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Quinlan CM, Chang X, March M, Mentch FD, Qu HQ, Liu Y, Glessner J, Sleiman PMA, Hakonarson H. Identification of novel loci in obstructive sleep apnea in European American and African American children. Sleep 2024; 47:zsac182. [PMID: 35902206 DOI: 10.1093/sleep/zsac182] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 02/07/2022] [Revised: 06/24/2022] [Indexed: 02/18/2024] Open
Abstract
STUDY OBJECTIVES To identify genetic susceptibility variants in pediatric obstructive sleep apnea in European American and African American children. METHODS A phenotyping algorithm using electronic medical records was developed to recruit cases with OSA and control subjects from the Center for Applied Genomics at Children's Hospital of Philadelphia (CHOP). Genome-wide association studies (GWAS) were performed in pediatric OSA cases and control subjects with European American (EA) and African American (AA) ancestry followed by meta-analysis and sex stratification. RESULTS The algorithm accrued 1486 subjects (46.3% European American, 53.7% African American). We identified genomic loci at 1p36.22 and 15q26.1 that associated with OSA risk in EA and AA, respectively. We also revealed a shared risk locus at 18p11.32 (rs114124196, p = 1.72 × 10-8) across EA and AA populations. Additionally, association at 1q43 (rs12754698) and 2p25.1 (rs72775219) was identified in the male-only analysis of EA children with OSA, while association at 8q21.11 (rs6472959), 11q24.3 (rs4370952) and 15q21.1 (rs149936782) was detected in the female-only analysis of EA children and association at 18p11.23 (rs9964029) was identified in the female-only analysis of African-American children. Moreover, the 18p11.32 locus was replicated in an EA cohort (rs114124196, p = 8.8 × 10-3). CONCLUSIONS We report the first GWAS for pediatric OSA in European Americans and African Americans. Our results provide novel insights to the genetic underpins of pediatric OSA.
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Affiliation(s)
- Courtney M Quinlan
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Pulmonary Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Xiao Chang
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Michael March
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Frank D Mentch
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Hui-Qi Qu
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Yichuan Liu
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Joseph Glessner
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Patrick M A Sleiman
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA, 19104, USA
- Divisions of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Hakon Hakonarson
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Pulmonary Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA, 19104, USA
- Divisions of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
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Glessner JT, Ningappa MB, Ngo KA, Zahid M, So J, Higgs BW, Sleiman PMA, Narayanan T, Ranganathan S, March M, Prasadan K, Vaccaro C, Reyes-Mugica M, Velazquez J, Salgado CM, Ebrahimkhani MR, Schmitt L, Rajasundaram D, Paul M, Pellegrino R, Gittes GK, Li D, Wang X, Billings J, Squires R, Ashokkumar C, Sharif K, Kelly D, Dhawan A, Horslen S, Lo CW, Shin D, Subramaniam S, Hakonarson H, Sindhi R. Biliary atresia is associated with polygenic susceptibility in ciliogenesis and planar polarity effector genes. J Hepatol 2023; 79:1385-1395. [PMID: 37572794 PMCID: PMC10729795 DOI: 10.1016/j.jhep.2023.07.039] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 07/07/2023] [Accepted: 07/18/2023] [Indexed: 08/14/2023]
Abstract
BACKGROUND & AIMS Biliary atresia (BA) is poorly understood and leads to liver transplantation (LT), with the requirement for and associated risks of lifelong immunosuppression, in most children. We performed a genome-wide association study (GWAS) to determine the genetic basis of BA. METHODS We performed a GWAS in 811 European BA cases treated with LT in US, Canadian and UK centers, and 4,654 genetically matched controls. Whole-genome sequencing of 100 cases evaluated synthetic association with rare variants. Functional studies included whole liver transcriptome analysis of 64 BA cases and perturbations in experimental models. RESULTS A GWAS of common single nucleotide polymorphisms (SNPs), i.e. allele frequencies >1%, identified intronic SNPs rs6446628 in AFAP1 with genome-wide significance (p = 3.93E-8) and rs34599046 in TUSC3 at sub-threshold genome-wide significance (p = 1.34E-7), both supported by credible peaks of neighboring SNPs. Like other previously reported BA-associated genes, AFAP1 and TUSC3 are ciliogenesis and planar polarity effectors (CPLANE). In gene-set-based GWAS, BA was associated with 6,005 SNPs in 102 CPLANE genes (p = 5.84E-15). Compared with non-CPLANE genes, more CPLANE genes harbored rare variants (allele frequency <1%) that were assigned Human Phenotype Ontology terms related to hepatobiliary anomalies by predictive algorithms, 87% vs. 40%, p <0.0001. Rare variants were present in multiple genes distinct from those with BA-associated common variants in most BA cases. AFAP1 and TUSC3 knockdown blocked ciliogenesis in mouse tracheal cells. Inhibition of ciliogenesis caused biliary dysgenesis in zebrafish. AFAP1 and TUSC3 were expressed in fetal liver organoids, as well as fetal and BA livers, but not in normal or disease-control livers. Integrative analysis of BA-associated variants and liver transcripts revealed abnormal vasculogenesis and epithelial tube formation, explaining portal vein anomalies that co-exist with BA. CONCLUSIONS BA is associated with polygenic susceptibility in CPLANE genes. Rare variants contribute to polygenic risk in vulnerable pathways via unique genes. IMPACT AND IMPLICATIONS Liver transplantation is needed to cure most children born with biliary atresia, a poorly understood rare disease. Transplant immunosuppression increases the likelihood of life-threatening infections and cancers. To improve care by preventing this disease and its progression to transplantation, we examined its genetic basis. We find that this disease is associated with both common and rare mutations in highly specialized genes which maintain normal communication and movement of cells, and their organization into bile ducts and blood vessels during early development of the human embryo. Because defects in these genes also cause other birth defects, our findings could lead to preventive strategies to lower the incidence of biliary atresia and potentially other birth defects.
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Affiliation(s)
- Joseph T Glessner
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mylarappa B Ningappa
- Hillman Center for Pediatric Transplantation, UPMC-Children's Hospital of Pittsburgh, and Thomas E Starzl Transplant Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kim A Ngo
- Department of Bioengineering, University of California, San Diego, San Diego, La Jolla, CA, USA
| | - Maliha Zahid
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Juhoon So
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Brandon W Higgs
- Hillman Center for Pediatric Transplantation, UPMC-Children's Hospital of Pittsburgh, and Thomas E Starzl Transplant Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Patrick M A Sleiman
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Tejaswini Narayanan
- Department of Bioengineering, University of California, San Diego, San Diego, La Jolla, CA, USA
| | - Sarangarajan Ranganathan
- Division of Pathology and Laboratory Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Michael March
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Krishna Prasadan
- Rangos Research Center Animal Imaging Core, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Courtney Vaccaro
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Miguel Reyes-Mugica
- Division of Pediatric Pathology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Jeremy Velazquez
- Department of Pathology, School of Medicine, Pittsburgh Liver Research Center, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Claudia M Salgado
- Division of Pediatric Pathology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Mo R Ebrahimkhani
- Department of Pathology, School of Medicine, Pittsburgh Liver Research Center, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lori Schmitt
- Histology Core Laboratory Manager, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Dhivyaa Rajasundaram
- Department of Pediatrics, Division of Health Informatics, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Morgan Paul
- Hillman Center for Pediatric Transplantation, UPMC-Children's Hospital of Pittsburgh, and Thomas E Starzl Transplant Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Renata Pellegrino
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - George K Gittes
- Surgeon-in-Chief Emeritus, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Dong Li
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Xiang Wang
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jonathan Billings
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Robert Squires
- Pediatric Gastroenterology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Chethan Ashokkumar
- Hillman Center for Pediatric Transplantation, UPMC-Children's Hospital of Pittsburgh, and Thomas E Starzl Transplant Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Khalid Sharif
- Paediatric Liver Unit Including Intestinal Transplantation, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Deirdre Kelly
- Paediatric Liver Unit Including Intestinal Transplantation, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Anil Dhawan
- Paediatric Liver GI and Nutrition Center and MowatLabs, NHS Foundation Trust, King's College Hospital, London, UK
| | - Simon Horslen
- Pediatric Gastroenterology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Cecilia W Lo
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Donghun Shin
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Shankar Subramaniam
- Department of Bioengineering, University of California, San Diego, San Diego, La Jolla, CA, USA; Department of Computer Science and Engineering, and Nanoengineering, University of California, San Diego, San Diego, La Jolla, CA, USA.
| | - Hakon Hakonarson
- Divisions of Human Genetics and Pulmonary Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Rakesh Sindhi
- Hillman Center for Pediatric Transplantation, UPMC-Children's Hospital of Pittsburgh, and Thomas E Starzl Transplant Institute, University of Pittsburgh, Pittsburgh, PA, USA.
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Glessner JT, Khan ME, Chang X, Liu Y, Otieno FG, Lemma M, Slaby I, Hain H, Mentch F, Li J, Kao C, Sleiman PMA, March ME, Connolly J, Hakonarson H. Rare recurrent copy number variations in metabotropic glutamate receptor interacting genes in children with neurodevelopmental disorders. J Neurodev Disord 2023; 15:14. [PMID: 37120522 PMCID: PMC10148449 DOI: 10.1186/s11689-023-09483-z] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 04/06/2023] [Indexed: 05/01/2023] Open
Abstract
BACKGROUND Neurodevelopmental disorders (NDDs), such as attention deficit hyperactivity disorder (ADHD) and autism spectrum disorder (ASD), are examples of complex and partially overlapping phenotypes that often lack definitive corroborating genetic information. ADHD and ASD have complex genetic associations implicated by rare recurrent copy number variations (CNVs). Both of these NDDs have been shown to share similar biological etiologies as well as genetic pleiotropy. METHODS Platforms aimed at investigating genetic-based associations, such as high-density microarray technologies, have been groundbreaking techniques in the field of complex diseases, aimed at elucidating the underlying disease biology. Previous studies have uncovered CNVs associated with genes within shared candidate genomic networks, including glutamate receptor genes, across multiple different NDDs. To examine shared biological pathways across two of the most common NDDs, we investigated CNVs across 15,689 individuals with ADHD (n = 7920), ASD (n = 4318), or both (n = 3,416), as well as 19,993 controls. Cases and controls were matched by genotype array (i.e., Illumina array versions). Three case-control association studies each calculated and compared the observed vs. expected frequency of CNVs across individual genes, loci, pathways, and gene networks. Quality control measures of confidence in CNV-calling, prior to association analyses, included visual inspection of genotype and hybridization intensity. RESULTS Here, we report results from CNV analysis in search for individual genes, loci, pathways, and gene networks. To extend our previous observations implicating a key role of the metabotropic glutamate receptor (mGluR) network in both ADHD and autism, we exhaustively queried patients with ASD and/or ADHD for CNVs associated with the 273 genomic regions of interest within the mGluR gene network (genes with one or two degrees protein-protein interaction with mGluR 1-8 genes). Among CNVs in mGluR network genes, we uncovered CNTN4 deletions enriched in NDD cases (P = 3.22E - 26, OR = 2.49). Additionally, we uncovered PRLHR deletions in 40 ADHD cases and 12 controls (P = 5.26E - 13, OR = 8.45) as well as clinically diagnostic relevant 22q11.2 duplications and 16p11.2 duplications in 23 ADHD + ASD cases and 9 controls (P = 4.08E - 13, OR = 15.05) and 22q11.2 duplications in 34 ADHD + ASD cases and 51 controls (P = 9.21E - 9, OR = 3.93); those control samples were not with previous 22qDS diagnosis in their EHR records. CONCLUSION Together, these results suggest that disruption in neuronal cell-adhesion pathways confers significant risk to NDDs and showcase that rare recurrent CNVs in CNTN4, 22q11.2, and 16p11.2 are overrepresented in NDDs that constitute patients predominantly suffering from ADHD and ASD. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT02286817 First Posted: 10 November 14, ClinicalTrials.gov Identifier: NCT02777931 first posted: 19 May 2016, ClinicalTrials.gov Identifier: NCT03006367 first posted: 30 December 2016, ClinicalTrials.gov Identifier: NCT02895906 first posted: 12 September 2016.
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Affiliation(s)
- Joseph T Glessner
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Munir E Khan
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, USA
| | - Xiao Chang
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, USA
| | - Yichuan Liu
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, USA
| | - F George Otieno
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, USA
| | - Maria Lemma
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, USA
| | - Isabella Slaby
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, USA
| | - Heather Hain
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, USA
| | - Frank Mentch
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, USA
| | - Jin Li
- Department of Cell Biology, the Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Charlly Kao
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, USA
| | - Patrick M A Sleiman
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Michael E March
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - John Connolly
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, USA.
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA.
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Singhal P, Veturi Y, Dudek SM, Lucas A, Frase A, van Steen K, Schrodi SJ, Fasel D, Weng C, Pendergrass R, Schaid DJ, Kullo IJ, Dikilitas O, Sleiman PMA, Hakonarson H, Moore JH, Williams SM, Ritchie MD, Verma SS. Evidence of epistasis in regions of long-range linkage disequilibrium across five complex diseases in the UK Biobank and eMERGE datasets. Am J Hum Genet 2023; 110:575-591. [PMID: 37028392 PMCID: PMC10119154 DOI: 10.1016/j.ajhg.2023.03.007] [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: 12/12/2022] [Accepted: 03/07/2023] [Indexed: 04/09/2023] Open
Abstract
Leveraging linkage disequilibrium (LD) patterns as representative of population substructure enables the discovery of additive association signals in genome-wide association studies (GWASs). Standard GWASs are well-powered to interrogate additive models; however, new approaches are required for invesigating other modes of inheritance such as dominance and epistasis. Epistasis, or non-additive interaction between genes, exists across the genome but often goes undetected because of a lack of statistical power. Furthermore, the adoption of LD pruning as customary in standard GWASs excludes detection of sites that are in LD but might underlie the genetic architecture of complex traits. We hypothesize that uncovering long-range interactions between loci with strong LD due to epistatic selection can elucidate genetic mechanisms underlying common diseases. To investigate this hypothesis, we tested for associations between 23 common diseases and 5,625,845 epistatic SNP-SNP pairs (determined by Ohta's D statistics) in long-range LD (>0.25 cM). Across five disease phenotypes, we identified one significant and four near-significant associations that replicated in two large genotype-phenotype datasets (UK Biobank and eMERGE). The genes that were most likely involved in the replicated associations were (1) members of highly conserved gene families with complex roles in multiple pathways, (2) essential genes, and/or (3) genes that were associated in the literature with complex traits that display variable expressivity. These results support the highly pleiotropic and conserved nature of variants in long-range LD under epistatic selection. Our work supports the hypothesis that epistatic interactions regulate diverse clinical mechanisms and might especially be driving factors in conditions with a wide range of phenotypic outcomes.
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Affiliation(s)
- Pankhuri Singhal
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yogasudha Veturi
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Scott M Dudek
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Anastasia Lucas
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alex Frase
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kristel van Steen
- Department of Human Genetics, Katholieke Universiteit Leuven, ON4 Herestraat 49, 3000 Leuven, Belgium
| | - Steven J Schrodi
- Laboratory of Genetics, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53706, USA
| | - David Fasel
- Columbia University, New York, NY 10027, USA
| | | | | | | | | | | | | | - Hakon Hakonarson
- Children's Hospital of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jason H Moore
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Scott M Williams
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Marylyn D Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Shefali S Verma
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Cardinale CJ, Abrams DJ, Mentch FD, Cardinale JA, Wang X, Kao C, Sleiman PMA, Hakonarson H. Elevated Levels of the Cytokine LIGHT in Pediatric Crohn's Disease. J Immunol 2023; 210:590-594. [PMID: 36688686 DOI: 10.4049/jimmunol.2200652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/28/2022] [Indexed: 01/24/2023]
Abstract
LIGHT (homologous to lymphotoxins, exhibits inducible expression, and competes with HSV glycoprotein D for herpes virus entry mediator, a receptor expressed by T lymphocytes), encoded by the TNFSF14 gene, is a cytokine belonging to the TNF superfamily. On binding to its receptors, herpes virus entry mediator and lymphotoxin β receptor, it activates inflammatory responses. We conducted this study to determine whether plasma LIGHT levels are elevated in Crohn's disease (CD) in a pediatric population with the aim of nominating this cytokine as a therapeutic target. We used a single-molecule immunoassay to determine the circulating levels of free LIGHT in plasma from pediatric patients with CD in our biobank (n = 183), a panel of healthy pediatric (n = 9) or adult (n = 22) reference samples, and pediatric biobank controls (n = 19). We performed correlational analyses between LIGHT levels and the clinical characteristics of the CD cohort, including age, Montreal classification, family history, medical/surgical therapy, and routine blood test parameters. LIGHT levels were greatly elevated in CD, with an average of 305 versus 32.4 pg/ml for controls from the biobank (p < 0.0001). The outside reference samples showed levels of 57 pg/ml in pediatric controls and 55 pg/ml in adults (p < 0.0001). We found a statistically significant correlation between white blood cell count and free LIGHT (p < 0.046). We conclude that free, soluble LIGHT is increased 5- to 10-fold in pediatric CD across an array of disease subtypes and characteristics.
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Affiliation(s)
| | - Debra J Abrams
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA; and
| | - Frank D Mentch
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA; and
| | - John A Cardinale
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA; and
| | - Xiang Wang
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA; and
| | - Charlly Kao
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA; and
| | - Patrick M A Sleiman
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA; and.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA; and.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
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Glessner JT, Li J, Liu Y, Khan M, Chang X, Sleiman PMA, Hakonarson H. ParseCNV2: efficient sequencing tool for copy number variation genome-wide association studies. Eur J Hum Genet 2023; 31:304-312. [PMID: 36316489 PMCID: PMC9995309 DOI: 10.1038/s41431-022-01222-7] [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: 12/07/2021] [Revised: 10/01/2022] [Accepted: 10/14/2022] [Indexed: 11/06/2022] Open
Abstract
Improved copy number variation (CNV) detection remains an area of heavy emphasis for algorithm development; however, both CNV curation and disease association approaches remain in its infancy. The current practice of focusing on candidate CNVs, where researchers study specific CNVs they believe to be pathological while discarding others, refrains from considering the full spectrum of CNVs in a hypothesis-free GWAS. To address this, we present a next-generation approach to CNV association by natively supporting the popular VCF specification for sequencing-derived variants as well as SNP array calls using a PennCNV format. The code is fast and efficient, allowing for the analysis of large (>100,000 sample) cohorts without dividing up the data on a compute cluster. The scripts are condensed into a single tool to promote simplicity and best practices. CNV curation pre and post-association is rigorously supported and emphasized to yield reliable results of highest quality. We benchmarked two large datasets, including the UK Biobank (n > 450,000) and CAG Biobank (n > 350,000) both of which are genotyped at >0.5 M probes, for our input files. ParseCNV has been actively supported and developed since 2008. ParseCNV2 presents a critical addition to formalizing CNV association for inclusion with SNP associations in GWAS Catalog. Clinical CNV prioritization, interactive quality control (QC), and adjustment for covariates are revolutionary new features of ParseCNV2 vs. ParseCNV. The software is freely available at: https://github.com/CAG-CNV/ParseCNV2 .
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Affiliation(s)
- Joseph T Glessner
- Department of Pediatrics, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA.
- Department of Pediatrics, Perelman School of Medicine, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA.
| | - Jin Li
- Department of Cell Biology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Yichuan Liu
- Department of Pediatrics, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA
- Department of Pediatrics, Perelman School of Medicine, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Munir Khan
- Department of Pediatrics, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA
- Department of Pediatrics, Perelman School of Medicine, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Xiao Chang
- Department of Pediatrics, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA
- Department of Pediatrics, Perelman School of Medicine, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Patrick M A Sleiman
- Department of Pediatrics, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA
- Department of Pediatrics, Perelman School of Medicine, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Hakon Hakonarson
- Department of Pediatrics, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA
- Department of Pediatrics, Perelman School of Medicine, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA
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Glessner JT, Chang X, Mentch F, Qu H, Abrams DJ, Thomas A, Sleiman PMA, Hakonarson H. COVID-19 in pediatrics: Genetic susceptibility. Front Genet 2022; 13:928466. [PMID: 36051697 PMCID: PMC9425045 DOI: 10.3389/fgene.2022.928466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/13/2022] [Indexed: 11/21/2022] Open
Abstract
The uptick in SARS-CoV-2 infection has resulted in a worldwide COVID-19 pandemic, which has created troublesome health and economic problems. We performed case–control meta-analyses in both African and European ethnicity COVID-19 disease cases based on laboratory test and phenotypic criteria. The cases had laboratory-confirmed SARS-CoV-2 infection. We uniquely investigated COVID infection genetics in a pediatric population. Our cohort has a large African ancestry component, also unique to our study. We tested for genetic variant association in 498 cases vs. 1,533 controls of African ancestry and 271 cases vs. 855 controls of European ancestry. We acknowledge that the sample size is relatively small, owing to the low prevalence of COVID infection among pediatric individuals. COVID-19 cases averaged 13 years of age. Pediatric genetic studies enhance the ability to detect genetic associations with a limited possible environment impact. Our findings support the notion that some genetic variants, most notably at the SEMA6D, FMN1, ACTN1, PDS5B, NFIA, ADGRL3, MMP27, TENM3, SPRY4, MNS1, and RSU1 loci, play a role in COVID-19 infection susceptibility. The pediatric cohort also shows nominal replication of previously reported adult study results: CCR9, CXCR6, FYCO1, LZTFL1, TDGF1, CCR1, CCR2, CCR3, CCR5, MAPT-AS1, and IFNAR2 gene variants. Reviewing the biological roles of genes implicated here, NFIA looks to be the most interesting as it binds to a palindromic sequence observed in both viral and cellular promoters and in the adenovirus type 2 origin of replication.
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Affiliation(s)
- Joseph T. Glessner
- Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- *Correspondence: Joseph T. Glessner,
| | - Xiao Chang
- Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Frank Mentch
- Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Huiqi Qu
- Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Debra J. Abrams
- Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Alexandria Thomas
- Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Patrick M. A. Sleiman
- Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Hakon Hakonarson
- Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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8
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Zeng C, Bastarache LA, Tao R, Venner E, Hebbring S, Andujar JD, Bland ST, Crosslin DR, Pratap S, Cooley A, Pacheco JA, Christensen KD, Perez E, Zawatsky CLB, Witkowski L, Zouk H, Weng C, Leppig KA, Sleiman PMA, Hakonarson H, Williams MS, Luo Y, Jarvik GP, Green RC, Chung WK, Gharavi AG, Lennon NJ, Rehm HL, Gibbs RA, Peterson JF, Roden DM, Wiesner GL, Denny JC. Association of Pathogenic Variants in Hereditary Cancer Genes With Multiple Diseases. JAMA Oncol 2022; 8:835-844. [PMID: 35446370 PMCID: PMC9026237 DOI: 10.1001/jamaoncol.2022.0373] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Importance Knowledge about the spectrum of diseases associated with hereditary cancer syndromes may improve disease diagnosis and management for patients and help to identify high-risk individuals. Objective To identify phenotypes associated with hereditary cancer genes through a phenome-wide association study. Design, Setting, and Participants This phenome-wide association study used health data from participants in 3 cohorts. The Electronic Medical Records and Genomics Sequencing (eMERGEseq) data set recruited predominantly healthy individuals from 10 US medical centers from July 16, 2016, through February 18, 2018, with a mean follow-up through electronic health records (EHRs) of 12.7 (7.4) years. The UK Biobank (UKB) cohort recruited participants from March 15, 2006, through August 1, 2010, with a mean (SD) follow-up of 12.4 (1.0) years. The Hereditary Cancer Registry (HCR) recruited patients undergoing clinical genetic testing at Vanderbilt University Medical Center from May 1, 2012, through December 31, 2019, with a mean (SD) follow-up through EHRs of 8.8 (6.5) years. Exposures Germline variants in 23 hereditary cancer genes. Pathogenic and likely pathogenic variants for each gene were aggregated for association analyses. Main Outcomes and Measures Phenotypes in the eMERGEseq and HCR cohorts were derived from the linked EHRs. Phenotypes in UKB were from multiple sources of health-related data. Results A total of 214 020 participants were identified, including 23 544 in eMERGEseq cohort (mean [SD] age, 47.8 [23.7] years; 12 611 women [53.6%]), 187 234 in the UKB cohort (mean [SD] age, 56.7 [8.1] years; 104 055 [55.6%] women), and 3242 in the HCR cohort (mean [SD] age, 52.5 [15.5] years; 2851 [87.9%] women). All 38 established gene-cancer associations were replicated, and 19 new associations were identified. These included the following 7 associations with neoplasms: CHEK2 with leukemia (odds ratio [OR], 3.81 [95% CI, 2.64-5.48]) and plasma cell neoplasms (OR, 3.12 [95% CI, 1.84-5.28]), ATM with gastric cancer (OR, 4.27 [95% CI, 2.35-7.44]) and pancreatic cancer (OR, 4.44 [95% CI, 2.66-7.40]), MUTYH (biallelic) with kidney cancer (OR, 32.28 [95% CI, 6.40-162.73]), MSH6 with bladder cancer (OR, 5.63 [95% CI, 2.75-11.49]), and APC with benign liver/intrahepatic bile duct tumors (OR, 52.01 [95% CI, 14.29-189.29]). The remaining 12 associations with nonneoplastic diseases included BRCA1/2 with ovarian cysts (OR, 3.15 [95% CI, 2.22-4.46] and 3.12 [95% CI, 2.36-4.12], respectively), MEN1 with acute pancreatitis (OR, 33.45 [95% CI, 9.25-121.02]), APC with gastritis and duodenitis (OR, 4.66 [95% CI, 2.61-8.33]), and PTEN with chronic gastritis (OR, 15.68 [95% CI, 6.01-40.92]). Conclusions and Relevance The findings of this genetic association study analyzing the EHRs of 3 large cohorts suggest that these new phenotypes associated with hereditary cancer genes may facilitate early detection and better management of cancers. This study highlights the potential benefits of using EHR data in genomic medicine.
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Affiliation(s)
- Chenjie Zeng
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Lisa A Bastarache
- Center for Precision Medicine, Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Ran Tao
- Department of Biostatistics, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Eric Venner
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Scott Hebbring
- Center for Human Genetics, Marshfield Clinic Research Institute, Marshfield, Wisconsin
| | - Justin D Andujar
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee.,Clinical and Translational Hereditary Cancer Program, Division of Genetic Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee
| | - Sarah T Bland
- Center for Precision Medicine, Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - David R Crosslin
- Department of Biomedical Informatics and Medical Education, University of Washington School of Medicine, Seattle
| | - Siddharth Pratap
- School of Graduate Studies and Research, Meharry Medical College, Nashville, Tennessee
| | - Ayorinde Cooley
- Department of Microbiology, Immunology and Physiology, Meharry Medical College, Nashville, Tennessee
| | - Jennifer A Pacheco
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Kurt D Christensen
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, Massachusetts.,Department of Population Medicine, Harvard Medical School, Boston, Massachusetts
| | - Emma Perez
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Carrie L Blout Zawatsky
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Leora Witkowski
- Centre Universitaire de Santé McGill, McGill University Health Centre, Montreal, Quebec, Canada
| | - Hana Zouk
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, New York
| | - Kathleen A Leppig
- Genetic Services and Kaiser Permanente Washington Health Research Institute, Kaiser Permanente of Washington, Seattle
| | - Patrick M A Sleiman
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Division of Human Genetics, Department of Pediatrics, The University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Division of Human Genetics, Department of Pediatrics, The University of Pennsylvania Perelman School of Medicine, Philadelphia
| | - Marc S Williams
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | - Yuan Luo
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Gail P Jarvik
- Department of Medicine (Medical Genetics), University of Washington, Seattle.,Department of Genome Sciences, University of Washington, Seattle
| | - Robert C Green
- Brigham and Women's Hospital, Broad Institute, Ariadne Labs and Harvard Medical School, Boston, Massachusetts
| | - Wendy K Chung
- Department of Pediatrics, Columbia University, New York, New York.,Department of Medicine, Columbia University, New York, New York
| | - Ali G Gharavi
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, New York.,Center for Precision Medicine and Genomics, Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - Niall J Lennon
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Heidi L Rehm
- Medical & Population Genetics Program and Genomics Platform, Broad Institute of MIT and Harvard Cambridge, Cambridge, Massachusetts.,Center for Genomic Medicine, Massachusetts General Hospital, Boston.,Department of Pathology, Harvard Medical School, Boston, Massachusetts
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Josh F Peterson
- Center for Precision Medicine, Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Dan M Roden
- Center for Precision Medicine, Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee.,Divisions of Cardiovascular Medicine and Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee.,Department of Pharmacology, Vanderbilt University, Nashville, Tennessee
| | - Georgia L Wiesner
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee.,Clinical and Translational Hereditary Cancer Program, Division of Genetic Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee
| | - Joshua C Denny
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
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9
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Dridi W, Kanfar S, Sleiman PMA, Liu Y, Hakonarson H, Rammah H, Matrouk A. Saudi Arabian CML patient with a novel four-way translocation at t(9;22;5;2)(q34;q11.2;p13;q44). Mol Genet Genomic Med 2022; 10:e1865. [PMID: 35543309 PMCID: PMC9184659 DOI: 10.1002/mgg3.1865] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 09/07/2021] [Accepted: 09/14/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The vast majority of chronic myeloid leukemia (CML) patients have a single translocation t(9;22)(q34;q11), BCR/ABL1 fusion genes, which is regarded as the hallmark of CML. However, around 5 to 10% of CML patients exhibit the involvement of a third chromosome. In some very rare cases a fourth or even fifth chromosome can be involved with the t(9;22). METHODS This case report is based on a 40-year-old Saudi Arabian male patient, diagnosed with CML in lymphoid blast crisis, and observed to have a four-way 46 XY, t(9;22;5;2)(q34;q11.2;p13;q44) translocation. The BCR/ABL1 fusion was identified by fluorescent in situ hybridization (FISH). Additionally, the BCR/ABL1 p210 mRNA fusion transcripts were identified by a molecular test. RESULTS The clinical and prognostic impact of additional partner chromosomes to t(9;22) remains unknown. The CML patient with this novel four-way translocation t(9;22;5;2) progressed to blast crisis and was resistant to Tyrosine Kinase Inhibitor (TKI) therapy. Therefore, this case is more in alignment with the negative impact of additional partner chromosomes to the translocation at t(9;22). CONCLUSION Here we report for the first time a novel four-way translocation at t(9;22;5;2)(q34;q11.2;p13;q44).
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Affiliation(s)
- Walid Dridi
- Cytogenetics Unit, Pathology and Laboratory Medicine Department, King Fahad Specialist Hospital-Dammam, Dammam, Saudi Arabia
| | - Solaf Kanfar
- Hemato-Oncology Adult Department, King Fahad Specialist Hospital-Dammam, Dammam, Saudi Arabia
| | - Patrick M A Sleiman
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yichuan Liu
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Hakon Hakonarson
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Hayaal Rammah
- Cytogenetics Unit, Pathology and Laboratory Medicine Department, King Fahad Specialist Hospital-Dammam, Dammam, Saudi Arabia
| | - Alia Matrouk
- Cytogenetics Unit, Pathology and Laboratory Medicine Department, King Fahad Specialist Hospital-Dammam, Dammam, Saudi Arabia
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10
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Liu Y, Qu HQ, Chang X, Qu J, Mentch FD, Nguyen K, Tian L, Glessner J, Sleiman PMA, Hakonarson H. Mutation Burden Analysis of Six Common Mental Disorders in African Americans by Whole Genome Sequencing. Hum Mol Genet 2022; 31:3769-3776. [PMID: 35642741 DOI: 10.1093/hmg/ddac129] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/12/2022] [Accepted: 05/27/2022] [Indexed: 11/14/2022] Open
Abstract
Mental disorders present a global health concern, with limited treatment options. In today's medical practice, medications such as antidepressants are prescribed not only for depression, but also for conditions such as anxiety and attention deficit hyperactivity disorder (ADHD). Therefore, identifying gene targets for specific disorders is important and offers improved precision. In this study, we performed a genetic analysis of six common mental disorders, ADHD, anxiety, depression, delays in mental developments, intellectual disabilities (ID), and speech/language disorder in the ethnic minority of African Americans (AA) using whole genome sequencing (WGS). WGS data was generated from blood-derived DNA from 4178 AA individuals, including 1384 patients with the diagnosis of at least one mental disorder. Mutation burden analysis was applied based on rare and deleterious mutations in the AA population between cases and controls, and further analyzed in the context of patients with single mental disorder diagnosis. Certain genes uncovered demonstrated significant p values in mutation burden analysis. In addition, exclusive recurrences in specific type of disorder were scanned through gene-drug interaction databases to assess for availability of potential medications. We uncovered 15 genes harboring deleterious mutations, including HMGCR and UST for ADHD; FNTB for anxiety, XIRP2, NPPC, , STK33, PANX1 and NTS for depression; RUNX3, TACR1, and NDUFS7 for delays in mental developments; HPN for ID; COL6A3, DDB1, and NDUFA11 for speech/language disorder. Taken together, we have established critical insight into the development of new precision medicine approaches for mental disorders in African Americans.
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Affiliation(s)
- Yichuan Liu
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Hui-Qi Qu
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Xiao Chang
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Jingchun Qu
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Frank D Mentch
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Kenny Nguyen
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Lifeng Tian
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Joseph Glessner
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Patrick M A Sleiman
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.,Division of Pulmonary Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 19104, USA.,Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
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11
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Liu Y, Qu HQ, Qu J, Chang X, Mentch FD, Nguyen K, Tian L, Glessner J, Sleiman PMA, Hakonarson H. Burden of rare coding variants reveals genetic heterogeneity between obese and non-obese asthma patients in the African American population. Respir Res 2022; 23:116. [PMID: 35524249 PMCID: PMC9078008 DOI: 10.1186/s12931-022-02039-0] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 04/19/2022] [Indexed: 11/23/2022] Open
Abstract
Background Asthma is a complex condition largely attributed to the interactions among genes and environments as a heterogeneous phenotype. Obesity is significantly associated with asthma development, and genetic studies on obese vs. non-obese asthma are warranted. Methods To investigate asthma in the minority African American (AA) population with or without obesity, we performed a whole genome sequencing (WGS) study on blood-derived DNA of 4289 AA individuals, included 2226 asthma patients (1364 with obesity and 862 without obesity) and 2006 controls without asthma. The burden analysis of functional rare coding variants was performed by comparing asthma vs. controls and by stratified analysis of obese vs. non-obese asthma, respectively. Results Among the top 66 genes with P < 0.01 in the asthma vs. control analysis, stratified analysis by obesity showed inverse correlation of natural logarithm (LN) of P value between obese and non-obese asthma (r = − 0.757, P = 1.90E−13). Five genes previously reported in a genome-wide association study (GWAS) on asthma, including TSLP, SLC9A4, PSMB8, IGSF5, and IKZF4 were demonstrated association in the asthma vs. control analysis. The associations of IKZF4 and IGSF5 are only associated with obese asthma; and the association of SLC9A4 is only observed in non-obese asthma. In addition, the association of RSPH3 (the gene is related to primary ciliary dyskinesia) is observed in non-obese asthma. Conclusions These findings highlight genetic heterogeneity between obese and non-obese asthma in patients of AA ancestry. Supplementary Information The online version contains supplementary material available at 10.1186/s12931-022-02039-0.
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Affiliation(s)
- Yichuan Liu
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Hui-Qi Qu
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Jingchun Qu
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Xiao Chang
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Frank D Mentch
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Kenny Nguyen
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Lifeng Tian
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Joseph Glessner
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Patrick M A Sleiman
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA. .,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA. .,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA. .,Division of Pulmonary Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA. .,Faculty of Medicine, University of Iceland, 101, Reykjavik, Iceland.
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12
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Li J, Li YR, Glessner JT, Yang J, March ME, Kao C, Vaccaro CN, Bradfield JP, Li J, Mentch FD, Qu H, Qi X, Chang X, Hou C, Abrams DJ, Qiu H, Wei Z, Connolly JJ, Wang F, Snyder J, Flatø B, Thompson SD, Langefeld CD, Lie BA, Munro JE, Wise C, Sleiman PMA, Hakonarson H. Identification of Novel Loci Shared by Juvenile Idiopathic Arthritis Subtypes through Integrative Genetic Analysis. Arthritis Rheumatol 2022; 74:1420-1429. [PMID: 35347896 PMCID: PMC9542075 DOI: 10.1002/art.42129] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 03/11/2022] [Accepted: 03/25/2022] [Indexed: 11/25/2022]
Abstract
Objective Juvenile idiopathic arthritis (JIA) is the most common chronic immune‐mediated joint disease among children and encompasses a heterogeneous group of immune‐mediated joint disorders classified into 7 subtypes according to clinical presentation. However, phenotype overlap and biologic evidence suggest a shared mechanistic basis between subtypes. This study was undertaken to systematically investigate shared genetic underpinnings of JIA subtypes. Methods We performed a heterogeneity‐sensitive genome‐wide association study encompassing a total of 1,245 JIA cases (classified into 7 subtypes) and 9,250 controls, followed by fine‐mapping of candidate causal variants at each genome‐wide significant locus, functional annotation, and pathway and network analysis. We further identified candidate drug targets and drug repurposing opportunities by in silico analyses. Results In addition to the major histocompatibility complex locus, we identified 15 genome‐wide significant loci shared between at least 2 JIA subtypes, including 10 novel loci. Functional annotation indicated that candidate genes at these loci were expressed in diverse immune cell types. Conclusion This study identified novel genetic loci shared by JIA subtypes. Our findings identified candidate mechanisms underlying JIA subtypes and candidate targets with drug repurposing opportunities for JIA treatment.
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Affiliation(s)
- Jin Li
- Department of Cell Biology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yun R Li
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,City of Hope Comprehensive Cancer Center, 1500 E Duarte Rd, Duarte, CA, 91010, USA.,Division of Quantitative Medicine & Systems Biology, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Joseph T Glessner
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jie Yang
- Department of Cell Biology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Michael E March
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Charlly Kao
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Courtney N Vaccaro
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jonathan P Bradfield
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Junyi Li
- Department of Cell Biology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Frank D Mentch
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Huiqi Qu
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Xiaohui Qi
- Department of Cell Biology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xiao Chang
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Cuiping Hou
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Debra J Abrams
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Haijun Qiu
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Zhi Wei
- Department of Computer Science, New Jersey Institute of Technology, Newark, New Jersey, USA
| | - John J Connolly
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Fengxiang Wang
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - James Snyder
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Berit Flatø
- Department of Rheumatology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Susan D Thompson
- Department of Pediatrics, University of Cincinnati College of Medicine, Division of Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Carl D Langefeld
- Department of Biostatistics and Data Science, Center for Precision Medicine, Wake Forest University School of Medicine, 27157, Winston-Salem, NC, USA
| | - Benedicte A Lie
- Department of Immunology, Oslo University Hospital, 0027 Rikshospitalet, Oslo, Norway
| | - Jane E Munro
- Murdoch Children's Research Institute, 3052 Parkville, Victoria, VIC, Australia.,Paediatric Rheumatology Unit, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Carol Wise
- Center for Pediatric Bone Biology and Translational Research, Scottish Rite for Children, 75219 Dallas, TX, USA
| | - Patrick M A Sleiman
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hakon Hakonarson
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Division of Pulmonary Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
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13
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Grosche S, Marenholz I, Esparza-Gordillo J, Arnau-Soler A, Pairo-Castineira E, Rüschendorf F, Ahluwalia TS, Almqvist C, Arnold A, Baurecht H, Bisgaard H, Bønnelykke K, Brown SJ, Bustamante M, Curtin JA, Custovic A, Dharmage SC, Esplugues A, Falchi M, Fernandez-Orth D, Ferreira MAR, Franke A, Gerdes S, Gieger C, Hakonarson H, Holt PG, Homuth G, Hubner N, Hysi PG, Jarvelin MR, Karlsson R, Koppelman GH, Lau S, Lutz M, Magnusson PKE, Marks GB, Müller-Nurasyid M, Nöthen MM, Paternoster L, Pennell CE, Peters A, Rawlik K, Robertson CF, Rodriguez E, Sebert S, Simpson A, Sleiman PMA, Standl M, Stölzl D, Strauch K, Szwajda A, Tenesa A, Thompson PJ, Ullemar V, Visconti A, Vonk JM, Wang CA, Weidinger S, Wielscher M, Worth CL, Xu CJ, Lee YA. Rare variant analysis in eczema identifies exonic variants in DUSP1, NOTCH4 and SLC9A4. Nat Commun 2021; 12:6618. [PMID: 34785669 PMCID: PMC8595373 DOI: 10.1038/s41467-021-26783-x] [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: 12/26/2020] [Accepted: 10/21/2021] [Indexed: 11/10/2022] Open
Abstract
Previous genome-wide association studies revealed multiple common variants involved in eczema but the role of rare variants remains to be elucidated. Here, we investigate the role of rare variants in eczema susceptibility. We meta-analyze 21 study populations including 20,016 eczema cases and 380,433 controls. Rare variants are imputed with high accuracy using large population-based reference panels. We identify rare exonic variants in DUSP1, NOTCH4, and SLC9A4 to be associated with eczema. In DUSP1 and NOTCH4 missense variants are predicted to impact conserved functional domains. In addition, five novel common variants at SATB1-AS1/KCNH8, TRIB1/LINC00861, ZBTB1, TBX21/OSBPL7, and CSF2RB are discovered. While genes prioritized based on rare variants are significantly up-regulated in the skin, common variants point to immune cell function. Over 20% of the single nucleotide variant-based heritability is attributable to rare and low-frequency variants. The identified rare/low-frequency variants located in functional protein domains point to promising targets for novel therapeutic approaches to eczema. Genetic studies of eczema to date have mostly explored common genetic variation. Here, the authors perform a large meta-analysis for common and rare variants and discover 8 loci associated with eczema. Over 20% of the heritability of the condition is attributable to rare variants.
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Affiliation(s)
- Sarah Grosche
- Max-Delbrück-Center (MDC) for Molecular Medicine, Berlin, Germany.,Clinic for Pediatric Allergy, Experimental and Clinical Research Center, Charité University Medical Center, Berlin, Germany.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Ingo Marenholz
- Max-Delbrück-Center (MDC) for Molecular Medicine, Berlin, Germany.,Clinic for Pediatric Allergy, Experimental and Clinical Research Center, Charité University Medical Center, Berlin, Germany
| | - Jorge Esparza-Gordillo
- Max-Delbrück-Center (MDC) for Molecular Medicine, Berlin, Germany.,Clinic for Pediatric Allergy, Experimental and Clinical Research Center, Charité University Medical Center, Berlin, Germany.,GlaxoSmithKline, Stevenage, UK
| | - Aleix Arnau-Soler
- Max-Delbrück-Center (MDC) for Molecular Medicine, Berlin, Germany.,Clinic for Pediatric Allergy, Experimental and Clinical Research Center, Charité University Medical Center, Berlin, Germany
| | - Erola Pairo-Castineira
- Roslin Institute, University of Edinburgh, Edinburgh, UK.,MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | | | - Tarunveer S Ahluwalia
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark.,Steno Diabetes Center Copenhagen, Gentofte, Denmark
| | - Catarina Almqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden.,Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Andreas Arnold
- Clinic and Polyclinic of Dermatology, University Medicine Greifswald, Greifswald, Germany
| | | | - Hansjörg Baurecht
- Department of Dermatology, Allergology and Venereology, University Hospital Schleswig-Holstein, Kiel, Germany.,Department of Epidemiology and Preventive Medicine, University Regensburg, Regensburg, Germany
| | - Hans Bisgaard
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Klaus Bønnelykke
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Sara J Brown
- Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Mariona Bustamante
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
| | - John A Curtin
- Division of Infection Immunity and Respiratory Medicine, School of Biological Sciences, The University of Manchester, Manchester Academic Health Science Centre and Manchester University NHS Foundation Trust, Manchester, UK
| | - Adnan Custovic
- National Lung and Heart Institute, Imperial College London, London, UK
| | - Shyamali C Dharmage
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Ana Esplugues
- Nursing School, University of Valencia, FISABIO-University Jaume I-University of Valencia Joint Research Unit of Epidemiology and Environmental Health, CIBERESP, Valencia, Spain
| | - Mario Falchi
- Department of Twins Research and Genetic Epidemiology, King's College London, London, UK
| | | | - Manuel A R Ferreira
- Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Sascha Gerdes
- Department of Dermatology, Allergology and Venereology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Christian Gieger
- Research Unit Molecular Epidemiology, Helmholtz Center Munich - German Research Center for Environmental Health, Neuherberg, Germany
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, and Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Patrick G Holt
- Telethon Kids Institute, The University of Western Australia, Perth, Australia
| | - Georg Homuth
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Norbert Hubner
- Max-Delbrück-Center (MDC) for Molecular Medicine, Berlin, Germany
| | - Pirro G Hysi
- Department of Twins Research and Genetic Epidemiology, King's College London, London, UK
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK.,Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Robert Karlsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Gerard H Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergology, University of Groningen, University Medical Center Groningen, GRIAC Research Institute, Groningen, the Netherlands
| | - Susanne Lau
- Department of Pediatric Pulmonology, Immunology and Intensive Care Medicine, Charité University Medical Center, Berlin, Germany
| | - Manuel Lutz
- Institute of Genetic Epidemiology, Helmholtz Center Munich-German Research Center for Environmental Health, Neuherberg, Germany
| | - Patrik K E Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Guy B Marks
- Woolcock Institute of Medical Research, University of Sydney, Sydney, Australia
| | - Martina Müller-Nurasyid
- Institute of Genetic Epidemiology, Helmholtz Center Munich-German Research Center for Environmental Health, Neuherberg, Germany.,Institute for Medical Information Processing, Biometry, and Epidemiology (IBE), Faculty of Medicine, LMU Munich, Munich, Germany.,Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Lavinia Paternoster
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Craig E Pennell
- School of Medicine and Public Health, Faculty of Medicine and Health, The University of Newcastle, Newcastle, Australia
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Center Munich-German Research Center for Environmental Health, Neuherberg, Germany
| | - Konrad Rawlik
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Colin F Robertson
- Respiratory Research, Murdoch Children's Research Institute, Melbourne, Australia
| | - Elke Rodriguez
- Department of Dermatology, Allergology and Venereology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Sylvain Sebert
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK.,Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Angela Simpson
- Division of Infection Immunity and Respiratory Medicine, School of Biological Sciences, The University of Manchester, Manchester Academic Health Science Centre and Manchester University NHS Foundation Trust, Manchester, UK
| | - Patrick M A Sleiman
- Center for Applied Genomics, Children's Hospital of Philadelphia, and Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marie Standl
- Institute of Epidemiology, Helmholtz Center Munich-German Research Center for Environmental Health, Neuherberg, Germany
| | - Dora Stölzl
- Department of Dermatology, Allergology and Venereology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Center Munich-German Research Center for Environmental Health, Neuherberg, Germany.,Institute for Medical Information Processing, Biometry, and Epidemiology (IBE), Faculty of Medicine, LMU Munich, Munich, Germany.,Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Agnieszka Szwajda
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Albert Tenesa
- Roslin Institute, University of Edinburgh, Edinburgh, UK.,MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK.,Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Edinburgh, UK
| | - Philip J Thompson
- Institute for Respiratory Health and Centre for Respiratory Health, School of Biomedical Sciences, University of Western Australia, Nedlands, Australia
| | - Vilhelmina Ullemar
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Alessia Visconti
- Department of Twins Research and Genetic Epidemiology, King's College London, London, UK
| | - Judith M Vonk
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, GRIAC Research Institute, Groningen, the Netherlands
| | - Carol A Wang
- School of Medicine and Public Health, Faculty of Medicine and Health, The University of Newcastle, Newcastle, Australia
| | - Stephan Weidinger
- Department of Dermatology, Allergology and Venereology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Matthias Wielscher
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK
| | | | - Chen-Jian Xu
- Department of Pediatric Pulmonology and Pediatric Allergology, University of Groningen, University Medical Center Groningen, GRIAC Research Institute, Groningen, the Netherlands.,Department of Gastroenterology, Hepatology and Endocrinology, Centre for individualized infection medicine (CIIM), Hannover Medical School, Hannover, Germany
| | - Young-Ae Lee
- Max-Delbrück-Center (MDC) for Molecular Medicine, Berlin, Germany. .,Clinic for Pediatric Allergy, Experimental and Clinical Research Center, Charité University Medical Center, Berlin, Germany.
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14
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Al-Harbi TM, Al-Rammah H, Al-Zahrani N, Liu Y, Sleiman PMA, Dridi W, Hakonarson H. Rare neurological manifestations in a Saudi Arabian patient with Ehlers-Danlos syndrome and a novel homozygous variant in the TNXB gene. Am J Med Genet A 2021; 188:618-623. [PMID: 34636138 DOI: 10.1002/ajmg.a.62539] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 09/14/2021] [Accepted: 09/18/2021] [Indexed: 11/08/2022]
Abstract
We report a 38-year-old Saudi male with Ehlers-Danlos Syndrome (EDS). The patient presented with rare and unusual neurological manifestations, including but not limited to ophthalmoplegia and myopathic pattern on his electromyography. In addition to hand weakness, there was skin hyperextensibility, joint hyperflexibility, and frontal baldness. Next-generation sequencing was performed on target exon sequences, using whole exome sequencing and Burrows-Wheeler Aligner for alignment/base calling. Genome Analysis Toolkit and reference genome Homo sapiens (UCSC hg19) were used for sequence processing and analysis. Variant classification was done according to standard international recommendations. A novel homozygous variant, NM_019105.6: c.8488C>T p.(Gln2830*), was detected in the TNXB gene. This variant is not reported in the literature nor dbSNP or gnomAD databases. Additionally, this variant is predicted to create a premature stop codon and produce a truncated protein or nonsense-mediated mRNA decay. Hence, it is classified as a likely pathogenic variant. The same point variant was found in a heterozygous state in the patient's father and sister. Both presented with milder symptoms associated with Ehlers-Danlos syndromes and heritable connective tissue disorders. Therefore, the patient was diagnosed as a tenascin-X (TNX) deficient type of EDS known as classical-like Ehlers-Danlos syndrome. TNX deficient patients may present with clinical and electrophysiological manifestations that are unusual in EDS like frontal baldness, ophthalmoplegia, and myotonia, which mimic myotonic dystrophy type I. Clinicians should be aware of the potential overlap of symptoms among these two diseases to ensure correct diagnosis is made.
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Affiliation(s)
- Talal M Al-Harbi
- Neurology Department, Neuroscience Centre, King Fahad Specialist Hospital-Dammam, Dammam, Saudi Arabia
| | - Haya Al-Rammah
- Genetic Unit, Pathology and Laboratory Medicine Department, King Fahad Specialist Hospital-Dammam, Dammam, Saudi Arabia
| | - Naif Al-Zahrani
- Neurology Department, Neuroscience Centre, King Fahad Specialist Hospital-Dammam, Dammam, Saudi Arabia
| | - Yichuan Liu
- Center for Applied Genomics (CAG), The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Patrick M A Sleiman
- Center for Applied Genomics (CAG), The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Walid Dridi
- Genetic Unit, Pathology and Laboratory Medicine Department, King Fahad Specialist Hospital-Dammam, Dammam, Saudi Arabia
| | - Hakon Hakonarson
- Center for Applied Genomics (CAG), The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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15
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Kelchtermans J, Chang X, March ME, Mentch F, Sleiman PMA, Hakonarson H. HIF-1α Pulmonary Phenotype Wide Association Study Unveils a Link to Inflammatory Airway Conditions. Front Genet 2021; 12:756645. [PMID: 34621299 PMCID: PMC8490729 DOI: 10.3389/fgene.2021.756645] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 08/10/2021] [Accepted: 09/08/2021] [Indexed: 11/21/2022] Open
Abstract
Despite experimental data linking HIF-1α dysfunction to inflammatory airway conditions, the effect of single nucleotide polymorphisms within the HIF1A gene on these conditions remains poorly understood. In the current study, we complete a phenotype wide association study to assess the link between SNPs with known disease associations and respiratory phenotypes. We report two SNPs of the HIF1A gene, the intronic rs79865957 and the missense rs41508050. In these positions the A and the T allele are significantly associated with allergic rhinitis and acute bronchitis and bronchiolitis, respectively. These findings further support the role of HIF-1α in inflammatory pulmonary conditions and may serve as a basis to refine our understanding of other HIF-1α associated phenotypes.
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Affiliation(s)
- Jelte Kelchtermans
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,The Center of Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Xiao Chang
- The Center of Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Michael E March
- The Center of Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Frank Mentch
- The Center of Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Patrick M A Sleiman
- The Center of Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Hakon Hakonarson
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,The Center of Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States
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16
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Glessner JT, Hou X, Zhong C, Zhang J, Khan M, Brand F, Krawitz P, Sleiman PMA, Hakonarson H, Wei Z. DeepCNV: a deep learning approach for authenticating copy number variations. Brief Bioinform 2021; 22:bbaa381. [PMID: 33429424 PMCID: PMC8681111 DOI: 10.1093/bib/bbaa381] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 09/14/2020] [Revised: 11/24/2020] [Accepted: 11/26/2020] [Indexed: 12/14/2022] Open
Abstract
Copy number variations (CNVs) are an important class of variations contributing to the pathogenesis of many disease phenotypes. Detecting CNVs from genomic data remains difficult, and the most currently applied methods suffer from an unacceptably high false positive rate. A common practice is to have human experts manually review original CNV calls for filtering false positives before further downstream analysis or experimental validation. Here, we propose DeepCNV, a deep learning-based tool, intended to replace human experts when validating CNV calls, focusing on the calls made by one of the most accurate CNV callers, PennCNV. The sophistication of the deep neural network algorithm is enriched with over 10 000 expert-scored samples that are split into training and testing sets. Variant confidence, especially for CNVs, is a main roadblock impeding the progress of linking CNVs with the disease. We show that DeepCNV adds to the confidence of the CNV calls with an optimal area under the receiver operating characteristic curve of 0.909, exceeding other machine learning methods. The superiority of DeepCNV was also benchmarked and confirmed using an experimental wet-lab validation dataset. We conclude that the improvement obtained by DeepCNV results in significantly fewer false positive results and failures to replicate the CNV association results.
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Affiliation(s)
- Joseph T Glessner
- Center for Applied Genomics, Department of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19102, USA
| | - Xiurui Hou
- Department of Computer Science, New Jersey Institute of Technology, Newark, NJ 07102, USA
| | - Cheng Zhong
- Department of Computer Science, New Jersey Institute of Technology, Newark, NJ 07102, USA
| | | | - Munir Khan
- Center for Applied Genomics, Department of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine, Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19102, USA
| | | | | | - Patrick M A Sleiman
- Perelman School of Medicine, Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19102, USA
| | - Hakon Hakonarson
- Perelman School of Medicine, Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19102, USA
| | - Zhi Wei
- Department of Computer Science, New Jersey Institute of Technology, Newark, NJ 07102, USA
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17
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Qu J, Qu HQ, Bradfield JP, Glessner JT, Chang X, Tian L, March M, Connolly JJ, Roizen JD, Sleiman PMA, Hakonarson H. Insights into non-autoimmune type 1 diabetes with 13 novel loci in low polygenic risk score patients. Sci Rep 2021; 11:16013. [PMID: 34362956 PMCID: PMC8346538 DOI: 10.1038/s41598-021-94994-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 04/06/2021] [Accepted: 07/20/2021] [Indexed: 01/21/2023] Open
Abstract
With polygenic risk score (PRS) for autoimmune type 1 diabetes (T1D), this study identified T1D cases with low T1D PRS and searched for susceptibility loci in these cases. Our hypothesis is that genetic effects (likely mediated by relatively rare genetic variants) of non-mainstream (or non-autoimmune) T1D might have been diluted in the previous studies on T1D cases in general. Two cohorts for the PRS modeling and testing respectively were included. The first cohort consisted of 3302 T1D cases and 6181 controls, and the independent second cohort consisted of 3297 T1D cases and 6169 controls. Cases with low T1D PRS were identified using PRSice-2 and compared to controls with low T1D PRS by genome-wide association (GWA) test. Thirteen novel genetic loci with high imputation quality (Quality Score r2 > 0.91) were identified of SNPs/SNVs associated with low PRS T1D at genome-wide significance (P ≤ 5.0 × E-08), in addition to 4 established T1D loci, 3 reported loci by our previous study, as well as 9 potential novel loci represented by rare SNVs, but with relatively low imputation quality (Quality Score r2 < 0.90). For the 13 novel loci, 9 regions have been reported of association with obesity related traits by previous GWA studies. Three loci encoding long intergenic non-protein coding RNAs (lncRNA), and 2 loci involved in N-linked glycosylation are also highlighted in this study.
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Affiliation(s)
- Jingchun Qu
- grid.239552.a0000 0001 0680 8770The Center for Applied Genomics, Children’s Hospital of Philadelphia, 3615 Civic Center Blvd, Abramson Building, Philadelphia, PA 19104 USA
| | - Hui-Qi Qu
- grid.239552.a0000 0001 0680 8770The Center for Applied Genomics, Children’s Hospital of Philadelphia, 3615 Civic Center Blvd, Abramson Building, Philadelphia, PA 19104 USA
| | | | - Joseph T. Glessner
- grid.239552.a0000 0001 0680 8770The Center for Applied Genomics, Children’s Hospital of Philadelphia, 3615 Civic Center Blvd, Abramson Building, Philadelphia, PA 19104 USA
| | - Xiao Chang
- grid.239552.a0000 0001 0680 8770The Center for Applied Genomics, Children’s Hospital of Philadelphia, 3615 Civic Center Blvd, Abramson Building, Philadelphia, PA 19104 USA
| | - Lifeng Tian
- grid.239552.a0000 0001 0680 8770The Center for Applied Genomics, Children’s Hospital of Philadelphia, 3615 Civic Center Blvd, Abramson Building, Philadelphia, PA 19104 USA
| | - Michael March
- grid.239552.a0000 0001 0680 8770The Center for Applied Genomics, Children’s Hospital of Philadelphia, 3615 Civic Center Blvd, Abramson Building, Philadelphia, PA 19104 USA
| | - John J. Connolly
- grid.239552.a0000 0001 0680 8770The Center for Applied Genomics, Children’s Hospital of Philadelphia, 3615 Civic Center Blvd, Abramson Building, Philadelphia, PA 19104 USA
| | - Jeffrey D. Roizen
- grid.25879.310000 0004 1936 8972Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Patrick M. A. Sleiman
- grid.239552.a0000 0001 0680 8770The Center for Applied Genomics, Children’s Hospital of Philadelphia, 3615 Civic Center Blvd, Abramson Building, Philadelphia, PA 19104 USA ,grid.25879.310000 0004 1936 8972Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA ,grid.239552.a0000 0001 0680 8770Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Hakon Hakonarson
- grid.239552.a0000 0001 0680 8770The Center for Applied Genomics, Children’s Hospital of Philadelphia, 3615 Civic Center Blvd, Abramson Building, Philadelphia, PA 19104 USA ,grid.25879.310000 0004 1936 8972Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA ,grid.239552.a0000 0001 0680 8770Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA ,grid.239552.a0000 0001 0680 8770Division of Pulmonary Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
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18
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Chang X, Bakay M, Liu Y, Glessner J, Rathi KS, Hou C, Qu H, Vaksman Z, Nguyen K, Sleiman PMA, Diskin SJ, Maris JM, Hakonarson H. Mitochondrial DNA Haplogroups and Susceptibility to Neuroblastoma. J Natl Cancer Inst 2021; 112:1259-1266. [PMID: 32096864 DOI: 10.1093/jnci/djaa024] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 01/24/2020] [Accepted: 02/19/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Neuroblastoma is a childhood malignancy that arises from the developing sympathetic nervous system. Although mitochondrial dysfunctions have been implicated in the pathophysiology of neuroblastoma, the role of mitochondrial DNA (mtDNA) has not been extensively investigated. METHODS A total of 2404 Caucasian children diagnosed with neuroblastoma and 9310 ancestry-matched controls were recruited at the Children's Hospital of Philadelphia. The mtDNA haplogroups were identified from SNP array data of two independent cohorts. We conducted a case-control study to explore potential associations of mtDNA haplogroups with the susceptibility of neuroblastoma. The genetic effect of neuroblastoma was measured by odds ratios (ORs) of mitochondrial haplogroups. All tests were two-sided. RESULTS Haplogroup K was statistically significantly associated with reduced risk of neuroblastoma in the discovery cohort consisting of 1474 cases and 5699 controls (OR = 0.72, 95% confidence interval [CI] = 0.57 to 0.90; P = 4.8 × 10-3). The association was replicated in an independent cohort (OR = 0.69, 95% CI = 0.53 to 0.92; P = .01) of 930 cases and 3611 controls. Pooled analysis was performed by combining the two data sets. The association remained highly statistically significant after correction for multiple testing (OR = 0.71, 95% CI = 0.59 to 0.84, P = 1.96 × 10-4, Pcorrected = .002). Further analysis focusing on neuroblastoma subtypes indicated haplogroup K was more associated with high-risk neuroblastoma (OR = 0.57, 95% CI = 0.43 to 0.76; P = 1.46 × 10-4) than low-risk and intermediate-risk neuroblastoma. CONCLUSIONS Haplogroup K is an independent genetic factor associated with reduced risk of developing neuroblastoma in European descents. These findings provide new insights into the genetic basis of neuroblastoma, implicating mitochondrial DNA encoded proteins in the etiology of neuroblastoma.
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Affiliation(s)
- Xiao Chang
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Marina Bakay
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Yichuan Liu
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Joseph Glessner
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Komal S Rathi
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Cuiping Hou
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Huiqi Qu
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Zalman Vaksman
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kenny Nguyen
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Patrick M A Sleiman
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sharon J Diskin
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - John M Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
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19
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Glessner JT, Chang X, Liu Y, Li J, Khan M, Wei Z, Sleiman PMA, Hakonarson H. MONTAGE: a new tool for high-throughput detection of mosaic copy number variation. BMC Genomics 2021; 22:133. [PMID: 33627065 PMCID: PMC7905641 DOI: 10.1186/s12864-021-07395-7] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 01/19/2021] [Indexed: 01/21/2023] Open
Abstract
Background Not all cells in a given individual are identical in their genomic makeup. Mosaicism describes such a phenomenon where a mixture of genotypic states in certain genomic segments exists within the same individual. Mosaicism is a prevalent and impactful class of non-integer state copy number variation (CNV). Mosaicism implies that certain cell types or subset of cells contain a CNV in a segment of the genome while other cells in the same individual do not. Several studies have investigated the impact of mosaicism in single patients or small cohorts but no comprehensive scan of mosaic CNVs has been undertaken to accurately detect such variants and interpret their impact on human health and disease. Results We developed a tool called Montage to improve the accuracy of detection of mosaic copy number variants in a high throughput fashion. Montage directly interfaces with ParseCNV2 algorithm to establish disease phenotype genome-wide association and determine which genomic ranges had more or less than expected frequency of mosaic events. We screened for mosaic events in over 350,000 samples using 1% allele frequency as the detection limit. Additionally, we uncovered disease associations of multiple phenotypes with mosaic CNVs at several genomic loci. We additionally investigated the allele imbalance observations genome-wide to define non-diploid and non-integer copy number states. Conclusions Our novel algorithm presents an efficient tool with fast computational runtime and high levels of accuracy of mosaic CNV detection. A curated mosaic CNV callset of 3716 events in 2269 samples is presented with comparability to previous reports and disease phenotype associations. The new algorithm can be freely accessed via: https://github.com/CAG-CNV/MONTAGE. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07395-7.
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Affiliation(s)
- Joseph T Glessner
- Department of Pediatrics, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA. .,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA.
| | - Xiao Chang
- Department of Pediatrics, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Yichuan Liu
- Department of Pediatrics, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Jin Li
- Department of Pediatrics, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Munir Khan
- Department of Pediatrics, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Zhi Wei
- New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Patrick M A Sleiman
- Department of Pediatrics, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Hakon Hakonarson
- Department of Pediatrics, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA
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20
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Meng X, Hou X, Wang P, Glessner JT, Qu HQ, March ME, Zhang S, Qi X, Zhu C, Nguyen K, Gao X, Li X, Liu Y, Zhou W, Zhang S, Li J, Sun Y, Yang J, Sleiman PMA, Xia Q, Hakonarson H, Li J. Association of novel rare coding variants with juvenile idiopathic arthritis. Ann Rheum Dis 2021; 80:626-631. [PMID: 33408077 DOI: 10.1136/annrheumdis-2020-218359] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 06/23/2020] [Revised: 11/16/2020] [Accepted: 12/08/2020] [Indexed: 11/04/2022]
Abstract
OBJECTIVE Juvenile idiopathic arthritis (JIA) is the most common type of arthritis among children, but a few studies have investigated the contribution of rare variants to JIA. In this study, we aimed to identify rare coding variants associated with JIA for the genome-wide landscape. METHODS We established a rare variant calling and filtering pipeline and performed rare coding variant and gene-based association analyses on three RNA-seq datasets composed of 228 JIA patients in the Gene Expression Omnibus against different sets of controls, and further conducted replication in our whole-exome sequencing (WES) data of 56 JIA patients. Then we conducted differential gene expression analysis and assessed the impact of recurrent functional coding variants on gene expression and signalling pathway. RESULTS By the RNA-seq data, we identified variants in two genes reported in literature as JIA causal variants, as well as additional 63 recurrent rare coding variants seen only in JIA patients. Among the 44 recurrent rare variants found in polyarticular patients, 10 were replicated by our WES of patients with the same JIA subtype. Several genes with recurrent functional rare coding variants have also common variants associated with autoimmune diseases. We observed immune pathways enriched for the genes with rare coding variants and differentially expressed genes. CONCLUSION This study elucidated a novel landscape of recurrent rare coding variants in JIA patients and uncovered significant associations with JIA at the gene pathway level. The convergence of common variants and rare variants for autoimmune diseases is also highlighted in this study.
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Affiliation(s)
- Xinyi Meng
- Department of Cell Biology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xiaoyuan Hou
- Department of Cell Biology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Ping Wang
- Department of Cell Biology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Joseph T Glessner
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Hui-Qi Qu
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Michael E March
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Sipeng Zhang
- Department of Cell Biology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xiaohui Qi
- Department of Cell Biology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Chonggui Zhu
- Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin, China
| | - Kenny Nguyen
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Xinyi Gao
- Department of Cell Biology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xiaoge Li
- Department of Pediatrics, Jinnan Hospital, Tianjin, China
| | - Yichuan Liu
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Wentao Zhou
- Department of Cell Biology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Shuyue Zhang
- Department of Cell Biology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Junyi Li
- Department of Cell Biology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yan Sun
- Department of Cell Biology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Jie Yang
- Department of Cell Biology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Patrick M A Sleiman
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Qianghua Xia
- Department of Cell Biology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA .,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jin Li
- Department of Cell Biology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China .,Tianjin Eye Hospital, Tianjin, China.,Tianjin Key Laboratory of Ophthalmology and Visual Science, Tianjin Eye Institute, Tianjin, China
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21
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Liu Y, Chang X, Glessner J, Qu H, Tian L, Li D, Nguyen K, Sleiman PMA, Hakonarson H. Association of Rare Recurrent Copy Number Variants With Congenital Heart Defects Based on Next-Generation Sequencing Data From Family Trios. Front Genet 2019; 10:819. [PMID: 31552105 PMCID: PMC6746959 DOI: 10.3389/fgene.2019.00819] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 08/07/2019] [Indexed: 01/17/2023] Open
Abstract
Congenital heart defects (CHDs) are a common birth defect, affecting approximately 1% of newborn children in the United States. As previously reported, a significant number of CHDs are potentially attributed to altered copy number variants (CNVs). However, as many genomic variants are rare, a large-scale CNV triad study is necessary to characterize the genetic architecture of CHD. We used whole-exome sequencing (WES) data generated by the Pediatric Cardiac Genomics Consortium (PCGC), including a discovery dataset of 2,103 individuals from 760 nuclear family trios and an independent replication set of 4,808 individuals from 1,712 trios. The candidate targets uncovered were further validated through different platforms, including the Omni single-nucleotide polymorphism (SNP) array chip in 1,860 individuals and the whole-genome sequencing (WGS) data in 33 trios. The genes harboring CNVs of interest were then investigated for expression alternations based on cardiac tissue RNA-Seq data. We identified multiple CNVs in the WES data that associated with specific sub-phenotypes of CHD in approximately 2,400 families, including 98 de novo CNV regions. We identified five CNV loci harboring LIMS1, GCC2, RANBP2, TTC3, and MAP3K7CL, respectively, where those genes are highly expressed in human heart and/or mouse embryo heart at 15 days. Five novel CNV loci were uncovered, demonstrating altered expression of the respective candidate genes involved. To our knowledge, this is the largest trio-based WES study of CHD and, in addition to uncovering novel CHD targets, presents an extensive resource with the potential to provide important insights to the architecture and impact of CNVs in CHD.
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Affiliation(s)
- Yichuan Liu
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Xiao Chang
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Joseph Glessner
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Huiqi Qu
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Lifeng Tian
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Dong Li
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Kenny Nguyen
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Patrick M. A. Sleiman
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Hakon Hakonarson
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Department of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
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22
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Sun Y, Yao X, March ME, Meng X, Li J, Wei Z, Sleiman PMA, Hakonarson H, Xia Q, Li J. Target Genes of Autism Risk Loci in Brain Frontal Cortex. Front Genet 2019; 10:707. [PMID: 31447881 PMCID: PMC6696877 DOI: 10.3389/fgene.2019.00707] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 10/11/2018] [Accepted: 07/04/2019] [Indexed: 12/12/2022] Open
Abstract
Autism spectrum disorder (ASD) is a complex neuropsychiatric disorder. A number of genetic risk loci have been identified for ASD from genome-wide association studies (GWAS); however, their target genes in relevant tissues and cell types remain to be investigated. The frontal cortex is a key region in the human brain for communication and cognitive function. To identify risk genes contributing to potential dysfunction in the frontal cortex of ASD patients, we took an in silico approach integrating multi-omics data. We first found genes with expression in frontal cortex tissue that correlates with ASD risk loci by leveraging expression quantitative trait loci (eQTLs) information. Among these genes, we then identified 76 genes showing significant differential expression in the frontal cortex between ASD cases and controls in microarray datasets and further replicated four genes with RNA-seq data. Among the ASD GWAS single nucleotide polymorphisms (SNPs) correlating with the 76 genes, 20 overlap with histone marks and 40 are associated with gene methylation level. Thus, through multi-omics data analyses, we identified genes that may work as target genes of ASD risk loci in the brain frontal cortex.
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Affiliation(s)
- Yan Sun
- Department of Cell Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin, China
| | - Xueming Yao
- Department of Cell Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin, China
| | - Michael E March
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Xinyi Meng
- Department of Cell Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin, China
| | - Junyi Li
- Department of Cell Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin, China
| | - Zhi Wei
- College of Computing Sciences, New Jersey Institute of Technology, University Heights, Newark, NJ, United States
| | - Patrick M A Sleiman
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States.,Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, PA, United States
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States.,Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, PA, United States
| | - Qianghua Xia
- Department of Cell Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin, China
| | - Jin Li
- Department of Cell Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin, China
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23
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Li D, March ME, Gutierrez-Uzquiza A, Kao C, Seiler C, Pinto E, Matsuoka LS, Battig MR, Bhoj EJ, Wenger TL, Tian L, Robinson N, Wang T, Liu Y, Weinstein BM, Swift M, Jung HM, Kaminski CN, Chiavacci R, Perkins JA, Levine MA, Sleiman PMA, Hicks PJ, Strausbaugh JT, Belasco JB, Dori Y, Hakonarson H. ARAF recurrent mutation causes central conducting lymphatic anomaly treatable with a MEK inhibitor. Nat Med 2019; 25:1116-1122. [DOI: 10.1038/s41591-019-0479-2] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 05/06/2019] [Indexed: 12/16/2022]
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24
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Tylee DS, Sun J, Hess JL, Tahir MA, Sharma E, Malik R, Worrall BB, Levine AJ, Martinson JJ, Nejentsev S, Speed D, Fischer A, Mick E, Walker BR, Crawford A, Grant SF, Polychronakos C, Bradfield JP, Sleiman PMA, Hakonarson H, Ellinghaus E, Elder JT, Tsoi LC, Trembath RC, Barker JN, Franke A, Dehghan A, Faraone SV, Glatt. SJ. Genetic correlations among psychiatric and immune-related phenotypes based on genome-wide association data. Am J Med Genet B Neuropsychiatr Genet 2018; 177:641-657. [PMID: 30325587 PMCID: PMC6230304 DOI: 10.1002/ajmg.b.32652] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 02/21/2018] [Accepted: 05/22/2018] [Indexed: 12/18/2022]
Abstract
Individuals with psychiatric disorders have elevated rates of autoimmune comorbidity and altered immune signaling. It is unclear whether these altered immunological states have a shared genetic basis with those psychiatric disorders. The present study sought to use existing summary-level data from previous genome-wide association studies to determine if commonly varying single nucleotide polymorphisms are shared between psychiatric and immune-related phenotypes. We estimated heritability and examined pair-wise genetic correlations using the linkage disequilibrium score regression (LDSC) and heritability estimation from summary statistics methods. Using LDSC, we observed significant genetic correlations between immune-related disorders and several psychiatric disorders, including anorexia nervosa, attention deficit-hyperactivity disorder, bipolar disorder, major depression, obsessive compulsive disorder, schizophrenia, smoking behavior, and Tourette syndrome. Loci significantly mediating genetic correlations were identified for schizophrenia when analytically paired with Crohn's disease, primary biliary cirrhosis, systemic lupus erythematosus, and ulcerative colitis. We report significantly correlated loci and highlight those containing genome-wide associations and candidate genes for respective disorders. We also used the LDSC method to characterize genetic correlations among the immune-related phenotypes. We discuss our findings in the context of relevant genetic and epidemiological literature, as well as the limitations and caveats of the study.
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Affiliation(s)
- Daniel S. Tylee
- Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab); Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology; SUNY Upstate Medical University; Syracuse, NY, U.S.A
| | - Jiayin Sun
- Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab); Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology; SUNY Upstate Medical University; Syracuse, NY, U.S.A
| | - Jonathan L. Hess
- Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab); Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology; SUNY Upstate Medical University; Syracuse, NY, U.S.A
| | - Muhammad A. Tahir
- Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab); Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology; SUNY Upstate Medical University; Syracuse, NY, U.S.A
| | - Esha Sharma
- Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab); Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology; SUNY Upstate Medical University; Syracuse, NY, U.S.A
| | - Rainer Malik
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians-University (LMU), Munich, Germany
| | - Bradford B. Worrall
- Departments of Neurology and Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, U.S.A
| | - Andrew J. Levine
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, U.S.A
| | - Jeremy J. Martinson
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, PA, U.S.A
| | | | - Doug Speed
- Aarhus Institute for Advanced Studies and University College London, London, U.K
| | - Annegret Fischer
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Eric Mick
- Department of Quantitative Health Sciences, University of Massachusetts Medical School, Worcester, MA, U.S.A
| | - Brian R. Walker
- BHF Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, EH16 4TJ, U.K
| | - Andrew Crawford
- School of Social and Community Medicine, MRC Integrated Epidemiology Unit, University of Bristol, Bristol, BS8 2BN, UK
- Center for Applied Genomics, Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA, U.S.A
| | - Struan F.A. Grant
- Center for Applied Genomics, Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA, U.S.A
- Division of Endocrinology and Diabetes, The Children’s Hospital of Philadelphia, Philadelphia, PA, U.S.A
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, U.S.A
- Institute of Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, U.S.A
| | - Constantin Polychronakos
- Endocrine Genetics Laboratory, Department of Pediatrics and the Child Health Program of the Research Institute, McGill University Health Centre, Montreal, Quebec, Canada
| | - Jonathan P. Bradfield
- Center for Applied Genomics, Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA, U.S.A
- Quantinuum Research LLC, San Diego, CA, U.S.A
| | - Patrick M. A. Sleiman
- Center for Applied Genomics, Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA, U.S.A
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, U.S.A
| | - Hakon Hakonarson
- Center for Applied Genomics, Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA, U.S.A
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, U.S.A
| | - Eva Ellinghaus
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - James T. Elder
- Department of Dermatology, Veterans Affairs Hospital, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Lam C. Tsoi
- Department of Dermatology, Veterans Affairs Hospital, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Richard C. Trembath
- Division of Genetics and Molecular Medicine, King’s College London, London, UK
| | - Jonathan N. Barker
- Department of Biostatistics and Epidemiology, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Abbas Dehghan
- Department of Biostatistics and Epidemiology, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London
| | | | | | - Stephen V. Faraone
- Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab); Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology; SUNY Upstate Medical University; Syracuse, NY, U.S.A
- K.G. Jebsen Centre for Research on Neuropsychiatric Disorders, University of Bergen, Bergen, Norway
| | - Stephen J. Glatt.
- Psychiatric Genetic Epidemiology & Neurobiology Laboratory (PsychGENe Lab); Departments of Psychiatry and Behavioral Sciences & Neuroscience and Physiology; SUNY Upstate Medical University; Syracuse, NY, U.S.A
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Chang X, Pellegrino R, Garifallou J, March M, Snyder J, Mentch F, Li J, Hou C, Liu Y, Sleiman PMA, Hakonarson H. Common variants at 5q33.1 predispose to migraine in African-American children. J Med Genet 2018; 55:831-836. [PMID: 30266756 DOI: 10.1136/jmedgenet-2018-105359] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [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: 02/28/2018] [Revised: 08/16/2018] [Accepted: 08/29/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND Genome-wide association studies (GWASs) have identified multiple susceptibility loci for migraine in European adults. However, no large-scale genetic studies have been performed in children or African Americans with migraine. METHODS We conducted a GWAS of 380 African-American children and 2129 ancestry-matched controls to identify variants associated with migraine. We then attempted to replicate our primary analysis in an independent cohort of 233 African-American patients and 4038 non-migraine control subjects. RESULTS The results of this study indicate that common variants at 5q33.1 associated with migraine risk in African-American children (rs72793414, p=1.94×10-9). The association was validated in an independent study (p=3.87×10-3) for an overall meta-analysis p value of 3.81×10-10. eQTL (Expression quantitative trait loci) analysis of the Genotype-Tissue Expression data also shows the genotypes of rs72793414 were strongly correlated with the mRNA expression levels of NMUR2 at 5q33.1. NMUR2 encodes a G protein-coupled receptor of neuromedin-U (NMU). NMU, a highly conserved neuropeptide, participates in diverse physiological processes of the central nervous system. CONCLUSIONS This study provides new insights into the genetic basis of childhood migraine and allow for precision therapeutic development strategies targeting migraine patients of African-American ancestry.
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Affiliation(s)
- Xiao Chang
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Renata Pellegrino
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - James Garifallou
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Michael March
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - James Snyder
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Frank Mentch
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jin Li
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Affiliated Cancer Hospital & Institute, Guangzhou Medical University, Guangzhou, China
| | - Cuiping Hou
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Yichuan Liu
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Patrick M A Sleiman
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Hakon Hakonarson
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
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Chang X, Lima LDA, Liu Y, Li J, Li Q, Sleiman PMA, Hakonarson H. Common and Rare Genetic Risk Factors Converge in Protein Interaction Networks Underlying Schizophrenia. Front Genet 2018; 9:434. [PMID: 30323833 PMCID: PMC6172705 DOI: 10.3389/fgene.2018.00434] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [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: 08/05/2018] [Accepted: 09/12/2018] [Indexed: 11/25/2022] Open
Abstract
Hundreds of genomic loci have been identified with the recent advances of schizophrenia in genome-wide association studies (GWAS) and sequencing studies. However, the functional interactions among those genes remain largely unknown. We developed a network-based approach to integrate multiple genetic risk factors, which lead to the discovery of new susceptibility genes and causal sub-networks, or pathways in schizophrenia. We identified significantly and consistently over-represented pathways in the largest schizophrenia GWA studies, which are highly relevant to synaptic plasticity, neural development and signaling transduction, such as long-term potentiation, neurotrophin signaling pathway, and the ERBB signaling pathway. We also demonstrated that genes targeted by common SNPs are more likely to interact with genes harboring de novo mutations (DNMs) in the protein-protein interaction (PPI) network, suggesting a mutual interplay of both common and rare variants in schizophrenia. We further developed an edge-based search algorithm to identify the top-ranked gene modules associated with schizophrenia risk. Our results suggest that the N-methyl-D-aspartate receptor (NMDAR) interactome may play a leading role in the pathology of schizophrenia, as it is highly targeted by multiple types of genetic risk factors.
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Affiliation(s)
- Xiao Chang
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Leandro de Araujo Lima
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Yichuan Liu
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Jin Li
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, United States.,Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Qingqin Li
- Janssen Research & Development, LLC, Titusville, NJ, United States
| | - Patrick M A Sleiman
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, United States.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Hakon Hakonarson
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, United States.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
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27
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Tian T, Wei Z, Chang X, Liu Y, Gur RE, Sleiman PMA, Hakonarson H. The Long Noncoding RNA Landscape in Amygdala Tissues from Schizophrenia Patients. EBioMedicine 2018; 34:171-181. [PMID: 30077719 PMCID: PMC6116417 DOI: 10.1016/j.ebiom.2018.07.022] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [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: 04/19/2018] [Revised: 07/14/2018] [Accepted: 07/16/2018] [Indexed: 12/13/2022] Open
Abstract
To date, most transcriptome studies of schizophrenia focus on the analysis of protein-coding genes. Long noncoding RNAs (lncRNAs) are emerging as key tissue-specific regulators of cellular and disease processes. The amygdala brain region has been implicated in the pathophysiology of schizophrenia. We performed unbiased whole transcriptome profiling of amygdala tissues from 22 schizophrenia patients and 24 non-psychiatric controls using RNA-seq. We reconstructed amygdala transcriptome and employed systems biology approaches to annotating the functional roles of lncRNAs. As a result, we identified 839 novel lncRNAs in amygdala. We found in amygdala lncRNAs are more subtype-specific than protein-coding genes. We identified functional modules associated with "synaptic transmission", "ribosome", and "immune responses" which were related to schizophrenia pathophysiology that involved lncRNAs. Integrative functional analyses associating individual lncRNAs with specific pathways and functions further show that amygdala lncRNAs are connected with all of these pathways. Our study presents the first systematic landscape of lncRNAs in amygdala tissue from schizophrenia cases.
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Affiliation(s)
- Tian Tian
- Department of Computer Science, New Jersey Institute of Technology, Newark, New Jersey, USA
| | - Zhi Wei
- Department of Computer Science, New Jersey Institute of Technology, Newark, New Jersey, USA.
| | - Xiao Chang
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Yichuan Liu
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Raquel E Gur
- Neuropsychiatry Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Patrick M A Sleiman
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA; Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA; Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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28
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Glessner JT, Li J, Wang D, March M, Lima L, Desai A, Hadley D, Kao C, Gur RE, Cohen N, Sleiman PMA, Li Q, Hakonarson H. Copy number variation meta-analysis reveals a novel duplication at 9p24 associated with multiple neurodevelopmental disorders. Genome Med 2017; 9:106. [PMID: 29191242 PMCID: PMC5709845 DOI: 10.1186/s13073-017-0494-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [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: 07/13/2017] [Accepted: 11/14/2017] [Indexed: 12/24/2022] Open
Abstract
Background Neurodevelopmental and neuropsychiatric disorders represent a wide spectrum of heterogeneous yet inter-related disease conditions. The overlapping clinical presentations of these diseases suggest a shared genetic etiology. We aim to identify shared structural variants spanning the spectrum of five neuropsychiatric disorders. Methods We investigated copy number variations (CNVs) in five cohorts, including schizophrenia (SCZ), bipolar disease (BD), autism spectrum disorders (ASD), attention deficit hyperactivity disorder (ADHD), and depression, from 7849 cases and 10,799 controls. CNVs were called based on intensity data from genome-wide SNP arrays and CNV frequency was compared between cases and controls in each disease cohort separately. Meta-analysis was performed via a gene-based approach. Quantitative PCR (qPCR) was employed to validate novel significant loci. Results In our meta-analysis, two genes containing CNVs with exonic overlap reached genome-wide significance threshold of meta P value < 9.4 × 10−6 for deletions and 7.5 × 10−6 for duplications. We observed significant overlap between risk CNV loci across cohorts. In addition, we identified novel significant associations of DOCK8/KANK1 duplications (meta P value = 7.5 × 10−7) across all cohorts, and further validated the CNV region with qPCR. Conclusions In the first large scale meta-analysis of CNVs across multiple neurodevelopmental/psychiatric diseases, we uncovered novel significant associations of structural variants in the locus of DOCK8/KANK1 shared by five diseases, suggesting common etiology of these clinically distinct neurodevelopmental conditions. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0494-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joseph T Glessner
- The Center for Applied Genomics, Abramson Research Center, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Jin Li
- The Center for Applied Genomics, Abramson Research Center, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Cell Biology, Tianjin Medical University, Tianjin, China
| | - Dai Wang
- Janssen Research & Development, LLC, Raritan, NJ, 08869, USA
| | - Michael March
- The Center for Applied Genomics, Abramson Research Center, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Leandro Lima
- The Center for Applied Genomics, Abramson Research Center, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Akshatha Desai
- The Center for Applied Genomics, Abramson Research Center, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Dexter Hadley
- The Center for Applied Genomics, Abramson Research Center, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Charlly Kao
- The Center for Applied Genomics, Abramson Research Center, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Raquel E Gur
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Nadine Cohen
- Janssen Research & Development, LLC, Raritan, NJ, 08869, USA
| | - Patrick M A Sleiman
- The Center for Applied Genomics, Abramson Research Center, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Qingqin Li
- Janssen Research & Development, LLC, Titusville, NJ, 08560, USA
| | - Hakon Hakonarson
- The Center for Applied Genomics, Abramson Research Center, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA. .,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA. .,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
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29
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Almoguera B, Vazquez L, Mentch F, Connolly J, Pacheco JA, Sundaresan AS, Peissig PL, Linneman JG, McCarty CA, Crosslin D, Carrell DS, Lingren T, Namjou-Khales B, Harley JB, Larson E, Jarvik GP, Brilliant M, Williams MS, Kullo IJ, Hysinger EB, Sleiman PMA, Hakonarson H. Identification of Four Novel Loci in Asthma in European American and African American Populations. Am J Respir Crit Care Med 2017; 195:456-463. [PMID: 27611488 DOI: 10.1164/rccm.201604-0861oc] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RATIONALE Despite significant advances in knowledge of the genetic architecture of asthma, specific contributors to the variability in the burden between populations remain uncovered. OBJECTIVES To identify additional genetic susceptibility factors of asthma in European American and African American populations. METHODS A phenotyping algorithm mining electronic medical records was developed and validated to recruit cases with asthma and control subjects from the Electronic Medical Records and Genomics network. Genome-wide association analyses were performed in pediatric and adult asthma cases and control subjects with European American and African American ancestry followed by metaanalysis. Nominally significant results were reanalyzed conditioning on allergy status. MEASUREMENTS AND MAIN RESULTS The validation of the algorithm yielded an average of 95.8% positive predictive values for both cases and control subjects. The algorithm accrued 21,644 subjects (65.83% European American and 34.17% African American). We identified four novel population-specific associations with asthma after metaanalyses: loci 6p21.31, 9p21.2, and 10q21.3 in the European American population, and the PTGES gene in African Americans. TEK at 9p21.2, which encodes TIE2, has been shown to be involved in remodeling the airway wall in asthma, and the association remained significant after conditioning by allergy. PTGES, which encodes the prostaglandin E synthase, has also been linked to asthma, where deficient prostaglandin E2 synthesis has been associated with airway remodeling. CONCLUSIONS This study adds to understanding of the genetic architecture of asthma in European Americans and African Americans and reinforces the need to study populations of diverse ethnic backgrounds to identify shared and unique genetic predictors of asthma.
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Affiliation(s)
- Berta Almoguera
- 1 Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Lyam Vazquez
- 1 Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Frank Mentch
- 1 Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - John Connolly
- 1 Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Jennifer A Pacheco
- 2 Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | | | - Peggy L Peissig
- 4 Marshfield Clinic Research Foundation, Marshfield, Wisconsin
| | | | | | - David Crosslin
- 6 University of Washington Medical Center, Seattle, Washington
| | | | - Todd Lingren
- 8 Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | | | - John B Harley
- 8 Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.,9 U.S. Department of Veterans Affairs Medical Center, Cincinnati, Ohio
| | - Eric Larson
- 7 Group Health Research Institute, Seattle, Washington
| | - Gail P Jarvik
- 6 University of Washington Medical Center, Seattle, Washington
| | | | | | | | - Erik B Hysinger
- 1 Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Patrick M A Sleiman
- 1 Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,11 Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Hakon Hakonarson
- 1 Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,11 Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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30
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Chang X, Liu Y, Hahn CG, Gur RE, Sleiman PMA, Hakonarson H. RNA-seq analysis of amygdala tissue reveals characteristic expression profiles in schizophrenia. Transl Psychiatry 2017; 7:e1203. [PMID: 28809853 PMCID: PMC5611723 DOI: 10.1038/tp.2017.154] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 05/02/2017] [Accepted: 05/30/2017] [Indexed: 12/15/2022] Open
Abstract
The amygdala brain region has been implicated in the pathophysiology of schizophrenia through emotion processing. However, transcriptome messages in the amygdala of schizophrenia patients have not been well studied. We used RNA sequencing to investigate gene-expression profiling in the amygdala tissues, and identified 569 upregulated and 192 downregulated genes from 22 schizophrenia patients and 24 non-psychiatric controls. Gene functional enrichment analysis demonstrated that the downregulated genes were enriched in pathways such as 'synaptic transmission' and 'behavior', whereas the upregulated genes were significantly over-represented in gene ontology pathways such as 'immune response' and 'blood vessel development'. Co-expression-based gene network analysis identified seven modules including four modules significantly associated with 'synaptic transmission', 'blood vessel development' or 'immune responses'. Taken together, our study provides novel insights into the molecular mechanism of schizophrenia, suggesting that precision-tailored therapeutic approaches aimed at normalizing the expression/function of specific gene networks could be a promising option in schizophrenia.
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Affiliation(s)
- X Chang
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Y Liu
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - C-G Hahn
- Neuropsychiatric Signaling Program, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - R E Gur
- Neuropsychiatry Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - P M A Sleiman
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA,Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - H Hakonarson
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA,Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA,Leonard Madlyn Abramson Research Center, 3615 Civic Center Boulevard, Room 1216E, Philadelphia, PA 19104-4318, USA. E-mail:
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31
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Sleiman PMA, March M, Nguyen K, Tian L, Pellegrino R, Hou C, Dridi W, Sager M, Housawi YH, Hakonarson H. Loss-of-Function Mutations in KIF15 Underlying a Braddock-Carey Genocopy. Hum Mutat 2017; 38:507-510. [PMID: 28150392 DOI: 10.1002/humu.23188] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [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: 08/22/2016] [Accepted: 01/24/2017] [Indexed: 11/09/2022]
Abstract
Braddock-Carey Syndrome (BCS) is characterized by microcephaly, congenital thrombocytopenia, Pierre-Robin sequence (PRS), and agenesis of the corpus callosum. BCS has been shown to be caused by a 21q22.11 microdeletion that encompasses multiple genes. Here, we report a BCS genocopy characterized by congenital thrombocytopenia and PRS that is caused by a loss-of-function mutation in KIF15 in a consanguineous Saudi Arabian family. Mutations of mitotic kinesins are a well-established cause of microcephaly. To our knowledge, KIF15 is the first kinesin to be associated with congenital thrombocytopenia.
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Affiliation(s)
- Patrick M A Sleiman
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Michael March
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Kenny Nguyen
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Lifeng Tian
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Renata Pellegrino
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Cuiping Hou
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Walid Dridi
- Departments of Pediatrics, Pediatric Oncology, Pathology and Laboratory Medicine and Research, King Fahad Specialist Hospital, Dammam, Saudi Arabia
| | - Mohamed Sager
- Departments of Pediatrics, Pediatric Oncology, Pathology and Laboratory Medicine and Research, King Fahad Specialist Hospital, Dammam, Saudi Arabia
| | - Yousef H Housawi
- Departments of Pediatrics, Pediatric Oncology, Pathology and Laboratory Medicine and Research, King Fahad Specialist Hospital, Dammam, Saudi Arabia
| | - Hakon Hakonarson
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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32
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Lima LDA, Feio-Dos-Santos AC, Belangero SI, Gadelha A, Bressan RA, Salum GA, Pan PM, Moriyama TS, Graeff-Martins AS, Tamanaha AC, Alvarenga P, Krieger FV, Fleitlich-Bilyk B, Jackowski AP, Brietzke E, Sato JR, Polanczyk GV, Mari JDJ, Manfro GG, do Rosário MC, Miguel EC, Puga RD, Tahira AC, Souza VN, Chile T, Gouveia GR, Simões SN, Chang X, Pellegrino R, Tian L, Glessner JT, Hashimoto RF, Rohde LA, Sleiman PMA, Hakonarson H, Brentani H. Corrigendum: An integrative approach to investigate the respective roles of single-nucleotide variants and copy-number variants in Attention-Deficit/Hyperactivity Disorder. Sci Rep 2016; 6:25861. [PMID: 27216920 PMCID: PMC4877574 DOI: 10.1038/srep25861] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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33
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Lima LDA, Feio-dos-Santos AC, Belangero SI, Gadelha A, Bressan RA, Salum GA, Pan PM, Moriyama TS, Graeff-Martins AS, Tamanaha AC, Alvarenga P, Krieger FV, Fleitlich-Bilyk B, Jackowski AP, Brietzke E, Sato JR, Polanczyk GV, Mari JDJ, Manfro GG, do Rosário MC, Miguel EC, Puga RD, Tahira AC, Souza VN, Chile T, Gouveia GR, Simões SN, Chang X, Pellegrino R, Tian L, Glessner JT, Hashimoto RF, Rohde LA, Sleiman PMA, Hakonarson H, Brentani H. An integrative approach to investigate the respective roles of single-nucleotide variants and copy-number variants in Attention-Deficit/Hyperactivity Disorder. Sci Rep 2016; 6:22851. [PMID: 26947246 PMCID: PMC4780010 DOI: 10.1038/srep22851] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [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: 07/21/2015] [Accepted: 02/23/2016] [Indexed: 02/07/2023] Open
Abstract
Many studies have attempted to investigate the genetic susceptibility of Attention-Deficit/Hyperactivity Disorder (ADHD), but without much success. The present study aimed to analyze both single-nucleotide and copy-number variants contributing to the genetic architecture of ADHD. We generated exome data from 30 Brazilian trios with sporadic ADHD. We also analyzed a Brazilian sample of 503 children/adolescent controls from a High Risk Cohort Study for the Development of Childhood Psychiatric Disorders, and also previously published results of five CNV studies and one GWAS meta-analysis of ADHD involving children/adolescents. The results from the Brazilian trios showed that cases with de novo SNVs tend not to have de novo CNVs and vice-versa. Although the sample size is small, we could also see that various comorbidities are more frequent in cases with only inherited variants. Moreover, using only genes expressed in brain, we constructed two "in silico" protein-protein interaction networks, one with genes from any analysis, and other with genes with hits in two analyses. Topological and functional analyses of genes in this network uncovered genes related to synapse, cell adhesion, glutamatergic and serotoninergic pathways, both confirming findings of previous studies and capturing new genes and genetic variants in these pathways.
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Affiliation(s)
- Leandro de Araújo Lima
- Inter-institutional Grad Program on Bioinformatics, University of São Paulo, São Paulo, SP, Brazil.,Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Sintia Iole Belangero
- National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil.,Department of Psychiatry, Federal University of São Paulo, São Paulo, SP, Brazil
| | - Ary Gadelha
- National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil.,Department of Psychiatry, Federal University of São Paulo, São Paulo, SP, Brazil
| | - Rodrigo Affonseca Bressan
- National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil.,Department of Psychiatry, Federal University of São Paulo, São Paulo, SP, Brazil
| | - Giovanni Abrahão Salum
- National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil.,Department of Psychiatry, Hospital de Clínicas de Porto Alegre, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Pedro Mario Pan
- National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil.,Department of Psychiatry, Federal University of São Paulo, São Paulo, SP, Brazil
| | - Tais Silveira Moriyama
- Department &Institute of Psychiatry, University of São Paulo Medical School, São Paulo, SP, Brazil.,National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil.,Department of Psychiatry, Federal University of São Paulo, São Paulo, SP, Brazil
| | - Ana Soledade Graeff-Martins
- Department &Institute of Psychiatry, University of São Paulo Medical School, São Paulo, SP, Brazil.,National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil
| | - Ana Carina Tamanaha
- National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil.,Department of Psychiatry, Federal University of São Paulo, São Paulo, SP, Brazil
| | - Pedro Alvarenga
- Department &Institute of Psychiatry, University of São Paulo Medical School, São Paulo, SP, Brazil.,National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil
| | - Fernanda Valle Krieger
- Department &Institute of Psychiatry, University of São Paulo Medical School, São Paulo, SP, Brazil.,National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil
| | - Bacy Fleitlich-Bilyk
- Department &Institute of Psychiatry, University of São Paulo Medical School, São Paulo, SP, Brazil.,National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil
| | - Andrea Parolin Jackowski
- National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil.,Department of Psychiatry, Federal University of São Paulo, São Paulo, SP, Brazil
| | - Elisa Brietzke
- National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil.,Department of Psychiatry, Federal University of São Paulo, São Paulo, SP, Brazil
| | - João Ricardo Sato
- National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil.,Center of Mathematics, Computation and Cognition. Universidade Federal do ABC, Santo André, Brazil
| | - Guilherme Vanoni Polanczyk
- Department &Institute of Psychiatry, University of São Paulo Medical School, São Paulo, SP, Brazil.,National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil
| | - Jair de Jesus Mari
- National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil.,Department of Psychiatry, Federal University of São Paulo, São Paulo, SP, Brazil
| | - Gisele Gus Manfro
- National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil.,Department of Psychiatry, Hospital de Clínicas de Porto Alegre, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Maria Conceição do Rosário
- National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil.,Department of Psychiatry, Federal University of São Paulo, São Paulo, SP, Brazil
| | - Eurípedes Constantino Miguel
- Department &Institute of Psychiatry, University of São Paulo Medical School, São Paulo, SP, Brazil.,National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil
| | - Renato David Puga
- Hospital Israelita Albert Einstein, Clinical Research, São Paulo, SP, Brazil
| | - Ana Carolina Tahira
- Department &Institute of Psychiatry, University of São Paulo Medical School, São Paulo, SP, Brazil
| | - Viviane Neri Souza
- Department &Institute of Psychiatry, University of São Paulo Medical School, São Paulo, SP, Brazil
| | - Thais Chile
- Department &Institute of Psychiatry, University of São Paulo Medical School, São Paulo, SP, Brazil
| | - Gisele Rodrigues Gouveia
- Department &Institute of Psychiatry, University of São Paulo Medical School, São Paulo, SP, Brazil
| | - Sérgio Nery Simões
- Inter-institutional Grad Program on Bioinformatics, University of São Paulo, São Paulo, SP, Brazil.,Federal Institute of Espírito Santo, Serra, ES, Brazil
| | - Xiao Chang
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Renata Pellegrino
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lifeng Tian
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Joseph T Glessner
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Ronaldo Fumio Hashimoto
- Inter-institutional Grad Program on Bioinformatics, University of São Paulo, São Paulo, SP, Brazil.,Mathematics &Statistics Institute, University of São Paulo, São Paulo, SP, Brazil
| | - Luis Augusto Rohde
- Department &Institute of Psychiatry, University of São Paulo Medical School, São Paulo, SP, Brazil.,National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil.,Department of Psychiatry, Hospital de Clínicas de Porto Alegre, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Patrick M A Sleiman
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania Philadelphia, PA, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania Philadelphia, PA, USA
| | - Helena Brentani
- Inter-institutional Grad Program on Bioinformatics, University of São Paulo, São Paulo, SP, Brazil.,Department &Institute of Psychiatry, University of São Paulo Medical School, São Paulo, SP, Brazil.,National Institute of Developmental Psychiatry for Children and Adolescents (INCT-CNPq), São Paulo, SP, Brazil
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Yang Y, Zhang L, Lynch DR, Lukas T, Ahmeti K, Sleiman PMA, Ryan E, Schadt KA, Newman JH, Deng HX, Siddique N, Siddique T. Compound heterozygote mutations in SPG7 in a family with adult-onset primary lateral sclerosis. Neurol Genet 2016; 2:e60. [PMID: 27123479 PMCID: PMC4830188 DOI: 10.1212/nxg.0000000000000060] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 01/07/2016] [Indexed: 12/11/2022]
Abstract
OBJECTIVE To identify the genetic defect for adult-onset primary lateral sclerosis (PLS) in a family with 5 patients. METHODS Whole-exome sequencing was performed to identify the shared genetic variants in 3 affected members in a PLS family with 5 affected individuals. Sanger sequencing was used for validation of the variants and for cosegregation analysis. Mitochondrial activity for both patients and unaffected siblings was measured using a SeaHorse metabolic analyzer. RESULTS Whole-exome sequencing and subsequent cosegregation analysis demonstrated that compound heterozygous missense variants L695P and I743T in SPG7 were the only mutations cosegregating with the disease in an autosomal recessive fashion in this family. The parents and siblings are genetically heterozygous and clinically unaffected. Functional studies suggested that the PLS-associated SPG7 mutants affect mitochondrial function when glucose is reduced. CONCLUSIONS Compound heterozygote mutations in SPG7 are associated with adult-onset PLS, extending the spectrum of SPG7-linked neurologic diseases. Patients with the PLS phenotype should have genetic testing for paraplegin, especially when the condition is familial.
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Affiliation(s)
- Yi Yang
- Department of Histology and Embryology (Y.Y., L.Z.), Hebei Medical University, China; Division of Neuromuscular Medicine (Y.Y., K.A., E.R., J.H.N., H.-X.D., N.S., T.S.), Davee Department of Neurology and Clinical Neurosciences and Department of Pharmacology (T.J.L.), Northwestern University Feinberg School of Medicine, Chicago, IL; Department of Neurology (D.L.) and Department of Pediatrics (P.M.A.S.), the Perelman School of Medicine, University of Pennsylvania, Philadelphia; and Department of Neurology (K.A.S.) and The Center for Applied Genomics (P.M.A.S.), The Children's Hospital of Philadelphia, PA
| | - Lei Zhang
- Department of Histology and Embryology (Y.Y., L.Z.), Hebei Medical University, China; Division of Neuromuscular Medicine (Y.Y., K.A., E.R., J.H.N., H.-X.D., N.S., T.S.), Davee Department of Neurology and Clinical Neurosciences and Department of Pharmacology (T.J.L.), Northwestern University Feinberg School of Medicine, Chicago, IL; Department of Neurology (D.L.) and Department of Pediatrics (P.M.A.S.), the Perelman School of Medicine, University of Pennsylvania, Philadelphia; and Department of Neurology (K.A.S.) and The Center for Applied Genomics (P.M.A.S.), The Children's Hospital of Philadelphia, PA
| | - David R Lynch
- Department of Histology and Embryology (Y.Y., L.Z.), Hebei Medical University, China; Division of Neuromuscular Medicine (Y.Y., K.A., E.R., J.H.N., H.-X.D., N.S., T.S.), Davee Department of Neurology and Clinical Neurosciences and Department of Pharmacology (T.J.L.), Northwestern University Feinberg School of Medicine, Chicago, IL; Department of Neurology (D.L.) and Department of Pediatrics (P.M.A.S.), the Perelman School of Medicine, University of Pennsylvania, Philadelphia; and Department of Neurology (K.A.S.) and The Center for Applied Genomics (P.M.A.S.), The Children's Hospital of Philadelphia, PA
| | - Thomas Lukas
- Department of Histology and Embryology (Y.Y., L.Z.), Hebei Medical University, China; Division of Neuromuscular Medicine (Y.Y., K.A., E.R., J.H.N., H.-X.D., N.S., T.S.), Davee Department of Neurology and Clinical Neurosciences and Department of Pharmacology (T.J.L.), Northwestern University Feinberg School of Medicine, Chicago, IL; Department of Neurology (D.L.) and Department of Pediatrics (P.M.A.S.), the Perelman School of Medicine, University of Pennsylvania, Philadelphia; and Department of Neurology (K.A.S.) and The Center for Applied Genomics (P.M.A.S.), The Children's Hospital of Philadelphia, PA
| | - Kreshnik Ahmeti
- Department of Histology and Embryology (Y.Y., L.Z.), Hebei Medical University, China; Division of Neuromuscular Medicine (Y.Y., K.A., E.R., J.H.N., H.-X.D., N.S., T.S.), Davee Department of Neurology and Clinical Neurosciences and Department of Pharmacology (T.J.L.), Northwestern University Feinberg School of Medicine, Chicago, IL; Department of Neurology (D.L.) and Department of Pediatrics (P.M.A.S.), the Perelman School of Medicine, University of Pennsylvania, Philadelphia; and Department of Neurology (K.A.S.) and The Center for Applied Genomics (P.M.A.S.), The Children's Hospital of Philadelphia, PA
| | - Patrick M A Sleiman
- Department of Histology and Embryology (Y.Y., L.Z.), Hebei Medical University, China; Division of Neuromuscular Medicine (Y.Y., K.A., E.R., J.H.N., H.-X.D., N.S., T.S.), Davee Department of Neurology and Clinical Neurosciences and Department of Pharmacology (T.J.L.), Northwestern University Feinberg School of Medicine, Chicago, IL; Department of Neurology (D.L.) and Department of Pediatrics (P.M.A.S.), the Perelman School of Medicine, University of Pennsylvania, Philadelphia; and Department of Neurology (K.A.S.) and The Center for Applied Genomics (P.M.A.S.), The Children's Hospital of Philadelphia, PA
| | - Eanna Ryan
- Department of Histology and Embryology (Y.Y., L.Z.), Hebei Medical University, China; Division of Neuromuscular Medicine (Y.Y., K.A., E.R., J.H.N., H.-X.D., N.S., T.S.), Davee Department of Neurology and Clinical Neurosciences and Department of Pharmacology (T.J.L.), Northwestern University Feinberg School of Medicine, Chicago, IL; Department of Neurology (D.L.) and Department of Pediatrics (P.M.A.S.), the Perelman School of Medicine, University of Pennsylvania, Philadelphia; and Department of Neurology (K.A.S.) and The Center for Applied Genomics (P.M.A.S.), The Children's Hospital of Philadelphia, PA
| | - Kimberly A Schadt
- Department of Histology and Embryology (Y.Y., L.Z.), Hebei Medical University, China; Division of Neuromuscular Medicine (Y.Y., K.A., E.R., J.H.N., H.-X.D., N.S., T.S.), Davee Department of Neurology and Clinical Neurosciences and Department of Pharmacology (T.J.L.), Northwestern University Feinberg School of Medicine, Chicago, IL; Department of Neurology (D.L.) and Department of Pediatrics (P.M.A.S.), the Perelman School of Medicine, University of Pennsylvania, Philadelphia; and Department of Neurology (K.A.S.) and The Center for Applied Genomics (P.M.A.S.), The Children's Hospital of Philadelphia, PA
| | - Jordan H Newman
- Department of Histology and Embryology (Y.Y., L.Z.), Hebei Medical University, China; Division of Neuromuscular Medicine (Y.Y., K.A., E.R., J.H.N., H.-X.D., N.S., T.S.), Davee Department of Neurology and Clinical Neurosciences and Department of Pharmacology (T.J.L.), Northwestern University Feinberg School of Medicine, Chicago, IL; Department of Neurology (D.L.) and Department of Pediatrics (P.M.A.S.), the Perelman School of Medicine, University of Pennsylvania, Philadelphia; and Department of Neurology (K.A.S.) and The Center for Applied Genomics (P.M.A.S.), The Children's Hospital of Philadelphia, PA
| | - Han-Xiang Deng
- Department of Histology and Embryology (Y.Y., L.Z.), Hebei Medical University, China; Division of Neuromuscular Medicine (Y.Y., K.A., E.R., J.H.N., H.-X.D., N.S., T.S.), Davee Department of Neurology and Clinical Neurosciences and Department of Pharmacology (T.J.L.), Northwestern University Feinberg School of Medicine, Chicago, IL; Department of Neurology (D.L.) and Department of Pediatrics (P.M.A.S.), the Perelman School of Medicine, University of Pennsylvania, Philadelphia; and Department of Neurology (K.A.S.) and The Center for Applied Genomics (P.M.A.S.), The Children's Hospital of Philadelphia, PA
| | - Nailah Siddique
- Department of Histology and Embryology (Y.Y., L.Z.), Hebei Medical University, China; Division of Neuromuscular Medicine (Y.Y., K.A., E.R., J.H.N., H.-X.D., N.S., T.S.), Davee Department of Neurology and Clinical Neurosciences and Department of Pharmacology (T.J.L.), Northwestern University Feinberg School of Medicine, Chicago, IL; Department of Neurology (D.L.) and Department of Pediatrics (P.M.A.S.), the Perelman School of Medicine, University of Pennsylvania, Philadelphia; and Department of Neurology (K.A.S.) and The Center for Applied Genomics (P.M.A.S.), The Children's Hospital of Philadelphia, PA
| | - Teepu Siddique
- Department of Histology and Embryology (Y.Y., L.Z.), Hebei Medical University, China; Division of Neuromuscular Medicine (Y.Y., K.A., E.R., J.H.N., H.-X.D., N.S., T.S.), Davee Department of Neurology and Clinical Neurosciences and Department of Pharmacology (T.J.L.), Northwestern University Feinberg School of Medicine, Chicago, IL; Department of Neurology (D.L.) and Department of Pediatrics (P.M.A.S.), the Perelman School of Medicine, University of Pennsylvania, Philadelphia; and Department of Neurology (K.A.S.) and The Center for Applied Genomics (P.M.A.S.), The Children's Hospital of Philadelphia, PA
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Abstract
Eosinophilic esophagitis is characterized by destructive responses of the immune system to environmental allergens, including food, on the human esophagus. EoE is now reported as a major cause of upper gastrointestinal morbidity in children and adults and the incidence is reported to be on the increase. It is known that EoE has a high degree of heritability, with a majority of the phenotypic variation believed to be genetic in origin as shown by genetic epidemiology studies of twins and families. Prior to 2010, there were no known genetic risk factors for the disease. Three GWAS have since been published identifying 5 loci which influence risk for EoE in both children and adults. The information gained from GWAS has been of value in elucidating the pathways involved, such as IL4/STAT6, and more unexpected pathways such as epithelial apical transport and wound healing. We will review the results of the EoE GWAS and the known associated genes, concluding with a discussion of some future directions for genetic studies in EoE.
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Affiliation(s)
- Patrick M A Sleiman
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, PA, USA; Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Michael March
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, PA, USA
| | - Hakon Hakonarson
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, PA, USA; Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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36
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Li YR, Li J, Zhao SD, Bradfield JP, Mentch FD, Maggadottir SM, Hou C, Abrams DJ, Chang D, Gao F, Guo Y, Wei Z, Connolly JJ, Cardinale CJ, Bakay M, Glessner JT, Li D, Kao C, Thomas KA, Qiu H, Chiavacci RM, Kim CE, Wang F, Snyder J, Richie MD, Flatø B, Førre Ø, Denson LA, Thompson SD, Becker ML, Guthery SL, Latiano A, Perez E, Resnick E, Russell RK, Wilson DC, Silverberg MS, Annese V, Lie BA, Punaro M, Dubinsky MC, Monos DS, Strisciuglio C, Staiano A, Miele E, Kugathasan S, Ellis JA, Munro JE, Sullivan KE, Wise CA, Chapel H, Cunningham-Rundles C, Grant SFA, Orange JS, Sleiman PMA, Behrens EM, Griffiths AM, Satsangi J, Finkel TH, Keinan A, Prak ETL, Polychronakos C, Baldassano RN, Li H, Keating BJ, Hakonarson H. Meta-analysis of shared genetic architecture across ten pediatric autoimmune diseases. Nat Med 2015; 21:1018-27. [PMID: 26301688 DOI: 10.1038/nm.3933] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Accepted: 07/23/2015] [Indexed: 12/15/2022]
Abstract
Genome-wide association studies (GWASs) have identified hundreds of susceptibility genes, including shared associations across clinically distinct autoimmune diseases. We performed an inverse χ(2) meta-analysis across ten pediatric-age-of-onset autoimmune diseases (pAIDs) in a case-control study including more than 6,035 cases and 10,718 shared population-based controls. We identified 27 genome-wide significant loci associated with one or more pAIDs, mapping to in silico-replicated autoimmune-associated genes (including IL2RA) and new candidate loci with established immunoregulatory functions such as ADGRL2, TENM3, ANKRD30A, ADCY7 and CD40LG. The pAID-associated single-nucleotide polymorphisms (SNPs) were functionally enriched for deoxyribonuclease (DNase)-hypersensitivity sites, expression quantitative trait loci (eQTLs), microRNA (miRNA)-binding sites and coding variants. We also identified biologically correlated, pAID-associated candidate gene sets on the basis of immune cell expression profiling and found evidence of genetic sharing. Network and protein-interaction analyses demonstrated converging roles for the signaling pathways of type 1, 2 and 17 helper T cells (TH1, TH2 and TH17), JAK-STAT, interferon and interleukin in multiple autoimmune diseases.
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Affiliation(s)
- Yun R Li
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Medical Scientist Training Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jin Li
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Sihai D Zhao
- Department of Biostatistics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jonathan P Bradfield
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Frank D Mentch
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - S Melkorka Maggadottir
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Division of Allergy and Immunology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Cuiping Hou
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Debra J Abrams
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Diana Chang
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA.,Program in Computational Biology and Medicine, Cornell University, Ithaca, New York, USA
| | - Feng Gao
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA
| | - Yiran Guo
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Zhi Wei
- Department of Computer Science, New Jersey Institute of Technology, Newark, New Jersey, USA
| | - John J Connolly
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Christopher J Cardinale
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Marina Bakay
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Joseph T Glessner
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Dong Li
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Charlly Kao
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Kelly A Thomas
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Haijun Qiu
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Rosetta M Chiavacci
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Cecilia E Kim
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Fengxiang Wang
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - James Snyder
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Marylyn D Richie
- Department of Biochemistry and Molecular Biology, Eberly College of Science, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Berit Flatø
- Department of Rheumatology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Øystein Førre
- Department of Rheumatology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Lee A Denson
- Division of Gastroenterology, The Center for Inflammatory Bowel Disease, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Susan D Thompson
- Divison of Rheumatology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Mara L Becker
- Division of Rheumatology, Children's Mercy Hospitals and Clinics, Kansas City, Missouri, USA
| | - Stephen L Guthery
- Department of Pediatrics, University of Utah School of Medicine and Primary Children's Medical Center, Salt Lake City, Utah, USA
| | - Anna Latiano
- Division of Gastroenterology, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Elena Perez
- Division of Pediatric Allergy and Immunology, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Elena Resnick
- Institute of Immunology and Department of Medicine, Mount Sinai School of Medicine, New York, New York, USA
| | - Richard K Russell
- Department of Paediatric Gastroenterology, Yorkhill Hospital for Sick Children, Glasgow, Scotland, UK
| | - David C Wilson
- Paediatric Gastroenterology and Nutrition, Royal Hospital for Sick Children, University of Edinburgh, Ediburgh, UK
| | - Mark S Silverberg
- Mount Sinai Hospital IBD Centre, University of Toronto, Toronto, Ontario, Canada
| | - Vito Annese
- Unit of Gastroenterology, Department of Medical and Surgical Specialties, Careggi University Hospital, Florence, Italy
| | - Benedicte A Lie
- Department of Immunology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Marilynn Punaro
- Department of Rheumatology, Texas Scottish Rite Hospital for Children, Dallas, Texas, USA
| | - Marla C Dubinsky
- Department of Pediatrics, Pediatric IBD Center, Cedars Sinai Medical Center, Los Angeles, California, USA
| | - Dimitri S Monos
- Department of Pathology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Caterina Strisciuglio
- Department of Translational Medical Science, Section of Pediatrics, University of Naples Federico II, Naples, Italy
| | - Annamaria Staiano
- Department of Translational Medical Science, Section of Pediatrics, University of Naples Federico II, Naples, Italy
| | - Erasmo Miele
- Department of Translational Medical Science, Section of Pediatrics, University of Naples Federico II, Naples, Italy
| | - Subra Kugathasan
- Department of Pediatrics, Emory University School of Medicine and Children's Health Care of Atlanta, Atlanta, Georgia, USA
| | - Justine A Ellis
- Genes, Environment and Complex Disease, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Pediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Jane E Munro
- Pediatric Rheumatology Unit, Royal Children's Hospital, Parkville, Victoria, Australia.,Arthritis and Rheumatology Research, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Kathleen E Sullivan
- Division of Allergy and Immunology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Carol A Wise
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, Texas, USA
| | - Helen Chapel
- Department of Clinical Immunology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Struan F A Grant
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jordan S Orange
- Section of Immunology, Allergy, and Rheumatology, Department of Pediatric Medicine, Texas Children's Hospital, Houston, Texas, USA
| | - Patrick M A Sleiman
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Edward M Behrens
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Division of Rheumatology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Anne M Griffiths
- The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Jack Satsangi
- Gastrointestinal Unit, Division of Medical Sciences, School of Molecular and Clinical Medicine, University of Edinburgh, Edinburgh, UK
| | - Terri H Finkel
- Department of Pediatrics, Nemours Children's Hospital, Orlando, Florida, USA
| | - Alon Keinan
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, USA.,Program in Computational Biology and Medicine, Cornell University, Ithaca, New York, USA
| | - Eline T Luning Prak
- Department of Pathology and Lab Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Constantin Polychronakos
- Departments of Pediatrics and Human Genetics, McGill University Health Centre Research Institute, Montréal, Québec, Canada
| | - Robert N Baldassano
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Division of Gastroenterology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Hongzhe Li
- Department of Pathology and Lab Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Brendan J Keating
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Hakon Hakonarson
- The Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Division of Pulmonary Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
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37
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Li J, Fung I, Glessner JT, Pandey R, Wei Z, Bakay M, Mentch FD, Pellegrino R, Wang T, Kim C, Hou C, Wang F, Chiavacci RM, Thomas KA, Spergel JM, Hakonarson H, Sleiman PMA. Copy Number Variations in CTNNA3 and RBFOX1 Associate with Pediatric Food Allergy. J Immunol 2015; 195:1599-607. [PMID: 26188062 DOI: 10.4049/jimmunol.1402310] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 05/20/2015] [Indexed: 11/19/2022]
Abstract
Food allergy is a significant public health concern, especially among children. Previous candidate gene studies suggested a few susceptibility loci for food allergy, but no study investigated the contribution of copy number variations (CNVs) to food allergy on a genome-wide scale. To investigate the genetics of food allergy, we performed CNV assessment using high-resolution genome-wide single nucleotide polymorphism arrays. CNV calls from a total of 357 cases with confirmed food allergy and 3980 controls were analyzed within a discovery cohort, followed by a replication analysis composed of 167 cases and 1573 controls. We identified that CNVs in CTNNA3 were significantly associated with food allergy in both the discovery cohort and the replication cohort. Of particular interest, CTNNA3 CNVs hit exons or intron regions rich in histone marker H3K4Me1. CNVs in a second gene (RBFOX1) showed a significant association (p = 7.35 × 10(-5)) with food allergy at the genome-wide level in our meta-analysis of the European ancestry cohorts. The presence of these CNVs was confirmed by quantitative PCR. Furthermore, knockdown of CTNNA3 resulted in upregulation of CD63 and CD203c in mononuclear cells upon PMA stimulation, suggesting a role in sensitization to allergen. We uncovered at least two plausible genes harboring CNV loci that are enriched in pediatric patients with food allergies. The novel gene candidates discovered in this study by genome-wide CNV analysis are compelling drug and diagnostic targets for food allergy.
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Affiliation(s)
- Jin Li
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Irene Fung
- Division of Allergy and Immunology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Joseph T Glessner
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Rahul Pandey
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Zhi Wei
- Department of Computer Science, New Jersey Institute of Technology, Newark, NJ 08540
| | - Marina Bakay
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Frank D Mentch
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Renata Pellegrino
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Tiancheng Wang
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Cecilia Kim
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Cuiping Hou
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Fengxiang Wang
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Rosetta M Chiavacci
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Kelly A Thomas
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Jonathan M Spergel
- Division of Allergy and Immunology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; Center for Pediatric Eosinophilic Disorders, The Children's Hospital of Philadelphia, Philadelphia, PA 19104; and
| | - Hakon Hakonarson
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA 19104; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Patrick M A Sleiman
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA 19104; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104; Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104
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38
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Chang X, Li J, Guo Y, Wei Z, Mentch FD, Hou C, Zhao Y, Qiu H, Kim C, Sleiman PMA, Hakonarson H. Genome-wide association study of serum minerals levels in children of different ethnic background. PLoS One 2015; 10:e0123499. [PMID: 25886283 PMCID: PMC4401557 DOI: 10.1371/journal.pone.0123499] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [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: 03/06/2014] [Accepted: 03/03/2015] [Indexed: 01/06/2023] Open
Abstract
Calcium, magnesium, potassium, sodium, chloride and phosphorus are the major dietary minerals involved in various biological functions and are commonly measured in the blood serum. Sufficient mineral intake is especially important for children due to their rapid growth. Currently, the genetic mechanisms influencing serum mineral levels are poorly understood, especially for children. We carried out a genome-wide association (GWA) study on 5,602 European-American children and 4,706 African-American children who had mineral measures available in their electronic medical records (EMR). While no locus met the criteria for genome-wide significant association, our results demonstrated a nominal association of total serum calcium levels with a missense variant in the calcium –sensing receptor (CASR) gene on 3q13 (rs1801725, P = 1.96 × 10-3) in the African-American pediatric cohort, a locus previously reported in Caucasians. We also confirmed the association result in our pediatric European-American cohort (P = 1.38 × 10-4). We further replicated two other loci associated with serum calcium levels in the European-American cohort (rs780094, GCKR, P = 4.26 × 10-3; rs10491003, GATA3, P = 0.02). In addition, we replicated a previously reported locus on 1q21, demonstrating association of serum magnesium levels with MUC1 (rs4072037, P = 2.04 × 10-6). Moreover, in an extended gene-based association analysis we uncovered evidence for association of calcium levels with the previously reported gene locus DGKD in both European-American children and African-American children. Taken together, our results support a role for CASR and DGKD mediated calcium regulation in both African-American and European-American children, and corroborate the association of calcium levels with GCKR and GATA3, and the association of magnesium levels with MUC1 in the European-American children.
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Affiliation(s)
- Xiao Chang
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Jin Li
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Yiran Guo
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Zhi Wei
- Department of Computer Science, New Jersey Institute of Technology, Newark, New Jersey, United States of America
| | - Frank D. Mentch
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Cuiping Hou
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Yan Zhao
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Haijun Qiu
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Cecilia Kim
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Patrick M. A. Sleiman
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- * E-mail: (PS); (HH)
| | - Hakon Hakonarson
- The Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- * E-mail: (PS); (HH)
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Satterthwaite TD, Connolly JJ, Ruparel K, Calkins ME, Jackson C, Elliott MA, Roalf DR, Hopson R, Prabhakaran K, Behr M, Qiu H, Mentch FD, Chiavacci R, Sleiman PMA, Gur RC, Hakonarson H, Gur RE. The Philadelphia Neurodevelopmental Cohort: A publicly available resource for the study of normal and abnormal brain development in youth. Neuroimage 2015; 124:1115-1119. [PMID: 25840117 DOI: 10.1016/j.neuroimage.2015.03.056] [Citation(s) in RCA: 195] [Impact Index Per Article: 21.7] [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: 01/28/2015] [Revised: 03/16/2015] [Accepted: 03/16/2015] [Indexed: 01/31/2023] Open
Abstract
The Philadelphia Neurodevelopmental Cohort (PNC) is a large-scale study of child development that combines neuroimaging, diverse clinical and cognitive phenotypes, and genomics. Data from this rich resource is now publicly available through the Database of Genotypes and Phenotypes (dbGaP). Here we focus on the data from the PNC that is available through dbGaP and describe how users can access this data, which is evolving to be a significant resource for the broader neuroscience community for studies of normal and abnormal neurodevelopment.
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Affiliation(s)
- Theodore D Satterthwaite
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - John J Connolly
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kosha Ruparel
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Monica E Calkins
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Chad Jackson
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mark A Elliott
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - David R Roalf
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ryan Hopson
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Karthik Prabhakaran
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Meckenzie Behr
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Haijun Qiu
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Frank D Mentch
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Rosetta Chiavacci
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Patrick M A Sleiman
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ruben C Gur
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Philadelphia Veterans Administration Medical Center, Philadelphia, PA 19104, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Raquel E Gur
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Ong BA, Li J, McDonough JM, Wei Z, Kim C, Chiavacci R, Mentch F, Caboot JB, Spergel J, Allen JL, Sleiman PMA, Hakonarson H. Gene network analysis in a pediatric cohort identifies novel lung function genes. PLoS One 2013; 8:e72899. [PMID: 24023788 PMCID: PMC3759429 DOI: 10.1371/journal.pone.0072899] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [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: 04/08/2013] [Accepted: 07/15/2013] [Indexed: 01/06/2023] Open
Abstract
Lung function is a heritable trait and serves as an important clinical predictor of morbidity and mortality for pulmonary conditions in adults, however, despite its importance, no studies have focused on uncovering pediatric-specific loci influencing lung function. To identify novel genetic determinants of pediatric lung function, we conducted a genome-wide association study (GWAS) of four pulmonary function traits, including FVC, FEV1, FEV1/FVC and FEF25–75% in 1556 children. Further, we carried out gene network analyses for each trait including all SNPs with a P-value of <1.0×10−3 from the individual GWAS. The GWAS identified SNPs with notable trends towards association with the pulmonary function measures, including the previously described INTS12 locus association with FEV1 (pmeta = 1.41×10−7). The gene network analyses identified 34 networks of genes associated with pulmonary function variables in Caucasians. Of those, the glycoprotein gene network reached genome-wide significance for all four variables. P-value range pmeta = 6.29×10−4 - 2.80×10−8 on meta-analysis. In this study, we report on specific pathways that are significantly associated with pediatric lung function at genome-wide significance. In addition, we report the first loci associated with lung function in both pediatric Caucasian and African American populations.
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Affiliation(s)
- Bruce A. Ong
- Division of Pulmonary Medicine and Cystic Fibrosis Center, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Jin Li
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Joseph M. McDonough
- Division of Pulmonary Medicine and Cystic Fibrosis Center, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Zhi Wei
- Department of Computer Science, New Jersey Institute of Technology, Newark, New Jersey, United States of America
| | - Cecilia Kim
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Rosetta Chiavacci
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Frank Mentch
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Jason B. Caboot
- Division of Pediatric Pulmonology, Madigan Army Medical Center, Tacoma, Washington, United States of America
| | - Jonathan Spergel
- Center for Pediatric Eosinophilic Disorders, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- Division of Allergy and Immunology, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Julian L. Allen
- Division of Pulmonary Medicine and Cystic Fibrosis Center, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Patrick M. A. Sleiman
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail: (HH); (PMAS)
| | - Hakon Hakonarson
- Division of Pulmonary Medicine and Cystic Fibrosis Center, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail: (HH); (PMAS)
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Chen Z, Tang H, Qayyum R, Schick UM, Nalls MA, Handsaker R, Li J, Lu Y, Yanek LR, Keating B, Meng Y, van Rooij FJA, Okada Y, Kubo M, Rasmussen-Torvik L, Keller MF, Lange L, Evans M, Bottinger EP, Linderman MD, Ruderfer DM, Hakonarson H, Papanicolaou G, Zonderman AB, Gottesman O, Thomson C, Ziv E, Singleton AB, Loos RJF, Sleiman PMA, Ganesh S, McCarroll S, Becker DM, Wilson JG, Lettre G, Reiner AP. Genome-wide association analysis of red blood cell traits in African Americans: the COGENT Network. Hum Mol Genet 2013; 22:2529-38. [PMID: 23446634 DOI: 10.1093/hmg/ddt087] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Laboratory red blood cell (RBC) measurements are clinically important, heritable and differ among ethnic groups. To identify genetic variants that contribute to RBC phenotypes in African Americans (AAs), we conducted a genome-wide association study in up to ~16 500 AAs. The alpha-globin locus on chromosome 16pter [lead SNP rs13335629 in ITFG3 gene; P < 1E-13 for hemoglobin (Hgb), RBC count, mean corpuscular volume (MCV), MCH and MCHC] and the G6PD locus on Xq28 [lead SNP rs1050828; P < 1E - 13 for Hgb, hematocrit (Hct), MCV, RBC count and red cell distribution width (RDW)] were each associated with multiple RBC traits. At the alpha-globin region, both the common African 3.7 kb deletion and common single nucleotide polymorphisms (SNPs) appear to contribute independently to RBC phenotypes among AAs. In the 2p21 region, we identified a novel variant of PRKCE distinctly associated with Hct in AAs. In a genome-wide admixture mapping scan, local European ancestry at the 6p22 region containing HFE and LRRC16A was associated with higher Hgb. LRRC16A has been previously associated with the platelet count and mean platelet volume in AAs, but not with Hgb. Finally, we extended to AAs the findings of association of erythrocyte traits with several loci previously reported in Europeans and/or Asians, including CD164 and HBS1L-MYB. In summary, this large-scale genome-wide analysis in AAs has extended the importance of several RBC-associated genetic loci to AAs and identified allelic heterogeneity and pleiotropy at several previously known genetic loci associated with blood cell traits in AAs.
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Affiliation(s)
- Zhao Chen
- Division of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ 85724, USA
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42
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Glessner JT, Smith AV, Panossian S, Kim CE, Takahashi N, Thomas KA, Wang F, Seidler K, Harris TB, Launer LJ, Keating B, Connolly J, Sleiman PMA, Buxbaum JD, Grant SFA, Gudnason V, Hakonarson H. Copy number variations in alternative splicing gene networks impact lifespan. PLoS One 2013; 8:e53846. [PMID: 23382853 PMCID: PMC3559729 DOI: 10.1371/journal.pone.0053846] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [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: 01/06/2012] [Accepted: 12/06/2012] [Indexed: 01/01/2023] Open
Abstract
Longevity has a strong genetic component evidenced by family-based studies. Lipoprotein metabolism, FOXO proteins, and insulin/IGF-1 signaling pathways in model systems have shown polygenic variations predisposing to shorter lifespan. To test the hypothesis that rare variants could influence lifespan, we compared the rates of CNVs in healthy children (0–18 years of age) with individuals 67 years or older. CNVs at a significantly higher frequency in the pediatric cohort were considered risk variants impacting lifespan, while those enriched in the geriatric cohort were considered longevity protective variants. We performed a whole-genome CNV analysis on 7,313 children and 2,701 adults of European ancestry genotyped with 302,108 SNP probes. Positive findings were evaluated in an independent cohort of 2,079 pediatric and 4,692 geriatric subjects. We detected 8 deletions and 10 duplications that were enriched in the pediatric group (P = 3.33×10−8–1.6×10−2 unadjusted), while only one duplication was enriched in the geriatric cohort (P = 6.3×10−4). Population stratification correction resulted in 5 deletions and 3 duplications remaining significant (P = 5.16×10−5–4.26×10−2) in the replication cohort. Three deletions and four duplications were significant combined (combined P = 3.7×10−4−3.9×10−2). All associated loci were experimentally validated using qPCR. Evaluation of these genes for pathway enrichment demonstrated ∼50% are involved in alternative splicing (P = 0.0077 Benjamini and Hochberg corrected). We conclude that genetic variations disrupting RNA splicing could have long-term biological effects impacting lifespan.
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Affiliation(s)
- Joseph T. Glessner
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Albert Vernon Smith
- Icelandic Heart Association, Heart Preventive Clinic and Research Institute, Kopavogur, Iceland
- University of Iceland, Reykjavik, Iceland
| | - Saarene Panossian
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Cecilia E. Kim
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Nagahide Takahashi
- Laboratory of Molecular Neuropsychiatry, Department of Psychiatry, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Kelly A. Thomas
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Fengxiang Wang
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Kallyn Seidler
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Tamara B. Harris
- Laboratory of Epidemiology, Demography, and Biometry, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Lenore J. Launer
- Laboratory of Epidemiology, Demography, and Biometry, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Brendan Keating
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - John Connolly
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Patrick M. A. Sleiman
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Joseph D. Buxbaum
- Laboratory of Molecular Neuropsychiatry, Department of Psychiatry, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Struan F. A. Grant
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Division of Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Vilmundur Gudnason
- Icelandic Heart Association, Heart Preventive Clinic and Research Institute, Kopavogur, Iceland
- University of Iceland, Reykjavik, Iceland
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Division of Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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Li J, Glessner JT, Zhang H, Hou C, Wei Z, Bradfield JP, Mentch FD, Guo Y, Kim C, Xia Q, Chiavacci RM, Thomas KA, Qiu H, Grant SFA, Furth SL, Hakonarson H, Sleiman PMA. GWAS of blood cell traits identifies novel associated loci and epistatic interactions in Caucasian and African-American children. Hum Mol Genet 2012; 22:1457-64. [PMID: 23263863 DOI: 10.1093/hmg/dds534] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Hematological traits are important clinical indicators, the genetic determinants of which have not been fully investigated. Common measures of hematological traits include red blood cell (RBC) count, hemoglobin concentration (HGB), hematocrit (HCT), mean corpuscular hemoglobin (MCH), MCH concentration (MCHC), mean corpuscular volume (MCV), platelet count (PLT) and white blood cell (WBC) count. We carried out a genome-wide association study of the eight common hematological traits among 7943 African-American children and 6234 Caucasian children. In African Americans, we report five novel associations of HBE1 variants with HCT and MCHC, the alpha-globin gene cluster variants with RBC and MCHC, and a variant at the ARHGEF3 locus with PLT, as well as replication of four previously reported loci at genome-wide significance. In Caucasians, we report a novel association of variants at the COPZ1 locus with PLT as well as replication of four previously reported loci at genome-wide significance. Extended analysis of an association observed between MCH and the alpha-globin gene cluster variants demonstrated independent effects and epistatic interaction at the locus, impacting the risk of iron deficiency anemia in African Americans with specific genotype states. In summary, we extend the understanding of genetic variants underlying hematological traits based on analyses in African-American children.
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Affiliation(s)
- Jin Li
- Center for Applied Genomics, Abramson Research Center and Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
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Bradfield JP, Taal HR, Timpson NJ, Scherag A, Lecoeur C, Warrington NM, Hypponen E, Holst C, Valcarcel B, Thiering E, Salem RM, Schumacher FR, Cousminer DL, Sleiman PMA, Zhao J, Berkowitz RI, Vimaleswaran KS, Jarick I, Pennell CE, Evans DM, St Pourcain B, Berry DJ, Mook-Kanamori DO, Hofman A, Rivadeneira F, Uitterlinden AG, van Duijn CM, van der Valk RJP, de Jongste JC, Postma DS, Boomsma DI, Gauderman WJ, Hassanein MT, Lindgren CM, Mägi R, Boreham CAG, Neville CE, Moreno LA, Elliott P, Pouta A, Hartikainen AL, Li M, Raitakari O, Lehtimäki T, Eriksson JG, Palotie A, Dallongeville J, Das S, Deloukas P, McMahon G, Ring SM, Kemp JP, Buxton JL, Blakemore AIF, Bustamante M, Guxens M, Hirschhorn JN, Gillman MW, Kreiner-Møller E, Bisgaard H, Gilliland FD, Heinrich J, Wheeler E, Barroso I, O'Rahilly S, Meirhaeghe A, Sørensen TIA, Power C, Palmer LJ, Hinney A, Widen E, Farooqi IS, McCarthy MI, Froguel P, Meyre D, Hebebrand J, Jarvelin MR, Jaddoe VWV, Smith GD, Hakonarson H, Grant SFA. A genome-wide association meta-analysis identifies new childhood obesity loci. Nat Genet 2012; 44:526-31. [PMID: 22484627 PMCID: PMC3370100 DOI: 10.1038/ng.2247] [Citation(s) in RCA: 270] [Impact Index Per Article: 22.5] [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: 10/21/2011] [Accepted: 03/14/2012] [Indexed: 12/19/2022]
Abstract
Multiple genetic variants have been associated with adult obesity and a few with severe obesity in childhood; however, less progress has been made in establishing genetic influences on common early-onset obesity. We performed a North American, Australian and European collaborative meta-analysis of 14 studies consisting of 5,530 cases (≥95th percentile of body mass index (BMI)) and 8,318 controls (<50th percentile of BMI) of European ancestry. Taking forward the eight newly discovered signals yielding association with P < 5 × 10(-6) in nine independent data sets (2,818 cases and 4,083 controls), we observed two loci that yielded genome-wide significant combined P values near OLFM4 at 13q14 (rs9568856; P = 1.82 × 10(-9); odds ratio (OR) = 1.22) and within HOXB5 at 17q21 (rs9299; P = 3.54 × 10(-9); OR = 1.14). Both loci continued to show association when two extreme childhood obesity cohorts were included (2,214 cases and 2,674 controls). These two loci also yielded directionally consistent associations in a previous meta-analysis of adult BMI(1).
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Affiliation(s)
- Jonathan P Bradfield
- Center for Applied Genomics, Abramson Research Center, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
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45
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Elia J, Glessner JT, Wang K, Takahashi N, Shtir CJ, Hadley D, Sleiman PMA, Zhang H, Kim CE, Robison R, Lyon GJ, Flory JH, Bradfield JP, Imielinski M, Hou C, Frackelton EC, Chiavacci RM, Sakurai T, Rabin C, Middleton FA, Thomas KA, Garris M, Mentch F, Freitag CM, Steinhausen HC, Todorov AA, Reif A, Rothenberger A, Franke B, Mick EO, Roeyers H, Buitelaar J, Lesch KP, Banaschewski T, Ebstein RP, Mulas F, Oades RD, Sergeant J, Sonuga-Barke E, Renner TJ, Romanos M, Romanos J, Warnke A, Walitza S, Meyer J, Pálmason H, Seitz C, Loo SK, Smalley SL, Biederman J, Kent L, Asherson P, Anney RJL, Gaynor JW, Shaw P, Devoto M, White PS, Grant SFA, Buxbaum JD, Rapoport JL, Williams NM, Nelson SF, Faraone SV, Hakonarson H. Genome-wide copy number variation study associates metabotropic glutamate receptor gene networks with attention deficit hyperactivity disorder. Nat Genet 2011; 44:78-84. [PMID: 22138692 PMCID: PMC4310555 DOI: 10.1038/ng.1013] [Citation(s) in RCA: 302] [Impact Index Per Article: 23.2] [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: 06/24/2011] [Accepted: 10/28/2011] [Indexed: 12/11/2022]
Abstract
Attention deficit hyperactivity disorder (ADHD) is a common, heritable neuropsychiatric disorder of unknown etiology. We performed a whole-genome copy number variation (CNV) study on 1,013 cases with ADHD and 4,105 healthy children of European ancestry using 550,000 SNPs. We evaluated statistically significant findings in multiple independent cohorts, with a total of 2,493 cases with ADHD and 9,222 controls of European ancestry, using matched platforms. CNVs affecting metabotropic glutamate receptor genes were enriched across all cohorts (P = 2.1 × 10(-9)). We saw GRM5 (encoding glutamate receptor, metabotropic 5) deletions in ten cases and one control (P = 1.36 × 10(-6)). We saw GRM7 deletions in six cases, and we saw GRM8 deletions in eight cases and no controls. GRM1 was duplicated in eight cases. We experimentally validated the observed variants using quantitative RT-PCR. A gene network analysis showed that genes interacting with the genes in the GRM family are enriched for CNVs in ∼10% of the cases (P = 4.38 × 10(-10)) after correction for occurrence in the controls. We identified rare recurrent CNVs affecting glutamatergic neurotransmission genes that were overrepresented in multiple ADHD cohorts.
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Affiliation(s)
- Josephine Elia
- Department of Psychiatry, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA
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Chen-Plotkin AS, Martinez-Lage M, Sleiman PMA, Hu W, Greene R, Wood EM, Bing S, Grossman M, Schellenberg GD, Hatanpaa KJ, Weiner MF, White CL, Brooks WS, Halliday GM, Kril JJ, Gearing M, Beach TG, Graff-Radford NR, Dickson DW, Rademakers R, Boeve BF, Pickering-Brown SM, Snowden J, van Swieten JC, Heutink P, Seelaar H, Murrell JR, Ghetti B, Spina S, Grafman J, Kaye JA, Woltjer RL, Mesulam M, Bigio E, Lladó A, Miller BL, Alzualde A, Moreno F, Rohrer JD, Mackenzie IRA, Feldman HH, Hamilton RL, Cruts M, Engelborghs S, De Deyn PP, Van Broeckhoven C, Bird TD, Cairns NJ, Goate A, Frosch MP, Riederer PF, Bogdanovic N, Lee VMY, Trojanowski JQ, Van Deerlin VM. Genetic and clinical features of progranulin-associated frontotemporal lobar degeneration. ACTA ACUST UNITED AC 2011; 68:488-97. [PMID: 21482928 DOI: 10.1001/archneurol.2011.53] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
OBJECTIVE To assess the relative frequency of unique mutations and their associated characteristics in 97 individuals with mutations in progranulin (GRN), an important cause of frontotemporal lobar degeneration (FTLD). PARTICIPANTS AND DESIGN A 46-site International Frontotemporal Lobar Degeneration Collaboration was formed to collect cases of FTLD with TAR DNA-binding protein of 43-kDa (TDP-43)-positive inclusions (FTLD-TDP). We identified 97 individuals with FTLD-TDP with pathogenic GRN mutations (GRN+ FTLD-TDP), assessed their genetic and clinical characteristics, and compared them with 453 patients with FTLD-TDP in which GRN mutations were excluded (GRN- FTLD-TDP). No patients were known to be related. Neuropathologic characteristics were confirmed as FTLD-TDP in 79 of the 97 GRN+ FTLD-TDP cases and all of the GRN- FTLD-TDP cases. RESULTS Age at onset of FTLD was younger in patients with GRN+ FTLD-TDP vs GRN- FTLD-TDP (median, 58.0 vs 61.0 years; P < .001), as was age at death (median, 65.5 vs 69.0 years; P < .001). Concomitant motor neuron disease was much less common in GRN+ FTLD-TDP vs GRN- FTLD-TDP (5.4% vs 26.3%; P < .001). Fifty different GRN mutations were observed, including 2 novel mutations: c.139delG (p.D47TfsX7) and c.378C>A (p.C126X). The 2 most common GRN mutations were c.1477C>T (p.R493X, found in 18 patients, representing 18.6% of GRN cases) and c.26C>A (p.A9D, found in 6 patients, representing 6.2% of cases). Patients with the c.1477C>T mutation shared a haplotype on chromosome 17; clinically, they resembled patients with other GRN mutations. Patients with the c.26C>A mutation appeared to have a younger age at onset of FTLD and at death and more parkinsonian features than those with other GRN mutations. CONCLUSION GRN+ FTLD-TDP differs in key features from GRN- FTLD-TDP.
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Affiliation(s)
- Alice S Chen-Plotkin
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, 19104, USA.
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47
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Zhao J, Bradfield JP, Li M, Zhang H, Mentch FD, Wang K, Sleiman PMA, Kim CE, Glessner JT, Frackelton EC, Chiavacci RM, Berkowitz RI, Zemel BS, Hakonarson H, Grant SFA. BMD-associated variation at the Osterix locus is correlated with childhood obesity in females. Obesity (Silver Spring) 2011; 19:1311-4. [PMID: 21212767 DOI: 10.1038/oby.2010.324] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Recent genome wide association studies (GWAS) have revealed a number of genetic variants robustly associated with bone mineral density (BMD) and/or osteoporosis. Evidence from epidemiological and clinical studies has shown an association between BMD and BMI, presumably as a consequence of bone loading. We investigated the 23 previously published BMD GWAS-derived loci in the context of childhood obesity by leveraging our existing genome-wide genotyped European American cohort of 1106 obese children (BMI ≥ 95th percentile) and 5997 controls (BMI < 95th percentile). Evidence of association was only observed at one locus, namely Osterix (SP7), with the G allele of rs2016266 being significantly over-represented among childhood obesity cases (P = 2.85 × 10(-3)). When restricting these analyses to each gender, we observed strong association between rs2016266 and childhood obesity in females (477 cases and 2867 controls; P = 3.56 × 10(-4)), which survived adjustment for all tests applied. However, no evidence of association was observed among males. Interestingly, Osterix is the only GWAS locus uncovered to date that has also been previously implicated in the determination of BMD in childhood. In conclusion, these findings indicate that a well established variant at the Osterix locus associated with increased BMD is also associated with childhood obesity primarily in females.
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Affiliation(s)
- Jianhua Zhao
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
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March ME, Sleiman PMA, Hakonarson H. The genetics of asthma and allergic disorders. Discov Med 2011; 11:35-45. [PMID: 21276409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Asthma and allergic diseases are complex conditions caused by a combination of genetic and environmental factors. More than 100 genes have been associated with asthma and related conditions through candidate gene approaches, but issues of insufficient replication have made conclusions difficult to draw. Despite this, several overarching themes in the biology and pathogenesis of asthma have been revealed as a result of this work. In mid-2007, the first genome wide association study (GWAS) targeting asthma was published, and in the intervening years more than a dozen such studies have been reported examining asthma, allergic diseases, and related intermediate phenotypes and quantitative traits. A few previously suspected genetic variants have been confirmed in these studies as asthma susceptibility loci, or as loci contributing to disease severity or response to treatment. Additionally, unexpected and largely uncharacterized genes have been identified as new susceptibility loci for asthma, altering lung function or perturbing immune function. In this review, we summarize these GWAS, as well as the functional themes and characteristics underlying asthma that have been revealed through decades of genetic and genomic research.
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Affiliation(s)
- Michael E March
- The Abramson Research Center of the Joseph Stokes Jr. Research Institute, The Children's Hospital of Philadelphia, Pennsylvania 19104, USA
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Abstract
BACKGROUND Observational epidemiology has been instrumental in identifying modifiable causes of common diseases, and, in turn, substantially impacting public health. Spurious associations in observational epidemiologic studies are most commonly caused by confounding due to social, behavioral, or environmental factors and can therefore be difficult to control. They may also be due to reverse causation-in which the phenotypic outcome subsequently influences an environmental exposure such that it is wrongly implicated in its pathogenesis-and selection bias. Randomized controlled trials are effective in dealing with the potential sources of error; however, their use is not always leveraged, for practical or ethical reasons. CONTENT An alternative method, mendelian randomization, entails the use of genetic variants as proxies for the environmental exposures under investigation. The power of mendelian randomization lies in its ability to avoid the often substantial confounding seen in conventional observational epidemiology. Underpinning mendelian randomization is the principle of the independent assortment of alleles during meiosis, which, importantly in this context, also implies that they are independent of those behavioral and environmental factors that confound epidemiologic studies. By selecting genetic variants that influence exposure patterns or are associated with an intermediate phenotype of the disease, one can effectively re-create a randomized comparison. SUMMARY In the past 4 years, genomewide association studies have yielded the first robust genetic associations with common diseases, which in turn should enable mendelian randomization to be even more informative, despite some limitations outlined in this review.
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Affiliation(s)
- Patrick M A Sleiman
- Center for Applied Genomics, The Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA.
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Wang K, Baldassano R, Zhang H, Qu HQ, Imielinski M, Kugathasan S, Annese V, Dubinsky M, Rotter JI, Russell RK, Bradfield JP, Sleiman PMA, Glessner JT, Walters T, Hou C, Kim C, Frackelton EC, Garris M, Doran J, Romano C, Catassi C, Van Limbergen J, Guthery SL, Denson L, Piccoli D, Silverberg MS, Stanley CA, Monos D, Wilson DC, Griffiths A, Grant SFA, Satsangi J, Polychronakos C, Hakonarson H. Comparative genetic analysis of inflammatory bowel disease and type 1 diabetes implicates multiple loci with opposite effects. Hum Mol Genet 2010; 19:2059-67. [PMID: 20176734 DOI: 10.1093/hmg/ddq078] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Inflammatory bowel disease, including Crohn's disease (CD) and ulcerative colitis (UC), and type 1 diabetes (T1D) are autoimmune diseases that may share common susceptibility pathways. We examined known susceptibility loci for these diseases in a cohort of 1689 CD cases, 777 UC cases, 989 T1D cases and 6197 shared control subjects of European ancestry, who were genotyped by the Illumina HumanHap550 SNP arrays. We identified multiple previously unreported or unconfirmed disease associations, including known CD loci (ICOSLG and TNFSF15) and T1D loci (TNFAIP3) that confer UC risk, known UC loci (HERC2 and IL26) that confer T1D risk and known UC loci (IL10 and CCNY) that confer CD risk. Additionally, we show that T1D risk alleles residing at the PTPN22, IL27, IL18RAP and IL10 loci protect against CD. Furthermore, the strongest risk alleles for T1D within the major histocompatibility complex (MHC) confer strong protection against CD and UC; however, given the multi-allelic nature of the MHC haplotypes, sequencing of the MHC locus will be required to interpret this observation. These results extend our current knowledge on genetic variants that predispose to autoimmunity, and suggest that many loci involved in autoimmunity may be under a balancing selection due to antagonistic pleiotropic effect. Our analysis implies that variants with opposite effects on different diseases may facilitate the maintenance of common susceptibility alleles in human populations, making autoimmune diseases especially amenable to genetic dissection by genome-wide association studies.
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Affiliation(s)
- Kai Wang
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
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