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Makarious MB, Lake J, Pitz V, Ye Fu A, Guidubaldi JL, Solsberg CW, Bandres-Ciga S, Leonard HL, Kim JJ, Billingsley KJ, Grenn FP, Jerez PA, Alvarado CX, Iwaki H, Ta M, Vitale D, Hernandez D, Torkamani A, Ryten M, Hardy J, Scholz SW, Traynor BJ, Dalgard CL, Ehrlich DJ, Tanaka T, Ferrucci L, Beach TG, Serrano GE, Real R, Morris HR, Ding J, Gibbs JR, Singleton AB, Nalls MA, Bhangale T, Blauwendraat C. Large-scale rare variant burden testing in Parkinson's disease. Brain 2023; 146:4622-4632. [PMID: 37348876 PMCID: PMC10629770 DOI: 10.1093/brain/awad214] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 05/01/2023] [Accepted: 05/30/2023] [Indexed: 06/24/2023] Open
Abstract
Parkinson's disease has a large heritable component and genome-wide association studies have identified over 90 variants with disease-associated common variants, providing deeper insights into the disease biology. However, there have not been large-scale rare variant analyses for Parkinson's disease. To address this gap, we investigated the rare genetic component of Parkinson's disease at minor allele frequencies <1%, using whole genome and whole exome sequencing data from 7184 Parkinson's disease cases, 6701 proxy cases and 51 650 healthy controls from the Accelerating Medicines Partnership Parkinson's disease (AMP-PD) initiative, the National Institutes of Health, the UK Biobank and Genentech. We performed burden tests meta-analyses on small indels and single nucleotide protein-altering variants, prioritized based on their predicted functional impact. Our work identified several genes reaching exome-wide significance. Two of these genes, GBA1 and LRRK2, have variants that have been previously implicated as risk factors for Parkinson's disease, with some variants in LRRK2 resulting in monogenic forms of the disease. We identify potential novel risk associations for variants in B3GNT3, AUNIP, ADH5, TUBA1B, OR1G1, CAPN10 and TREML1 but were unable to replicate the observed associations across independent datasets. Of these, B3GNT3 and TREML1 could provide new evidence for the role of neuroinflammation in Parkinson's disease. To date, this is the largest analysis of rare genetic variants in Parkinson's disease.
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Affiliation(s)
- Mary B Makarious
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- UCL Movement Disorders Centre, University College London, London WC1N 3BG, UK
| | - Julie Lake
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
| | - Vanessa Pitz
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
| | - Allen Ye Fu
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
| | - Joseph L Guidubaldi
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20814, USA
| | - Caroline Warly Solsberg
- Memory and Aging Center, Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA
- Pharmaceutical Sciences and Pharmacogenomics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Sara Bandres-Ciga
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20814, USA
| | - Hampton L Leonard
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20814, USA
- Data Tecnica International, Washington, DC 20812, USA
| | - Jonggeol Jeffrey Kim
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- Preventive Neurology Unit, Wolfson Institute of Preventive Medicine, Queen Mary University of London, London EC1M 6BQ, UK
| | - Kimberley J Billingsley
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20814, USA
| | - Francis P Grenn
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
| | - Pilar Alvarez Jerez
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20814, USA
| | - Chelsea X Alvarado
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20814, USA
- Data Tecnica International, Washington, DC 20812, USA
| | - Hirotaka Iwaki
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20814, USA
- Data Tecnica International, Washington, DC 20812, USA
| | - Michael Ta
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20814, USA
- Data Tecnica International, Washington, DC 20812, USA
| | - Dan Vitale
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20814, USA
- Data Tecnica International, Washington, DC 20812, USA
| | - Dena Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
| | - Ali Torkamani
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Mina Ryten
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London WC1N 1EH, UK
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - John Hardy
- UK Dementia Research Institute and Department of Neurodegenerative Disease and Reta Lila Weston Institute, UCL Queen Square Institute of Neurology and UCL Movement Disorders Centre, University College London, London WC1N 3BG, UK
- Institute for Advanced Study, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | | | - Sonja W Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD 20814, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD 21287, USA
| | - Bryan J Traynor
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD 21287, USA
| | - Clifton L Dalgard
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Debra J Ehrlich
- Parkinson’s Disease Clinic, Office of the Clinical Director, National Institute of Neurological Disorders and Stroke, Bethesda, MD 20814, USA
| | - Toshiko Tanaka
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Thomas G Beach
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, AZ 85351, USA
| | - Geidy E Serrano
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Sun City, AZ 85351, USA
| | - Raquel Real
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- UCL Movement Disorders Centre, University College London, London WC1N 3BG, UK
| | - Huw R Morris
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- UCL Movement Disorders Centre, University College London, London WC1N 3BG, UK
| | - Jinhui Ding
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
| | - J Raphael Gibbs
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
| | - Andrew B Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20814, USA
| | - Mike A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20814, USA
- Data Tecnica International, Washington, DC 20812, USA
| | - Tushar Bhangale
- Department of Human Genetics, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Cornelis Blauwendraat
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20814, USA
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20814, USA
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2
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Loomis SJ, Sadhu N, Fisher E, Gafson AR, Huang Y, Yang C, Hughes EE, Marshall E, Herman A, John S, Runz H, Jia X, Bhangale T, Bronson PG. Genome-wide study of longitudinal brain imaging measures of multiple sclerosis progression across six clinical trials. Sci Rep 2023; 13:14313. [PMID: 37652990 PMCID: PMC10471679 DOI: 10.1038/s41598-023-41099-0] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 08/22/2023] [Indexed: 09/02/2023] Open
Abstract
While the genetics of MS risk susceptibility are well-described, and recent progress has been made on the genetics of disease severity, the genetics of disease progression remain elusive. We therefore investigated the genetic determinants of MS progression on longitudinal brain MRI: change in brain volume (BV) and change in T2 lesion volume (T2LV), reflecting progressive tissue loss and increasing disease burden, respectively. We performed genome-wide association studies of change in BV (N = 3401) and change in T2LV (N = 3513) across six randomized clinical trials from Biogen and Roche/Genentech: ADVANCE, ASCEND, DECIDE, OPERA I & II, and ORATORIO. Analyses were adjusted for randomized treatment arm, age, sex, and ancestry. Results were pooled in a meta-analysis, and were evaluated for enrichment of MS risk variants. Variant colocalization and cell-specific expression analyses were performed using published cohorts. The strongest peaks were in PTPRD (rs77321193-C/A, p = 3.9 × 10-7) for BV change, and NEDD4L (rs11398377-GC/G, p = 9.3 × 10-8) for T2LV change. Evidence of colocalization was observed for NEDD4L, and both genes showed increased expression in neuronal and/or glial populations. No association between MS risk variants and MRI outcomes was observed. In this unique, precompetitive industry partnership, we report putative regions of interest in the neurodevelopmental gene PTPRD, and the ubiquitin ligase gene NEDD4L. These findings are distinct from known MS risk genetics, indicating an added role for genetic progression analyses and informing drug discovery.
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3
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Khan Z, Jung M, Crow M, Mohindra R, Maiya V, Kaminker JS, Hackos DH, Chandler GS, McCarthy MI, Bhangale T. Whole genome sequencing across clinical trials identifies rare coding variants in GPR68 associated with chemotherapy-induced peripheral neuropathy. Genome Med 2023; 15:45. [PMID: 37344884 DOI: 10.1186/s13073-023-01193-4] [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: 11/30/2022] [Accepted: 05/17/2023] [Indexed: 06/23/2023] Open
Abstract
BACKGROUND Dose-limiting toxicities significantly impact the benefit/risk profile of many drugs. Whole genome sequencing (WGS) in patients receiving drugs with dose-limiting toxicities can identify therapeutic hypotheses to prevent these toxicities. Chemotherapy-induced peripheral neuropathy (CIPN) is a common dose-limiting neurological toxicity of chemotherapies with no effective approach for prevention. METHODS We conducted a genetic study of time-to-first peripheral neuropathy event using 30× germline WGS data from whole blood samples from 4900 European-ancestry cancer patients in 14 randomized controlled trials. A substantial number of patients in these trials received taxane and platinum-based chemotherapies as part of their treatment regimen, either standard of care or in combination with the PD-L1 inhibitor atezolizumab. The trials spanned several cancers including renal cell carcinoma, triple negative breast cancer, non-small cell lung cancer, small cell lung cancer, bladder cancer, ovarian cancer, and melanoma. RESULTS We identified a locus consisting of low-frequency variants in intron 13 of GRID2 associated with time-to-onset of first peripheral neuropathy (PN) indexed by rs17020773 (p = 2.03 × 10-8, all patients, p = 6.36 × 10-9, taxane treated). Gene-level burden analysis identified rare coding variants associated with increased PN risk in the C-terminus of GPR68 (p = 1.59 × 10-6, all patients, p = 3.47 × 10-8, taxane treated), a pH-sensitive G-protein coupled receptor (GPCR). The variants driving this signal were found to alter predicted arrestin binding motifs in the C-terminus of GPR68. Analysis of snRNA-seq from human dorsal root ganglia (DRG) indicated that expression of GPR68 was highest in mechano-thermo-sensitive nociceptors. CONCLUSIONS Our genetic study provides insight into the impact of low-frequency and rare coding genetic variation on PN risk and suggests that further study of GPR68 in sensory neurons may yield a therapeutic hypothesis for prevention of CIPN.
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Affiliation(s)
- Zia Khan
- Genentech, 1 DNA Way, South San Francisco, 94080, USA.
| | - Min Jung
- Genentech, 1 DNA Way, South San Francisco, 94080, USA
| | - Megan Crow
- Genentech, 1 DNA Way, South San Francisco, 94080, USA
| | - Rajat Mohindra
- F. Hoffmann-La Roche, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Vidya Maiya
- Genentech, 1 DNA Way, South San Francisco, 94080, USA
| | | | | | - G Scott Chandler
- F. Hoffmann-La Roche, Grenzacherstrasse 124, 4070, Basel, Switzerland
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4
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Wall JD, Sathirapongsasuti JF, Gupta R, Rasheed A, Venkatesan R, Belsare S, Menon R, Phalke S, Mittal A, Fang J, Tanneeru D, Deshmukh M, Bassi A, Robinson J, Chaudhary R, Murugan S, Ul-Asar Z, Saleem I, Ishtiaq U, Fatima A, Sheikh SS, Hameed S, Ishaq M, Rasheed SZ, Memon FUR, Jalal A, Abbas S, Frossard P, Fuchsberger C, Forer L, Schoenherr S, Bei Q, Bhangale T, Tom J, Gadde SGK, B V P, Naik NK, Wang M, Kwok PY, Khera AV, Lakshmi BR, Butterworth AS, Chowdhury R, Danesh J, di Angelantonio E, Naheed A, Goyal V, Kandadai RM, Kumar H, Borgohain R, Mukherjee A, Wadia PM, Yadav R, Desai S, Kumar N, Biswas A, Pal PK, Muthane UB, Das SK, Ramprasad VL, Kukkle PL, Seshagiri S, Kathiresan S, Ghosh A, Mohan V, Saleheen D, Stawiski EW, Peterson AS. South Asian medical cohorts reveal strong founder effects and high rates of homozygosity. Nat Commun 2023; 14:3377. [PMID: 37291107 PMCID: PMC10250394 DOI: 10.1038/s41467-023-38766-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 05/15/2023] [Indexed: 06/10/2023] Open
Abstract
The benefits of large-scale genetic studies for healthcare of the populations studied are well documented, but these genetic studies have traditionally ignored people from some parts of the world, such as South Asia. Here we describe whole genome sequence (WGS) data from 4806 individuals recruited from the healthcare delivery systems of Pakistan, India and Bangladesh, combined with WGS from 927 individuals from isolated South Asian populations. We characterize population structure in South Asia and describe a genotyping array (SARGAM) and imputation reference panel that are optimized for South Asian genomes. We find evidence for high rates of reproductive isolation, endogamy and consanguinity that vary across the subcontinent and that lead to levels of rare homozygotes that reach 100 times that seen in outbred populations. Founder effects increase the power to associate functional variants with disease processes and make South Asia a uniquely powerful place for population-scale genetic studies.
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Affiliation(s)
- Jeffrey D Wall
- Institute for Human Genetics, University of California, San Francisco, CA, 94143, USA.
- Dept of Ornithology and Mammology, California Academy of Sciences, San Francisco, CA, 94118, USA.
| | - J Fah Sathirapongsasuti
- MedGenome Inc., Foster City, CA, 94404, USA
- GenomeAsia 100K Foundation, Foster City, CA, 94404, USA
| | - Ravi Gupta
- MedGenome Labs Pvt. Ltd., Bengaluru, Karnataka, 560099, India
| | - Asif Rasheed
- Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan
| | - Radha Venkatesan
- Madras Diabetes Research Foundation and Dr. Mohan's Diabetes Specialties Centre, Chennai, Tamil Nadu, 600086, India
| | - Saurabh Belsare
- Institute for Human Genetics, University of California, San Francisco, CA, 94143, USA
| | - Ramesh Menon
- MedGenome Labs Pvt. Ltd., Bengaluru, Karnataka, 560099, India
| | - Sameer Phalke
- MedGenome Labs Pvt. Ltd., Bengaluru, Karnataka, 560099, India
| | | | - John Fang
- Thermo Fisher Scientific, Santa Clara, CA, 95051, USA
| | - Deepak Tanneeru
- MedGenome Labs Pvt. Ltd., Bengaluru, Karnataka, 560099, India
| | | | - Akshi Bassi
- MedGenome Labs Pvt. Ltd., Bengaluru, Karnataka, 560099, India
| | - Jacqueline Robinson
- Institute for Human Genetics, University of California, San Francisco, CA, 94143, USA
| | | | | | - Zameer Ul-Asar
- Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan
| | - Imran Saleem
- Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan
| | - Unzila Ishtiaq
- Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan
| | - Areej Fatima
- Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan
| | | | | | | | | | | | - Anjum Jalal
- Faisalabad Institute of Cardiology, Faisalabad, Pakistan
| | - Shahid Abbas
- Faisalabad Institute of Cardiology, Faisalabad, Pakistan
| | - Philippe Frossard
- Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan
| | - Christian Fuchsberger
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
- Institute for Biomedicine, Eurac Research, Bolzano, Italy
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Lukas Forer
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Sebastian Schoenherr
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Qixin Bei
- Department of Molecular Biology, Genentech, South San Francisco, CA, 94080, USA
| | - Tushar Bhangale
- Department of Human Genetics, Genentech, South San Francisco, CA, 94080, USA
| | - Jennifer Tom
- Product Development Data Sciences, Genentech, South San Francisco, CA, 94080, USA
| | | | - Priya B V
- Narayana Nethralaya Foundation, Bengaluru, Karnataka, 560010, India
| | | | - Minxian Wang
- Program in Medical and Population Genetics & Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Pui-Yan Kwok
- Institute for Human Genetics, University of California, San Francisco, CA, 94143, USA
- Cardiovascular Research Institute and Department of Dermatology, University of California San Francisco, San Francisco, CA, 94143, USA
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Amit V Khera
- Harvard Medical School, Boston, MA, 02115, USA
- Division of Cardiology, Department of Medicine, Brigham and Women's Hospital, MA, 02115, Boston, USA
- Verve Therapeutics, Cambridge, MA, 02139, USA
| | - B R Lakshmi
- MDCRC, Royal Care Super Speciality Hospital 1/520, Neelambur, Coimbatore, Tamil Nadu, 641062, India
| | - Adam S Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK
- National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Rajiv Chowdhury
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - John Danesh
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK
- National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Emanuele di Angelantonio
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK
- National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Aliya Naheed
- Initiative for Non Communicable Diseases, Health Systems and Population Studies Division, icddr,b, Dhaka, Bangladesh
| | - Vinay Goyal
- All India Institute of Medical Sciences (AIIMS), New Delhi, India
- Medanta Hospital, New Delhi, India
- Medanta, The Medicity, Gurgaon, India
| | | | | | - Rupam Borgohain
- Nizams Institute of Medical Sciences (NIMS), Hyderabad, India
| | - Adreesh Mukherjee
- Bangur Institute of Neurosciences and Institute of Post Graduate Medical Education and Research (IPGME&R), Kolkata, India
| | | | - Ravi Yadav
- National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
| | - Soaham Desai
- Shree Krishna Hospital and Pramukhaswami Medical College, Bhaikaka University, Karamsad, Gujarat, India
| | - Niraj Kumar
- All India Institute of Medical Sciences, Rishikesh, India
| | - Atanu Biswas
- Bangur Institute of Neurosciences and Institute of Post Graduate Medical Education and Research (IPGME&R), Kolkata, India
| | - Pramod Kumar Pal
- National Institute of Mental Health and Neurosciences (NIMHANS), Bengaluru, India
| | - Uday B Muthane
- Parkinson and Ageing Research Foundation, Bengaluru, India
| | - Shymal K Das
- Bangur Institute of Neurosciences and Institute of Post Graduate Medical Education and Research (IPGME&R), Kolkata, India
| | | | - Prashanth L Kukkle
- All India Institute of Medical Sciences, Rishikesh, India
- Manipal Hospital, Miller Road, Bengaluru, India
- Parkinson's Disease and Movement Disorders Clinic, Bengaluru, India
| | - Somasekar Seshagiri
- GenomeAsia 100K Foundation, Foster City, CA, 94404, USA
- Department of Molecular Biology, Genentech, South San Francisco, CA, 94080, USA
| | - Sekar Kathiresan
- Program in Medical and Population Genetics & Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Verve Therapeutics, Cambridge, MA, 02139, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Arkasubhra Ghosh
- Narayana Nethralaya Foundation, Bengaluru, Karnataka, 560010, India
| | - V Mohan
- Madras Diabetes Research Foundation and Dr. Mohan's Diabetes Specialties Centre, Chennai, Tamil Nadu, 600086, India
| | - Danish Saleheen
- Center for Non-Communicable Disease, Karachi, Karachi City, Sindh, 75300, Pakistan
- Seymour, Paul and Gloria Milstein Division of Cardiology at Columbia University, New York, NY, 10032, USA
| | - Eric W Stawiski
- MedGenome Inc., Foster City, CA, 94404, USA
- GenomeAsia 100K Foundation, Foster City, CA, 94404, USA
- Department of Molecular Biology, Genentech, South San Francisco, CA, 94080, USA
- Caribou Biosciences, Berkeley, CA, 94710, USA
| | - Andrew S Peterson
- MedGenome Inc., Foster City, CA, 94404, USA.
- GenomeAsia 100K Foundation, Foster City, CA, 94404, USA.
- Department of Molecular Biology, Genentech, South San Francisco, CA, 94080, USA.
- Broadwing Bio, South San Francisco, CA, 94080, USA.
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5
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Kayagaki N, Stowe IB, Alegre K, Deshpande I, Wu S, Lin Z, Kornfeld OS, Lee BL, Zhang J, Liu J, Suto E, Lee WP, Schneider K, Lin W, Seshasayee D, Bhangale T, Chalouni C, Johnson MC, Joshi P, Mossemann J, Zhao S, Ali D, Goldenberg NM, Sayed BA, Steinberg BE, Newton K, Webster JD, Kelly RL, Dixit VM. Inhibiting membrane rupture with NINJ1 antibodies limits tissue injury. Nature 2023:10.1038/s41586-023-06191-5. [PMID: 37196676 DOI: 10.1038/s41586-023-06191-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 05/10/2023] [Indexed: 05/19/2023]
Abstract
Plasma membrane rupture (PMR) in dying cells undergoing pyroptosis or apoptosis requires the cell-surface protein NINJ11. PMR releases proinflammatory cytoplasmic molecules, collectively called damage-associated molecular patterns (DAMPs), that activate immune cells. Therefore, inhibiting NINJ1 and PMR may limit the inflammation that is associated with excessive cell death. Here we describe an anti-NINJ1 monoclonal antibody, specifically targeting murine NINJ1, that blocks oligomerization of NINJ1 and prevents PMR. By electron microscopy, this antibody prevented NINJ1 from forming oligomeric filaments. In mice, inhibition of NINJ1 or Ninj1 deficiency ameliorated hepatocellular PMR induced with TNF plus D-Galactosamine, concanavalin A, Jo2 anti-Fas agonist antibody, or ischemia-reperfusion injury (IRI). Accordingly, serum levels of lactate dehydrogenase (LDH), liver enzymes alanine aminotransaminase (ALT) and aspartate aminotransferase (AST), and DAMPs interleukin 18 (IL-18) and HMGB1 were reduced. Moreover, in the liver IRI model, there was an attendant reduction in neutrophil infiltration. These data indicate that NINJ1 mediates PMR and inflammation in diseases driven by aberrant hepatocellular death.
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Affiliation(s)
- Nobuhiko Kayagaki
- Department of Physiological Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, California, USA.
| | - Irma B Stowe
- Department of Physiological Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Kamela Alegre
- Department of Physiological Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Ishan Deshpande
- Department of Physiological Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
- Department of Structural Biology, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Shuang Wu
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Zhonghua Lin
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Opher S Kornfeld
- Department of Physiological Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Bettina L Lee
- Department of Physiological Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Juan Zhang
- Department of Translational Immunology, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - John Liu
- Department of Translational Immunology, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Eric Suto
- Department of Translational Immunology, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Wyne P Lee
- Department of Translational Immunology, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Kellen Schneider
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - WeiYu Lin
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Dhaya Seshasayee
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Tushar Bhangale
- Department of Human Genetics, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Cecile Chalouni
- Department of Pathology, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Matthew C Johnson
- Department of Structural Biology, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Prajakta Joshi
- Department of Biomolecular Resources, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Jan Mossemann
- Program in Cell Biology, Hospital for Sick Children, 555 University Ave, Toronto, Ontario, Canada
| | - Sarah Zhao
- Program in Neuroscience and Mental Health, Hospital for Sick Children, 555 University Ave, Toronto, Ontario, Canada
| | - Danish Ali
- Program in Cell Biology, Hospital for Sick Children, 555 University Ave, Toronto, Ontario, Canada
| | - Neil M Goldenberg
- Program in Cell Biology, Hospital for Sick Children, 555 University Ave, Toronto, Ontario, Canada
- Department of Anesthesia and Pain Medicine, Hospital for Sick Children, 555 University Ave, Toronto, Ontario, Canada
| | - Blayne A Sayed
- Program in Cell Biology, Hospital for Sick Children, 555 University Ave, Toronto, Ontario, Canada
- Division of General Surgery, Hospital for Sick Children, 555 University Ave, Toronto, Ontario, Canada
| | - Benjamin E Steinberg
- Program in Neuroscience and Mental Health, Hospital for Sick Children, 555 University Ave, Toronto, Ontario, Canada
- Department of Anesthesia and Pain Medicine, Hospital for Sick Children, 555 University Ave, Toronto, Ontario, Canada
| | - Kim Newton
- Department of Physiological Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Joshua D Webster
- Department of Pathology, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Ryan L Kelly
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, California, USA
| | - Vishva M Dixit
- Department of Physiological Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, California, USA.
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6
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Orozco LD, Chen HH, Cox C, Katschke KJ, Rommel Arceo, Espiritu C, Caplazi P, Nghiem SS, Chen YJ, Modrusan Z, Dressen A, Goldstein LD, Clarke C, Bhangale T, Yaspan B, Jeanne M, Townsend MJ, van Lookeren Campagne M, Hackney JA. Integration of eQTL and a Single-Cell Atlas in the Human Eye Identifies Causal Genes for Age-Related Macular Degeneration. Cell Rep 2023; 42:112298. [PMID: 36952338 DOI: 10.1016/j.celrep.2023.112298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023] Open
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7
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Chang D, Hunkapiller J, Bhangale T, Reeder J, Mukhyala K, Tom J, Cowgill A, Vogel J, Forrest WF, Khan Z, Stockwell A, McCarthy MI, Staton TL, Olsson J, Holweg CTJ, Cheung DS, Chen H, Brauer MJ, Graham RR, Behrens T, Wilson MS, Arron JR, Choy DF, Yaspan BL. A whole genome sequencing study of moderate to severe asthma identifies a lung function locus associated with asthma risk. Sci Rep 2022; 12:5574. [PMID: 35368043 PMCID: PMC8976834 DOI: 10.1038/s41598-022-09447-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/23/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractGenome-wide association studies (GWAS) have identified many common variant loci associated with asthma susceptibility, but few studies investigate the genetics underlying moderate-to-severe asthma risk. Here, we present a whole-genome sequencing study comparing 3181 moderate-to-severe asthma patients to 3590 non-asthma controls. We demonstrate that asthma risk is genetically correlated with lung function measures and that this component of asthma risk is orthogonal to the eosinophil genetics that also contribute to disease susceptibility. We find that polygenic scores for reduced lung function are associated with younger asthma age of onset. Genome-wide, seven previously reported common asthma variant loci and one previously reported lung function locus, near THSD4, reach significance. We replicate association of the lung function locus in a recently published GWAS of moderate-to-severe asthma patients. We additionally replicate the association of a previously reported rare (minor allele frequency < 1%) coding variant in IL33 and show significant enrichment of rare variant burden in genes from common variant allergic disease loci. Our findings highlight the contribution of lung function genetics to moderate-to-severe asthma risk, and provide initial rare variant support for associations with moderate-to-severe asthma risk at several candidate genes from common variant loci.
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8
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Farrell K, Kim S, Han N, Iida MA, Gonzalez EM, Otero-Garcia M, Walker JM, Richardson TE, Renton AE, Andrews SJ, Fulton-Howard B, Humphrey J, Vialle RA, Bowles KR, de Paiva Lopes K, Whitney K, Dangoor DK, Walsh H, Marcora E, Hefti MM, Casella A, Sissoko CT, Kapoor M, Novikova G, Udine E, Wong G, Tang W, Bhangale T, Hunkapiller J, Ayalon G, Graham RR, Cherry JD, Cortes EP, Borukov VY, McKee AC, Stein TD, Vonsattel JP, Teich AF, Gearing M, Glass J, Troncoso JC, Frosch MP, Hyman BT, Dickson DW, Murray ME, Attems J, Flanagan ME, Mao Q, Mesulam MM, Weintraub S, Woltjer RL, Pham T, Kofler J, Schneider JA, Yu L, Purohit DP, Haroutunian V, Hof PR, Gandy S, Sano M, Beach TG, Poon W, Kawas CH, Corrada MM, Rissman RA, Metcalf J, Shuldberg S, Salehi B, Nelson PT, Trojanowski JQ, Lee EB, Wolk DA, McMillan CT, Keene CD, Latimer CS, Montine TJ, Kovacs GG, Lutz MI, Fischer P, Perrin RJ, Cairns NJ, Franklin EE, Cohen HT, Raj T, Cobos I, Frost B, Goate A, White Iii CL, Crary JF. Genome-wide association study and functional validation implicates JADE1 in tauopathy. Acta Neuropathol 2022; 143:33-53. [PMID: 34719765 PMCID: PMC8786260 DOI: 10.1007/s00401-021-02379-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [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: 08/27/2021] [Revised: 10/13/2021] [Accepted: 10/24/2021] [Indexed: 01/07/2023]
Abstract
Primary age-related tauopathy (PART) is a neurodegenerative pathology with features distinct from but also overlapping with Alzheimer disease (AD). While both exhibit Alzheimer-type temporal lobe neurofibrillary degeneration alongside amnestic cognitive impairment, PART develops independently of amyloid-β (Aβ) plaques. The pathogenesis of PART is not known, but evidence suggests an association with genes that promote tau pathology and others that protect from Aβ toxicity. Here, we performed a genetic association study in an autopsy cohort of individuals with PART (n = 647) using Braak neurofibrillary tangle stage as a quantitative trait. We found some significant associations with candidate loci associated with AD (SLC24A4, MS4A6A, HS3ST1) and progressive supranuclear palsy (MAPT and EIF2AK3). Genome-wide association analysis revealed a novel significant association with a single nucleotide polymorphism on chromosome 4 (rs56405341) in a locus containing three genes, including JADE1 which was significantly upregulated in tangle-bearing neurons by single-soma RNA-seq. Immunohistochemical studies using antisera targeting JADE1 protein revealed localization within tau aggregates in autopsy brains with four microtubule-binding domain repeats (4R) isoforms and mixed 3R/4R, but not with 3R exclusively. Co-immunoprecipitation in post-mortem human PART brain tissue revealed a specific binding of JADE1 protein to four repeat tau lacking N-terminal inserts (0N4R). Finally, knockdown of the Drosophila JADE1 homolog rhinoceros (rno) enhanced tau-induced toxicity and apoptosis in vivo in a humanized 0N4R mutant tau knock-in model, as quantified by rough eye phenotype and terminal deoxynucleotidyl transferase dUTP nick end-labeling (TUNEL) in the fly brain. Together, these findings indicate that PART has a genetic architecture that partially overlaps with AD and other tauopathies and suggests a novel role for JADE1 as a modifier of neurofibrillary degeneration.
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Affiliation(s)
- Kurt Farrell
- Department of Pathology, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place Box 1194, New York, NY, 10029, USA
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - SoongHo Kim
- Department of Pathology, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place Box 1194, New York, NY, 10029, USA
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Natalia Han
- Department of Pathology, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place Box 1194, New York, NY, 10029, USA
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Megan A Iida
- Department of Pathology, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place Box 1194, New York, NY, 10029, USA
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elias M Gonzalez
- Department of Cell Systems and Anatomy, Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, the Sam and Ann Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Marcos Otero-Garcia
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, University of California, Los Angeles, CA, USA
| | - Jamie M Walker
- Department of Pathology and Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, UT Health San Antonio, San Antonio, TX, USA
| | - Timothy E Richardson
- Department of Pathology and Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, UT Health San Antonio, San Antonio, TX, USA
| | - Alan E Renton
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shea J Andrews
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brian Fulton-Howard
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jack Humphrey
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ricardo A Vialle
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kathryn R Bowles
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Katia de Paiva Lopes
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kristen Whitney
- Department of Pathology, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place Box 1194, New York, NY, 10029, USA
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Diana K Dangoor
- Department of Pathology, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place Box 1194, New York, NY, 10029, USA
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hadley Walsh
- Department of Pathology, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place Box 1194, New York, NY, 10029, USA
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edoardo Marcora
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marco M Hefti
- Department of Pathology, University of Iowa, Iowa City, IA, USA
| | - Alicia Casella
- Department of Pathology, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place Box 1194, New York, NY, 10029, USA
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Cheick T Sissoko
- Department of Pathology, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place Box 1194, New York, NY, 10029, USA
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Manav Kapoor
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gloriia Novikova
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Evan Udine
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Garrett Wong
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Weijing Tang
- Department of Pathology, Stanford University, Palo Alto, USA
| | - Tushar Bhangale
- Department of Human Genetics, Genentech, South San Francisco, CA, USA
| | - Julie Hunkapiller
- Department of Human Genetics, Genentech, South San Francisco, CA, USA
| | - Gai Ayalon
- Neumora Therapeutics, South San Francisco, CA, USA
| | | | - Jonathan D Cherry
- Department of Pathology (Neuropathology), VA Medical Center, Boston University School of Medicine, Boston, MA, USA
| | - Etty P Cortes
- Department of Pathology, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place Box 1194, New York, NY, 10029, USA
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Valeriy Y Borukov
- Department of Pathology, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place Box 1194, New York, NY, 10029, USA
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ann C McKee
- Department of Pathology (Neuropathology), VA Medical Center, Boston University School of Medicine, Boston, MA, USA
| | - Thor D Stein
- Department of Pathology (Neuropathology), VA Medical Center, Boston University School of Medicine, Boston, MA, USA
| | - Jean-Paul Vonsattel
- Department of Pathology and Cell Biology, Department of Neurology, and the Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA
| | - Andy F Teich
- Department of Pathology and Cell Biology, Department of Neurology, and the Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA
| | - Marla Gearing
- Department of Pathology and Laboratory Medicine (Neuropathology) and Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Jonathan Glass
- Department of Pathology and Laboratory Medicine (Neuropathology) and Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Juan C Troncoso
- Department of Pathology, Division of Neuropathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Matthew P Frosch
- Department of Neurology and Pathology, Harvard Medical School and Massachusetts General Hospital, Charlestown, MA, USA
| | - Bradley T Hyman
- Department of Neurology and Pathology, Harvard Medical School and Massachusetts General Hospital, Charlestown, MA, USA
| | | | | | - Johannes Attems
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Margaret E Flanagan
- Department of Pathology (Neuropathology), Northwestern Cognitive Neurology and Alzheimer Disease Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Qinwen Mao
- Department of Pathology (Neuropathology), Northwestern Cognitive Neurology and Alzheimer Disease Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - M-Marsel Mesulam
- Department of Pathology (Neuropathology), Northwestern Cognitive Neurology and Alzheimer Disease Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Sandra Weintraub
- Department of Pathology (Neuropathology), Northwestern Cognitive Neurology and Alzheimer Disease Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Randy L Woltjer
- Department of Pathology, Oregon Health Sciences University, Portland, OR, USA
| | - Thao Pham
- Department of Pathology, Oregon Health Sciences University, Portland, OR, USA
| | - Julia Kofler
- Department of Pathology (Neuropathology), University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Julie A Schneider
- Departments of Pathology (Neuropathology) and Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Lei Yu
- Departments of Pathology (Neuropathology) and Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Dushyant P Purohit
- Department of Pathology, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place Box 1194, New York, NY, 10029, USA
- Department of Psychiatry, Alzheimer's Disease Research Center, James J. Peters VA Medical Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vahram Haroutunian
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Alzheimer's Disease Research Center, James J. Peters VA Medical Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Patrick R Hof
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sam Gandy
- Department of Psychiatry, Alzheimer's Disease Research Center, James J. Peters VA Medical Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neurology, Center for Cognitive Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mary Sano
- Department of Psychiatry, Alzheimer's Disease Research Center, James J. Peters VA Medical Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas G Beach
- Department of Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, USA
| | - Wayne Poon
- Department of Neurology, Department of Epidemiology, Institute for Memory Impairments and Neurological Disorders, UC Irvine, Irvine, CA, USA
| | - Claudia H Kawas
- Department of Neurology, Department of Neurobiology and Behavior, Institute for Memory Impairments and Neurological Disorders, UC Irvine, Irvine, CA, USA
| | - María M Corrada
- Department of Neurology, Department of Epidemiology, Institute for Memory Impairments and Neurological Disorders, UC Irvine, Irvine, CA, USA
| | - Robert A Rissman
- Department of Neurosciences University of California and the Veterans Affairs San Diego Healthcare System, La Jolla, San Diego, California, USA
| | - Jeff Metcalf
- Department of Neurosciences University of California and the Veterans Affairs San Diego Healthcare System, La Jolla, San Diego, California, USA
| | - Sara Shuldberg
- Department of Neurosciences University of California and the Veterans Affairs San Diego Healthcare System, La Jolla, San Diego, California, USA
| | - Bahar Salehi
- Department of Neurosciences University of California and the Veterans Affairs San Diego Healthcare System, La Jolla, San Diego, California, USA
| | - Peter T Nelson
- Department of Pathology (Neuropathology) and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - John Q Trojanowski
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Edward B Lee
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - David A Wolk
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Corey T McMillan
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - C Dirk Keene
- Department of Laboratory Medicine and Pathology, University of f Medicine, Seattle, WA, USA
| | - Caitlin S Latimer
- Department of Laboratory Medicine and Pathology, University of f Medicine, Seattle, WA, USA
| | - Thomas J Montine
- Department of Laboratory Medicine and Pathology, University of f Medicine, Seattle, WA, USA
- Department of Pathology, Stanford University, Palo Alto, USA
| | - Gabor G Kovacs
- Laboratory Medicine Program, Krembil Brain Institute, University Health Network, Toronto, ON, Canada
- Tanz Centre for Research in Neurodegenerative Disease and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Institute of Neurology, Medical University of Vienna, Vienna, Austria
| | - Mirjam I Lutz
- Institute of Neurology, Medical University of Vienna, Vienna, Austria
| | - Peter Fischer
- Department of Psychiatry, Danube Hospital, Vienna, Austria
| | - Richard J Perrin
- Department of Pathology and Immunology, Department of Neurology, Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Nigel J Cairns
- College of Medicine and Health, University of Exeter, Exeter, UK
| | - Erin E Franklin
- Department of Pathology and Immunology, Department of Neurology, Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Herbert T Cohen
- Departments of Medicine, Pathology, and Pharmacology, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Towfique Raj
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Inma Cobos
- Department of Pathology, Stanford University, Palo Alto, USA
| | - Bess Frost
- Department of Cell Systems and Anatomy, Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, the Sam and Ann Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Alison Goate
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Charles L White Iii
- Department of Pathology (Neuropathology), University of Texas Southwestern Medical School, Dallas, TX, USA
| | - John F Crary
- Department of Pathology, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place Box 1194, New York, NY, 10029, USA.
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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9
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Brendza R, Lin H, Stark K, Foreman O, Tao J, Pierce A, Ngu H, Shen K, Easton AE, Bhangale T, Chang D, Bingol B, Friedman BA. Genetic ablation of Gpnmb does not alter synuclein-related pathology. Neurobiol Dis 2021; 159:105494. [PMID: 34464706 DOI: 10.1016/j.nbd.2021.105494] [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: 03/14/2021] [Revised: 08/03/2021] [Accepted: 08/26/2021] [Indexed: 11/29/2022] Open
Abstract
The gene GPNMB is known to play roles in phagocytosis and tissue repair, and is upregulated in microglia in many mouse models of neurodegenerative disease as well as in human patients. Nearby genomic variants are associated with both elevated Parkinson's disease (PD) risk and higher expression of this gene, suggesting that inhibiting GPNMB activity might be protective in Parkinson's disease. We tested this hypothesis in three different mouse models of neurological diseases: a remyelination model and two models of alpha-synuclein pathology. We found that Gpnmb deletion had no effect on histological, cellular, behavioral, neurochemical or gene expression phenotypes in any of these models. These data suggest that Gpnmb does not play a major role in the development of pathology or functional defects in these models and that further work is necessary to study its role in the development or progression of Parkinson's disease.
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Affiliation(s)
- Robert Brendza
- Department of Neuroscience, Genentech, Inc., South San Francisco, CA, USA
| | - Han Lin
- Department of Neuroscience, Genentech, Inc., South San Francisco, CA, USA
| | - Kimberly Stark
- Department of Neuroscience, Genentech, Inc., South San Francisco, CA, USA
| | - Oded Foreman
- Department of Pathology, Genentech, Inc., South San Francisco, CA, USA
| | - Janet Tao
- Department of Pathology, Genentech, Inc., South San Francisco, CA, USA
| | - Andrew Pierce
- Department of Pathology, Genentech, Inc., South San Francisco, CA, USA
| | - Hai Ngu
- Department of Pathology, Genentech, Inc., South San Francisco, CA, USA
| | - Kimberle Shen
- Department of Neuroscience, Genentech, Inc., South San Francisco, CA, USA
| | - Amy E Easton
- Department of Neuroscience, Genentech, Inc., South San Francisco, CA, USA
| | - Tushar Bhangale
- Department of Human Genetics, Genentech, Inc., South San Francisco, CA, USA
| | - Diana Chang
- Department of Human Genetics, Genentech, Inc., South San Francisco, CA, USA
| | - Baris Bingol
- Department of Neuroscience, Genentech, Inc., South San Francisco, CA, USA.
| | - Brad A Friedman
- Department of OMNI Bioinformatics, Genentech, Inc., South San Francisco, CA, USA.
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10
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Khan Z, Hammer C, Carroll J, Di Nucci F, Acosta SL, Maiya V, Bhangale T, Hunkapiller J, Mellman I, Albert ML, McCarthy MI, Chandler GS. Genetic variation associated with thyroid autoimmunity shapes the systemic immune response to PD-1 checkpoint blockade. Nat Commun 2021; 12:3355. [PMID: 34099659 PMCID: PMC8184890 DOI: 10.1038/s41467-021-23661-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 05/05/2021] [Indexed: 12/19/2022] Open
Abstract
Activation of systemic immune responses using PD-1 checkpoint inhibitors is an essential approach to cancer therapy. Yet, the extent of benefit relative to risk of immune related adverse events (irAE) varies widely among patients. Here, we study endocrine irAE from 7 clinical trials across 6 cancers where atezolizumab (anti-PD-L1) was combined with chemotherapies and compared to standard of care. We show that atezolizumab-induced thyroid dysfunction is associated with longer survival. We construct a polygenic risk score (PRS) for lifetime risk of hypothyroidism using a GWAS from the UK Biobank and apply this PRS to genetic data collected from 2,616 patients of European ancestry from these trials. Patients with high PRS are at increased risk of atezolizumab-induced thyroid dysfunction and lower risk of death in triple negative breast cancer. Our results indicate that genetic variation associated with thyroid autoimmunity interacts with biological pathways driving the systemic immune response to PD-1 blockade.
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Affiliation(s)
- Zia Khan
- Genentech, South San Francisco, CA, USA.
| | | | | | | | | | | | | | | | | | - Matthew L Albert
- Genentech, South San Francisco, CA, USA
- insitro, South San Francisco, CA, USA
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11
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Orozco LD, Chen HH, Cox C, Katschke KJ, Arceo R, Espiritu C, Caplazi P, Nghiem SS, Chen YJ, Modrusan Z, Dressen A, Goldstein LD, Clarke C, Bhangale T, Yaspan B, Jeanne M, Townsend MJ, van Lookeren Campagne M, Hackney JA. Integration of eQTL and a Single-Cell Atlas in the Human Eye Identifies Causal Genes for Age-Related Macular Degeneration. Cell Rep 2020; 30:1246-1259.e6. [PMID: 31995762 DOI: 10.1016/j.celrep.2019.12.082] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 11/04/2019] [Accepted: 12/19/2019] [Indexed: 12/11/2022] Open
Abstract
Age-related macular degeneration (AMD) is a leading cause of vision loss. To better understand disease pathogenesis and identify causal genes in GWAS loci for AMD risk, we present a comprehensive database of human retina and retinal pigment epithelium (RPE). Our database comprises macular and non-macular RNA sequencing (RNA-seq) profiles from 129 donors, a genome-wide expression quantitative trait loci (eQTL) dataset that includes macula-specific retina and RPE/choroid, and single-nucleus RNA-seq (NucSeq) from human retina and RPE with subtype resolution from more than 100,000 cells. Using NucSeq, we find enriched expression of AMD candidate genes in RPE cells. We identify 15 putative causal genes for AMD on the basis of co-localization of genetic association signals for AMD risk and eye eQTL, including the genes TSPAN10 and TRPM1. These results demonstrate the value of our human eye database for elucidating genetic pathways and potential therapeutic targets for ocular diseases.
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Affiliation(s)
- Luz D Orozco
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA
| | - Hsu-Hsin Chen
- Department of Biomarker Discovery OMNI, Genentech, South San Francisco, CA 94080, USA
| | - Christian Cox
- Department of Immunology Discovery, Genentech, South San Francisco, CA 94080, USA
| | - Kenneth J Katschke
- Department of Immunology Discovery, Genentech, South San Francisco, CA 94080, USA
| | - Rommel Arceo
- Department of Pathology, Genentech, South San Francisco, CA 94080, USA
| | - Carmina Espiritu
- Department of Pathology, Genentech, South San Francisco, CA 94080, USA
| | - Patrick Caplazi
- Department of Pathology, Genentech, South San Francisco, CA 94080, USA
| | | | - Ying-Jiun Chen
- Department of Molecular Biology, Genentech, South San Francisco, CA 94080, USA
| | - Zora Modrusan
- Department of Molecular Biology, Genentech, South San Francisco, CA 94080, USA
| | - Amy Dressen
- Department of Human Genetics, Genentech, South San Francisco, CA 94080, USA
| | - Leonard D Goldstein
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA; Department of Molecular Biology, Genentech, South San Francisco, CA 94080, USA
| | - Christine Clarke
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA
| | - Tushar Bhangale
- Department of Human Genetics, Genentech, South San Francisco, CA 94080, USA
| | - Brian Yaspan
- Department of Human Genetics, Genentech, South San Francisco, CA 94080, USA
| | - Marion Jeanne
- Department of Immunology Discovery, Genentech, South San Francisco, CA 94080, USA
| | - Michael J Townsend
- Department of Biomarker Discovery OMNI, Genentech, South San Francisco, CA 94080, USA.
| | | | - Jason A Hackney
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA.
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12
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Fleck D, Phu L, Verschueren E, Hinkle T, Reichelt M, Bhangale T, Haley B, Wang Y, Graham R, Kirkpatrick DS, Sheng M, Bingol B. PTCD1 Is Required for Mitochondrial Oxidative-Phosphorylation: Possible Genetic Association with Alzheimer's Disease. J Neurosci 2019; 39:4636-4656. [PMID: 30948477 PMCID: PMC6561697 DOI: 10.1523/jneurosci.0116-19.2019] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/26/2019] [Accepted: 03/28/2019] [Indexed: 12/30/2022] Open
Abstract
In addition to amyloid-β plaques and tau tangles, mitochondrial dysfunction is implicated in the pathology of Alzheimer's disease (AD). Neurons heavily rely on mitochondrial function, and deficits in brain energy metabolism are detected early in AD; however, direct human genetic evidence for mitochondrial involvement in AD pathogenesis is limited. We analyzed whole-exome sequencing data of 4549 AD cases and 3332 age-matched controls and discovered that rare protein altering variants in the gene pentatricopeptide repeat-containing protein 1 (PTCD1) show a trend for enrichment in cases compared with controls. We show here that PTCD1 is required for normal mitochondrial rRNA levels, proper assembly of the mitochondrial ribosome and hence for mitochondrial translation and assembly of the electron transport chain. Loss of PTCD1 function impairs oxidative phosphorylation and forces cells to rely on glycolysis for energy production. Cells expressing the AD-linked variant of PTCD1 fail to sustain energy production under increased metabolic stress. In neurons, reduced PTCD1 expression leads to lower ATP levels and impacts spontaneous synaptic activity. Thus, our study uncovers a possible link between a protein required for mitochondrial function and energy metabolism and AD risk.SIGNIFICANCE STATEMENT Mitochondria are the main source of cellular energy and mitochondrial dysfunction is implicated in the pathology of Alzheimer's disease (AD) and other neurodegenerative disorders. Here, we identify a variant in the gene PTCD1 that is enriched in AD patients and demonstrate that PTCD1 is required for ATP generation through oxidative phosphorylation. PTCD1 regulates the level of 16S rRNA, the backbone of the mitoribosome, and is essential for mitochondrial translation and assembly of the electron transport chain. Cells expressing the AD-associated variant fail to maintain adequate ATP production during metabolic stress, and reduced PTCD1 activity disrupts neuronal energy homeostasis and dampens spontaneous transmission. Our work provides a mechanistic link between a protein required for mitochondrial function and genetic AD risk.
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Affiliation(s)
| | - Lilian Phu
- Microchemistry, Proteomics, and Lipidomics
| | | | | | | | | | - Benjamin Haley
- Molecular Biology, Genentech Inc., South San Francisco, California 94080
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13
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Ye CJ, Chen J, Villani AC, Gate RE, Subramaniam M, Bhangale T, Lee MN, Raj T, Raychowdhury R, Li W, Rogel N, Simmons S, Imboywa SH, Chipendo PI, McCabe C, Lee MH, Frohlich IY, Stranger BE, De Jager PL, Regev A, Behrens T, Hacohen N. Genetic analysis of isoform usage in the human anti-viral response reveals influenza-specific regulation of ERAP2 transcripts under balancing selection. Genome Res 2018; 28:1812-1825. [PMID: 30446528 PMCID: PMC6280757 DOI: 10.1101/gr.240390.118] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [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: 06/08/2018] [Accepted: 10/09/2018] [Indexed: 02/02/2023]
Abstract
While genetic variants are known to be associated with overall gene abundance in stimulated immune cells, less is known about their effects on alternative isoform usage. By analyzing RNA-seq profiles of monocyte-derived dendritic cells from 243 individuals, we uncovered thousands of unannotated isoforms synthesized in response to influenza infection and type 1 interferon stimulation. We identified more than a thousand quantitative trait loci (QTLs) associated with alternate isoform usage (isoQTLs), many of which are independent of expression QTLs (eQTLs) for the same gene. Compared with eQTLs, isoQTLs are enriched for splice sites and untranslated regions, but depleted of sequences upstream of annotated transcription start sites. Both eQTLs and isoQTLs explain a significant proportion of the disease heritability attributed to common genetic variants. At the ERAP2 locus, we shed light on the function of the gene and how two frequent, highly differentiated haplotypes with intermediate frequencies could be maintained by balancing selection. At baseline and following type 1 interferon stimulation, the major haplotype is associated with low ERAP2 expression caused by nonsense-mediated decay, while the minor haplotype, known to increase Crohn's disease risk, is associated with high ERAP2 expression. In response to influenza infection, we found two uncharacterized isoforms expressed from the major haplotype, likely the result of multiple perfectly linked variants affecting the transcription and splicing at the locus. Thus, genetic variants at a single locus could modulate independent gene regulatory processes in innate immune responses and, in the case of ERAP2, may confer a historical fitness advantage in response to virus.
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Affiliation(s)
- Chun Jimmie Ye
- Institute for Human Genetics, Institute for Health and Computational Sciences, Department of Biostatistics and Epidemiology, Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94143, USA
| | - Jenny Chen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Alexandra-Chloé Villani
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, Massachusetts 02114, USA
| | - Rachel E Gate
- Institute for Human Genetics, Institute for Health and Computational Sciences, Department of Biostatistics and Epidemiology, Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94143, USA.,Biomedical Informatics Program, University of California, San Francisco, California 94143, USA
| | - Meena Subramaniam
- Institute for Human Genetics, Institute for Health and Computational Sciences, Department of Biostatistics and Epidemiology, Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94143, USA.,Biomedical Informatics Program, University of California, San Francisco, California 94143, USA
| | - Tushar Bhangale
- Genentech Incorporated, South San Francisco, California 94080, USA
| | - Mark N Lee
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, Massachusetts 02114, USA.,Harvard Medical School, Boston, Massachusetts 02116, USA
| | - Towfique Raj
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Harvard Medical School, Boston, Massachusetts 02116, USA.,Departments of Neurology and Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | | | - Weibo Li
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Noga Rogel
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Sean Simmons
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | | | | | - Cristin McCabe
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Departments of Neurology and Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Michelle H Lee
- Harvard Medical School, Boston, Massachusetts 02116, USA
| | | | - Barbara E Stranger
- Section of Genetic Medicine, Department of Medicine, Institute for Genomics and Systems Biology, Center for Data Intensive Science, The University of Chicago, Chicago, Illinois 60637, USA
| | - Philip L De Jager
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Harvard Medical School, Boston, Massachusetts 02116, USA.,Departments of Neurology and Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Tim Behrens
- Genentech Incorporated, South San Francisco, California 94080, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, Massachusetts 02114, USA
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14
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Rathore N, Ramani SR, Pantua H, Payandeh J, Bhangale T, Wuster A, Kapoor M, Sun Y, Kapadia SB, Gonzalez L, Zarrin AA, Goate A, Hansen DV, Behrens TW, Graham RR. Paired Immunoglobulin-like Type 2 Receptor Alpha G78R variant alters ligand binding and confers protection to Alzheimer's disease. PLoS Genet 2018; 14:e1007427. [PMID: 30388101 PMCID: PMC6235402 DOI: 10.1371/journal.pgen.1007427] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [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: 05/16/2018] [Revised: 11/14/2018] [Accepted: 09/26/2018] [Indexed: 12/31/2022] Open
Abstract
Paired Immunoglobulin-like Type 2 Receptor Alpha (PILRA) is a cell surface inhibitory receptor that recognizes specific O-glycosylated proteins and is expressed on various innate immune cell types including microglia. We show here that a common missense variant (G78R, rs1859788) of PILRA is the likely causal allele for the confirmed Alzheimer’s disease risk locus at 7q21 (rs1476679). The G78R variant alters the interaction of residues essential for sialic acid engagement, resulting in >50% reduced binding for several PILRA ligands including a novel ligand, complement component 4A, and herpes simplex virus 1 (HSV-1) glycoprotein B. PILRA is an entry receptor for HSV-1 via glycoprotein B, and macrophages derived from R78 homozygous donors showed significantly decreased levels of HSV-1 infection at several multiplicities of infection compared to homozygous G78 macrophages. We propose that PILRA G78R protects individuals from Alzheimer’s disease risk via reduced inhibitory signaling in microglia and reduced microglial infection during HSV-1 recurrence. Alzheimer’s disease (AD) is a devastating neurodegenerative disorder resulting from a complex interaction of environmental and genetic risk factors. Despite considerable progress in defining the genetic component of AD risk, understanding the biology of common variant associations is a challenge. We find that PILRA G78R (rs1859788) is the likely AD risk variant from the 7q21 locus (rs1476679) and PILRA G78R reduces PILRA endogenous and exogenous ligand binding. Our study highlights a new immune signaling axis in AD and suggests a role for exogenous ligands (HSV-1). Further, we have identified that reduced function of a negative regulator of microglia and neutrophils is protective from AD risk, providing a new candidate therapeutic target.
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Affiliation(s)
- Nisha Rathore
- Department of OMNI Human Genetics, Genentech Inc., South San Francisco, California, United States of America
| | - Sree Ranjani Ramani
- Department of Microchemistry, Proteomics & Lipidomics, Genentech Inc., South San Francisco, California, United States of America
| | - Homer Pantua
- Department of Immunology and Infectious Diseases, Genentech Inc., South San Francisco, California, United States of America
| | - Jian Payandeh
- Department of Structural Biology, Genentech Inc., South San Francisco, California, United States of America
| | - Tushar Bhangale
- Department of OMNI Human Genetics, Genentech Inc., South San Francisco, California, United States of America.,Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, California, United States of America
| | - Arthur Wuster
- Department of OMNI Human Genetics, Genentech Inc., South San Francisco, California, United States of America.,Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, California, United States of America
| | - Manav Kapoor
- Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, New York, United States of America
| | - Yonglian Sun
- Department of Immunology, Genentech Inc., South San Francisco, California, United States of America
| | - Sharookh B Kapadia
- Department of Immunology and Infectious Diseases, Genentech Inc., South San Francisco, California, United States of America
| | - Lino Gonzalez
- Department of Proteomics & Biological Resources, Genentech Inc., South San Francisco, California, United States of America
| | - Ali A Zarrin
- Department of Immunology, Genentech Inc., South San Francisco, California, United States of America
| | - Alison Goate
- Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, New York, United States of America
| | - David V Hansen
- Department of Neuroscience, Genentech Inc., South San Francisco, California, United States of America
| | - Timothy W Behrens
- Department of OMNI Human Genetics, Genentech Inc., South San Francisco, California, United States of America
| | - Robert R Graham
- Department of OMNI Human Genetics, Genentech Inc., South San Francisco, California, United States of America
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15
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Chang D, Choy D, Bhangale T, Wuster A, Khan Z, Dressen A, Cuenco K, Riol Blanco L, Arron JR, Wilson M, Pappu R, Yi T, Lafkas D, Staton T, Cai F, Bauer R, Holweg C, Cheung D, Chen H, Lin J, Abbas A, Matthews J, Olsson J, Reeder J, Mukhyala K, Tom J, Cowgill A, Vogel J, Forrest B, Brauer M, Hunkapiller J, Graham RR, Behrens T, Yaspan B. A whole genome sequencing association study of severe, uncontrolled asthma. Genes Environ 2018. [DOI: 10.1183/13993003.congress-2018.oa2194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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16
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Farrell KW, Iida M, White C, Walker J, Richardson T, Graham R, Bhangale T, Crary J. P4‐247: A PILOT GENETIC STUDY REVEALS CANDIDATE RISK ALLELES FOR PRIMARY AGE‐RELATED TAUOPATHY (PART). Alzheimers Dement 2018. [DOI: 10.1016/j.jalz.2018.07.068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
| | - Megan Iida
- Icahn School of Medicine at Mount SinaiNew YorkNYUSA
| | | | - Jamie Walker
- University of Texas SouthwesternDallasTXUSA
- Northwestern UniversityChicagoILUSA
| | | | | | | | - John Crary
- Icahn School of Medicine at Mount SinaiNew YorkNYUSA
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17
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Mohan V, Radha V, Nguyen TT, Stawiski EW, Pahuja KB, Goldstein LD, Tom J, Anjana RM, Kong-Beltran M, Bhangale T, Jahnavi S, Chandni R, Gayathri V, George P, Zhang N, Murugan S, Phalke S, Chaudhuri S, Gupta R, Zhang J, Santhosh S, Stinson J, Modrusan Z, Ramprasad VL, Seshagiri S, Peterson AS. Comprehensive genomic analysis identifies pathogenic variants in maturity-onset diabetes of the young (MODY) patients in South India. BMC Med Genet 2018; 19:22. [PMID: 29439679 PMCID: PMC5811965 DOI: 10.1186/s12881-018-0528-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 01/19/2018] [Indexed: 12/22/2022]
Abstract
BACKGROUND Maturity-onset diabetes of the young (MODY) is an early-onset, autosomal dominant form of non-insulin dependent diabetes. Genetic diagnosis of MODY can transform patient management. Earlier data on the genetic predisposition to MODY have come primarily from familial studies in populations of European origin. METHODS In this study, we carried out a comprehensive genomic analysis of 289 individuals from India that included 152 clinically diagnosed MODY cases to identify variants in known MODY genes. Further, we have analyzed exome data to identify putative MODY relevant variants in genes previously not implicated in MODY. Functional validation of MODY relevant variants was also performed. RESULTS We found MODY 3 (HNF1A; 7.2%) to be most frequently mutated followed by MODY 12 (ABCC8; 3.3%). They together account for ~ 11% of the cases. In addition to known MODY genes, we report the identification of variants in RFX6, WFS1, AKT2, NKX6-1 that may contribute to development of MODY. Functional assessment of the NKX6-1 variants showed that they are functionally impaired. CONCLUSIONS Our findings showed HNF1A and ABCC8 to be the most frequently mutated MODY genes in south India. Further we provide evidence for additional MODY relevant genes, such as NKX6-1, and these require further validation.
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Affiliation(s)
- Viswanathan Mohan
- Madras Diabetes Research Foundation & Dr. Mohan's Diabetes Specialities Centre, No. 4, Conran Smith Road, Gopalapuram, Chennai, Tamil Nadu, 600 086, India.
| | - Venkatesan Radha
- Madras Diabetes Research Foundation & Dr. Mohan's Diabetes Specialities Centre, No. 4, Conran Smith Road, Gopalapuram, Chennai, Tamil Nadu, 600 086, India
| | - Thong T Nguyen
- Department of Molecular Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Eric W Stawiski
- Department of Molecular Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA.,Department of Bioinformatics and Computational Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Kanika Bajaj Pahuja
- Department of Molecular Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Leonard D Goldstein
- Department of Molecular Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA.,Department of Bioinformatics and Computational Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Jennifer Tom
- Department of Bioinformatics and Computational Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Ranjit Mohan Anjana
- Madras Diabetes Research Foundation & Dr. Mohan's Diabetes Specialities Centre, No. 4, Conran Smith Road, Gopalapuram, Chennai, Tamil Nadu, 600 086, India
| | - Monica Kong-Beltran
- Department of Molecular Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Tushar Bhangale
- Department of Bioinformatics and Computational Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA.,Department of Human Genetics, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Suresh Jahnavi
- Madras Diabetes Research Foundation & Dr. Mohan's Diabetes Specialities Centre, No. 4, Conran Smith Road, Gopalapuram, Chennai, Tamil Nadu, 600 086, India
| | | | - Vijay Gayathri
- Madras Diabetes Research Foundation & Dr. Mohan's Diabetes Specialities Centre, No. 4, Conran Smith Road, Gopalapuram, Chennai, Tamil Nadu, 600 086, India
| | - Paul George
- MedGenome, Bangalore, Karnataka, 560 099, India
| | - Na Zhang
- Department of Molecular Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | | | | | - Subhra Chaudhuri
- Department of Molecular Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Ravi Gupta
- MedGenome, Bangalore, Karnataka, 560 099, India
| | - Jingli Zhang
- Department of Molecular Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | | | - Jeremy Stinson
- Department of Molecular Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Zora Modrusan
- Department of Molecular Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | | | - Somasekar Seshagiri
- Department of Molecular Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA.
| | - Andrew S Peterson
- Department of Molecular Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA.
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Hung T, Pratt GA, Sundararaman B, Townsend MJ, Chaivorapol C, Bhangale T, Graham RR, Ortmann W, Criswell LA, Yeo GW, Behrens TW. The Ro60 autoantigen binds endogenous retroelements and regulates inflammatory gene expression. Science 2015; 350:455-9. [PMID: 26382853 DOI: 10.1126/science.aac7442] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 09/03/2015] [Indexed: 12/16/2022]
Abstract
Autoantibodies target the RNA binding protein Ro60 in systemic lupus erythematosus (SLE) and Sjögren's syndrome. However, it is unclear whether Ro60 and its associated RNAs contribute to disease pathogenesis. We catalogued the Ro60-associated RNAs in human cell lines and found that among other RNAs, Ro60 bound an RNA motif derived from endogenous Alu retroelements. Alu transcripts were induced by type I interferon and stimulated proinflammatory cytokine secretion by human peripheral blood cells. Ro60 deletion resulted in enhanced expression of Alu RNAs and interferon-regulated genes. Anti-Ro60-positive SLE immune complexes contained Alu RNAs, and Alu transcripts were up-regulated in SLE whole blood samples relative to controls. These findings establish a link among the lupus autoantigen Ro60, Alu retroelements, and type I interferon.
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Affiliation(s)
- T Hung
- Genentech, South San Francisco, CA 94080, USA.
| | - G A Pratt
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, Stem Cell Program, University of California at San Diego, Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA 92037, USA
| | - B Sundararaman
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, Stem Cell Program, University of California at San Diego, Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA 92037, USA
| | | | | | - T Bhangale
- Genentech, South San Francisco, CA 94080, USA
| | - R R Graham
- Genentech, South San Francisco, CA 94080, USA
| | - W Ortmann
- Genentech, South San Francisco, CA 94080, USA
| | - L A Criswell
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, University of California, San Francisco, CA 94143, USA
| | - G W Yeo
- Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, Stem Cell Program, University of California at San Diego, Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA 92037, USA. Department of Physiology, National University of Singapore, Singapore. Genome Institute of Singapore and Molecular Engineering Laboratory, Agency for Science, Technology and Research, Singapore.
| | - T W Behrens
- Genentech, South San Francisco, CA 94080, USA.
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19
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Lee JH, Cheng R, Vardarajan B, Lantigua R, Reyes-Dumeyer D, Ortmann W, Graham RR, Bhangale T, Behrens TW, Medrano M, Jiménez-Velázquez IZ, Mayeux R. Genetic Modifiers of Age at Onset in Carriers of the G206A Mutation in PSEN1 With Familial Alzheimer Disease Among Caribbean Hispanics. JAMA Neurol 2015; 72:1043-51. [PMID: 26214276 PMCID: PMC5010776 DOI: 10.1001/jamaneurol.2015.1424] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [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
IMPORTANCE The present study identified potential genetic modifiers that may delay or accelerate age at onset of familial Alzheimer disease (AD) by examining age at onset in PSEN1 mutation carrier families, and further investigation of these modifiers may provide insight into the pathobiology of AD and potential therapeutic measures. OBJECTIVE To identify genetic variants that modify age at onset of AD. DESIGN, SETTING, AND PARTICIPANTS Using a subset of Caribbean Hispanic families that carry the PSEN1 p.G206A mutation, we performed a 2-stage genome study. The mutation carrier families from an ongoing genetic study served as a discovery set, and the cohort of those with LOAD served as a confirmation set. To identify candidate loci, we performed linkage analysis using 5 p.G206A carrier families (n = 56), and we also performed whole-exome association analysis using 31 p.G206A carriers from 26 families. To confirm the genetic modifiers identified from the p.G206A carrier families, we analyzed the GWAS data for 2888 elderly individuals with LOAD. All study participants were Caribbean Hispanics. MAIN OUTCOMES AND MEASURES Age at onset of AD. RESULTS Linkage analysis of AD identified the strongest linkage support at 4q35 (LOD [logarithm of odds] score, 3.69), and the GWAS of age at onset identified variants on 1p13.1, 2q13, 4q25, and 17p11. In the confirmation stage, genewise analysis identified SNX25, PDLIM3, and 3 SH3 domain genes (SORBS2, SH3RF3, and NPHP1) to be significantly associated with LOAD. Subsequent allelic association analysis confirmed SNX25, PDLIM3, and SORBS2 as genetic modifiers of age at onset of EOAD and LOAD and provided modest support for SH3RF3 and NPHP1. CONCLUSIONS AND RELEVANCE Our 2-stage analysis revealed that SNX25, PDLIM3, and SORBS2 may serve as genetic modifiers of age at onset in both EOAD and LOAD.
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Affiliation(s)
- Joseph H. Lee
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, New York2Gertrude H. Sergievsky Center, Columbia University, New York, New York3Department of Epidemiology, School of Public Health, Columbia Univer
| | - Rong Cheng
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, New York2Gertrude H. Sergievsky Center, Columbia University, New York, New York
| | - Badri Vardarajan
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, New York2Gertrude H. Sergievsky Center, Columbia University, New York, New York
| | - Rafael Lantigua
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, New York4Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Dolly Reyes-Dumeyer
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, New York
| | | | | | | | - Timothy W. Behrens
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Martin Medrano
- School of Medicine, Pontificia Universidad Catolica Madre y Maestra, Santiago, Dominican Republic
| | | | - Richard Mayeux
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, New York2Gertrude H. Sergievsky Center, Columbia University, New York, New York3Department of Epidemiology, School of Public Health, Columbia Univer
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20
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Chung SA, Brown EE, Williams AH, Ramos PS, Berthier CC, Bhangale T, Alarcon-Riquelme ME, Behrens TW, Criswell LA, Graham DC, Demirci FY, Edberg JC, Gaffney PM, Harley JB, Jacob CO, Kamboh MI, Kelly JA, Manzi S, Moser-Sivils KL, Russell LP, Petri M, Tsao BP, Vyse TJ, Zidovetzki R, Kretzler M, Kimberly RP, Freedman BI, Graham RR, Langefeld CD. Lupus nephritis susceptibility loci in women with systemic lupus erythematosus. J Am Soc Nephrol 2014; 25:2859-70. [PMID: 24925725 DOI: 10.1681/asn.2013050446] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Lupus nephritis is a manifestation of SLE resulting from glomerular immune complex deposition and inflammation. Lupus nephritis demonstrates familial aggregation and accounts for significant morbidity and mortality. We completed a meta-analysis of three genome-wide association studies of SLE to identify lupus nephritis-predisposing loci. Through genotyping and imputation, >1.6 million markers were assessed in 2000 unrelated women of European descent with SLE (588 patients with lupus nephritis and 1412 patients with lupus without nephritis). Tests of association were computed using logistic regression adjusting for population substructure. The strongest evidence for association was observed outside the MHC and included markers localized to 4q11-q13 (PDGFRA, GSX2; P=4.5×10(-7)), 16p12 (SLC5A11; P=5.1×10(-7)), 6p22 (ID4; P=7.4×10(-7)), and 8q24.12 (HAS2, SNTB1; P=1.1×10(-6)). Both HLA-DR2 and HLA-DR3, two well established lupus susceptibility loci, showed evidence of association with lupus nephritis (P=0.06 and P=3.7×10(-5), respectively). Within the class I region, rs9263871 (C6orf15-HCG22) had the strongest evidence of association with lupus nephritis independent of HLA-DR2 and HLA-DR3 (P=8.5×10(-6)). Consistent with a functional role in lupus nephritis, intra-renal mRNA levels of PDGFRA and associated pathway members showed significant enrichment in patients with lupus nephritis (n=32) compared with controls (n=15). Results from this large-scale genome-wide investigation of lupus nephritis provide evidence of multiple biologically relevant lupus nephritis susceptibility loci.
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Affiliation(s)
- Sharon A Chung
- Division of Rheumatology, Rosalind Russell-Ephraim P. Engleman Medical Research Center for Arthritis, University of California, San Francisco, California
| | - Elizabeth E Brown
- Department of Epidemiology, University of Alabama, Birmingham, Alabama; Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama, Birmingham, Alabama
| | - Adrienne H Williams
- Department of Biostatistical Sciences, Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Paula S Ramos
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Celine C Berthier
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | | | - Marta E Alarcon-Riquelme
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma; Human DNA Variability Area, Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research, Granada, Spain
| | - Timothy W Behrens
- Immunology Tissue Growth and Repair Human Genetics Group, Genentech Inc., South San Francisco, California
| | - Lindsey A Criswell
- Division of Rheumatology, Rosalind Russell-Ephraim P. Engleman Medical Research Center for Arthritis, University of California, San Francisco, California
| | - Deborah Cunninghame Graham
- Divisions of Genetics and Molecular Medicine and Immunology, Infection, and Inflammatory Disease, Kings College, London, United Kingdom
| | - F Yesim Demirci
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jeffrey C Edberg
- Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama, Birmingham, Alabama
| | - Patrick M Gaffney
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma
| | - John B Harley
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma; Division of Rheumatology, Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma; US Department of Veterans Affairs Medical Center, Oklahoma City, Oklahoma
| | - Chaim O Jacob
- Department of Medicine, University of Southern California, Los Angeles, California
| | - M Ilyas Kamboh
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jennifer A Kelly
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma
| | - Susan Manzi
- Department of Medicine, West Penn Allegheny Health System, University of Pittsburgh, Pittsburgh, Pennsylvania; Temple University School of Medicine, Philadelphia, Pennsylvania
| | - Kathy L Moser-Sivils
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma; College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Laurie P Russell
- Department of Biostatistical Sciences, Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Michelle Petri
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Betty P Tsao
- Division of Rheumatology, Department of Medicine, University of California, Los Angeles, California
| | - Tim J Vyse
- Divisions of Genetics and Molecular Medicine and Immunology, Infection, and Inflammatory Disease, Kings College, London, United Kingdom
| | - Raphael Zidovetzki
- Department of Cell Biology and Neuroscience, University of California, Riverside, California; and
| | - Matthias Kretzler
- Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Robert P Kimberly
- Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama, Birmingham, Alabama
| | - Barry I Freedman
- Section on Nephrology, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Robert R Graham
- Immunology Tissue Growth and Repair Human Genetics Group, Genentech Inc., South San Francisco, California
| | - Carl D Langefeld
- Department of Biostatistical Sciences, Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, North Carolina;
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21
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Benitez BA, Jin SC, Guerreiro R, Graham R, Lord J, Harold D, Sims R, Lambert JC, Gibbs JR, Bras J, Sassi C, Harari O, Bertelsen S, Lupton MK, Powell J, Bellenguez C, Brown K, Medway C, Haddick PCG, van der Brug MP, Bhangale T, Ortmann W, Behrens T, Mayeux R, Pericak-Vance MA, Farrer LA, Schellenberg GD, Haines JL, Turton J, Braae A, Barber I, Fagan AM, Holtzman DM, Morris JC, Williams J, Kauwe JS, Amouyel P, Morgan K, Singleton A, Hardy J, Goate AM, Cruchaga C, Singleton A, Hardy J, Goate AM, Cruchaga C. Missense variant in TREML2 protects against Alzheimer's disease. Neurobiol Aging 2014; 35:1510.e19-26. [PMID: 24439484 PMCID: PMC3961557 DOI: 10.1016/j.neurobiolaging.2013.12.010] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 12/09/2013] [Accepted: 12/13/2013] [Indexed: 01/22/2023]
Abstract
TREM and TREM-like receptors are a structurally similar protein family encoded by genes clustered on chromosome 6p21.11. Recent studies have identified a rare coding variant (p.R47H) in TREM2 that confers a high risk for Alzheimer's disease (AD). In addition, common single nucleotide polymorphisms in this genomic region are associated with cerebrospinal fluid biomarkers for AD and a common intergenic variant found near the TREML2 gene has been identified to be protective for AD. However, little is known about the functional variant underlying the latter association or its relationship with the p.R47H. Here, we report comprehensive analyses using whole-exome sequencing data, cerebrospinal fluid biomarker analyses, meta-analyses (16,254 cases and 20,052 controls) and cell-based functional studies to support the role of the TREML2 coding missense variant p.S144G (rs3747742) as a potential driver of the meta-analysis AD-associated genome-wide association studies signal. Additionally, we demonstrate that the protective role of TREML2 in AD is independent of the role of TREM2 gene as a risk factor for AD.
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Affiliation(s)
- Bruno A. Benitez
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Sheng Chih Jin
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Rita Guerreiro
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK,Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Rob Graham
- Diagnostic Discovery Department, Genentech Inc, South San Francisco, CA, USA
| | - Jenny Lord
- Human Genetics, School of Molecular Medical Sciences, University of Nottingham, Nottingham, UK
| | - Denise Harold
- Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Rebecca Sims
- Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Jean-Charles Lambert
- Inserm, Lille, France,Universite Lille 2, Lille, France,Institut Pasteur de Lille, Lille, France
| | - J. Raphael Gibbs
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK,Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Jose Bras
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Celeste Sassi
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK,Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Oscar Harari
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Sarah Bertelsen
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | | | - John Powell
- Institute of Psychiatry, King's College London, London, UK
| | - Celine Bellenguez
- Inserm, Lille, France,Universite Lille 2, Lille, France,Institut Pasteur de Lille, Lille, France
| | - Kristelle Brown
- Human Genetics, School of Molecular Medical Sciences, University of Nottingham, Nottingham, UK
| | - Christopher Medway
- Human Genetics, School of Molecular Medical Sciences, University of Nottingham, Nottingham, UK
| | - Patrick CG. Haddick
- Diagnostic Discovery Department, Genentech Inc, South San Francisco, CA, USA
| | | | - Tushar Bhangale
- Department of Bioinformatics and Computational Biology, Genentech Inc, South San Francisco, CA, USA
| | - Ward Ortmann
- Human Genetics Department, Genentech Inc, South San Francisco, CA, USA
| | - Tim Behrens
- Human Genetics Department, Genentech Inc, South San Francisco, CA, USA
| | - Richard Mayeux
- Department of Neurology, Taub Institute on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA,Gertrude H. Sergievsky Center, Columbia University, New York, NY, USA
| | - Margaret A. Pericak-Vance
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA,Dr John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, USA
| | - Lindsay A. Farrer
- Department of Medicine, Boston University Schools of Medicine and Public Health, Boston, MA, USA,Department of Biomedical Genetics, Boston University Schools of Medicine and Public Health, Boston, MA, USA,Department of Neurology, Boston University Schools of Medicine and Public Health, Boston, MA, USA,Department of Ophthalmology, Boston University Schools of Medicine and Public Health, Boston, MA, USA,Department of Epidemiology, Boston University Schools of Medicine and Public Health, Boston, MA, USA,Department of Biostatistics, Boston University Schools of Medicine and Public Health, Boston, MA, USA
| | - Gerard D. Schellenberg
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Jonathan L. Haines
- Department of Molecular Physiology and Biophysics, Vanderbilt Center for Human Genetics Research, Vanderbilt University, Nashville, TN, USA
| | - Jim Turton
- Human Genetics, School of Molecular Medical Sciences, University of Nottingham, Nottingham, UK
| | - Anne Braae
- Human Genetics, School of Molecular Medical Sciences, University of Nottingham, Nottingham, UK
| | - Imelda Barber
- Human Genetics, School of Molecular Medical Sciences, University of Nottingham, Nottingham, UK
| | - Anne M. Fagan
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA,Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA,Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - David M. Holtzman
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA,Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA,Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA,Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | - John C. Morris
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA,Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA,Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Julie Williams
- Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - John S.K. Kauwe
- Department of Biology, Brigham Young University, Provo, UT, USA
| | - Philippe Amouyel
- Inserm, Lille, France,Universite Lille 2, Lille, France,Institut Pasteur de Lille, Lille, France
| | - Kevin Morgan
- Human Genetics, School of Molecular Medical Sciences, University of Nottingham, Nottingham, UK
| | - Andy Singleton
- Human Genetics Department, Genentech Inc, South San Francisco, CA, USA
| | - John Hardy
- Human Genetics Department, Genentech Inc, South San Francisco, CA, USA
| | - Alison M. Goate
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA,Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA,Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA,Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA,Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA,Alternate corresponding author at: Department of Psychiatry, Washington University School of Medicine, 660 South Euclid Avenue B8134, St. Louis, MO 63110, USA. Tel.: +314 286 0546; fax: +314 747 2983.
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA; Universite Lille 2, Lille, France.
| | - Andy Singleton
- Human Genetics Department, Genentech Inc, South San Francisco, CA, USA
| | - John Hardy
- Human Genetics Department, Genentech Inc, South San Francisco, CA, USA
| | - Alison M Goate
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA; Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA; Knight Alzheimer's Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA.
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, USA; Universite Lille 2, Lille, France.
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22
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Lee J, Cheng R, Ortmann W, Lantigua R, Graham R, Bhangale T, Perez‐Horta G, Medrano M, Behrens T, Mayeux R. O4–06–01: Genetic modifiers in early‐onset familial Alzheimer's disease in Caribbean Hispanics. Alzheimers Dement 2013. [DOI: 10.1016/j.jalz.2013.04.365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Joseph Lee
- Columbia University, College of Physicians and Surgeons New York New York United States
| | - Rong Cheng
- Columbia University, College of Physicians and Surgeons New York New York United States
| | - Ward Ortmann
- Genentech South San Francisco California United States
| | | | - Robert Graham
- Genentech South San Francisco California United States
| | | | | | - Martin Medrano
- Pontificia Universidad Catolica Madre y Maestra Santiago Dominican Republic
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23
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Gogarten SM, Bhangale T, Conomos MP, Laurie CA, McHugh CP, Painter I, Zheng X, Crosslin DR, Levine D, Lumley T, Nelson SC, Rice K, Shen J, Swarnkar R, Weir BS, Laurie CC. GWASTools: an R/Bioconductor package for quality control and analysis of genome-wide association studies. Bioinformatics 2012; 28:3329-31. [PMID: 23052040 DOI: 10.1093/bioinformatics/bts610] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
GWASTools is an R/Bioconductor package for quality control and analysis of genome-wide association studies (GWAS). GWASTools brings the interactive capability and extensive statistical libraries of R to GWAS. Data are stored in NetCDF format to accommodate extremely large datasets that cannot fit within R's memory limits. The documentation includes instructions for converting data from multiple formats, including variants called from sequencing. GWASTools provides a convenient interface for linking genotypes and intensity data with sample and single nucleotide polymorphism annotation.
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Lanktree M, Guo Y, Murtaza M, Glessner J, Bailey S, Onland-Moret N, Lettre G, Ongen H, Rajagopalan R, Johnson T, Shen H, Nelson C, Klopp N, Baumert J, Padmanabhan S, Pankratz N, Pankow J, Shah S, Taylor K, Barnard J, Peters B, Maloney C, Lobmeyer M, Stanton A, Zafarmand M, Romaine S, Mehta A, van Iperen E, Gong Y, Price T, Smith E, Kim C, Li Y, Asselbergs F, Atwood L, Bailey K, Bhatt D, Bauer F, Behr E, Bhangale T, Boer J, Boehm B, Bradfield J, Brown M, Braund P, Burton P, Carty C, Chandrupatla H, Chen W, Connell J, Dalgeorgou C, de Boer A, Drenos F, Elbers C, Fang J, Fox C, Frackelton E, Fuchs B, Furlong C, Gibson Q, Gieger C, Goel A, Grobbee D, Hastie C, Howard P, Huang GH, Johnson W, Li Q, Kleber M, Klein B, Klein R, Kooperberg C, Ky B, LaCroix A, Lanken P, Lathrop M, Li M, Marshall V, Melander O, Mentch F, Meyer N, Monda K, Montpetit A, Murugesan G, Nakayama K, Nondahl D, Onipinla A, Rafelt S, Newhouse S, Otieno F, Patel S, Putt M, Rodriguez S, Safa R, Sawyer D, Schreiner P, Simpson C, Sivapalaratnam S, Srinivasan S, Suver C, Swergold G, Sweitzer N, Thomas K, Thorand B, Timpson N, Tischfield S, Tobin M, Tomaszewski M, Verschuren W, Wallace C, Winkelmann B, Zhang H, Zheng D, Zhang L, Zmuda J, Clarke R, Balmforth A, Danesh J, Day I, Schork N, de Bakker P, Delles C, Duggan D, Hingorani A, Hirschhorn J, Hofker M, Humphries S, Kivimaki M, Lawlor D, Kottke-Marchant K, Mega J, Mitchell B, Morrow D, Palmen J, Redline S, Shields D, Shuldiner A, Sleiman P, Smith G, Farrall M, Jamshidi Y, Christiani D, Casas J, Hall A, Doevendans P, Christie J, Berenson G, Murray S, Illig T, Dorn G, Cappola T, Boerwinkle E, Sever P, Rader D, Reilly M, Caulfield M, Talmud P, Topol E, Engert J, Wang K, Dominiczak A, Hamsten A, Curtis S, Silverstein R, Lange L, Sabatine M, Trip M, Saleheen D, Peden J, Cruickshanks K, März W, O'Connell J, Klungel O, Wijmenga C, Maitland-van der Zee A, Schadt E, Johnson J, Jarvik G, Papanicolaou G, Grant S, Munroe P, North K, Samani N, Koenig W, Gaunt T, Anand S, van der Schouw Y, Soranzo N, FitzGerald G, Reiner A, Hegele R, Hakonarson H, Keating B. Meta-analysis of Dense Genecentric Association Studies Reveals Common and Uncommon Variants Associated with Height. Am J Hum Genet 2012. [DOI: 10.1016/j.ajhg.2012.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Saxena R, Elbers C, Guo Y, Peter I, Gaunt T, Mega J, Lanktree M, Tare A, Castillo B, Li Y, Johnson T, Bruinenberg M, Gilbert-Diamond D, Rajagopalan R, Voight B, Balasubramanyam A, Barnard J, Bauer F, Baumert J, Bhangale T, Böhm B, Braund P, Burton P, Chandrupatla H, Clarke R, Cooper-DeHoff R, Crook E, Davey-Smith G, Day I, de Boer A, de Groot MC, Drenos F, Ferguson J, Fox C, Furlong C, Gibson Q, Gieger C, Gilhuijs-Pederson L, Glessner J, Goel A, Gong Y, Grant S, Grobbee D, Hastie C, Humphries S, Kim C, Kivimaki M, Kleber M, Meisinger C, Kumari M, Langaee T, Lawlor D, Li M, Lobmeyer M, Maitland-van der Zee AH, Meijs M, Molony C, Morrow D, Murugesan G, Musani S, Nelson C, Newhouse S, O'Connell J, Padmanabhan S, Palmen J, Patel S, Pepine C, Pettinger M, Price T, Rafelt S, Ranchalis J, Rasheed A, Rosenthal E, Ruczinski I, Shah S, Shen H, Silbernagel G, Smith E, Spijkerman A, Stanton A, Steffes M, Thorand B, Trip M, van der Harst P, van der A D, van Iperen E, van Setten J, van Vliet-Ostaptchouk J, Verweij N, Wolffenbuttel B, Young T, Hadi Zafarmand M, Zmuda J, Boehnke M, Altshuler D, McCarthy M, Linda Kao W, Pankow J, Cappola T, Sever P, Poulter N, Caulfield M, Dominiczak A, Shields D, Bhatt D, Zhang L, Curtis S, Danesh J, Casas J, van der Schouw Y, Onland-Moret N, Doevendans P, Dorn G, Farrall M, FitzGerald G, Robert Hegele A, Hingorani A, Hofker M, Huggins G, Illig T, Jarvik G, Johnson J, Klungel O, Knowler W, Koenig W, März W, Meigs J, Melander O, Munroe P, Mitchell B, Bielinski S, Rader D, Reilly M, Rich S, Rotter J, Saleheen D, Samani N, Schadt E, Shuldiner A, Silverstein R, Kottke-Marchant K, Talmud P, Watkins H, Asselbergs F, de Bakker P, McCaffery J, Wijmenga C, Sabatine M, Wilson J, Reiner A, Bowden D, Hakonarson H, Siscovick D, Keating B. Large-Scale Gene-Centric Meta-Analysis across 39 Studies Identifies Type 2 Diabetes Loci. Am J Hum Genet 2012. [DOI: 10.1016/j.ajhg.2012.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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Saxena R, Elbers C, Guo Y, Peter I, Gaunt T, Mega J, Lanktree M, Tare A, Castillo B, Li Y, Johnson T, Bruinenberg M, Gilbert-Diamond D, Rajagopalan R, Voight B, Balasubramanyam A, Barnard J, Bauer F, Baumert J, Bhangale T, Böhm B, Braund P, Burton P, Chandrupatla H, Clarke R, Cooper-DeHoff R, Crook E, Davey-Smith G, Day I, de Boer A, de Groot M, Drenos F, Ferguson J, Fox C, Furlong C, Gibson Q, Gieger C, Gilhuijs-Pederson L, Glessner J, Goel A, Gong Y, Grant S, Grobbee D, Hastie C, Humphries S, Kim C, Kivimaki M, Kleber M, Meisinger C, Kumari M, Langaee T, Lawlor D, Li M, Lobmeyer M, Maitland-van der Zee AH, Meijs M, Molony C, Morrow D, Murugesan G, Musani S, Nelson C, Newhouse S, O'Connell J, Padmanabhan S, Palmen J, Patel S, Pepine C, Pettinger M, Price T, Rafelt S, Ranchalis J, Rasheed A, Rosenthal E, Ruczinski I, Shah S, Shen H, Silbernagel G, Smith E, Spijkerman A, Stanton A, Steffes M, Thorand B, Trip M, van der Harst P, van der A D, van Iperen E, van Setten J, van Vliet-Ostaptchouk J, Verweij N, Wolffenbuttel B, Young T, Zafarmand M, Zmuda J, Boehnke M, Altshuler D, McCarthy M, Kao W, Pankow J, Cappola T, Sever P, Poulter N, Caulfield M, Dominiczak A, Shields D, Bhatt DL, Zhang L, Curtis S, Danesh J, Casas J, van der Schouw Y, Onland-Moret N, Doevendans P, Dorn G, Farrall M, FitzGerald G, Hamsten A, Hegele R, Hingorani A, Hofker M, Huggins G, Illig T, Jarvik G, Johnson J, Klungel O, Knowler W, Koenig W, März W, Meigs J, Melander O, Munroe P, Mitchell B, Bielinski S, Rader D, Reilly M, Rich S, Rotter J, Saleheen D, Samani N, Schadt E, Shuldiner A, Silverstein R, Kottke-Marchant K, Talmud P, Watkins H, Asselbergs FW, de Bakker P, McCaffery J, Wijmenga C, Sabatine M, Wilson J, Reiner A, Bowden D, Hakonarson H, Siscovick D, Keating B. Large-scale gene-centric meta-analysis across 39 studies identifies type 2 diabetes loci. Am J Hum Genet 2012; 90:410-25. [PMID: 22325160 PMCID: PMC3309185 DOI: 10.1016/j.ajhg.2011.12.022] [Citation(s) in RCA: 195] [Impact Index Per Article: 16.3] [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: 08/22/2011] [Revised: 12/06/2011] [Accepted: 12/31/2011] [Indexed: 01/12/2023] Open
Abstract
To identify genetic factors contributing to type 2 diabetes (T2D), we performed large-scale meta-analyses by using a custom ∼50,000 SNP genotyping array (the ITMAT-Broad-CARe array) with ∼2000 candidate genes in 39 multiethnic population-based studies, case-control studies, and clinical trials totaling 17,418 cases and 70,298 controls. First, meta-analysis of 25 studies comprising 14,073 cases and 57,489 controls of European descent confirmed eight established T2D loci at genome-wide significance. In silico follow-up analysis of putative association signals found in independent genome-wide association studies (including 8,130 cases and 38,987 controls) performed by the DIAGRAM consortium identified a T2D locus at genome-wide significance (GATAD2A/CILP2/PBX4; p = 5.7 × 10(-9)) and two loci exceeding study-wide significance (SREBF1, and TH/INS; p < 2.4 × 10(-6)). Second, meta-analyses of 1,986 cases and 7,695 controls from eight African-American studies identified study-wide-significant (p = 2.4 × 10(-7)) variants in HMGA2 and replicated variants in TCF7L2 (p = 5.1 × 10(-15)). Third, conditional analysis revealed multiple known and novel independent signals within five T2D-associated genes in samples of European ancestry and within HMGA2 in African-American samples. Fourth, a multiethnic meta-analysis of all 39 studies identified T2D-associated variants in BCL2 (p = 2.1 × 10(-8)). Finally, a composite genetic score of SNPs from new and established T2D signals was significantly associated with increased risk of diabetes in African-American, Hispanic, and Asian populations. In summary, large-scale meta-analysis involving a dense gene-centric approach has uncovered additional loci and variants that contribute to T2D risk and suggests substantial overlap of T2D association signals across multiple ethnic groups.
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Affiliation(s)
- Richa Saxena
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Clara C. Elbers
- Department of Genetics, University of Pennsylvania, School of Medicine, Philadelphia, PA 19104, USA
- Complex Genetics Section, Department of Medical Genetics, University Medical Center Utrecht, The Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, The Netherlands
| | - Yiran Guo
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- BGI Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, NY 10029 USA
| | - Tom R. Gaunt
- Medical Research Council Centre for Causal Analyses in Translational Epidemiology, Department of Social Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Jessica L. Mega
- Thrombolysis in Myocardial Infarction Study Group, Cardiovascular Division, Brigham and Women's Hospital, Boston, MA 021155 USA
| | - Matthew B. Lanktree
- Department of Biochemistry, University of Western Ontario, London, ON N6A 5C1, Canada
| | - Archana Tare
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
| | - Berta Almoguera Castillo
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Servicio de Genética Instituto de Investigación Sanitaria-Fundación Jiménez Díaz, Avda. Reyes Católicos 228040, Madrid, Spain
| | - Yun R. Li
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Toby Johnson
- Clinical Pharmacology, Barts and the London Genome Centre, Queen Mary University of London, London EC1M 6BQ, UK
- William Harvey Research Institute, Barts and the London School of Medicine, Queen Mary University of London, London EC1M 6BQ, UK
| | - Marcel Bruinenberg
- LifeLines Cohort Study and Biobank, University Medical Center Groningen, University of Groningen, the Netherlands
| | - Diane Gilbert-Diamond
- Children's Environmental Health and Disease Prevention Center at Dartmouth, Hanover, NH 03755, USA
- Section of Biostatistics and Epidemiology, Department of Community and Family Medicine, Dartmouth Medical School, Hanover, NH 03756, USA
| | | | - Benjamin F. Voight
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
| | - Ashok Balasubramanyam
- Translational Metabolism Unit, Division of Diabetes, Endocrinology and Metabolism, Baylor College of Medicine, Houston, TX 77030, USA
| | - John Barnard
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Florianne Bauer
- Complex Genetics Section, Department of Medical Genetics, University Medical Center Utrecht, The Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, The Netherlands
| | - Jens Baumert
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Tushar Bhangale
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Bernhard O. Böhm
- Cardiology Group Frankfurt-Sachsenhausen, Frankfurt 60598, Germany
| | - Peter S. Braund
- Department of Cardiovascular Sciences, University of Leicester, Glenfield Hospital, Leicester, LE3 9QP, UK
| | - Paul R. Burton
- Department of Health Sciences, University of Leicester, University Rd, Leicester LE1 7RH, UK
| | - Hareesh R. Chandrupatla
- Cardiovascular Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Robert Clarke
- Clinical Trial Service Unit, Richard Doll Building, Old Road Campus, Roosevelt Drive, Oxford OX37LF, UK
| | - Rhonda M. Cooper-DeHoff
- Department of Pharmacotherapy and Translational Research, University of Florida College of Pharmacy, Gainesville, FL 32610, USA
- Division of Cardiovascular Medicine, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | | | - George Davey-Smith
- Medical Research Council Centre for Causal Analyses in Translational Epidemiology, Department of Social Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Ian N. Day
- Medical Research Council Centre for Causal Analyses in Translational Epidemiology, Department of Social Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Anthonius de Boer
- Division of Pharmacoepidemiology and Clinical Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Mark C.H. de Groot
- Division of Pharmacoepidemiology and Clinical Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Fotios Drenos
- Centre for Cardiovascular Genetics, Department of Medicine, University College London, 5 University Street, London, WC1E 6JF, UK
| | - Jane Ferguson
- Cardiovascular Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Caroline S. Fox
- Framingham Heart Study, Boston University School of Medicine, Boston, MA 02118, USA
| | - Clement E. Furlong
- Department of Medicine (Medical Genetics), University of Washington, Seattle, WA 98195, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Quince Gibson
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Lisa A. Gilhuijs-Pederson
- Division of Pharmacoepidemiology and Clinical Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Joseph T. Glessner
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Anuj Goel
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Yan Gong
- Division of Cardiovascular Medicine, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Struan F.A. Grant
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Diederick E. Grobbee
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, The Netherlands
| | - Claire Hastie
- British Heart Foundation Glasgow Cardiovascular Research Centre, Division of Cardiovascular and Medical Sciences, Western Infirmary, University of Glasgow, Glasgow G12 8TA, UK
| | - Steve E. Humphries
- Centre for Cardiovascular Genetics, Department of Medicine, University College London, 5 University Street, London, WC1E 6JF, UK
| | - Cecilia E. Kim
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Mika Kivimaki
- Department of Epidemiology and Public Health, University College London, London, UK
- Genetic Epidemiology Group, Department of Epidemiology and Public Health, University College London, London WC1E 6BT, UK
| | - Marcus Kleber
- LURIC Study, Freiburg im Breisgau 79098, Germany
- Synlab Center of Laboratory Diagnostics Heidelberg, Heidelberg 69037, Germany
| | - Christa Meisinger
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Meena Kumari
- Genetic Epidemiology Group, Department of Epidemiology and Public Health, University College London, London WC1E 6BT, UK
| | - Taimour Y. Langaee
- Department of Pharmacotherapy and Translational Research, University of Florida College of Pharmacy, Gainesville, FL 32610, USA
| | - Debbie A. Lawlor
- Medical Research Council Centre for Causal Analyses in Translational Epidemiology, Department of Social Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Mingyao Li
- Cardiovascular Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Maximilian T. Lobmeyer
- Division of Cardiovascular Medicine, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Anke-Hilse Maitland-van der Zee
- Division of Pharmacoepidemiology and Clinical Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Matthijs F.L. Meijs
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Cliona M. Molony
- Department of Genetics, Rosetta Inpharmatics, Seattle, WA 98109, USA
| | - David A. Morrow
- Thrombolysis in Myocardial Infarction Study Group, Cardiovascular Division, Brigham and Women's Hospital, Boston, MA 021155 USA
| | - Gurunathan Murugesan
- Department of Clinical Pathology, Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH 44106, USA
| | - Solomon K. Musani
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Christopher P. Nelson
- Department of Cardiovascular Sciences, University of Leicester, Glenfield Hospital, Leicester, LE3 9QP, UK
| | - Stephen J. Newhouse
- Clinical Pharmacology, Barts and the London Genome Centre, Queen Mary University of London, London EC1M 6BQ, UK
- William Harvey Research Institute, Barts and the London School of Medicine, Queen Mary University of London, London EC1M 6BQ, UK
| | - Jeffery R. O'Connell
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Sandosh Padmanabhan
- British Heart Foundation Glasgow Cardiovascular Research Centre, Division of Cardiovascular and Medical Sciences, Western Infirmary, University of Glasgow, Glasgow G12 8TA, UK
| | - Jutta Palmen
- Centre for Cardiovascular Genetics, Department of Medicine, University College London, 5 University Street, London, WC1E 6JF, UK
| | - Sanjey R. Patel
- Division of Sleep Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Carl J. Pepine
- Division of Cardiovascular Medicine, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Mary Pettinger
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Thomas S. Price
- Medical Research Council Social, Genetic, and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London WC2R 2LS, UK
| | - Suzanne Rafelt
- Department of Cardiovascular Sciences, University of Leicester, Glenfield Hospital, Leicester, LE3 9QP, UK
| | - Jane Ranchalis
- Department of Medicine (Medical Genetics), University of Washington, Seattle, WA 98195, USA
| | - Asif Rasheed
- Center for Non-Communicable Diseases, Karachi, Pakistan
| | - Elisabeth Rosenthal
- Department of Medicine (Medical Genetics), University of Washington, Seattle, WA 98195, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Sonia Shah
- University College Genetics Institute, University College London, 5 University St London, WC1E 6BT, UK
| | - Haiqing Shen
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Günther Silbernagel
- Division of Endocrinology, Diabetology, Nephrology, Vascular Disease, and Clinical Chemistry, Department of Internal Medicine, Eberhard-Karls-University Tübingen, Tübingen 72074, Germany
| | | | | | - Alice Stanton
- Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Michael W. Steffes
- Department of Laboratory Medicine and Pathology, Medical School, University of Minnesota, Minneapolis, MN 55455, USA
| | - Barbara Thorand
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Mieke Trip
- Department of Vascular Medicine, Academic Medical Center, Amsterdam, The Netherlands
| | - Pim van der Harst
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University Medical Center Groningen and Groningen University, 9700 RB Groningen, The Netherlands
| | - Daphne L. van der A
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | | | - Jessica van Setten
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jana V. van Vliet-Ostaptchouk
- Molecular Genetics, Department of Pathology and Medical Biology, University Medical Center Groningen and University of Groningen, The Netherlands
- Department of Endocrinology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Niek Verweij
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Bruce H.R. Wolffenbuttel
- Department of Internal Medicine, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Taylor Young
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
| | - M. Hadi Zafarmand
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Joseph M. Zmuda
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, 130 DeSoto St, Pittsburgh, PA 15261, USA
| | | | | | - Michael Boehnke
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - David Altshuler
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Mark McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford OX3 7LJ, UK
| | - W.H. Linda Kao
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21287, USA
| | - James S. Pankow
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN 55454, USA
| | - Thomas P. Cappola
- Cardiovascular Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Peter Sever
- International Centre for Circulatory Health, Imperial College London, London W2 1PG, UK
| | - Neil Poulter
- International Centre for Circulatory Health, Imperial College London, London W2 1PG, UK
| | - Mark Caulfield
- Clinical Pharmacology, Barts and the London Genome Centre, Queen Mary University of London, London EC1M 6BQ, UK
- William Harvey Research Institute, Barts and the London School of Medicine, Queen Mary University of London, London EC1M 6BQ, UK
| | - Anna Dominiczak
- British Heart Foundation Glasgow Cardiovascular Research Centre, Division of Cardiovascular and Medical Sciences, Western Infirmary, University of Glasgow, Glasgow G12 8TA, UK
| | - Denis C. Shields
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | | | - Li Zhang
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Sean P. Curtis
- Merck Research Laboratories, P.O. Box 2000, Rahway, NJ 07065, USA
| | - John Danesh
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Juan P. Casas
- Department of Epidemiology and Public Health, University College London, London, UK
- Department of Non-communicable Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Yvonne T. van der Schouw
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, The Netherlands
| | - N. Charlotte Onland-Moret
- Complex Genetics Section, Department of Medical Genetics, University Medical Center Utrecht, The Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, The Netherlands
| | - Pieter A. Doevendans
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Gerald W. Dorn
- Washington University Center for Pharmacogenetics, 660 S. Euclid Ave, Campus Box 8220, St. Louis, MO 63110, USA
| | - Martin Farrall
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Department of Cardiovascular Medicine, University of Oxford, Level 6 West Wing, John Radcliffe Hospital, Headley Way, Headington, Oxford OX3 9DU, UK
| | - Garret A. FitzGerald
- The Institute for Translational Medicine and Therapeutics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19146, USA
| | - Anders Hamsten
- Cardiovascular Genetics Group, Atherosclerosis Research Unit, Department of Medicine Solna, Karolinska Institutet, SE-17176 Stockholm, Sweden
| | - Robert Hegele
- Department of Biochemistry, University of Western Ontario, London, ON N6A 5C1, Canada
| | - Aroon D. Hingorani
- Centre for Clinical Pharmacology, Department of Medicine, University College London, London WC1E 6JF, UK
| | - Marten H. Hofker
- University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Gordon S. Huggins
- Molecular Cardiology Research Institute, Center for Translational Genomics, Tufts Medical Center and Tufts University, Boston, MA 02114, USA
| | - Thomas Illig
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Hannover Unified Biobank, Hannover Medical School, 30625 Hannover, Germany
| | - Gail P. Jarvik
- Department of Medicine (Medical Genetics), University of Washington, Seattle, WA 98195, USA
| | - Julie A. Johnson
- Department of Pharmacotherapy and Translational Research, University of Florida College of Pharmacy, Gainesville, FL 32610, USA
- Division of Cardiovascular Medicine, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Olaf H. Klungel
- Division of Pharmacoepidemiology and Clinical Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - William C. Knowler
- National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ 85104, USA
| | - Wolfgang Koenig
- Department of Internal Medicine II-Cardiology, University of Ulm Medical Center, Ulm, Germany
| | - Winfried März
- Synlab Center of Laboratory Diagnostics Heidelberg, Heidelberg 69037, Germany
- Mannheim Institute of Public Health, Social and Preventive Medicine, Medical Faculty Mannheim, University of Heidelberg D-68167 Mannheim, Germany
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, 8010 Graz, Austria
| | - James B. Meigs
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- General Medicine Division, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Olle Melander
- Clinical Research Center, Malmö University Hospital, Malmö SE-205 02, Sweden
| | - Patricia B. Munroe
- Clinical Pharmacology, Barts and the London Genome Centre, Queen Mary University of London, London EC1M 6BQ, UK
- William Harvey Research Institute, Barts and the London School of Medicine, Queen Mary University of London, London EC1M 6BQ, UK
| | - Braxton D. Mitchell
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Susan J. Bielinski
- Division of Epidemiology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Daniel J. Rader
- Cardiovascular Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Muredach P. Reilly
- Cardiovascular Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22902, USA
| | - Jerome I. Rotter
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Danish Saleheen
- Center for Non-Communicable Diseases, Karachi, Pakistan
- Merck Research Laboratories, P.O. Box 2000, Rahway, NJ 07065, USA
| | - Nilesh J. Samani
- Department of Cardiovascular Sciences, University of Leicester, Glenfield Hospital, Leicester, LE3 9QP, UK
| | | | - Alan R. Shuldiner
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Roy Silverstein
- Department of Cell Biology, Lerner Research Institute, Cleveland Clinic Foundation, Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, 9500 Euclid Avenue Cleveland, OH 44195, USA
| | | | - Philippa J. Talmud
- Centre for Cardiovascular Genetics, Department of Medicine, University College London, 5 University Street, London, WC1E 6JF, UK
| | - Hugh Watkins
- Washington University Center for Pharmacogenetics, 660 S. Euclid Ave, Campus Box 8220, St. Louis, MO 63110, USA
| | - Folkert W. Asselbergs
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, The Netherlands
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Paul I.W. de Bakker
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
- Complex Genetics Section, Department of Medical Genetics, University Medical Center Utrecht, The Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, The Netherlands
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jeanne McCaffery
- Weight Control and Diabetes Research Center, The Miriam Hospital and Warren Alpert School of Medicine at Brown University, Providence, RI 02906, USA
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen and Groningen University, 9700 RB Groningen, The Netherlands
| | - Marc S. Sabatine
- Thrombolysis in Myocardial Infarction Study Group, Cardiovascular Division, Brigham and Women's Hospital, Boston, MA 021155 USA
| | - James G. Wilson
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Alex Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Donald W. Bowden
- Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, NC 27106, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Human Genetics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - David S. Siscovick
- Cardiovascular Health Research Unit, Departments of Medicine and Epidemiology, University of Washington, Seattle, WA 98101, USA
| | - Brendan J. Keating
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Human Genetics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
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27
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Laurie CC, Doheny KF, Mirel DB, Pugh EW, Bierut LJ, Bhangale T, Boehm F, Caporaso NE, Cornelis MC, Edenberg HJ, Gabriel SB, Harris EL, Hu FB, Jacobs KB, Kraft P, Landi MT, Lumley T, Manolio TA, McHugh C, Painter I, Paschall J, Rice JP, Rice KM, Zheng X, Weir BS. Quality control and quality assurance in genotypic data for genome-wide association studies. Genet Epidemiol 2011; 34:591-602. [PMID: 20718045 DOI: 10.1002/gepi.20516] [Citation(s) in RCA: 318] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Genome-wide scans of nucleotide variation in human subjects are providing an increasing number of replicated associations with complex disease traits. Most of the variants detected have small effects and, collectively, they account for a small fraction of the total genetic variance. Very large sample sizes are required to identify and validate findings. In this situation, even small sources of systematic or random error can cause spurious results or obscure real effects. The need for careful attention to data quality has been appreciated for some time in this field, and a number of strategies for quality control and quality assurance (QC/QA) have been developed. Here we extend these methods and describe a system of QC/QA for genotypic data in genome-wide association studies (GWAS). This system includes some new approaches that (1) combine analysis of allelic probe intensities and called genotypes to distinguish gender misidentification from sex chromosome aberrations, (2) detect autosomal chromosome aberrations that may affect genotype calling accuracy, (3) infer DNA sample quality from relatedness and allelic intensities, (4) use duplicate concordance to infer SNP quality, (5) detect genotyping artifacts from dependence of Hardy-Weinberg equilibrium test P-values on allelic frequency, and (6) demonstrate sensitivity of principal components analysis to SNP selection. The methods are illustrated with examples from the "Gene Environment Association Studies" (GENEVA) program. The results suggest several recommendations for QC/QA in the design and execution of GWAS.
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Affiliation(s)
- Cathy C Laurie
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
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28
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Keating BJ, Tischfield S, Murray SS, Bhangale T, Price TS, Glessner JT, Galver L, Barrett JC, Grant SFA, Farlow DN, Chandrupatla HR, Hansen M, Ajmal S, Papanicolaou GJ, Guo Y, Li M, DerOhannessian S, de Bakker PIW, Bailey SD, Montpetit A, Edmondson AC, Taylor K, Gai X, Wang SS, Fornage M, Shaikh T, Groop L, Boehnke M, Hall AS, Hattersley AT, Frackelton E, Patterson N, Chiang CWK, Kim CE, Fabsitz RR, Ouwehand W, Price AL, Munroe P, Caulfield M, Drake T, Boerwinkle E, Reich D, Whitehead AS, Cappola TP, Samani NJ, Lusis AJ, Schadt E, Wilson JG, Koenig W, McCarthy MI, Kathiresan S, Gabriel SB, Hakonarson H, Anand SS, Reilly M, Engert JC, Nickerson DA, Rader DJ, Hirschhorn JN, FitzGerald GA. Concept, design and implementation of a cardiovascular gene-centric 50 k SNP array for large-scale genomic association studies. PLoS One 2008; 3:e3583. [PMID: 18974833 PMCID: PMC2571995 DOI: 10.1371/journal.pone.0003583] [Citation(s) in RCA: 327] [Impact Index Per Article: 20.4] [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: 06/16/2008] [Accepted: 09/16/2008] [Indexed: 11/19/2022] Open
Abstract
A wealth of genetic associations for cardiovascular and metabolic phenotypes in humans has been accumulating over the last decade, in particular a large number of loci derived from recent genome wide association studies (GWAS). True complex disease-associated loci often exert modest effects, so their delineation currently requires integration of diverse phenotypic data from large studies to ensure robust meta-analyses. We have designed a gene-centric 50 K single nucleotide polymorphism (SNP) array to assess potentially relevant loci across a range of cardiovascular, metabolic and inflammatory syndromes. The array utilizes a "cosmopolitan" tagging approach to capture the genetic diversity across approximately 2,000 loci in populations represented in the HapMap and SeattleSNPs projects. The array content is informed by GWAS of vascular and inflammatory disease, expression quantitative trait loci implicated in atherosclerosis, pathway based approaches and comprehensive literature searching. The custom flexibility of the array platform facilitated interrogation of loci at differing stringencies, according to a gene prioritization strategy that allows saturation of high priority loci with a greater density of markers than the existing GWAS tools, particularly in African HapMap samples. We also demonstrate that the IBC array can be used to complement GWAS, increasing coverage in high priority CVD-related loci across all major HapMap populations. DNA from over 200,000 extensively phenotyped individuals will be genotyped with this array with a significant portion of the generated data being released into the academic domain facilitating in silico replication attempts, analyses of rare variants and cross-cohort meta-analyses in diverse populations. These datasets will also facilitate more robust secondary analyses, such as explorations with alternative genetic models, epistasis and gene-environment interactions.
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Affiliation(s)
- Brendan J. Keating
- The Institute for Translational Medicine and Therapeutics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvannia, United States of America
| | - Sam Tischfield
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Divisions of Genetics, Endocrinology & Program in Genomics, Children's Hospital, Boston, Massachusetts, United States of America
| | - Sarah S. Murray
- Scripps Genomic Medicine, La Jolla, California, United States of America
| | - Tushar Bhangale
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Thomas S. Price
- MRC SGDP Centre, Institute of Psychiatry, London, United Kingdom
| | - Joseph T. Glessner
- The Center for Applied Genomics, Division of Human Genetics, Department of Pediatrics, The Childrens' Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Luana Galver
- Illumina Incorporated, San Diego, California, United States of America
| | - Jeffrey C. Barrett
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Struan F. A. Grant
- The Center for Applied Genomics, Division of Human Genetics, Department of Pediatrics, The Childrens' Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Deborah N. Farlow
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Hareesh R. Chandrupatla
- The Cardiovascular Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Mark Hansen
- Illumina Incorporated, San Diego, California, United States of America
| | - Saad Ajmal
- The Cardiovascular Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - George J. Papanicolaou
- Division of Prevention and Population Sciences, National Heart, Lung, and Blood Institute, Bethesda, Maryland, United States of America
| | - Yiran Guo
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Mingyao Li
- The Cardiovascular Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Stephanie DerOhannessian
- The Cardiovascular Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Paul I. W. de Bakker
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Swneke D. Bailey
- Departments of Medicine and Human Genetics, McGill University, Montréal, Québec, Canada
| | | | - Andrew C. Edmondson
- The Cardiovascular Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Kent Taylor
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Xiaowu Gai
- The Center for Applied Genomics, Division of Human Genetics, Department of Pediatrics, The Childrens' Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Susanna S. Wang
- Department of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Myriam Fornage
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Tamim Shaikh
- The Center for Applied Genomics, Division of Human Genetics, Department of Pediatrics, The Childrens' Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Leif Groop
- Department of Clinical Science Malmoe, Diabetes and Endocrinology, Lund University, Sweden and Department of Medicine, Helsinki University Hospital, Helsinki, Finland
| | - Michael Boehnke
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Alistair S. Hall
- Leeds Institute of Genetics, Health & Therapeutics, University of Leeds, Leeds, United Kingdom
| | - Andrew T. Hattersley
- Diabetes Genetics Group, Institute of Biomedical and Clinical Science, Peninsula Medical School, Exeter, United Kingdom
| | - Edward Frackelton
- The Center for Applied Genomics, Division of Human Genetics, Department of Pediatrics, The Childrens' Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Nick Patterson
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Charleston W. K. Chiang
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Cecelia E. Kim
- The Center for Applied Genomics, Division of Human Genetics, Department of Pediatrics, The Childrens' Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Richard R. Fabsitz
- Division of Prevention and Population Sciences, National Heart, Lung, and Blood Institute, Bethesda, Maryland, United States of America
| | - Willem Ouwehand
- Department of Haematology and NHS Blood and Transplant, University of Cambridge, Cambridge, United Kingdom
| | - Alkes L. Price
- Departments of Epidemiology and Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Patricia Munroe
- Department of Clinical Pharmacology, Barts and The London, Charterhouse Square, London, United Kingdom
- William Harvey Research Institute, Barts and The London, Charterhouse Square, London, United Kingdom
| | - Mark Caulfield
- William Harvey Research Institute, Barts and The London, Charterhouse Square, London, United Kingdom
| | - Thomas Drake
- Department of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Eric Boerwinkle
- Human Genetics Center, University of Texas Health Science Center, Houston, Texas, United States of America
| | - David Reich
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - A. Stephen Whitehead
- The Institute for Translational Medicine and Therapeutics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvannia, United States of America
| | - Thomas P. Cappola
- The Cardiovascular Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Nilesh J. Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester, United Kingdom
| | - A. Jake Lusis
- Department of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles School of Medicine, Los Angeles, California, United States of America
| | - Eric Schadt
- Rosetta Inpharmatics, LLC, Merck & Co. Inc., Seattle, Washington, United States of America
| | - James G. Wilson
- V.A. Medical Center and the University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Wolfgang Koenig
- Department of Internal Medicine II - Cardiology, University of Ulm Medical Center, Ulm, Germany
| | - Mark I. McCarthy
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Oxford Center for Diabetes, Endocrinology and Metabolism and Oxford NIHR Biomedical Research Center, Churchill Hospital, University of Oxford, Oxford, United Kingdom
| | - Sekar Kathiresan
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Cardiology Division, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Stacey B. Gabriel
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Hakon Hakonarson
- The Center for Applied Genomics, Division of Human Genetics, Department of Pediatrics, The Childrens' Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Sonia S. Anand
- Department of Medicine and Clinical Epidemiology and Biostatistics, Population Genomics Program, McMaster University, Hamilton Health Sciences, Hamilton General Hospital, Hamilton, Ontario, Canada
| | - Muredach Reilly
- The Institute for Translational Medicine and Therapeutics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvannia, United States of America
- The Cardiovascular Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - James C. Engert
- Departments of Medicine and Human Genetics, McGill University, Montréal, Québec, Canada
| | - Deborah A. Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Daniel J. Rader
- The Institute for Translational Medicine and Therapeutics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvannia, United States of America
- The Cardiovascular Institute, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Joel N. Hirschhorn
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Divisions of Genetics, Endocrinology & Program in Genomics, Children's Hospital, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Garret A. FitzGerald
- The Institute for Translational Medicine and Therapeutics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvannia, United States of America
- * E-mail:
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29
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Crawford DC, Bhangale T, Li N, Hellenthal G, Rieder MJ, Nickerson DA, Stephens M. Evidence for substantial fine-scale variation in recombination rates across the human genome. Nat Genet 2004; 36:700-6. [PMID: 15184900 DOI: 10.1038/ng1376] [Citation(s) in RCA: 229] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2004] [Accepted: 05/13/2004] [Indexed: 11/09/2022]
Abstract
Characterizing fine-scale variation in human recombination rates is important, both to deepen understanding of the recombination process and to aid the design of disease association studies. Current genetic maps show that rates vary on a megabase scale, but studying finer-scale variation using pedigrees is difficult. Sperm-typing experiments have characterized regions where crossovers cluster into 1-2-kb hot spots, but technical difficulties limit the number of studies. An alternative is to use population variation to infer fine-scale characteristics of the recombination process. Several surveys reported 'block-like' patterns of diversity, which may reflect fine-scale recombination rate variation, but limitations of available methods made this impossible to assess. Here, we applied a new statistical method, which overcomes these limitations, to infer patterns of fine-scale recombination rate variation in 74 genes. We found extensive rate variation both within and among genes. In particular, recombination hot spots are a common feature of the human genome: 47% (35 of 74) of genes showed substantive evidence for a hot spot, and many more showed evidence for some rate variation. No primary sequence characteristics are consistently associated with precise hot-spot location, although G+C content and nucleotide diversity are correlated with local recombination rate.
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Affiliation(s)
- Dana C Crawford
- Department of Genome Sciences, University of Washington, Box 354322, Seattle, Washington 98195, USA
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