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas Health Sciences Center, San Antonio, TX, USA
| | - Myriam Fornage
- Department of Neuromedicine and Movement Science, Norwegian University of Science and Technology, Trondheim, Norway
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Juan Fortea
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
- Department of Neurology, II B Sant Pau, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Tatiana M Foroud
- Department of Medical and Molecular Genetics, Indiana University, Indianapolis, IN, USA
| | - Silvia Fostinelli
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Nick C Fox
- Dementia Research Centre, UCL Queen Square Institute of Neurology, London, UK
| | - Emlio Franco-Macías
- Unidad de Demencias, Servicio de Neurología y Neurofisiología. Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
| | - María J Bullido
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
- Instituto de Investigacion Sanitaria 'Hospital la Paz' (IdIPaz), Madrid, Spain
- Centro de Biología Molecular Severo Ochoa (UAM-CSIC), Madrid, Spain
| | - Ana Frank-García
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
- Instituto de Investigacion Sanitaria 'Hospital la Paz' (IdIPaz), Madrid, Spain
- Hospital Universitario la Paz, Madrid, Spain
| | - Lutz Froelich
- Department of Geriatric Psychiatry, Central Institute for Mental Health, Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Brian Fulton-Howard
- Department of Genetics and Genomic Sciences, Ronald M. Loeb Center for Alzheimer's Disease Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniela Galimberti
- Fondazione IRCCS Ca'Granda, Ospedale Policlinico, Milan, Italy
- University of Milan, Milan, Italy
| | - Jose Maria García-Alberca
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
- Alzheimer Research Center & Memory Clinic, Andalusian Institute for Neuroscience, Málaga, Spain
| | - Pablo García-González
- Research Center and Memory Clinic Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | | | | | - Roberta Ghidoni
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Ina Giegling
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Vienna, Austria
| | - Giaccone Giorgio
- Fondazione IRCCS, Istituto Neurologico Carlo Besta, Milan, Italy
| | - Alison M Goate
- Department of Genetics and Genomic Sciences, Ronald M. Loeb Center for Alzheimer's Disease Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Oliver Goldhardt
- Klinikum rechts der Isar, Department of Psychiatry and Psychotherapy, Technical University of Munich, School of Medicine, Munich, Germany
| | - Duber Gomez-Fonseca
- Department of Biostatistics, Epidemiology, and Informatics Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Caroline Graff
- Center for Alzheimer Research, Department NVS, Division of Neurogeriatrics, Karolinska Institutet, Stockholm, Sweden
- Unit for Hereditary Dementias, Karolinska University Hospital-Solna, Stockholm, Sweden
| | - Giulia Grande
- Aging Research Center, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet and Stockholm University, Stockholm, Sweden
| | - Emma Green
- Institute of Public Health, University of Cambridge, Cambridge, UK
| | - Timo Grimmer
- Klinikum rechts der Isar, Department of Psychiatry and Psychotherapy, Technical University of Munich, School of Medicine, Munich, Germany
| | - Edna Grünblatt
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry Zurich, University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland
- Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | - Michelle Grunin
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Vilmundur Gudnason
- Icelandic Heart Association, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Tamar Guetta-Baranes
- Human Genetics, School of Life Sciences, Life Sciences Building, University Park, University of Nottingham, Nottingham, UK
| | - Annakaisa Haapasalo
- AI Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | | | - Jonathan L Haines
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | | | - Harald Hampel
- GRC 21, Alzheimer Precision Medicine Initiative (APMI), Sorbonne University, AP-HP, Pitié-Salpêtrière Hospital, Paris, France
| | - Olivier Hanon
- EA 4468, Université de Paris, APHP, Hôpital Broca, Paris, France
| | - John Hardy
- Reta Lila Weston Research Laboratories, Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Annette M Hartmann
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Vienna, Austria
| | - Lucrezia Hausner
- Department of Geriatric Psychiatry, Central Institute for Mental Health, Mannheim, University of Heidelberg, Heidelberg, Germany
| | - Janet Harwood
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neuroscience, School of Medicine, Cardiff University, Cardiff, UK
| | - Stefanie Heilmann-Heimbach
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Seppo Helisalmi
- Institute of Clinical Medicine, Neurology, University of Eastern, Kuopio, Finland
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Michael T Heneka
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE Bonn), Bonn, Germany
| | - Isabel Hernández
- Research Center and Memory Clinic Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Martin J Herrmann
- Department of Psychiatry, Psychosomatics and Psychotherapy, Center of Mental Health, University Hospital, Wuerzburg, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Clive Holmes
- Clinical and Experimental Science, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Henne Holstege
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
- Section Genomics of Neurodegenerative Diseases and Aging, Department of Human Genetics Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
| | - Raquel Huerto Vilas
- Unitat Trastorns Cognitius, Hospital Universitari Santa Maria de Lleida, Lleida, Spain
- Institut de Recerca Biomedica de Lleida (IRBLLeida), Lleida, Spain
| | - Marc Hulsman
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
- Section Genomics of Neurodegenerative Diseases and Aging, Department of Human Genetics Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
| | - Jack Humphrey
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Geert Jan Biessels
- Department of Neurology, UMC Utrecht Brain Center, Utrecht, the Netherlands
| | - Xueqiu Jian
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas Health Sciences Center, San Antonio, TX, USA
| | - Charlotte Johansson
- Center for Alzheimer Research, Department NVS, Division of Neurogeriatrics, Karolinska Institutet, Stockholm, Sweden
| | - Gyungah R Jun
- Medicine Biomedical Genetics Boston University School of Medicine, Boston, MA, USA
| | - Yuriko Kastumata
- Biostatistics, University of Kentucky College of Public Health, Lexington, KY, USA
| | - John Kauwe
- Department of Biology, Brigham Young University, Provo, UT, USA
| | - Patrick G Kehoe
- Translational Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Lena Kilander
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Anne Kinhult Ståhlbom
- Center for Alzheimer Research, Department NVS, Division of Neurogeriatrics, Karolinska Institutet, Stockholm, Sweden
| | - Miia Kivipelto
- Division of Clinical Geriatrics, Center for Alzheimer Research, Care Sciences and Society (NVS), Karolinska Institutet, Stockholm, Sweden
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
- Neuroepidemiology and Ageing Research Unit, School of Public Health, Imperial College London, London, UK
- Research & Development, UnitStockholms Sjukhem, Stockholm, Sweden
| | - Anne Koivisto
- Institute of Clinical Medicine, Neurology, University of Eastern, Kuopio, Finland
- Department of Neurology, Kuopio University Hospital, Kuopio, Finland
- Department of Neurosciences, University of Helsinki and Department of Geriatrics, Helsinki University Hospital, Helsinki, Finland
| | - Johannes Kornhuber
- Department of Psychiatry and Psychotherapy, Universitätsklinikum Erlangen, and Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Mary H Kosmidis
- Laboratory of Cognitive Neuroscience, School of Psychology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Walter A Kukull
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Pavel P Kuksa
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Brian W Kunkle
- Department of Neurology, Medical School, University of Cyprus, Nicosia, Cyprus
| | - Amanda B Kuzma
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Carmen Lage
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
- Neurology Service, Marqués de Valdecilla University Hospital (University of Cantabria and IDIVAL), Santander, Spain
| | - Erika J Laukka
- Aging Research Center, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet and Stockholm University, Stockholm, Sweden
- Stockholm Gerontology Research Center, Stockholm, Sweden
| | - Lenore Launer
- Laboratory of Epidemiology, Demography, and Biometry, National Institute of Aging, The National Institutes of Health, Bethesda, MD, USA
- Intramural Research Program/National Institute on Aging/National Institutes of Health, Bethesda, MD, USA
| | - Alessandra Lauria
- Geriatrics Unit, Fondazione Policlinico A. Gemelli IRCCS, Rome, Italy
| | - Chien-Yueh Lee
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jenni Lehtisalo
- Institute of Clinical Medicine, Neurology, University of Eastern, Kuopio, Finland
- Public Health Promotion Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Ondrej Lerch
- Memory Clinic, Department of Neurology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Praha, Czechia
- International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czechia
| | - Alberto Lleó
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
- Department of Neurology, II B Sant Pau, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - William Longstreth
- Departments of Neurology and Epidemiology, University of Washington, Seattle, WA, USA
| | | | - Adolfo Lopez de Munain
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
- Department of Neurology, Hospital Universitario Donostia, OSAKIDETZA-Servicio Vasco de Salud, San Sebastian, Spain
| | - Seth Love
- Translational Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Malin Löwemark
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Lauren Luckcuck
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neuroscience, School of Medicine, Cardiff University, Cardiff, UK
| | - Kathryn L Lunetta
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Yiyi Ma
- Section Genomics of Neurodegenerative Diseases and Aging, Department of Human Genetics Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
- Department of Neurology, Columbia University, New York, NY, USA
| | - Juan Macías
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario de Valme, Sevilla, Spain
| | | | - Wolfgang Maier
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE Bonn), Bonn, Germany
| | - Francesca Mangialasche
- Division of Clinical Geriatrics, Center for Alzheimer Research, Care Sciences and Society (NVS), Karolinska Institutet, Stockholm, Sweden
| | - Marco Spallazzi
- Unit of Neurology, University of Parma and AOU, Parma, Italy
| | - Marta Marquié
- Research Center and Memory Clinic Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Rachel Marshall
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neuroscience, School of Medicine, Cardiff University, Cardiff, UK
| | - Eden R Martin
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Angel Martín Montes
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
- Instituto de Investigacion Sanitaria 'Hospital la Paz' (IdIPaz), Madrid, Spain
- Hospital Universitario la Paz, Madrid, Spain
| | - Carmen Martínez Rodríguez
- Servicio de Neurología, Hospital Universitario Central de Asturias- Oviedo and Instituto de Investigación Biosanitaria del Principado de Asturias, Oviedo, Spain
| | - Carlo Masullo
- Institute of Neurology, Catholic University of the Sacred Heart, Rome, Italy
| | - Richard Mayeux
- Taub Institute on Alzheimer's Disease and the Aging Brain, Department of Neurology, Columbia University, New York, NY, USA
- Gertrude H. Sergievsky Center, Columbia University, New York, NY, USA
| | - Simon Mead
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, London, UK
| | - Patrizia Mecocci
- Institute of Gerontology and Geriatrics, Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Miguel Medina
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
- CIEN Foundation/Queen Sofia Foundation Alzheimer Center, Madrid, Spain
| | - Alun Meggy
- UKDRI@ Cardiff, School of Medicine, Cardiff University, Cardiff, UK
| | - Shima Mehrabian
- Clinic of Neurology, UH 'Alexandrovska', Medical University - Sofia, Sofia, Bulgaria
| | - Silvia Mendoza
- Alzheimer Research Center & Memory Clinic, Andalusian Institute for Neuroscience, Málaga, Spain
| | - Manuel Menéndez-González
- Servicio de Neurología, Hospital Universitario Central de Asturias- Oviedo and Instituto de Investigación Biosanitaria del Principado de Asturias, Oviedo, Spain
| | - Pablo Mir
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
- Unidad de Trastornos del Movimiento, Servicio de Neurología y Neurofisiología. Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
| | - Susanne Moebus
- Institute for Urban Public Health, University Hospital of University Duisburg-Essen, Essen, Germany
| | - Merel Mol
- Department of Neurology, Erasmus MC, Rotterdam, the Netherlands
| | - Laura Molina-Porcel
- Neurological Tissue Bank of the Biobanc-Hospital Clinic-IDIBAPS, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Department, Hospital Clinic, Barcelona, Spain
| | - Laura Montrreal
- Research Center and Memory Clinic Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Laura Morelli
- Laboratory of Brain Aging and Neurodegeneration, FIL-CONICET, Buenos Aires, Argentina
| | - Fermin Moreno
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
- Department of Neurology, Hospital Universitario Donostia, OSAKIDETZA-Servicio Vasco de Salud, San Sebastian, Spain
| | - Kevin Morgan
- Human Genetics, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Thomas Mosley
- Memory Impairment and Neurodegenerative Dementia (MIND) Center, University of Mississippi Medical Center, Jackson, MS, USA
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Carolina Muchnik
- Centro de Neuropsiquiatría y Neurología de la Conducta (CENECON), Facultad de Medicina, Universidad de Buenos Aires (UBA), C.A.B.A., Buenos Aires, Argentina
- Laboratorio de Bioquímica Molecular, Facultad de Medicina, Instituto de Investigaciones Médicas A. Lanari, UBA, C.A.B.A, Buenos Aires, Argentina
| | | | - Benedetta Nacmias
- Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, Florence, Italy
- IRCCS Fondazione Don Carlo Gnocchi, Florence, Italy
| | - Tiia Ngandu
- Public Health Promotion Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Gael Nicolas
- Department of Genetics and CNR-MAJ, Normandie University, UNIROUEN, INSERM U1245, CHU Rouen, Rouen, France
| | - Børge G Nordestgaard
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Herlev, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Robert Olaso
- CEA, Centre National de Recherche en Génomique Humaine, Université Paris-Saclay, Evry, France
| | - Adelina Orellana
- Research Center and Memory Clinic Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Michela Orsini
- Department of Neuroscience, Catholic University of Sacred Heart, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Gemma Ortega
- Research Center and Memory Clinic Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Alessandro Padovani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | | | - Goran Papenberg
- Aging Research Center, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet and Stockholm University, Stockholm, Sweden
| | - Lucilla Parnetti
- Centre for Memory Disturbances, Lab of Clinical Neurochemistry, Section of Neurology, University of Perugia, Perugia, Italy
| | - Florence Pasquier
- Resources and Research Memory Center (MRRC) of Distalz, LicendUniversity of Lille, INSERM, CHU Lille, UMR1172, Lille, France
| | - Pau Pastor
- Fundació Docència i Recerca MútuaTerrassa and Movement Disorders Unit, Department of Neurology, University Hospital MútuaTerrassa, Terrassa, Spain
- Memory Disorders Unit, Department of Neurology, Hospital Universitari Mutua de Terrassa, Terrassa, Spain
| | - Gina Peloso
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
- Boston University and the NHLBI's Framingham Heart Study, Boston, MA, USA
| | - Alba Pérez-Cordón
- Research Center and Memory Clinic Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Jordi Pérez-Tur
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
- Institut de Biomedicina de València-CSIC CIBERNED, València, Spain
- Unitat Mixta de de Neurología y Genética, Institut d'Investigació Sanitària La Fe, València, Spain
| | - Pierre Pericard
- US 41-UMS 2014-PLBS, bilille, Université de Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Lille, France
| | - Oliver Peters
- Institute of Psychiatry and Psychotherapy, Charité-Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany
| | - Yolande A L Pijnenburg
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
| | - Juan A Pineda
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario de Valme, Sevilla, Spain
| | - Gerard Piñol-Ripoll
- Unitat Trastorns Cognitius, Hospital Universitari Santa Maria de Lleida, Lleida, Spain
- Institut de Recerca Biomedica de Lleida (IRBLLeida), Lleida, Spain
| | - Claudia Pisanu
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Thomas Polak
- Department of Psychiatry, Psychosomatics and Psychotherapy, Center of Mental Health, University Hospital, Wuerzburg, Germany
| | - Julius Popp
- CHUV, Old Age Psychiatry, Department of Psychiatry, Lausanne, Switzerland
- Old Age Psychiatry, Department of Psychiatry, Lausanne University Hospital, Lausanne, Switzerland
- Department of Geriatric Psychiatry, University Hospital of Psychiatry Zürich, Zürich, Switzerland
| | - Danielle Posthuma
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije University, Amsterdam, the Netherlands
| | - Josef Priller
- German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany
- Department of Neuropsychiatry and Laboratory of Molecular Psychiatry, Charité, Charitéplatz 1, Berlin, Germany
| | - Raquel Puerta
- Research Center and Memory Clinic Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Olivier Quenez
- Department of Genetics and CNR-MAJ, Normandie University, UNIROUEN, INSERM U1245, CHU Rouen, Rouen, France
| | - Inés Quintela
- Grupo de Medicina Xenómica, Centro Nacional de Genotipado (CEGEN-PRB3-ISCIII), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | | | - Alberto Rábano
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
- CIEN Foundation/Queen Sofia Foundation Alzheimer Center, Madrid, Spain
| | - Innocenzo Rainero
- Centre for Neurodegenerative Disorders, Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
| | - Farid Rajabli
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Inez Ramakers
- Department of Psychiatry & Neuropsychologie, Maastricht University, Alzheimer Center Limburg, Maastricht, the Netherlands
| | - Luis M Real
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario de Valme, Sevilla, Spain
- Depatamento de Especialidades Quirúrgicas Bioquímica e Inmunología, Facultad de Medicina, Universidad de Málaga, Málaga, Spain
| | - Marcel J T Reinders
- Delft Bioinformatics Lab, Delft University of Technology, Delft, the Netherlands
| | - Christiane Reitz
- Gertrude H. Sergievsky Center, Columbia University, New York, NY, USA
- Delft Bioinformatics Lab, Delft University of Technology, Delft, the Netherlands
- Taub Institute, Columbia University, New York, NY, USA
| | - Dolly Reyes-Dumeyer
- Department of Neurology, Columbia University, New York, NY, USA
- Taub Institute, Columbia University, New York, NY, USA
| | - Perry Ridge
- Bioinformatics, College of Life Sciences, Brigham Young University, Provo, UT, USA
| | - Steffi Riedel-Heller
- Institute of Social Medicine, Occupational Health and Public Health, University of Leipzig, Leipzig, Germany
| | - Peter Riederer
- Center of Mental Health, Clinic and Policlinic of Psychiatry, Psychosomatics and Psychotherapy, University Hospital of Würzburg, Wuerzburg, Germany
| | - Natalia Roberto
- Research Center and Memory Clinic Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Eloy Rodriguez-Rodriguez
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
- Neurology Service, Marqués de Valdecilla University Hospital (University of Cantabria and IDIVAL), Santander, Spain
| | - Arvid Rongve
- Department of Research and Innovation, Helse Fonna, Haugesund Hospital, Haugesund, Norway
- Institute of Clinical Medicine (K1), The University of Bergen, Bergen, Norway
| | - Irene Rosas Allende
- Laboratorio de Genética, Hospital Universitario Central de Asturias, Oviedo, Spain
- Servicio de Neurología, Hospital Universitario Central de Asturias- Oviedo and Instituto de Investigación Biosanitaria del Principado de Asturias, Oviedo, Spain
| | - Maitée Rosende-Roca
- Research Center and Memory Clinic Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Jose Luis Royo
- Departamento de Especialidades Quirúrgicas, Bioquímicas e Inmunología, School of Medicine, University of Málaga, Málaga, Spain
| | - Elisa Rubino
- Department of Neuroscience and Mental Health, AOU Città della Salute e della Scienza di Torino, Torino, Italy
| | - Dan Rujescu
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Vienna, Austria
| | | | - Paraskevi Sakka
- Athens Association of Alzheimer's Disease and Related Disorders, Athens, Greece
| | - Ingvild Saltvedt
- Department of Neurology and Clinical Neurophysiology, University Hospital of Trondheim, Trondheim, Norway
- Department of Geriatrics, St. Olav's Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Ángela Sanabria
- Research Center and Memory Clinic Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - María Bernal Sánchez-Arjona
- Unidad de Demencias, Servicio de Neurología y Neurofisiología. Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
| | - Florentino Sanchez-Garcia
- Department of Immunology, Hospital Universitario Doctor Negrín, Las Palmas de Gran Canaria, Las Palmas, Spain
| | - Pascual Sánchez Juan
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
- Neurology Service, Marqués de Valdecilla University Hospital (University of Cantabria and IDIVAL), Santander, Spain
| | - Raquel Sánchez-Valle
- Neurology Department-Hospital Clínic, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
| | - Sigrid B Sando
- Experimental Neuro-psychobiology Laboratory, Department of Clinical and Behavioral Neurology, IRCCS Santa Lucia Foundation, Rome, Italy
- Department of Neurology and Clinical Neurophysiology, University Hospital of Trondheim, Trondheim, Norway
| | - Chloé Sarnowski
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Claudia L Satizabal
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas Health Sciences Center, San Antonio, TX, USA
| | - Michela Scamosci
- Institute of Gerontology and Geriatrics, Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Nikolaos Scarmeas
- Taub Institute on Alzheimer's Disease and the Aging Brain, Department of Neurology, Columbia University, New York, NY, USA
- First Department of Neurology, Aiginition Hospital, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Elio Scarpini
- Fondazione IRCCS Ca'Granda, Ospedale Policlinico, Milan, Italy
- University of Milan, Milan, Italy
| | - Philip Scheltens
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
| | - Norbert Scherbaum
- LVR-Hospital Essen, Department of Psychiatry and Psychotherapy, Medical Faculty, University of Duisburg-Essen, Essen, Germany
| | - Martin Scherer
- Department of Primary Medical Care, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Matthias Schmid
- German Center for Neurodegenerative Diseases (DZNE Bonn), Bonn, Germany
- Institute of Medical Biometry, Informatics and Epidemiology, University Hospital of Bonn, Bonn, Germany
| | - Anja Schneider
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE Bonn), Bonn, Germany
| | - Jonathan M Schott
- Dementia Research Centre, UCL Queen Square Institute of Neurology, London, UK
| | - Geir Selbæk
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Geriatric Medicine, Oslo University Hospital, Oslo, Norway
| | - Davide Seripa
- Laboratory for Advanced Hematological Diagnostics, Department of Hematology and Stem Cell Transplant, Vito Fazzi Hospital, Lecce, Italy
| | - Manuel Serrano
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas, CIBERDEM, Hospital Clínico San Carlos, Madrid, Spain
| | - Jin Sha
- Department of Biostatistics, Epidemiology, and Informatics, Penn Neurodegeneration Genomics Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | - Olivia Skrobot
- Translational Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Susan Slifer
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Gijsje J L Snijders
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hilkka Soininen
- Institute of Clinical Medicine, Neurology, University of Eastern, Kuopio, Finland
| | | | - Alina Solomon
- Institute of Clinical Medicine, Neurology, University of Eastern, Kuopio, Finland
- Division of Clinical Geriatrics, Center for Alzheimer Research, Care Sciences and Society (NVS), Karolinska Institutet, Stockholm, Sweden
| | - Yeunjoo Song
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Sandro Sorbi
- Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, Florence, Italy
- IRCCS Fondazione Don Carlo Gnocchi, Florence, Italy
| | - Oscar Sotolongo-Grau
- Research Center and Memory Clinic Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Gianfranco Spalletta
- Laboratory of Neuropsychiatry, Department of Clinical and Behavioral Neurology, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Annika Spottke
- German Center for Neurodegenerative Diseases (DZNE Bonn), Bonn, Germany
- Department of Neurology, University of Bonn, Bonn, Germany
| | - Alessio Squassina
- Department of Biomedical Sciences, Section of Neuroscience and Clinical Pharmacology, University of Cagliari, Cagliari, Italy
| | | | - Juan Pablo Tartan
- Research Center and Memory Clinic Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Lluís Tárraga
- Research Center and Memory Clinic Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Niccolo Tesí
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
- Section Genomics of Neurodegenerative Diseases and Aging, Department of Human Genetics Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
| | - Anbupalam Thalamuthu
- Centre for Healthy Brain Ageing, School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Tegos Thomas
- First Department of Neurology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Alzheimer Hellas, Thessaloniki, Greece
| | - Giuseppe Tosto
- Taub Institute on Alzheimer's Disease and the Aging Brain, Department of Neurology, Columbia University, New York, NY, USA
- Department of Neurology, Columbia University, New York, NY, USA
| | - Latchezar Traykov
- Clinic of Neurology, UH 'Alexandrovska', Medical University - Sofia, Sofia, Bulgaria
| | - Lucio Tremolizzo
- School of Medicine and Surgery, University of Milano-Bicocca, Milano, Italy
- Neurology Unit, San Gerardo Hospital, Monza, Italy
| | - Anne Tybjærg-Hansen
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Rigshospitalet, Copenhagen, Denmark
| | - Andre Uitterlinden
- Department of Internal Medicine and Biostatistics, Erasmus MC, Rotterdam, the Netherlands
| | - Abbe Ullgren
- Center for Alzheimer Research, Department NVS, Division of Neurogeriatrics, Karolinska Institutet, Stockholm, Sweden
| | - Ingun Ulstein
- Department of Geriatric Medicine, Oslo University Hospital, Oslo, Norway
| | - Sergi Valero
- Research Center and Memory Clinic Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Otto Valladares
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Christine Van Broeckhoven
- Complex Genetics of Alzheimer's Disease Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Laboratory of Neurogenetics, Institute Born - Bunge, Antwerp, Belgium
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
| | - Jeffery Vance
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, USA
| | - Badri N Vardarajan
- Taub Institute on Alzheimer's Disease and the Aging Brain, Department of Neurology, Columbia University, New York, NY, USA
| | | | - Jasper Van Dongen
- Complex Genetics of Alzheimer's Disease Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Laboratory of Neurogenetics, Institute Born - Bunge, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Jeroen van Rooij
- Department of Neurology, Erasmus MC, Rotterdam, the Netherlands
- Department of Neurology, ErasmusMC, Rotterdam, the Netherlands
| | | | - Rik Vandenberghe
- Laboratory for Cognitive Neurology, Department of Neurosciences, University of Leuven, Leuven, Belgium
- Neurology Department, University Hospitals Leuven, Leuven, Belgium
| | - Frans Verhey
- Department of Psychiatry & Neuropsychologie, Maastricht University, Alzheimer Center Limburg, Maastricht, the Netherlands
| | | | - Jonathan Vogelgsang
- Department of Psychiatry and Psychotherapy, University Medical Center Goettingen, Goettingen, Germany
- Department of Psychiatry, Harvard Medical School, McLean Hospital, Belmont, MA, USA
| | - Martin Vyhnalek
- Memory Clinic, Department of Neurology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Praha, Czechia
- International Clinical Research Center, St. Anne's University Hospital Brno, Brno, Czechia
| | - Michael Wagner
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE Bonn), Bonn, Germany
| | - David Wallon
- Department of Neurology and CNR-MAJ, F 76000, Normandy Center for Genomic and Personalized Medicine, Normandie University, UNIROUEN, INSERM U1245, CHU Rouen, Rouen, France
| | - Li-San Wang
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ruiqi Wang
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Leonie Weinhold
- Institute of Medical Biometry, Informatics and Epidemiology, University Hospital of Bonn, Bonn, Germany
| | - Jens Wiltfang
- Department of Psychiatry and Psychotherapy, University Medical Center Goettingen, Goettingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Goettingen, Germany
- Medical Science Department, iBiMED, Aveiro, Portugal
| | - Gill Windle
- School of Health Sciences, Bangor University, Bangor, UK
| | - Bob Woods
- School of Health Sciences, Bangor University, Bangor, UK
| | - Mary Yannakoulia
- Department of Nutrition and Diatetics, Harokopio University, Athens, Greece
| | - Habil Zare
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas Health Sciences Center, San Antonio, TX, USA
| | - Yi Zhao
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Xiaoling Zhang
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Congcong Zhu
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Miren Zulaica
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
- Neurosciences Area, Instituto Biodonostia, San Sebastian, Spain
| | - Lindsay A Farrer
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
- Medicine Biomedical Genetics Boston University School of Medicine, Boston, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Bruce M Psaty
- Framingham Heart Study, Framingham, MA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Health Service, University of Washington, Seattle, WA, USA
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands
| | - Towfique Raj
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Perminder Sachdev
- Centre for Healthy Brain Ageing, School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Karen Mather
- Centre for Healthy Brain Ageing, School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Frank Jessen
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE Bonn), Bonn, Germany
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands
| | | | - Jakub Hort
- Intramural Research Program/National Institute on Aging/National Institutes of Health, Bethesda, MD, USA
- Memory Clinic, Department of Neurology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Praha, Czechia
| | - Magda Tsolaki
- First Department of Neurology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Alzheimer Hellas, Thessaloniki, Greece
| | | | - Philippe Amouyel
- Université de Lille, INSERM, CHU Lille, Institut Pasteur Lille, U1167-RID-AGE, Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, Lille, France
| | - Julie Williams
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neuroscience, School of Medicine, Cardiff University, Cardiff, UK
- UKDRI@ Cardiff, School of Medicine, Cardiff University, Cardiff, UK
| | - Ruth Frikke-Schmidt
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Biochemistry, Rigshospitalet, Copenhagen, Denmark
| | - Jordi Clarimon
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
- Department of Neurology, II B Sant Pau, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jean-François Deleuze
- CEA, Centre National de Recherche en Génomique Humaine, Université Paris-Saclay, Evry, France
| | - Giacomina Rossi
- Fondazione IRCCS, Istituto Neurologico Carlo Besta, Milan, Italy
| | - Sudha Seshadri
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas Health Sciences Center, San Antonio, TX, USA
| | | | - Martin Ingelsson
- Department of Public Health and Carins Sciences/Geriatrics, Uppsala University, Uppsala, Sweden
| | - Mikko Hiltunen
- Brain Institute, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Kristel Sleegers
- Complex Genetics of Alzheimer's Disease Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Laboratory of Neurogenetics, Institute Born - Bunge, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Gerard D Schellenberg
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus MC, Rotterdam, the Netherlands
- Nuffield Department of Population Health, Oxford University, Oxford, UK
| | - Rebecca Sims
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neuroscience, School of Medicine, Cardiff University, Cardiff, UK
| | - Wiesje M van der Flier
- Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, the Netherlands
| | - Agustín Ruiz
- Research Center and Memory Clinic Fundació ACE, Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Alfredo Ramirez
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, Bonn, Germany
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, University of Cologne, Medical Faculty, Cologne, Germany
- German Center for Neurodegenerative Diseases (DZNE Bonn), Bonn, Germany
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, University of Texas Health Sciences Center, San Antonio, TX, USA
- Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Jean-Charles Lambert
- Université de Lille, INSERM, CHU Lille, Institut Pasteur Lille, U1167-RID-AGE, Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, Lille, France.
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Jin B, Capra JA, Benchek P, Wheeler N, Naj AC, Hamilton-Nelson KL, Farrell JJ, Leung YY, Kunkle B, Vadarajan B, Schellenberg GD, Mayeux R, Wang LS, Farrer LA, Pericak-Vance MA, Martin ER, Haines JL, Crawford DC, Bush WS. An association test of the spatial distribution of rare missense variants within protein structures identifies Alzheimer's disease-related patterns. Genome Res 2022; 32:778-790. [PMID: 35210353 PMCID: PMC8997344 DOI: 10.1101/gr.276069.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 02/17/2022] [Indexed: 11/24/2022]
Abstract
More than 90% of genetic variants are rare in most modern sequencing studies, such as the Alzheimer's Disease Sequencing Project (ADSP) whole-exome sequencing (WES) data. Furthermore, 54% of the rare variants in ADSP WES are singletons. However, both single variant and unit-based tests are limited in their statistical power to detect an association between rare variants and phenotypes. To best use missense rare variants and investigate their biological effect, we examine their association with phenotypes in the context of protein structures. We developed a protein structure-based approach, protein optimized kernel evaluation of missense nucleotides (POKEMON), which evaluates rare missense variants based on their spatial distribution within a protein rather than their allele frequency. The hypothesis behind this test is that the three-dimensional spatial distribution of variants within a protein structure provides functional context to power an association test. POKEMON identified three candidate genes (TREM2, SORL1, and EXOC3L4) and another suggestive gene from the ADSP WES data. For TREM2 and SORL1, two known Alzheimer's disease (AD) genes, the signal from the spatial cluster is stable even if we exclude known AD risk variants, indicating the presence of additional low-frequency risk variants within these genes. EXOC3L4 is a novel AD risk gene that has a cluster of variants primarily shared by case subjects around the Sec6 domain. This cluster is also validated in an independent replication data set and a validation data set with a larger sample size.
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Affiliation(s)
- Bowen Jin
- Graduate Program in Systems Biology and Bioinformatics, Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - John A Capra
- The Bakar Computational Health Sciences Institute, Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California 94143, USA
| | - Penelope Benchek
- Cleveland Institute for Computational Biology, Department for Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Nicholas Wheeler
- Cleveland Institute for Computational Biology, Department for Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Adam C Naj
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Kara L Hamilton-Nelson
- The John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida 33136, USA
| | - John J Farrell
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Yuk Yee Leung
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Brian Kunkle
- The John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida 33136, USA
- Dr. John T. Macdonald Foundation, Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida 33136, USA
| | - Badri Vadarajan
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Department of Neurology, Gertrude H. Sergievsky Center, Department of Neurology, Columbia University, New York, New York 10032, USA
| | - Gerard D Schellenberg
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Richard Mayeux
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Department of Neurology, Gertrude H. Sergievsky Center, Department of Neurology, Columbia University, New York, New York 10032, USA
| | - Li-San Wang
- Department of Pathology and Laboratory Medicine, Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Lindsay A Farrer
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Margaret A Pericak-Vance
- The John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida 33136, USA
- Dr. John T. Macdonald Foundation, Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida 33136, USA
| | - Eden R Martin
- The John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida 33136, USA
- Dr. John T. Macdonald Foundation, Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida 33136, USA
| | - Jonathan L Haines
- Cleveland Institute for Computational Biology, Department for Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Dana C Crawford
- Cleveland Institute for Computational Biology, Department for Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - William S Bush
- Cleveland Institute for Computational Biology, Department for Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio 44106, USA
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Gao XR, Li Y, Martin ER. Alzheimer’s disease risk prediction using automated machine learning. Alzheimers Dement 2021. [DOI: 10.1002/alz.053953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Yi‐Ju Li
- Department of Biostatistics and Bioinformatics, Duke University Medical Center Durham NC USA
| | - Eden R. Martin
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine Miami FL USA
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Wang L, Zhang L, Young J, Gomez L, Silva TC, Schmidt MA, Cai Z, Kunkle BW, Martin ER. Sex‐specific analysis of DNA methylation changes implicates new loci in Alzheimer’s disease pathology. Alzheimers Dement 2021. [DOI: 10.1002/alz.049363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Lily Wang
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
- University of Miami Miller School of Medicine Miami FL USA
| | - Lanyu Zhang
- University of Miami Miller School of Medicine Miami FL USA
| | - Juan Young
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
- University of Miami Miller School of Medicine Miami FL USA
| | - Lissette Gomez
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Tiago C Silva
- University of Miami Miller School of Medicine Miami FL USA
| | - Michael A. Schmidt
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
- University of Miami Miller School of Medicine Miami FL USA
| | - Zixi Cai
- Brentwood High School Brentwood TN USA
| | - Brian W. Kunkle
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics University of Miami Miller School of Medicine Miami FL USA
| | - Eden R Martin
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
- University of Miami Miller School of Medicine Miami FL USA
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Wang L, Silva TC, Young J, Martin ER, Kunkle BW, Chen X. Estimating the regulatory potential of DNA methylation in Alzheimer's disease. Alzheimers Dement 2021. [DOI: 10.1002/alz.049365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Lily Wang
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
- University of Miami Miller School of Medicine Miami FL USA
| | - Tiago C Silva
- University of Miami Miller School of Medicine Miami FL USA
| | - Juan Young
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
- University of Miami Miller School of Medicine Miami FL USA
| | - Eden R Martin
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
- University of Miami Miller School of Medicine Miami FL USA
| | - Brian W. Kunkle
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
- Dr. John T. Macdonald Foundation Department of Human Genetics University of Miami Miller School of Medicine Miami FL USA
| | - Xi Chen
- University of Miami Miller School of Medicine Miami FL USA
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da Fonseca EL, Jean‐Francois MN, Kurup JT, Slifer SH, Martin ER, Kunkle BW, Schellenberg GD, Pericak‐Vance MA, Fernandez V, Cruchaga C, Reitz C, Beecham GW. Heritability analyses show partial genetic overlap between (non‐Mendelian) early and late onset Alzheimer disease due to an intriguing APOE effect. Alzheimers Dement 2021. [DOI: 10.1002/alz.056143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Eder Lucio da Fonseca
- University of Miami, Miller School of Medicine, John P. Hussman Institute for Human Genomics Miami FL USA
| | - Melissa N. Jean‐Francois
- University of Miami, Miller School of Medicine, John P. Hussman Institute for Human Genomics Miami FL USA
| | | | - Susan H. Slifer
- University of Miami, Miller School of Medicine, John P. Hussman Institute for Human Genomics Miami FL USA
| | - Eden R. Martin
- University of Miami, Miller School of Medicine, John P. Hussman Institute for Human Genomics Miami FL USA
| | - Brian W. Kunkle
- University of Miami, Miller School of Medicine, John P. Hussman Institute for Human Genomics Miami FL USA
| | - Gerard D. Schellenberg
- University of Pennsylvania Perelman School of Medicine, Path & Lab Med, Stellar Chance Philadelphia PA USA
| | - Margaret A. Pericak‐Vance
- University of Miami, Miller School of Medicine, John P. Hussman Institute for Human Genomics Miami FL USA
| | | | - Carlos Cruchaga
- Washington University in St. Louis School of Medicine St. Louis MO USA
| | - Christiane Reitz
- Columbia University, Departments of Neurology and Epidemiology New York NY USA
| | - Gary W. Beecham
- University of Miami, Miller School of Medicine, John P. Hussman Institute for Human Genomics Miami FL USA
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Kunkle BW, Jean‐Francois MN, Hamilton‐Nelson KL, Schmidt MA, Naj AC, Martin ER, Vance JM, Cuccaro ML, Rajabli F, Jun GR, Wang L, Farrer LA, Haines JL, Byrd GS, Schellenberg GD, Mayeux R, Beecham GW, Pericak‐Vance MA, Reitz C. APOE‐stratified genome‐wide association analysis identifies novel Alzheimer disease candidate risk loci for African Americans. Alzheimers Dement 2021. [DOI: 10.1002/alz.056383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Brian W. Kunkle
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Melissa N. Jean‐Francois
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Kara L. Hamilton‐Nelson
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Michael A. Schmidt
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Adam C Naj
- University of Pennsylvania Perelman School of Medicine Philadelphia PA USA
| | - Eden R Martin
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Jeffery M. Vance
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Michael L. Cuccaro
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Farid Rajabli
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | | | - Li‐San Wang
- University of Pennsylvania Perelman School of Medicine Philadelphia PA USA
| | | | - Jonathan L. Haines
- Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland OH USA
| | - Goldie S. Byrd
- Maya Angelou Center for Health Equity (MACHE) / Wake Forest School of Medicine Winston Salem NC USA
| | | | - Richard Mayeux
- The Taub Institute for Research on Alzheimer’s Disease and The Aging Brain Columbia University New York NY USA
| | - Gary W. Beecham
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Margaret A. Pericak‐Vance
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami FL USA
| | - Christiane Reitz
- The Taub Institute for Research on Alzheimer’s Disease and The Aging Brain Columbia University New York NY USA
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Sanders AR, Beecham GW, Guo S, Badner JA, Bocklandt S, Mustanski BS, Hamer DH, Martin ER. Genome-Wide Linkage Study Meta-Analysis of Male Sexual Orientation. Arch Sex Behav 2021; 50:3371-3375. [PMID: 34080073 PMCID: PMC8604844 DOI: 10.1007/s10508-021-02035-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 05/01/2021] [Accepted: 05/04/2021] [Indexed: 05/26/2023]
Abstract
Male sexual orientation is a scientifically and socially important trait shown by family and twin studies to be influenced by environmental and complex genetic factors. Individual genome-wide linkage studies (GWLS) have been conducted, but not jointly analyzed. Two main datasets account for > 90% of the published GWLS concordant sibling pairs on the trait and are jointly analyzed here: MGSOSO (Molecular Genetic Study of Sexual Orientation; 409 concordant sibling pairs in 384 families, Sanders et al. (2015)) and Hamer (155 concordant sibling pairs in 145 families, Mustanski et al. (2005)). We conducted multipoint linkage analyses with Merlin on the datasets separately since they were genotyped differently, integrated genetic marker positions, and combined the resultant LOD (logarithm of the odds) scores at each 1 cM grid position. We continue to find the strongest linkage support at pericentromeric chromosome 8 and chromosome Xq28. We also incorporated the remaining published GWLS dataset (on 55 families) by using meta-analytic approaches on published summary statistics. The meta-analysis has maximized the positional information from GWLS of currently available family resources and can help prioritize findings from genome-wide association studies (GWAS) and other approaches. Although increasing evidence highlights genetic contributions to male sexual orientation, our current understanding of contributory loci is still limited, consistent with the complexity of the trait. Further increasing genetic knowledge about male sexual orientation, especially via large GWAS, should help advance our understanding of the biology of this important trait.
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Affiliation(s)
- Alan R Sanders
- Department of Psychiatry and Behavioral Sciences, NorthShore University HealthSystem, 1001 University Place, Evanston, IL, 60201, USA.
- Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL, USA.
| | - Gary W Beecham
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Shengru Guo
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | - Sven Bocklandt
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Brian S Mustanski
- Department of Medical Social Sciences, Northwestern University, Evanston, IL, USA
| | - Dean H Hamer
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Eden R Martin
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
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46
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Sanders AR, Beecham GW, Guo S, Dawood K, Rieger G, Krishnappa RS, Kolundzija AB, Bailey JM, Martin ER. Genome-Wide Linkage and Association Study of Childhood Gender Nonconformity in Males. Arch Sex Behav 2021; 50:3377-3383. [PMID: 34518958 PMCID: PMC8604823 DOI: 10.1007/s10508-021-02146-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 06/13/2023]
Abstract
Male sexual orientation is influenced by environmental and complex genetic factors. Childhood gender nonconformity (CGN) is one of the strongest correlates of homosexuality with substantial familiality. We studied brothers in families with two or more homosexual brothers (409 concordant sibling pairs in 384 families, as well as their heterosexual brothers), who self-recalled their CGN. To map loci for CGN, we conducted a genome-wide linkage scan (GWLS) using SNP genotypes. The strongest linkage peaks, each with significant or suggestive two-point LOD scores and multipoint LOD score support, were on chromosomes 5q31 (maximum two-point LOD = 4.45), 6q12 (maximum two-point LOD = 3.64), 7q33 (maximum two-point LOD = 3.09), and 8q24 (maximum two-point LOD = 3.67), with the latter not overlapping with previously reported strongest linkage region for male sexual orientation on pericentromeric chromosome 8. Family-based association analyses were used to identify associated variants in the linkage regions, with a cluster of SNPs (minimum association p = 1.3 × 10-8) found at the 5q31 linkage peak. Genome-wide, clusters of multiple SNPs in the 10-6 to 10-8 p-value range were found at chromosomes 5p13, 5q31, 7q32, 8p22, and 10q23, highlighting glutamate-related genes. This is the first reported GWLS and genome-wide association study on CGN. Further increasing genetic knowledge about CGN and its relationships to male sexual orientation should help advance our understanding of the biology of these associated traits.
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Affiliation(s)
- Alan R Sanders
- Department of Psychiatry and Behavioral Sciences, NorthShore University HealthSystem Research Institute, 1001 University Place, Evanston, IL, 60201, USA.
- Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL, USA.
| | - Gary W Beecham
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Shengru Guo
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Khytam Dawood
- Department of Psychology, Pennsylvania State University, University Park, PA, USA
| | - Gerulf Rieger
- Department of Psychology, University of Essex, Colchester, UK
| | - Ritesha S Krishnappa
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, Elmhurst, NY, USA
| | | | - J Michael Bailey
- Department of Psychology, Northwestern University, Evanston, IL, USA
| | - Eden R Martin
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
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Zietsch BP, Sidari MJ, Abdellaoui A, Maier R, Långström N, Guo S, Beecham GW, Martin ER, Sanders AR, Verweij KJH. Author Correction: Genomic evidence consistent with antagonistic pleiotropy may help explain the evolutionary maintenance of same-sex sexual behaviour in humans. Nat Hum Behav 2021; 5:1259. [PMID: 34518664 DOI: 10.1038/s41562-021-01210-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Brendan P Zietsch
- Centre for Psychology and Evolution, School of Psychology, University of Queensland, Brisbane, Queensland, Australia.
| | - Morgan J Sidari
- Centre for Psychology and Evolution, School of Psychology, University of Queensland, Brisbane, Queensland, Australia
| | - Abdel Abdellaoui
- Department of Psychiatry, Amsterdam UMC location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Robert Maier
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Niklas Långström
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Shengru Guo
- Department of Human Genetics, University of Miami, Miami, FL, USA
| | - Gary W Beecham
- Department of Human Genetics, University of Miami, Miami, FL, USA
| | - Eden R Martin
- Department of Human Genetics, University of Miami, Miami, FL, USA
| | - Alan R Sanders
- Department of Psychiatry and Behavioral Sciences, NorthShore University HealthSystem Research Institute, Evanston, IL, USA.,Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL, USA
| | - Karin J H Verweij
- Department of Psychiatry, Amsterdam UMC location AMC, University of Amsterdam, Amsterdam, the Netherlands
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Zietsch BP, Sidari MJ, Abdellaoui A, Maier R, Långström N, Guo S, Beecham GW, Martin ER, Sanders AR, Verweij KJH. Genomic evidence consistent with antagonistic pleiotropy may help explain the evolutionary maintenance of same-sex sexual behaviour in humans. Nat Hum Behav 2021; 5:1251-1258. [PMID: 34426668 DOI: 10.1038/s41562-021-01168-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 06/18/2021] [Indexed: 01/31/2023]
Abstract
Human same-sex sexual behaviour (SSB) is heritable, confers no immediately obvious direct reproductive or survival benefit and can divert mating effort from reproductive opportunities. This presents a Darwinian paradox: why has SSB been maintained despite apparent selection against it? We show that genetic effects associated with SSB may, in individuals who only engage in opposite-sex sexual behaviour (OSB individuals), confer a mating advantage. Using results from a recent genome-wide association study of SSB and a new genome-wide association study on number of opposite-sex sexual partners in 358,426 individuals, we show that, among OSB individuals, genetic effects associated with SSB are associated with having more opposite-sex sexual partners. Computer simulations suggest that such a mating advantage for alleles associated with SSB could help explain how it has been evolutionarily maintained. Caveats include the cultural specificity of our UK and US samples, the societal regulation of sexual behaviour in these populations, the difficulty of measuring mating success and the fact that measured variants capture a minority of the total genetic variation in the traits.
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Affiliation(s)
- Brendan P Zietsch
- Centre for Psychology and Evolution, School of Psychology, University of Queensland, Brisbane, Queensland, Australia.
| | - Morgan J Sidari
- Centre for Psychology and Evolution, School of Psychology, University of Queensland, Brisbane, Queensland, Australia
| | - Abdel Abdellaoui
- Department of Psychiatry, Amsterdam UMC location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Robert Maier
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Niklas Långström
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Shengru Guo
- Department of Human Genetics, University of Miami, Miami, FL, USA
| | - Gary W Beecham
- Department of Human Genetics, University of Miami, Miami, FL, USA
| | - Eden R Martin
- Department of Human Genetics, University of Miami, Miami, FL, USA
| | - Alan R Sanders
- Department of Psychiatry and Behavioral Sciences, NorthShore University HealthSystem Research Institute, Evanston, IL, USA.,Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL, USA
| | - Karin J H Verweij
- Department of Psychiatry, Amsterdam UMC location AMC, University of Amsterdam, Amsterdam, the Netherlands
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Lai D, Alipanahi B, Fontanillas P, Schwantes-An TH, Aasly J, Alcalay RN, Beecham GW, Berg D, Bressman S, Brice A, Brockman K, Clark L, Cookson M, Das S, Van Deerlin V, Follett J, Farrer MJ, Trinh J, Gasser T, Goldwurm S, Gustavsson E, Klein C, Lang AE, Langston JW, Latourelle J, Lynch T, Marder K, Marras C, Martin ER, McLean CY, Mejia-Santana H, Molho E, Myers RH, Nuytemans K, Ozelius L, Payami H, Raymond D, Rogaeva E, Rogers MP, Ross OA, Samii A, Saunders-Pullman R, Schüle B, Schulte C, Scott WK, Tanner C, Tolosa E, Tomkins JE, Vilas D, Trojanowski JQ, Uitti R, Vance JM, Visanji NP, Wszolek ZK, Zabetian CP, Mirelman A, Giladi N, Orr Urtreger A, Cannon P, Fiske B, Foroud T. Genomewide Association Studies of LRRK2 Modifiers of Parkinson's Disease. Ann Neurol 2021; 90:76-88. [PMID: 33938021 PMCID: PMC8252519 DOI: 10.1002/ana.26094] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/28/2021] [Accepted: 04/29/2021] [Indexed: 02/03/2023]
Abstract
Objective The aim of this study was to search for genes/variants that modify the effect of LRRK2 mutations in terms of penetrance and age‐at‐onset of Parkinson's disease. Methods We performed the first genomewide association study of penetrance and age‐at‐onset of Parkinson's disease in LRRK2 mutation carriers (776 cases and 1,103 non‐cases at their last evaluation). Cox proportional hazard models and linear mixed models were used to identify modifiers of penetrance and age‐at‐onset of LRRK2 mutations, respectively. We also investigated whether a polygenic risk score derived from a published genomewide association study of Parkinson's disease was able to explain variability in penetrance and age‐at‐onset in LRRK2 mutation carriers. Results A variant located in the intronic region of CORO1C on chromosome 12 (rs77395454; p value = 2.5E‐08, beta = 1.27, SE = 0.23, risk allele: C) met genomewide significance for the penetrance model. Co‐immunoprecipitation analyses of LRRK2 and CORO1C supported an interaction between these 2 proteins. A region on chromosome 3, within a previously reported linkage peak for Parkinson's disease susceptibility, showed suggestive associations in both models (penetrance top variant: p value = 1.1E‐07; age‐at‐onset top variant: p value = 9.3E‐07). A polygenic risk score derived from publicly available Parkinson's disease summary statistics was a significant predictor of penetrance, but not of age‐at‐onset. Interpretation This study suggests that variants within or near CORO1C may modify the penetrance of LRRK2 mutations. In addition, common Parkinson's disease associated variants collectively increase the penetrance of LRRK2 mutations. ANN NEUROL 2021;90:82–94
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Affiliation(s)
- Dongbing Lai
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
| | | | | | - Tae-Hwi Schwantes-An
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
| | - Jan Aasly
- Department of Neurology, St. Olavs Hospital, Trondheim, Norway
| | - Roy N Alcalay
- Department of Neurology, Columbia University, New York, NY
| | - Gary W Beecham
- John P. Hussman Institute for Human Genomics and Dr. John T. Macdonald Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL
| | - Daniela Berg
- Department of Neurology, Christian-Albrechts-University of Kiel, Kiel, Germany.,Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Susan Bressman
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Alexis Brice
- Sorbonne Université, Institut du Cerveau et de la Moelle épinière (ICM), AP-HP, Inserm, CNRS, University Hospital Pitié-Salpêtrière, Paris, France
| | - Kathrin Brockman
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Lorraine Clark
- Department of Pathology and Cell Biology, Columbia University, New York, NY
| | - Mark Cookson
- Laboratory of Neurogenetics, National Institute of Aging, National Institute of Health, Bethesda, MD
| | | | - Vivianna Van Deerlin
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA
| | - Jordan Follett
- Laboratory of Neurogenetics and Neuroscience, Fixel Institute for Neurological Diseases, McKnight Brain Institute, L5-101D, UF Clinical and Translational Science Institute, University of Florida, Gainesville, FL
| | - Matthew J Farrer
- Laboratory of Neurogenetics and Neuroscience, Fixel Institute for Neurological Diseases, McKnight Brain Institute, L5-101D, UF Clinical and Translational Science Institute, University of Florida, Gainesville, FL
| | - Joanne Trinh
- Institute of Neurogenetics, University of Luebeck, Luebeck, Germany
| | - Thomas Gasser
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | | | - Emil Gustavsson
- Centre for Applied Neurogenetics, University of British Columbia, Vancouver, Canada
| | - Christine Klein
- Institute of Neurogenetics, University of Luebeck, Luebeck, Germany
| | - Anthony E Lang
- The Edmond J. Safra Program in Parkinson's Disease and the Morton and Gloria Shulman Movement Disorders Clinic, Toronto Western Hospital, Toronto, Canada
| | - J William Langston
- Departments of Neurology, Neuroscience, and Pathology, Stanford University School of Medicine, Stanford, CA
| | | | - Timothy Lynch
- Dublin Neurological Institute at the Mater Misericordiae University Hospital, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Karen Marder
- Department of Neurology and Psychiatry, Taub Institute and Sergievsky Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY
| | - Connie Marras
- The Edmond J. Safra Program in Parkinson's Disease and the Morton and Gloria Shulman Movement Disorders Clinic, Toronto Western Hospital, Toronto, Canada
| | - Eden R Martin
- John P. Hussman Institute for Human Genomics and Dr. John T. Macdonald Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL
| | - Cory Y McLean
- 23andMe, Inc., Sunnyvale, CA.,Google LLC, Cambridge, MA
| | | | - Eric Molho
- Department of Neurology, Albany Medical College, Albany, NY
| | | | - Karen Nuytemans
- John P. Hussman Institute for Human Genomics and Dr. John T. Macdonald Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL
| | - Laurie Ozelius
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Haydeh Payami
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL
| | - Deborah Raymond
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Ekaterina Rogaeva
- Tanz Centre for Research in Neurodegenerative Diseases and Department of Neurology, University of Toronto, Toronto, Canada
| | - Michael P Rogers
- Department of General Surgery, University of South Florida Morsani College of Medicine, Tampa, FL
| | - Owen A Ross
- Departments of Neuroscience and Clinical Genomics, Mayo Clinic, Jacksonville, FL.,School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| | - Ali Samii
- VA Puget Sound Health Care System and Department of Neurology, University of Washington, Seattle, WA
| | | | - Birgitt Schüle
- Department of Pathology, Stanford University School of Medicine, Stanford, CA
| | - Claudia Schulte
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - William K Scott
- John P. Hussman Institute for Human Genomics and Dr. John T. Macdonald Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL
| | - Caroline Tanner
- University of California, San Francisco Veterans Affairs Health Care System, San Francisco, CA
| | - Eduardo Tolosa
- Parkinson Disease and Movement Disorders Unit, Hospital Clínic Universitari, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona (UB), Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain
| | | | - Dolores Vilas
- Parkinson Disease and Movement Disorders Unit, Hospital Clínic Universitari, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona (UB), Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain
| | - John Q Trojanowski
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA
| | -
- 23andMe, Inc., Sunnyvale, CA
| | - Ryan Uitti
- Department of Neurology, Mayo Clinic, Jacksonville, FL
| | - Jeffery M Vance
- John P. Hussman Institute for Human Genomics and Dr. John T. Macdonald Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL
| | - Naomi P Visanji
- The Edmond J. Safra Program in Parkinson's Disease and the Morton and Gloria Shulman Movement Disorders Clinic, Toronto Western Hospital, Toronto, Canada
| | | | - Cyrus P Zabetian
- VA Puget Sound Health Care System and Department of Neurology, University of Washington, Seattle, WA
| | - Anat Mirelman
- Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Nir Giladi
- Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Avi Orr Urtreger
- Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | | | - Brian Fiske
- The Michael J. Fox Foundation for Parkinson's Research, New York, NY
| | - Tatiana Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
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Zhang L, Young JI, Gomez L, Silva TC, Schmidt MA, Cai J, Chen X, Martin ER, Wang L. Sex-specific DNA methylation differences in Alzheimer's disease pathology. Acta Neuropathol Commun 2021; 9:77. [PMID: 33902726 PMCID: PMC8074512 DOI: 10.1186/s40478-021-01177-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 04/10/2021] [Indexed: 12/14/2022] Open
Abstract
Sex is an important factor that contributes to the clinical and biological heterogeneities in Alzheimer's disease (AD), but the regulatory mechanisms underlying sex disparity in AD are still not well understood. DNA methylation is an important epigenetic modification that regulates gene transcription and is known to be involved in AD. We performed the first large-scale sex-specific meta-analysis of DNA methylation differences in AD neuropathology, by re-analyzing four recent epigenome-wide association studies totaling more than 1000 postmortem prefrontal cortex brain samples using a uniform analytical pipeline. For each cohort, we employed two complementary analytical strategies, a sex-stratified analysis that examined methylation-Braak stage associations in male and female samples separately, and a sex-by-Braak stage interaction analysis that compared the magnitude of these associations between different sexes. Our analysis uncovered 14 novel CpGs, mapped to genes such as TMEM39A and TNXB that are associated with the AD Braak stage in a sex-specific manner. TMEM39A is known to be involved in inflammation, dysregulated type I interferon responses, and other immune processes. TNXB encodes tenascin proteins, which are extracellular matrix glycoproteins demonstrated to modulate synaptic plasticity in the brain. Moreover, for many previously implicated genes in AD neuropathology, such as MBP and AZU1, our analysis provided the new insights that they were predominately driven by effects in only one sex. These sex-specific DNA methylation differences were enriched in divergent biological processes such as integrin activation in females and complement activation in males. Our study implicated multiple new loci and biological processes that affected AD neuropathology in a sex-specific manner.
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Affiliation(s)
- Lanyu Zhang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
| | - Juan I Young
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
| | - Lissette Gomez
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
| | - Tiago C Silva
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
| | - Michael A Schmidt
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
| | - Jesse Cai
- Brentwood High School, 5304 Murray Ln, Brentwood, TN, 37027, USA
| | - Xi Chen
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
| | - Eden R Martin
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
| | - Lily Wang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA.
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA.
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA.
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA.
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