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Chan Y, Tang X, Cai D, Liu Y, Li D, Su J, Neng G, Yin Y, Geng Z, Zhu S, Zhang J, Jiang L, Zhu B. The relationship of maternal polymorphisms of genes related to meiosis and DNA damage repair with fetal chromosomal stability. J Perinat Med 2023; 51:1082-1096. [PMID: 37486214 DOI: 10.1515/jpm-2022-0613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 06/24/2023] [Indexed: 07/25/2023]
Abstract
OBJECTIVES To evaluate the association between maternal polymorphisms of NANOS3 rs2016163, HELQ rs4693089, PRIM1 rs2277339, TLK1 rs10183486, ERCC6 rs2228526, EXO1 rs1635501, DMC1 rs5757133, and MSH5 rs2075789 and fetal chromosomal abnormality. METHODS This retrospective case-control study included 571 women with fetal chromosome abnormalities (330 pregnant women diagnosed with fetal aneuploidy, 241 with fetal de novo structural chromosome pregnancy) and 811 healthy pregnant women between January 2018 and April 2022. All the above polymorphisms were tested using SNaPshot. RESULTS All the eight polymorphisms were analyzed for genotypes, alleles, under dominant and recessive genetic models. Significant distribution differences of TLK1 rs10183486 in fetal chromosome structural abnormality were found between the case group and control subjects who were <35 years of age [Genotype: p=0.029; Dominant: OR (95 %CI)=0.46 (0.25-0.82), p=0.01 and allele: OR (95 %CI)=0.47 (0.27-0.82), p=0.01 respectively], while no difference was found in the recessive model [OR (95 %CI)=2.49 (0.31-20.40), p=0.39]. In advanced age subgroups for fetal aneuploidy, significant differences were found in genotypes analysis of PRIM1 rs2277339 (p=0.008), allele analysis of TLK1 rs10183486 [OR (95 %CI)=0.62 (0.42-0.91), p=0.02]. For the fetal chromosome structural abnormality population, HELQ rs4693089 revealed a significant distribution difference (p=0.01) but not in the allele, dominant and recessive genetic models analysis (p>0.05 individually). CONCLUSIONS For older women, maternal PRIM1 rs2277339 and TLK1 rs10183486 polymorphisms may be associated with fetal aneuploidy, while HELQ rs4693089 may be associated with fetal chromosome structural abnormality. Also, carriers of T allele of TLK1 rs10183486 have a lower risk of fetal chromosome structural abnormality in younger women.
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Affiliation(s)
- Ying Chan
- Department of Medical Genetics, NHC Key Laboratory of Periconception Health Birth in Western China, Yunnan Provincial Key Laboratory for Birth Defects and Genetic Diseases, The First People's Hospital of Yunnan Province, Kunming, P.R. China
| | - Xinhua Tang
- Department of Medical Genetics, NHC Key Laboratory of Periconception Health Birth in Western China, Yunnan Provincial Key Laboratory for Birth Defects and Genetic Diseases, The First People's Hospital of Yunnan Province, Kunming, P.R. China
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan Province, P.R. China
| | - Dongling Cai
- School of Medicine, Kunming University of Science and Technology, Kunming, 650500, Yunnan Province, P.R. China
| | - Yize Liu
- School of Medicine, Kunming University of Science and Technology, Kunming, 650500, Yunnan Province, P.R. China
| | - Dongmei Li
- Department of Medical Genetics, NHC Key Laboratory of Periconception Health Birth in Western China, Yunnan Provincial Key Laboratory for Birth Defects and Genetic Diseases, The First People's Hospital of Yunnan Province, Kunming, P.R. China
| | - Jie Su
- Department of Medical Genetics, NHC Key Laboratory of Periconception Health Birth in Western China, Yunnan Provincial Key Laboratory for Birth Defects and Genetic Diseases, The First People's Hospital of Yunnan Province, Kunming, P.R. China
| | - Guowei Neng
- Department of Medical Genetics, NHC Key Laboratory of Periconception Health Birth in Western China, Yunnan Provincial Key Laboratory for Birth Defects and Genetic Diseases, The First People's Hospital of Yunnan Province, Kunming, P.R. China
| | - Yifei Yin
- Department of Medical Genetics, NHC Key Laboratory of Periconception Health Birth in Western China, Yunnan Provincial Key Laboratory for Birth Defects and Genetic Diseases, The First People's Hospital of Yunnan Province, Kunming, P.R. China
| | - Zibiao Geng
- Department of Medical Genetics, NHC Key Laboratory of Periconception Health Birth in Western China, Yunnan Provincial Key Laboratory for Birth Defects and Genetic Diseases, The First People's Hospital of Yunnan Province, Kunming, P.R. China
| | - Shu Zhu
- Department of Medical Genetics, NHC Key Laboratory of Periconception Health Birth in Western China, Yunnan Provincial Key Laboratory for Birth Defects and Genetic Diseases, The First People's Hospital of Yunnan Province, Kunming, P.R. China
| | - Jinman Zhang
- Department of Medical Genetics, NHC Key Laboratory of Periconception Health Birth in Western China, Yunnan Provincial Key Laboratory for Birth Defects and Genetic Diseases, The First People's Hospital of Yunnan Province, Kunming, P.R. China
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan Province, P.R. China
| | - Lihong Jiang
- Department of Cardiothoracic Surgery, First People's Hospital of Yunnan Province, 157, Jinbi Road, Kunming, 650032, China
| | - Baosheng Zhu
- Department of Medical Genetics, NHC Key Laboratory of Periconception Health Birth in Western China, Yunnan Provincial Key Laboratory for Birth Defects and Genetic Diseases, The First People's Hospital of Yunnan Province, Kunming, P.R. China
- School of Medicine, Kunming University of Science and Technology, Kunming, 650500, Yunnan Province, P.R. China
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming, Yunnan Province, P.R. China
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Massidda M, Flore L, Scorcu M, Monteleone G, Tiloca A, Salvi M, Tocco F, Calò CM. Collagen Gene Variants and Anterior Cruciate Ligament Rupture in Italian Athletes: A Preliminary Report. Genes (Basel) 2023; 14:1418. [PMID: 37510322 PMCID: PMC10379389 DOI: 10.3390/genes14071418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/28/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
Several studies have investigated the role of genetics in anterior cruciate ligament (ACL) rupture, often returning conflicting results. The present pilot study aimed to analyze the association between six Single Nucleotide Polymorphisms (SNPs) (rs1800012; rs12722; rs13946; rs240736; rs970547; and rs4870723, located on the COL1A1, COL5A1, COL12A1, and COL14A1 genes), and ACL rupture, among Italian athletes. A hypothesis-driven association study was conducted. In total, 181 male and female athletes (n = 86 injured; n = 96 non-injured) were genotyped for the prioritized variants. All polymorphisms were genotyped using PCR RFLP, with the only exception being the rs1800012 on the COL1A1 gene, which was detected using MTPA PCR. The allele frequency distribution fell within the worldwide range. Despite the evident population variability, no selective pressure signals were recorded using PBS analysis. No significant difference was detected between the cases and controls for any of the SNPs (rs1800012; rs13946; rs240736; rs970547, and rs4870723) included in the analyses (p > 0.008, Bonferroni-adjusted for multiple comparisons). Moreover, no significant differences were found when males and females were assessed separately. Further investigations based on a larger sample size are needed, in order to draw solid conclusions for the influence between collagen genes and ACL rupture.
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Affiliation(s)
- Myosotis Massidda
- Department of Medical Sciences and Public Health, University of Cagliari, 09042 Monserrato, Italy
| | - Laura Flore
- Department of Sciences of Life and Environment, University of Cagliari, 09042 Monserrato, Italy
| | - Marco Scorcu
- Italian Federation of Sports Medicine (FIMS), CR Sardegna, 00196 Rome, Italy
| | - Giovanni Monteleone
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Alessandra Tiloca
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
| | | | - Filippo Tocco
- Department of Medical Sciences and Public Health, University of Cagliari, 09042 Monserrato, Italy
| | - Carla M Calò
- Department of Sciences of Life and Environment, University of Cagliari, 09042 Monserrato, Italy
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3
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Sahana G, Cai Z, Sanchez MP, Bouwman AC, Boichard D. Invited review: Good practices in genome-wide association studies to identify candidate sequence variants in dairy cattle. J Dairy Sci 2023:S0022-0302(23)00357-0. [PMID: 37349208 DOI: 10.3168/jds.2022-22694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 02/01/2023] [Indexed: 06/24/2023]
Abstract
Genotype data from dairy cattle selection programs have greatly facilitated GWAS to identify variants related to economic traits. Results can enhance the accuracy of genomic prediction, analyze more complex models that go beyond additive effects, elucidate the genetic architecture of a trait, and finally, decipher the underlying biology of traits. The entire process, comprising data generation, quality control, statistical analyses, interpretation of association results, and linking results to biology should be designed and executed to minimize the generation of false-positive and false-negative associations and misleading links to biological processes. This review aims to provide general guidelines for data analysis that address data quality control, association tests, adjustment for population stratification, and significance evaluation to improve the reliability of conclusions. We also provide guidance on post-GWAS strategy and the interpretation of results. These guidelines are tailored to dairy cattle, which are characterized by long-range linkage disequilibrium, large half-sib families, and routinely collected phenotypes, requiring different approaches than those applied in human GWAS. We discuss common limitations and challenges that have been overlooked in the analysis and interpretation of GWAS to identify candidate sequence variants in dairy cattle.
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Affiliation(s)
- G Sahana
- Aarhus University, Center for Quantitative Genetic and Genomics, 8830 Tjele, Denmark.
| | - Z Cai
- Aarhus University, Center for Quantitative Genetic and Genomics, 8830 Tjele, Denmark
| | - M P Sanchez
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France
| | - A C Bouwman
- Wageningen University & Research, Animal Breeding and Genomics, 6700 AH Wageningen, the Netherlands
| | - D Boichard
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France
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4
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Wei J, Zhang H, Ma X, Li Y, Zhou W, Guo J, Jin T, Hu M. Effect of OR51E1 Single Nucleotide Polymorphisms on Glioma Susceptibility in the Chinese Han Population. Gene 2023; 875:147489. [PMID: 37207826 DOI: 10.1016/j.gene.2023.147489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/27/2023] [Accepted: 05/12/2023] [Indexed: 05/21/2023]
Abstract
BACKGROUND Glioma is one of the common primary intracranial tumors, which is heterogeneous among individuals with a low cure rate. Our study aimed to investigate the association between single nucleotide polymorphisms (SNPs) of the OR51E1 gene and glioma susceptibility in the Chinese Han population. METHODS A total of six SNPs on OR51E1 in 1,026 subjects (526 cases and 500 controls) were genotyped by MassARRAY iPLEX GOLD assay. The association between these SNPs and glioma susceptibility was analyzed using logistic regression, and odds ratios (ORs) and 95% confidence intervals (CIs) were also calculated. The multifactor dimensionality reduction (MDR) method was applied to detect "SNP-SNP" interactions. RESULTS In the overall sample, polymorphisms rs10768148, rs7102992, and rs10500608 were identified to be associated with glioma risk. In the stratified analysis based on gender, only polymorphism rs10768148 was observed to be associated with the risk of glioma. In the age-stratified analysis, rs7102992, rs74052483, and rs10500609 contributed to the risk of glioma in subjects aged > 40 years. And polymorphisms rs10768148 and rs7102992 were associated with the risk of glioma in subjects aged ≤ 40 years and subjects with astrocytoma. In addition, a strong synergistic relationship between rs74052483 and rs10768148, and a strong redundant relationship between rs7102992 and rs10768148 were identified in the study. CONCLUSIONS This study demonstrated the association of OR51E1 polymorphisms with glioma susceptibility, providing a basis for assessing glioma risk-associated variants in the Chinese Han population.
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Affiliation(s)
- Jie Wei
- The College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Huan Zhang
- The College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Xiaoya Ma
- The College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Yujie Li
- The College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Wenqian Zhou
- The College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Jinping Guo
- The College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Tianbo Jin
- School of Medicine, Northwest University, Xi'an 710069, China
| | - Mingjun Hu
- School of Medicine, Northwest University, Xi'an 710069, China; Department of Neurosurgery, Xi'an Changan District Hospital, Xi'an 710199, China.
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5
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Yap CX, Henders AK, Alvares GA, Giles C, Huynh K, Nguyen A, Wallace L, McLaren T, Yang Y, Hernandez LM, Gandal MJ, Hansell NK, Cleary D, Grove R, Hafekost C, Harun A, Holdsworth H, Jellett R, Khan F, Lawson LP, Leslie J, Levis Frenk M, Masi A, Mathew NE, Muniandy M, Nothard M, Miller JL, Nunn L, Strike LT, Cadby G, Moses EK, de Zubicaray GI, Thompson PM, McMahon KL, Wright MJ, Visscher PM, Dawson PA, Dissanayake C, Eapen V, Heussler HS, Whitehouse AJO, Meikle PJ, Wray NR, Gratten J. Interactions between the lipidome and genetic and environmental factors in autism. Nat Med 2023; 29:936-949. [PMID: 37076741 PMCID: PMC10115648 DOI: 10.1038/s41591-023-02271-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 02/22/2023] [Indexed: 04/21/2023]
Abstract
Autism omics research has historically been reductionist and diagnosis centric, with little attention paid to common co-occurring conditions (for example, sleep and feeding disorders) and the complex interplay between molecular profiles and neurodevelopment, genetics, environmental factors and health. Here we explored the plasma lipidome (783 lipid species) in 765 children (485 diagnosed with autism spectrum disorder (ASD)) within the Australian Autism Biobank. We identified lipids associated with ASD diagnosis (n = 8), sleep disturbances (n = 20) and cognitive function (n = 8) and found that long-chain polyunsaturated fatty acids may causally contribute to sleep disturbances mediated by the FADS gene cluster. We explored the interplay of environmental factors with neurodevelopment and the lipidome, finding that sleep disturbances and unhealthy diet have a convergent lipidome profile (with potential mediation by the microbiome) that is also independently associated with poorer adaptive function. In contrast, ASD lipidome differences were accounted for by dietary differences and sleep disturbances. We identified a large chr19p13.2 copy number variant genetic deletion spanning the LDLR gene and two high-confidence ASD genes (ELAVL3 and SMARCA4) in one child with an ASD diagnosis and widespread low-density lipoprotein-related lipidome derangements. Lipidomics captures the complexity of neurodevelopment, as well as the biological effects of conditions that commonly affect quality of life among autistic people.
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Affiliation(s)
- Chloe X Yap
- Mater Research Institute, The University of Queensland, Brisbane, Queensland, Australia.
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia.
| | - Anjali K Henders
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
| | - Gail A Alvares
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia, Australia
| | - Corey Giles
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Baker Department of Cardiometabolic Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Kevin Huynh
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Baker Department of Cardiometabolic Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Anh Nguyen
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Baker Department of Cardiometabolic Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Leanne Wallace
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
| | - Tiana McLaren
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
| | - Yuanhao Yang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
| | - Leanna M Hernandez
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Michael J Gandal
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Lifespan Brain Institute at Penn Medicine and The Children's Hospital of Philadelphia, Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Narelle K Hansell
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Dominique Cleary
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia, Australia
| | - Rachel Grove
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Faculty of Health, University of Technology Sydney, Sydney, New South Wales, Australia
- School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Claire Hafekost
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia, Australia
| | - Alexis Harun
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia, Australia
| | - Helen Holdsworth
- Mater Research Institute, The University of Queensland, Brisbane, Queensland, Australia
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Child Health Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Rachel Jellett
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Olga Tennison Autism Research Centre, La Trobe University, Melbourne, Victoria, Australia
| | - Feroza Khan
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Lauren P Lawson
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Department of Psychology, Counselling and Therapy, La Trobe University, Melbourne, Victoria, Australia
| | - Jodie Leslie
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia, Australia
| | - Mira Levis Frenk
- Mater Research Institute, The University of Queensland, Brisbane, Queensland, Australia
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Child Health Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Anne Masi
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Nisha E Mathew
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Melanie Muniandy
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Olga Tennison Autism Research Centre, La Trobe University, Melbourne, Victoria, Australia
| | - Michaela Nothard
- Mater Research Institute, The University of Queensland, Brisbane, Queensland, Australia
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Olga Tennison Autism Research Centre, La Trobe University, Melbourne, Victoria, Australia
| | - Jessica L Miller
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Lorelle Nunn
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Lachlan T Strike
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Gemma Cadby
- School of Population and Global Health, The University of Western Australia, Perth, Western Australia, Australia
| | - Eric K Moses
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
- School of Biomedical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Greig I de Zubicaray
- School of Psychology and Counselling, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Paul M Thompson
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Katie L McMahon
- School of Clinical Sciences, Centre for Biomedical Technologies, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Margaret J Wright
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
- Centre for Advanced Imaging, The University of Queensland, Brisbane, Queensland, Australia
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Paul A Dawson
- Mater Research Institute, The University of Queensland, Brisbane, Queensland, Australia
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
| | - Cheryl Dissanayake
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Olga Tennison Autism Research Centre, La Trobe University, Melbourne, Victoria, Australia
| | - Valsamma Eapen
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
- Academic Unit of Child Psychiatry South West Sydney, Ingham Institute for Applied Medical Research, Liverpool Hospital, Sydney, New South Wales, Australia
| | - Helen S Heussler
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Child Health Research Centre, The University of Queensland, Brisbane, Queensland, Australia
- Child Development Program, Children's Health Queensland, Brisbane, Queensland, Australia
| | - Andrew J O Whitehouse
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia, Australia
| | - Peter J Meikle
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Baker Department of Cardiometabolic Health, The University of Melbourne, Melbourne, Victoria, Australia
- Baker Department of Cardiovascular Research, Translation and Implementation, La Trobe University, Melbourne, Victoria, Australia
| | - Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Jacob Gratten
- Mater Research Institute, The University of Queensland, Brisbane, Queensland, Australia.
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
- Cooperative Research Centre for Living with Autism, Long Pocket, Queensland, Australia.
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Wendel B, Heidenreich M, Budde M, Heilbronner M, Oraki Kohshour M, Papiol S, Falkai P, Schulze TG, Heilbronner U, Bickeböller H. Kalpra: A kernel approach for longitudinal pathway regression analysis integrating network information with an application to the longitudinal PsyCourse Study. Front Genet 2022; 13:1015885. [PMID: 36561312 PMCID: PMC9767414 DOI: 10.3389/fgene.2022.1015885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 11/24/2022] [Indexed: 12/12/2022] Open
Abstract
A popular approach to reduce the high dimensionality resulting from genome-wide association studies is to analyze a whole pathway in a single test for association with a phenotype. Kernel machine regression (KMR) is a highly flexible pathway analysis approach. Initially, KMR was developed to analyze a simple phenotype with just one measurement per individual. Recently, however, the investigation into the influence of genomic factors in the development of disease-related phenotypes across time (trajectories) has gained in importance. Thus, novel statistical approaches for KMR analyzing longitudinal data, i.e. several measurements at specific time points per individual are required. For longitudinal pathway analysis, we extend KMR to long-KMR using the estimation equivalence of KMR and linear mixed models. We include additional random effects to correct for the dependence structure. Moreover, within long-KMR we created a topology-based pathway analysis by combining this approach with a kernel including network information of the pathway. Most importantly, long-KMR not only allows for the investigation of the main genetic effect adjusting for time dependencies within an individual, but it also allows to test for the association of the pathway with the longitudinal course of the phenotype in the form of testing the genetic time-interaction effect. The approach is implemented as an R package, kalpra. Our simulation study demonstrates that the power of long-KMR exceeded that of another KMR method previously developed to analyze longitudinal data, while maintaining (slightly conservatively) the type I error. The network kernel improved the performance of long-KMR compared to the linear kernel. Considering different pathway densities, the power of the network kernel decreased with increasing pathway density. We applied long-KMR to cognitive data on executive function (Trail Making Test, part B) from the PsyCourse Study and 17 candidate pathways selected from Reactome. We identified seven nominally significant pathways.
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Affiliation(s)
- Bernadette Wendel
- Department of Genetic Epidemiology, University Medical Center Göttingen, Georg-August-University Göttingen, Göttingen, Germany,*Correspondence: Bernadette Wendel,
| | - Markus Heidenreich
- Department of Genetic Epidemiology, University Medical Center Göttingen, Georg-August-University Göttingen, Göttingen, Germany
| | - Monika Budde
- Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich, Germany
| | - Maria Heilbronner
- Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich, Germany
| | - Mojtaba Oraki Kohshour
- Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich, Germany
| | - Sergi Papiol
- Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich, Germany,Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany
| | - Peter Falkai
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany
| | - Thomas G. Schulze
- Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich, Germany,Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, United States,Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Urs Heilbronner
- Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich, Germany
| | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center Göttingen, Georg-August-University Göttingen, Göttingen, Germany
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Liu W, Lu L, Pan H, He X, Zhang M, Wang N, Zhu J, Yi H, Tang S. Haem oxygenase-1 and haemopexin gene polymorphisms and the risk of anti-tuberculosis drug-induced hepatotoxicity in China. Pharmacogenomics 2022; 23:431-441. [PMID: 35470713 DOI: 10.2217/pgs-2022-0015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Objective: To assess whether the risk of anti-tuberculosis drug-induced hepatotoxicity (ATDH) might be influenced by haem oxygenase-1 (HMOX1) and haemopexin (HPX) gene polymorphisms. Methods: A dynamic anti-tuberculosis treatment cohort was constructed, and the 1:4 matched nested case-control study was analysed. Eight single nucleotide polymorphisms (SNPs) of the two genes were selected for genotyping and Bonferroni correction was performed to correct for multiple comparison. Results: Overall, 7.8% of patients developed ATDH. SNP rs1807714 in the HMOX1 gene had decreased effects on the risk of moderate and severe hepatotoxicity under the dominant and additive models, and hepatocellular injury under the additive model. SNP rs2682099 in the HPX gene had increased effects on the risk of moderate and severe hepatotoxicity under the recessive model. However, these associations disappeared after Bonferroni correction. Conclusion: HMOX1 and HPX gene polymorphisms might not be associated with susceptibility to ATDH in the Chinese population.
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Affiliation(s)
- Wenpei Liu
- Department of Epidemiology & Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Lihuan Lu
- Department of Tuberculosis, The Second People's Hospital of Changshu, Changshu, 215500, China
| | - Hongqiu Pan
- Department of Tuberculosis, The Third People's Hospital of Zhenjiang Affiliated to Jiangsu University, Zhenjiang, 212021, China
| | - Xiaomin He
- Department of Infectious Disease, The People's Hospital of Taixing, Taixing, 225400, China
| | - Meiling Zhang
- Department of Infectious Disease, The Jurong Hospital Affiliated to Jiangsu University, Jurong, 212400, China
| | - Nannan Wang
- Department of Epidemiology & Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Jia Zhu
- Department of Epidemiology & Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Honggang Yi
- Department of Epidemiology & Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Shaowen Tang
- Department of Epidemiology & Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
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8
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Tsekmekidou X, Tsetsos F, Koufakis T, Georgitsi M, Papanas N, Papazoglou D, Roumeliotis A, Panagoutsos S, Thodis E, Theodoridis M, Passadakis P, Maltezos E, Paschou P, Kotsa K. Variants in clock genes could be associated with lower risk of type 2 diabetes in an elderly Greek population. Maturitas 2021; 152:20-25. [PMID: 34674804 DOI: 10.1016/j.maturitas.2021.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 06/16/2021] [Accepted: 07/06/2021] [Indexed: 11/26/2022]
Abstract
OBJECTIVES Recent evidence has linked circadian rhythm dysregulation to an increased risk of metabolic disorders. This study explores a potential association between variation in genes regulating the endogenous circadian timing system (clock genes) and the risk of type 2 diabetes (T2D) in a sample of Greek elderly people. STUDY DESIGN Variants within and upstream or downstream of PPARA, PPARD, CLOCK/TMEM165, PER1, PER2 and PER3 genes were genotyped in 716 individuals with T2D (A) and 569 normoglycemic controls (B), and allele frequencies were compared between the groups in a case control study design. MAIN OUTCOME MEASURES Samples were genotyped on Illumina Human PsychArray. Permutation test analysis was implemented to determine statistical significance. To avoid the possibility of subjects with prediabetes being included in the control group, people with HbA1c <5.7% and fasting glucose <100 mg/dl comprised group C (n = 393), for whom a separate analysis was performed (secondary analysis). RESULTS A protective role against T2D was identified for 14 variants in the PPARA gene. The rs7291444, rs36125344, rs6008384 in PKDREJ, located upstream of PPARA, and rs2859389 in UTS2, located upstream of PER3, demonstrated a protective role against T2D in both analyses. In contrast, rs6744132, located between HES6 and PER2, was positively correlated with T2D risk. Only in the secondary analysis, rs2278637 in VAMP2, located downstream of PER1, and rs11943456 in CLOCK/TMEM165 were found to confer protection against T2D. In a recessive model analysis of all groups, PPARD variants exhibited a protective role against disease. CONCLUSIONS Our findings suggest a possible implication of clock genes in T2D susceptibility. Further studies are needed to clarify the mechanisms that connect circadian rhythm dysfunction and T2D pathogenesis.
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Affiliation(s)
- Xanthippi Tsekmekidou
- Division of Endocrinology and Metabolism and Diabetes Center, First Department of Internal Medicine, AHEPA University Hospital, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Greece
| | - Fotis Tsetsos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Theocharis Koufakis
- Division of Endocrinology and Metabolism and Diabetes Center, First Department of Internal Medicine, AHEPA University Hospital, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Greece
| | - Marianthi Georgitsi
- 1st Laboratory of Medical Biology-Genetics, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Greece
| | - Nikolaos Papanas
- Diabetes Centre, Second Department of Internal Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Dimitrios Papazoglou
- Diabetes Centre, Second Department of Internal Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Athanasios Roumeliotis
- Division of Nephrology and Hypertension, First Department of Internal Medicine, AHEPA University Hospital, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Greece
| | - Stylianos Panagoutsos
- Department of Nephrology, Alexandroupolis University General Hospital, Democritus University of Thrace School of Health Sciences
| | - Elias Thodis
- Department of Nephrology, Alexandroupolis University General Hospital, Democritus University of Thrace School of Health Sciences
| | - Marios Theodoridis
- Department of Nephrology, Alexandroupolis University General Hospital, Democritus University of Thrace School of Health Sciences
| | - Ploumis Passadakis
- Department of Nephrology, Alexandroupolis University General Hospital, Democritus University of Thrace School of Health Sciences
| | - Efstratios Maltezos
- Diabetes Centre, Second Department of Internal Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Peristera Paschou
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
| | - Kalliopi Kotsa
- Division of Endocrinology and Metabolism and Diabetes Center, First Department of Internal Medicine, AHEPA University Hospital, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Greece.
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9
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Lin CH, Ho CJ, Lu YT, Tsai MH. Response to Sodium Channel blocking Antiseizure medications and coding polymorphisms of Sodium Channel genes in Taiwanese epilepsy patients. BMC Neurol 2021; 21:367. [PMID: 34556045 PMCID: PMC8459515 DOI: 10.1186/s12883-021-02395-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 09/06/2021] [Indexed: 11/13/2022] Open
Abstract
Background Many antiseizure medications (ASMs) control seizures by blocking voltage-dependent sodium channels. Polymorphisms of sodium channel genes may affect the response to ASMs due to altering the effect of ASMs on blocking sodium channels. Methods We conducted a retrospective study of epilepsy patients followed up at the Neurological Department of Kaohsiung Chang Gung Memorial Hospital, Taiwan between January 2010 and December 2018. We categorized the patients into response, partial response, and failure to sodium channel blocking ASM groups. Sodium channel blocking ASMs included phenytoin, carbamazepine, lamotrigine, oxcarbazepine, lacosamide, zonisamide, topiramate, and valproic acid. A subgroup of predominant sodium channel blocking ASMs included phenytoin, carbamazepine, lamotrigine, oxcarbazepine, and lacosamide. Associations between the response of ASMs and single-nucleotide polymorphisms of SCN1A, SCN1B, SCN2A, and SCN9A were analyzed. Results Two hundred Taiwanese patients and 21 single-nucleotide polymorphisms among SCN1A, SCN1B, SCN2A, and SCN9A were evaluated. We found allele C of rs55742440 in SCN1B was statistically significantly associated with not achieving seizure-free with sodium channel blocking ASMs. For the predominant sodium channel blocking ASMs group, no SNPs were associated with the response of ASMs. Conclusion Single-nucleotide polymorphism in SCN1B was associated with the response to sodium channel blocking ASMs. This highlights the possibility that beta subunits may affect the function of sodium channels and resulted in different responsiveness to ASMs. Supplementary Information The online version contains supplementary material available at 10.1186/s12883-021-02395-2.
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Affiliation(s)
- Chih-Hsiang Lin
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital, Colleague of Medicine, Chang Gung University, Kaohsiung, Kaohsiung City, 83301, Taiwan
| | - Chen-Jui Ho
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital, Colleague of Medicine, Chang Gung University, Kaohsiung, Kaohsiung City, 83301, Taiwan
| | - Yan-Ting Lu
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital, Colleague of Medicine, Chang Gung University, Kaohsiung, Kaohsiung City, 83301, Taiwan
| | - Meng-Han Tsai
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital, Colleague of Medicine, Chang Gung University, Kaohsiung, Kaohsiung City, 83301, Taiwan. .,School of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
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10
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Dennis EL, Disner SG, Fani N, Salminen LE, Logue M, Clarke EK, Haswell CC, Averill CL, Baugh LA, Bomyea J, Bruce SE, Cha J, Choi K, Davenport ND, Densmore M, du Plessis S, Forster GL, Frijling JL, Gonenc A, Gruber S, Grupe DW, Guenette JP, Hayes J, Hofmann D, Ipser J, Jovanovic T, Kelly S, Kennis M, Kinzel P, Koch SBJ, Koerte I, Koopowitz S, Korgaonkar M, Krystal J, Lebois LAM, Li G, Magnotta VA, Manthey A, May GJ, Menefee DS, Nawijn L, Nelson SM, Neufeld RWJ, Nitschke JB, O'Doherty D, Peverill M, Ressler KJ, Roos A, Sheridan MA, Sierk A, Simmons A, Simons RM, Simons JS, Stevens J, Suarez-Jimenez B, Sullivan DR, Théberge J, Tran JK, van den Heuvel L, van der Werff SJA, van Rooij SJH, van Zuiden M, Velez C, Verfaellie M, Vermeiren RRJM, Wade BSC, Wager T, Walter H, Winternitz S, Wolff J, York G, Zhu Y, Zhu X, Abdallah CG, Bryant R, Daniels JK, Davidson RJ, Fercho KA, Franz C, Geuze E, Gordon EM, Kaufman ML, Kremen WS, Lagopoulos J, Lanius RA, Lyons MJ, McCauley SR, McGlinchey R, McLaughlin KA, Milberg W, Neria Y, Olff M, Seedat S, Shenton M, Sponheim SR, Stein DJ, Stein MB, Straube T, Tate DF, van der Wee NJA, Veltman DJ, Wang L, Wilde EA, Thompson PM, Kochunov P, Jahanshad N, Morey RA. Altered white matter microstructural organization in posttraumatic stress disorder across 3047 adults: results from the PGC-ENIGMA PTSD consortium. Mol Psychiatry 2021; 26:4315-4330. [PMID: 31857689 PMCID: PMC7302988 DOI: 10.1038/s41380-019-0631-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 11/20/2019] [Accepted: 12/02/2019] [Indexed: 01/08/2023]
Abstract
A growing number of studies have examined alterations in white matter organization in people with posttraumatic stress disorder (PTSD) using diffusion MRI (dMRI), but the results have been mixed which may be partially due to relatively small sample sizes among studies. Altered structural connectivity may be both a neurobiological vulnerability for, and a result of, PTSD. In an effort to find reliable effects, we present a multi-cohort analysis of dMRI metrics across 3047 individuals from 28 cohorts currently participating in the PGC-ENIGMA PTSD working group (a joint partnership between the Psychiatric Genomics Consortium and the Enhancing NeuroImaging Genetics through Meta-Analysis consortium). Comparing regional white matter metrics across the full brain in 1426 individuals with PTSD and 1621 controls (2174 males/873 females) between ages 18-83, 92% of whom were trauma-exposed, we report associations between PTSD and disrupted white matter organization measured by lower fractional anisotropy (FA) in the tapetum region of the corpus callosum (Cohen's d = -0.11, p = 0.0055). The tapetum connects the left and right hippocampus, for which structure and function have been consistently implicated in PTSD. Results were consistent even after accounting for the effects of multiple potentially confounding variables: childhood trauma exposure, comorbid depression, history of traumatic brain injury, current alcohol abuse or dependence, and current use of psychotropic medications. Our results show that PTSD may be associated with alterations in the broader hippocampal network.
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Affiliation(s)
- Emily L Dennis
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Boston, MA, USA.
- Imaging Genetics Center, Stevens Neuroimaging & Informatics Institute, Keck School of Medicine of USC, Marina del Rey, CA, USA.
- Department of Neurology, University of Utah, Salt Lake City, UT, USA.
- Stanford Neurodevelopment, Affect, and Psychopathology Laboratory, Stanford, CA, USA.
| | - Seth G Disner
- Minneapolis VA Health Care System, Minneapolis, MN, USA
- Department of Psychiatry, University of Minnesota, Minneapolis, MN, USA
| | - Negar Fani
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Lauren E Salminen
- Imaging Genetics Center, Stevens Neuroimaging & Informatics Institute, Keck School of Medicine of USC, Marina del Rey, CA, USA
| | - Mark Logue
- National Center for PTSD, VA Boston Healthcare System, Boston, MA, USA
- Department of Psychiatry, Boston University School of Medicine, Boston, MA, USA
- Biomedical Genetics, Boston University School of Medicine, Boston, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Emily K Clarke
- Brain Imaging and Analysis Center, Duke University, Durham, NC, USA
- VISN 6 MIRECC, Durham VA, Durham, NC, USA
| | - Courtney C Haswell
- Brain Imaging and Analysis Center, Duke University, Durham, NC, USA
- VISN 6 MIRECC, Durham VA, Durham, NC, USA
| | - Christopher L Averill
- Clinical Neuroscience Division, National Center for PTSD; Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Lee A Baugh
- Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, SD, USA
- Center for Brain and Behavior Research, University of South Dakota, Vermillion, SD, USA
- Sioux Falls VA Health Care System, Sioux Falls, SD, USA
| | - Jessica Bomyea
- Center of Excellence for Stress and Mental Health, VA San Diego Healthcare System, La Jolla, CA, USA
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Steven E Bruce
- Department of Psychological Sciences, Center for Trauma Recovery University of Missouri-St. Louis, St. Louis, MO, USA
| | - Jiook Cha
- Department of Psychiatry, Columbia University Medical Center, New York, NY, USA
- New York State Psychiatric Institute, New York, NY, USA
| | - Kyle Choi
- Health Services Research Center, University of California, San Diego, CA, USA
| | - Nicholas D Davenport
- Minneapolis VA Health Care System, Minneapolis, MN, USA
- Department of Psychiatry, University of Minnesota, Minneapolis, MN, USA
| | - Maria Densmore
- Department of Psychiatry, Western University, London, ON, Canada
- Imaging Division, Lawson Health Research Institute, London, ON, Canada
| | - Stefan du Plessis
- Department of Psychiatry, Stellenbosch University, Stellenbosch, South Africa
| | - Gina L Forster
- Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, SD, USA
- Center for Brain and Behavior Research, University of South Dakota, Vermillion, SD, USA
- Brain Health Research Centre, Department of Anatomy, University of Otago, Dunedin, 9054, New Zealand
| | - Jessie L Frijling
- Department of Psychiatry, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Atilla Gonenc
- Cognitive and Clinical Neuroimaging Core, McLean Hospital, Belmont, MA, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - Staci Gruber
- Cognitive and Clinical Neuroimaging Core, McLean Hospital, Belmont, MA, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - Daniel W Grupe
- Center for Healthy Minds, University of Wisconsin-Madison, Madison, WI, USA
| | - Jeffrey P Guenette
- Division of Neuroradiology, Brigham and Women's Hospital, Boston, MA, USA
| | - Jasmeet Hayes
- Department of Psychology, The Ohio State University, Columbus, OH, USA
| | - David Hofmann
- Institute of Medical Psychology and Systems Neuroscience, University of Münster, Münster, Germany
| | - Jonathan Ipser
- SA Medical Research Council Unit on Risk & Resilience in Mental Disorders, Dept of Psychiatry & Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Tanja Jovanovic
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
- Department of Psychiatry and Behavioral Neuroscience, Wayne State University School of Medicine, Detroit, MI, USA
| | - Sinead Kelly
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Boston, MA, USA
- Department of Psychiatry, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Mitzy Kennis
- Brain Center Rudolf Magnus, Department of Psychiatry, UMCU, Utrecht, The Netherlands
- Brain Research and Innovation Centre, Ministry of Defence, Utrecht, The Netherlands
| | - Philipp Kinzel
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Boston, MA, USA
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital, Ludwig-Maximilians-Universität, Munich, Germany
| | - Saskia B J Koch
- Department of Psychiatry, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- Donders Institute for Brain, Cognition and Behavior, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Inga Koerte
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Boston, MA, USA
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital, Ludwig-Maximilians-Universität, Munich, Germany
| | - Sheri Koopowitz
- SA Medical Research Council Unit on Risk & Resilience in Mental Disorders, Dept of Psychiatry & Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Mayuresh Korgaonkar
- Brain Dynamics Centre, Westmead Institute of Medical Research, University of Sydney, Westmead, NSW, Australia
| | - John Krystal
- Clinical Neuroscience Division, National Center for PTSD; Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Lauren A M Lebois
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- Division of Depression and Anxiety Disorders, McLean Hospital, Belmont, MA, USA
| | - Gen Li
- Laboratory for Traumatic Stress Studies, CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing, China
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, China
| | - Vincent A Magnotta
- Departments of Radiology, Psychiatry, and Biomedical Engineering, University of Iowa, Iowa City, IA, USA
| | | | - Geoff J May
- VISN 17 Center of Excellence for Research on Returning War Veterans, Waco, TX, USA
- Department of Psychology and Neuroscience, Baylor University, Waco, TX, USA
- Department of Psychiatry and Behavioral Science, Texas A&M Health Science Center, Bryan, TX, USA
- Center for Vital Longevity, School of Behavioral and Brain Sciences, University of Texas at Dallas, Dallas, TX, USA
| | - Deleene S Menefee
- Menninger Department of Psychiatry, Baylor College of Medicine, Houston, TX, USA
- South Central MIRECC, Houston, TX, USA
| | - Laura Nawijn
- Department of Psychiatry, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- Department of Psychiatry, Amsterdam University Medical Centers, Location VU University Medical Center, VU University, Amsterdam, The Netherlands
| | - Steven M Nelson
- VISN 17 Center of Excellence for Research on Returning War Veterans, Waco, TX, USA
- Department of Psychology and Neuroscience, Baylor University, Waco, TX, USA
- Center for Vital Longevity, School of Behavioral and Brain Sciences, University of Texas at Dallas, Dallas, TX, USA
| | - Richard W J Neufeld
- Department of Psychiatry, Western University, London, ON, Canada
- Department of Psychology, Western University, London, ON, Canada
- Department of Neuroscience, Western University, London, ON, Canada
- Department of Psychology, University of British Columbia, Okanagan, BC, Canada
| | - Jack B Nitschke
- Department of Psychiatry, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Matthew Peverill
- Department of Psychology, University of Washington, Seattle, WA, USA
| | - Kerry J Ressler
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- Donders Institute for Brain, Cognition and Behavior, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Annerine Roos
- South African Medical Research Council / Stellenbosch University Genomics of Brain Disorders Research Unit, Department of Psychiatry, Stellenbosch University, Cape Town, South Africa
| | - Margaret A Sheridan
- Department of Psychology and Brain Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Anika Sierk
- University Medical Centre Charite, Berlin, Germany
| | - Alan Simmons
- Center of Excellence for Stress and Mental Health, VA San Diego Healthcare System, La Jolla, CA, USA
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Raluca M Simons
- Center for Brain and Behavior Research, University of South Dakota, Vermillion, SD, USA
- Department of Psychology, University of South Dakota, Vermillion, SD, USA
| | - Jeffrey S Simons
- Sioux Falls VA Health Care System, Sioux Falls, SD, USA
- Department of Psychology, University of South Dakota, Vermillion, SD, USA
| | - Jennifer Stevens
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Benjamin Suarez-Jimenez
- Department of Psychiatry, Columbia University Medical Center, New York, NY, USA
- New York State Psychiatric Institute, New York, NY, USA
| | - Danielle R Sullivan
- National Center for PTSD, VA Boston Healthcare System, Boston, MA, USA
- Department of Psychiatry, Boston University School of Medicine, Boston, MA, USA
| | - Jean Théberge
- Department of Psychiatry, Western University, London, ON, Canada
- Imaging Division, Lawson Health Research Institute, London, ON, Canada
- Department of Medical Biophysics, Western University, London, ON, Canada
| | | | | | - Steven J A van der Werff
- Department of Psychiatry, LUMC, Leiden, The Netherlands
- Leiden Institute for Brain and Cognition, Leiden, The Netherlands
| | - Sanne J H van Rooij
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Mirjam van Zuiden
- Department of Psychiatry, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Carmen Velez
- Department of Neurology, University of Utah, Salt Lake City, UT, USA
- Missouri Institute of Mental Health and University of Missouri, St Louis, MO, USA
| | - Mieke Verfaellie
- Department of Psychiatry, Boston University School of Medicine, Boston, MA, USA
- Memory Disorders Research Center, VA Boston Healthcare System, Boston, MA, USA
| | | | - Benjamin S C Wade
- Department of Neurology, University of Utah, Salt Lake City, UT, USA
- Missouri Institute of Mental Health and University of Missouri, St Louis, MO, USA
- Ahmanson-Lovelace Brain Mapping Center, Department of Neurology, University of California, Los Angeles, Los Angeles, CA, USA
| | | | | | - Sherry Winternitz
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- Division of Women's Mental Health, McLean Hospital, Belmont, MA, USA
| | - Jonathan Wolff
- Division of Depression and Anxiety Disorders, McLean Hospital, Belmont, MA, USA
| | - Gerald York
- Joint Trauma System, 3698 Chambers Pass, Joint Base San Antonio, Fort Sam Houston, TX, USA
- Alaska Radiology Associates, Anchorage, AK, USA
| | - Ye Zhu
- Laboratory for Traumatic Stress Studies, CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing, China
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, China
| | - Xi Zhu
- Department of Psychiatry, Columbia University Medical Center, New York, NY, USA
- New York State Psychiatric Institute, New York, NY, USA
| | - Chadi G Abdallah
- Clinical Neuroscience Division, National Center for PTSD; Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Richard Bryant
- School of Psychology, University of New South Wales, Sydney, NSW, Australia
| | - Judith K Daniels
- Department of Clinical Psychology, University of Groningen, Groningen, The Netherlands
| | - Richard J Davidson
- Center for Healthy Minds, University of Wisconsin-Madison, Madison, WI, USA
- Department of Psychiatry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Psychology, University of Wisconsin-Madison, Madison, WI, USA
| | - Kelene A Fercho
- Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, SD, USA
- Center for Brain and Behavior Research, University of South Dakota, Vermillion, SD, USA
- Sioux Falls VA Health Care System, Sioux Falls, SD, USA
- Civil Aerospace Medical Institute, US Federal Aviation Administration, Oklahoma City, OK, USA
| | - Carol Franz
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
- Center for Behavior Genetics of Aging, University of California, San Diego, La Jolla, CA, USA
| | - Elbert Geuze
- Brain Center Rudolf Magnus, Department of Psychiatry, UMCU, Utrecht, The Netherlands
- Brain Research and Innovation Centre, Ministry of Defence, Utrecht, The Netherlands
| | - Evan M Gordon
- VISN 17 Center of Excellence for Research on Returning War Veterans, Waco, TX, USA
- Department of Psychology and Neuroscience, Baylor University, Waco, TX, USA
- Center for Vital Longevity, School of Behavioral and Brain Sciences, University of Texas at Dallas, Dallas, TX, USA
| | - Milissa L Kaufman
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- Division of Women's Mental Health, McLean Hospital, Belmont, MA, USA
| | - William S Kremen
- Center of Excellence for Stress and Mental Health, VA San Diego Healthcare System, La Jolla, CA, USA
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
- Center for Behavior Genetics of Aging, University of California, San Diego, La Jolla, CA, USA
| | - Jim Lagopoulos
- University of the Sunshine Coast, Birtinya, QLD, Australia
| | - Ruth A Lanius
- Department of Psychiatry, Western University, London, ON, Canada
- Imaging Division, Lawson Health Research Institute, London, ON, Canada
- Department of Neuroscience, Western University, London, ON, Canada
| | - Michael J Lyons
- Dept. of Psychological & Brain Sciences, Boston University, Boston, MA, USA
| | - Stephen R McCauley
- Departments of Neurology and Pediatrics, Baylor College of Medicine, Houston, TX, USA
- H. Ben Taub Department of Physical Medicine and Rehabilitation, Baylor College of Medicine, Houston, TX, USA
| | - Regina McGlinchey
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- Geriatric Research Educational and Clinical Center and Translational Research Center for TBI and Stress Disorders, VA Boston Healthcare System, Boston, MA, USA
| | | | - William Milberg
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- ARQ National Psychotrauma Centre, Diemen, The Netherlands
| | - Yuval Neria
- Department of Psychiatry, Columbia University Medical Center, New York, NY, USA
- New York State Psychiatric Institute, New York, NY, USA
| | - Miranda Olff
- Department of Psychiatry, Amsterdam Neuroscience, Amsterdam University Medical Centers, Location Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- ARQ National Psychotrauma Centre, Diemen, The Netherlands
| | - Soraya Seedat
- South African Medical Research Council / Stellenbosch University Genomics of Brain Disorders Research Unit, Department of Psychiatry, Stellenbosch University, Cape Town, South Africa
| | - Martha Shenton
- Psychiatry Neuroimaging Laboratory, Department of Psychiatry, Brigham and Women's Hospital, Boston, MA, USA
- VA Boston Healthcare System, Brockton Division, Brockton, MA, USA
| | - Scott R Sponheim
- Minneapolis VA Health Care System, Minneapolis, MN, USA
- Department of Psychiatry, University of Minnesota, Minneapolis, MN, USA
| | - Dan J Stein
- SA Medical Research Council Unit on Risk & Resilience in Mental Disorders, Dept of Psychiatry & Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Murray B Stein
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
- Department of Family Medicine and Public Health, University of California, San Diego, La Jolla, CA, USA
| | - Thomas Straube
- Institute of Medical Psychology and Systems Neuroscience, University of Münster, Münster, Germany
| | - David F Tate
- Department of Neurology, University of Utah, Salt Lake City, UT, USA
- Missouri Institute of Mental Health and University of Missouri, St Louis, MO, USA
| | - Nic J A van der Wee
- Department of Psychiatry, LUMC, Leiden, The Netherlands
- Leiden Institute for Brain and Cognition, Leiden, The Netherlands
| | - Dick J Veltman
- Department of Psychiatry, Amsterdam University Medical Centers, Location VU University Medical Center, VU University, Amsterdam, The Netherlands
| | - Li Wang
- Laboratory for Traumatic Stress Studies, CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing, China
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, China
| | - Elisabeth A Wilde
- Department of Neurology, University of Utah, Salt Lake City, UT, USA
- H. Ben Taub Department of Physical Medicine and Rehabilitation, Baylor College of Medicine, Houston, TX, USA
- George E. Whalen Veterans Affairs Medical Center, Salt Lake City, UT, USA
| | - Paul M Thompson
- Imaging Genetics Center, Stevens Neuroimaging & Informatics Institute, Keck School of Medicine of USC, Marina del Rey, CA, USA
| | - Peter Kochunov
- Maryland Psychiatric Research Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Neda Jahanshad
- Imaging Genetics Center, Stevens Neuroimaging & Informatics Institute, Keck School of Medicine of USC, Marina del Rey, CA, USA
| | - Rajendra A Morey
- Brain Imaging and Analysis Center, Duke University, Durham, NC, USA
- VISN 6 MIRECC, Durham VA, Durham, NC, USA
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11
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Asif H, Alliey-Rodriguez N, Keedy S, Tamminga CA, Sweeney JA, Pearlson G, Clementz BA, Keshavan MS, Buckley P, Liu C, Neale B, Gershon ES. GWAS significance thresholds for deep phenotyping studies can depend upon minor allele frequencies and sample size. Mol Psychiatry 2021; 26:2048-2055. [PMID: 32066829 PMCID: PMC7429341 DOI: 10.1038/s41380-020-0670-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 01/28/2020] [Accepted: 01/29/2020] [Indexed: 02/01/2023]
Abstract
An important issue affecting genome-wide association studies with deep phenotyping (multiple correlated phenotypes) is determining the suitable family-wise significance threshold. Straightforward family-wise correction (Bonferroni) of p < 0.05 for 4.3 million genotypes and 335 phenotypes would give a threshold of p < 3.46E-11. This would be too conservative because it assumes all tests are independent. The effective number of tests, both phenotypic and genotypic, must be adjusted for the correlations between them. Spectral decomposition of the phenotype matrix and LD-based correction of the number of tested SNPs are currently used to determine an effective number of tests. In this paper, we compare these calculated estimates with permutation-determined family-wise significance thresholds. Permutations are performed by shuffling individual IDs of the genotype vector for this dataset, to preserve correlation of phenotypes. Our results demonstrate that the permutation threshold is influenced by minor allele frequency (MAF) of the SNPs, and by the number of individuals tested. For the more common SNPs (MAF > 0.1), the permutation family-wise threshold was in close agreement with spectral decomposition methods. However, for less common SNPs (0.05 < MAF ≤ 0.1), the permutation threshold calculated over all SNPs was off by orders of magnitude. This applies to the number of individuals studied (here 777) but not to very much larger numbers. Based on these findings, we propose that the threshold to find a particular level of family-wise significance may need to be established using separate permutations of the actual data for several MAF bins.
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Affiliation(s)
- Huma Asif
- Department of Psychiatry and Behavioral Neurosciences, University of Chicago, 924 East 57th Street Room. R016, Chicago, IL, 60637, USA.
| | - Ney Alliey-Rodriguez
- Department of Psychiatry and Behavioral Neurosciences, University of Chicago, 924 East 57th Street Room. R016, Chicago, IL, 60637, USA
| | - Sarah Keedy
- Department of Psychiatry and Behavioral Neurosciences, University of Chicago, 924 East 57th Street Room. R016, Chicago, IL, 60637, USA
| | - Carol A Tamminga
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - John A Sweeney
- Department of Psychiatry, University of Cincinnati, Cincinnati, OH, USA
| | - Godfrey Pearlson
- Departments of Psychiatry & Neuroscience, Yale University, New Haven, CT, USA
| | - Brett A Clementz
- Department of Psychology, University of Georgia, Athens, GA, USA
| | | | | | - Chunyu Liu
- Department of Psychiatry, SUNY Upstate Medical University, Binghamton, NY, USA
| | | | - Elliot S Gershon
- Department of Psychiatry and Behavioral Neurosciences, University of Chicago, 924 East 57th Street Room. R016, Chicago, IL, 60637, USA. .,Department of Human Genetics, University of Chicago, 924 East 57th Street Room. R016, Chicago, IL, 60637, USA.
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12
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Multiple functional variants in the IL1RL1 region are pretransplant markers for risk of GVHD and infection deaths. Blood Adv 2020; 3:2512-2524. [PMID: 31455667 DOI: 10.1182/bloodadvances.2019000075] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 06/16/2019] [Indexed: 01/31/2023] Open
Abstract
Graft-versus-host disease (GVHD) and infections are the 2 main causes of death without relapse after allogeneic hematopoietic cell transplantation (HCT). Elevated soluble serum simulation-2 (sST2), the product of IL1RL1 in plasma/serum post-HCT, is a validated GVHD biomarker. Hundreds of SNPs at 2q12.1 have been shown to be strongly associated with sST2 concentrations in healthy populations. We therefore hypothesized that the donor genetic variants in IL1RL1 correlate with sST2 protein levels associated with patient survival outcomes after HCT. We used DISCOVeRY-BMT (Determining the Influence of Susceptibility Conveying Variants Related to 1-Year Mortality after Blood and Marrow Transplantation), a genomic study of >3000 donor-recipient pairs, to inform our hypothesis. We first measured pre-HCT plasma/serum sST2 levels in a subset of DISCOVeRY-BMT donors (n = 757) and tested the association of donor sST2 levels with donor single nucleotide polymorphisms (SNPs) in the 2q12.1 region. Donor SNPs associated with sST2 levels were then tested for association with recipient death caused by acute GVHD (aGVHD)-, infection-, and transplant-related mortality in cohorts 1 and 2. Meta-analyses of cohorts 1 and 2 were performed using fixed-effects inverse variance weighting, and P values were corrected for multiple comparisons. Donor risk alleles in rs22441131 (P meta = .00026) and rs2310241 (P meta = .00033) increased the cumulative incidence of aGVHD death up to fourfold and were associated with high sST2 levels. Donor risk alleles at rs4851601 (P meta = 9.7 × 10-7), rs13019803 (P meta = 8.9 × 10-6), and rs13015714 (P meta = 5.3 × 10-4) increased cumulative incidence of infection death to almost sevenfold and were associated with low sST2 levels. These functional variants are biomarkers of infection or aGVHD death and could facilitate donor selection, prophylaxis, and a conditioning regimen to reduce post-HCT mortality.
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13
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Zhang H, Ahearn TU, Lecarpentier J, Barnes D, Beesley J, Qi G, Jiang X, O'Mara TA, Zhao N, Bolla MK, Dunning AM, Dennis J, Wang Q, Ful ZA, Aittomäki K, Andrulis IL, Anton-Culver H, Arndt V, Aronson KJ, Arun BK, Auer PL, Azzollini J, Barrowdale D, Becher H, Beckmann MW, Behrens S, Benitez J, Bermisheva M, Bialkowska K, Blanco A, Blomqvist C, Bogdanova NV, Bojesen SE, Bonanni B, Bondavalli D, Borg A, Brauch H, Brenner H, Briceno I, Broeks A, Brucker SY, Brüning T, Burwinkel B, Buys SS, Byers H, Caldés T, Caligo MA, Calvello M, Campa D, Castelao JE, Chang-Claude J, Chanock SJ, Christiaens M, Christiansen H, Chung WK, Claes KBM, Clarke CL, Cornelissen S, Couch FJ, Cox A, Cross SS, Czene K, Daly MB, Devilee P, Diez O, Domchek SM, Dörk T, Dwek M, Eccles DM, Ekici AB, Evans DG, Fasching PA, Figueroa J, Foretova L, Fostira F, Friedman E, Frost D, Gago-Dominguez M, Gapstur SM, Garber J, García-Sáenz JA, Gaudet MM, Gayther SA, Giles GG, Godwin AK, Goldberg MS, Goldgar DE, González-Neira A, Greene MH, Gronwald J, Guénel P, Häberle L, Hahnen E, Haiman CA, Hake CR, Hall P, Hamann U, Harkness EF, Heemskerk-Gerritsen BAM, Hillemanns P, Hogervorst FBL, Holleczek B, Hollestelle A, Hooning MJ, Hoover RN, Hopper JL, Howell A, Huebner H, Hulick PJ, Imyanitov EN, Isaacs C, Izatt L, Jager A, Jakimovska M, Jakubowska A, James P, Janavicius R, Janni W, John EM, Jones ME, Jung A, Kaaks R, Kapoor PM, Karlan BY, Keeman R, Khan S, Khusnutdinova E, Kitahara CM, Ko YD, Konstantopoulou I, Koppert LB, Koutros S, Kristensen VN, Laenkholm AV, Lambrechts D, Larsson SC, Laurent-Puig P, Lazaro C, Lazarova E, Lejbkowicz F, Leslie G, Lesueur F, Lindblom A, Lissowska J, Lo WY, Loud JT, Lubinski J, Lukomska A, MacInnis RJ, Mannermaa A, Manoochehri M, Manoukian S, Margolin S, Martinez ME, Matricardi L, McGuffog L, McLean C, Mebirouk N, Meindl A, Menon U, Miller A, Mingazheva E, Montagna M, Mulligan AM, Mulot C, Muranen TA, Nathanson KL, Neuhausen SL, Nevanlinna H, Neven P, Newman WG, Nielsen FC, Nikitina-Zake L, Nodora J, Offit K, Olah E, Olopade OI, Olsson H, Orr N, Papi L, Papp J, Park-Simon TW, Parsons MT, Peissel B, Peixoto A, Peshkin B, Peterlongo P, Peto J, Phillips KA, Piedmonte M, Plaseska-Karanfilska D, Prajzendanc K, Prentice R, Prokofyeva D, Rack B, Radice P, Ramus SJ, Rantala J, Rashid MU, Rennert G, Rennert HS, Risch HA, Romero A, Rookus MA, Rübner M, Rüdiger T, Saloustros E, Sampson S, Sandler DP, Sawyer EJ, Scheuner MT, Schmutzler RK, Schneeweiss A, Schoemaker MJ, Schöttker B, Schürmann P, Senter L, Sharma P, Sherman ME, Shu XO, Singer CF, Smichkoska S, Soucy P, Southey MC, Spinelli JJ, Stone J, Stoppa-Lyonnet D, Swerdlow AJ, Szabo CI, Tamimi RM, Tapper WJ, Taylor JA, Teixeira MR, Terry M, Thomassen M, Thull DL, Tischkowitz M, Toland AE, Tollenaar RAEM, Tomlinson I, Torres D, Troester MA, Truong T, Tung N, Untch M, Vachon CM, van den Ouweland AMW, van der Kolk LE, van Veen EM, vanRensburg EJ, Vega A, Wappenschmidt B, Weinberg CR, Weitzel JN, Wildiers H, Winqvist R, Wolk A, Yang XR, Yannoukakos D, Zheng W, Zorn KK, Milne RL, Kraft P, Simard J, Pharoah PDP, Michailidou K, Antoniou AC, Schmidt MK, Chenevix-Trench G, Easton DF, Chatterjee N, García-Closas M. Genome-wide association study identifies 32 novel breast cancer susceptibility loci from overall and subtype-specific analyses. Nat Genet 2020; 52:572-581. [PMID: 32424353 PMCID: PMC7808397 DOI: 10.1038/s41588-020-0609-2] [Citation(s) in RCA: 227] [Impact Index Per Article: 56.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 03/05/2020] [Indexed: 11/18/2022]
Abstract
Breast cancer susceptibility variants frequently show heterogeneity in associations by tumor subtype1-3. To identify novel loci, we performed a genome-wide association study including 133,384 breast cancer cases and 113,789 controls, plus 18,908 BRCA1 mutation carriers (9,414 with breast cancer) of European ancestry, using both standard and novel methodologies that account for underlying tumor heterogeneity by estrogen receptor, progesterone receptor and human epidermal growth factor receptor 2 status and tumor grade. We identified 32 novel susceptibility loci (P < 5.0 × 10-8), 15 of which showed evidence for associations with at least one tumor feature (false discovery rate < 0.05). Five loci showed associations (P < 0.05) in opposite directions between luminal and non-luminal subtypes. In silico analyses showed that these five loci contained cell-specific enhancers that differed between normal luminal and basal mammary cells. The genetic correlations between five intrinsic-like subtypes ranged from 0.35 to 0.80. The proportion of genome-wide chip heritability explained by all known susceptibility loci was 54.2% for luminal A-like disease and 37.6% for triple-negative disease. The odds ratios of polygenic risk scores, which included 330 variants, for the highest 1% of quantiles compared with middle quantiles were 5.63 and 3.02 for luminal A-like and triple-negative disease, respectively. These findings provide an improved understanding of genetic predisposition to breast cancer subtypes and will inform the development of subtype-specific polygenic risk scores.
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Affiliation(s)
- Haoyu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Department of Health and Human Services, Bethesda, MD, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Thomas U Ahearn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Department of Health and Human Services, Bethesda, MD, USA
| | - Julie Lecarpentier
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Daniel Barnes
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Jonathan Beesley
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Guanghao Qi
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Xia Jiang
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Tracy A O'Mara
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Ni Zhao
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Zumuruda Abu Ful
- Clalit National Cancer Control Center, Carmel Medical Center and Technion Faculty of Medicine, Haifa, Israel
| | - Kristiina Aittomäki
- Department of Clinical Genetics, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Irene L Andrulis
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Hoda Anton-Culver
- Department of Epidemiology, Genetic Epidemiology Research Institute, University of California, Irvine, Irvine, CA, USA
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kristan J Aronson
- Department of Public Health Sciences and Cancer Research Institute, Queen's University, Kingston, Ontario, Canada
| | - Banu K Arun
- Department of Breast Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Paul L Auer
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Jacopo Azzollini
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Daniel Barrowdale
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Heiko Becher
- Institute of Medical Biometry and Epidemiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Matthias W Beckmann
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center ER-EMN, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen, Germany
| | - Sabine Behrens
- Division of Cancer Epidemiology, DKFZ, Heidelberg, Germany
| | - Javier Benitez
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Valencia, Spain
| | - Marina Bermisheva
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
| | - Katarzyna Bialkowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Ana Blanco
- Molecular Medicine Unit, Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, Servicio Galego de Saude (SERGAS), Santiago de Compostela, Spain
- CIBERER, Santiago de Compostela, Spain
| | - Carl Blomqvist
- Department of Oncology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
- Department of Oncology, Örebro University Hospital, Örebro, Sweden
| | - Natalia V Bogdanova
- N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
- Department of Radiation Oncology, Hannover Medical School, Hannover, Germany
| | - Stig E Bojesen
- Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Bernardo Bonanni
- Division of Cancer Prevention and Genetics, European Institute of Oncology (IEO) IRCCS, Milan, Italy
| | - Davide Bondavalli
- Division of Cancer Prevention and Genetics, European Institute of Oncology (IEO) IRCCS, Milan, Italy
| | - Ake Borg
- Department of Oncology, Lund University and Skåne University Hospital, Lund, Sweden
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
- iFIT Cluster of Excellence, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK), DKFZ, Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), DKFZ, Heidelberg, Germany
- Division of Preventive Oncology, DKFZ and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Ignacio Briceno
- Bioscience Department, Faculty of Medicine, Universidad de la Sabana, Chia, Colombia
| | - Annegien Broeks
- Division of Molecular Pathology, The Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Sara Y Brucker
- Department of Women's Health, University of Tübingen, Tübingen, Germany
| | - Thomas Brüning
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance (IPA), Ruhr University Bochum, Bochum, Germany
| | - Barbara Burwinkel
- Molecular Epidemiology Group (C080), DKFZ, Heidelberg, Germany
- Molecular Biology of Breast Cancer, University Women's Clinic Heidelberg, University of Heidelberg, Heidelberg, Germany
| | - Saundra S Buys
- Department of Medicine, Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Helen Byers
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester NIHR Biomedical Research Centre, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Trinidad Caldés
- Medical Oncology Department, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Maria A Caligo
- Section of Molecular Genetics, Department of Laboratory Medicine, University Hospital of Pisa, Pisa, Italy
| | - Mariarosaria Calvello
- Division of Cancer Prevention and Genetics, European Institute of Oncology (IEO) IRCCS, Milan, Italy
| | - Daniele Campa
- Division of Cancer Epidemiology, DKFZ, Heidelberg, Germany
- Department of Biology, University of Pisa, Pisa, Italy
| | - Jose E Castelao
- Oncology and Genetics Unit, Instituto de Investigacion Sanitaria Galicia Sur (IISGS), Xerencia de Xestion Integrada de Vigo-SERGAS, Vigo, Spain
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, DKFZ, Heidelberg, Germany
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Department of Health and Human Services, Bethesda, MD, USA
| | - Melissa Christiaens
- Leuven Multidisciplinary Breast Center, Department of Oncology, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Hans Christiansen
- Department of Radiation Oncology, Hannover Medical School, Hannover, Germany
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, USA
| | | | - Christine L Clarke
- Westmead Institute for Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | - Sten Cornelissen
- Division of Molecular Pathology, The Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Angela Cox
- Sheffield Institute for Nucleic Acids (SInFoNiA), Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Simon S Cross
- Academic Unit of Pathology, Department of Neuroscience, University of Sheffield, Sheffield, UK
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Mary B Daly
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Peter Devilee
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Orland Diez
- Oncogenetics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Susan M Domchek
- Department of Medicine, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Miriam Dwek
- Department of Biomedical Sciences, Faculty of Science and Technology, University of Westminster, London, UK
| | - Diana M Eccles
- Cancer Sciences Academic Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Arif B Ekici
- Institute of Human Genetics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center ER-EMN, Erlangen, Germany
| | - D Gareth Evans
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester NIHR Biomedical Research Centre, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
- Division of Evolution and Genomic Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Peter A Fasching
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center ER-EMN, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen, Germany
- David Geffen School of Medicine, Department of Medicine, Division of Hematology and Oncology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jonine Figueroa
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh Medical School, Edinburgh, UK
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, INRASTES, National Centre for Scientific Research 'Demokritos', Athens, Greece
| | - Eitan Friedman
- The Susanne Levy Gertner Oncogenetics Unit, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Debra Frost
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, Galician Foundation of Genomic Medicine, IDIS, Complejo Hospitalario Universitario de Santiago, SERGAS, Santiago de Compostela, Spain
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
| | - Susan M Gapstur
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, USA
| | - Judy Garber
- Cancer Risk and Prevention Clinic, Dana-Farber Cancer Institute, Boston, MA, USA
| | - José A García-Sáenz
- Medical Oncology Department, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Mia M Gaudet
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, USA
| | - Simon A Gayther
- Center for Bioinformatics and Functional Genomics and the Cedars-Sinai Genomics Core, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, Victoria, Australia
| | - Andrew K Godwin
- Department of Pathology and Laboratory Medicine, Kansas University Medical Center, Kansas City, KS, USA
| | - Mark S Goldberg
- Department of Medicine, McGill University, Montréal, Québec, Canada
- Division of Clinical Epidemiology, Royal Victoria Hospital, McGill University, Montréal, Québec, Canada
- Breast Cancer Research Unit, Cancer Research Institute, University Malaya Medical Centre, Kuala Lumpur, Malaysia
| | - David E Goldgar
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Anna González-Neira
- Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Mark H Greene
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jacek Gronwald
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Pascal Guénel
- Cancer and Environment Group, Center for Research in Epidemiology and Population Health (CESP), INSERM, University Paris-Sud, University of Paris-Saclay, Paris, France
| | - Lothar Häberle
- Department of Gynaecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center ER-EMN, Erlangen, Germany
| | - Eric Hahnen
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Oncology, Södersjukhuset, Stockholm, Sweden
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, DKFZ, Heidelberg, Germany
| | - Elaine F Harkness
- Division of Informatics, Imaging and Data Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- Nightingale Breast Screening Centre, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | | | - Peter Hillemanns
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Frans B L Hogervorst
- Family Cancer Clinic, The Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | | | - Antoinette Hollestelle
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Maartje J Hooning
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Robert N Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Department of Health and Human Services, Bethesda, MD, USA
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Anthony Howell
- Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Hanna Huebner
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center ER-EMN, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen, Germany
| | - Peter J Hulick
- Center for Medical Genetics, NorthShore University HealthSystem, Evanston, IL, USA
| | | | - Claudine Isaacs
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Louise Izatt
- Clinical Genetics, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Agnes Jager
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Milena Jakimovska
- Research Centre for Genetic Engineering and Biotechnology 'Georgi D. Efremov', Macedonian Academy of Sciences and Arts, Skopje, Republic of Macedonia
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
- Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University, Szczecin, Poland
| | - Paul James
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Center, Melbourne, Victoria, Australia
| | - Ramunas Janavicius
- Hematology, Oncology and Transfusion Medicine Center, Department of Molecular and Regenerative Medicine, Vilnius University Hospital Santariskiu Clinics, Vilnius, Lithuania
- State Research Institute Center for Innovative Medicine, Vilnius, Lithuania
| | - Wolfgang Janni
- Department of Gynaecology and Obstetrics, University Hospital Ulm, Ulm, Germany
| | - Esther M John
- Department of Medicine, Division of Oncology, Stanford Cancer Institute, School of Medicine, Stanford University, Stanford, CA, USA
| | - Michael E Jones
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Audrey Jung
- Division of Cancer Epidemiology, DKFZ, Heidelberg, Germany
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, DKFZ, Heidelberg, Germany
| | - Pooja Middha Kapoor
- Division of Cancer Epidemiology, DKFZ, Heidelberg, Germany
- Faculty of Medicine, University of Heidelberg, Heidelberg, Germany
| | - Beth Y Karlan
- David Geffen School of Medicine, Department of Obstetrics and Gynecology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Renske Keeman
- Division of Molecular Pathology, The Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Sofia Khan
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State Medical University, Ufa, Russia
| | - Cari M Kitahara
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Yon-Dschun Ko
- Department of Internal Medicine, Evangelische Kliniken Bonn, Johanniter Krankenhaus, Bonn, Germany
| | - Irene Konstantopoulou
- Molecular Diagnostics Laboratory, INRASTES, National Centre for Scientific Research 'Demokritos', Athens, Greece
| | - Linetta B Koppert
- Department of Surgical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Stella Koutros
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Department of Health and Human Services, Bethesda, MD, USA
| | - Vessela N Kristensen
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | | | - Diether Lambrechts
- VIB Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory of Translational Genetics, Department of Human Genetics, University of Leuven, Leuven, Belgium
| | - Susanna C Larsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | | | - Conxi Lazaro
- Molecular Diagnostic Unit, Hereditary Cancer Program, Bellvitge Biomedical Research Institute (IDIBELL), Catalan Institute of Oncology (ICO), CIBERONC, Barcelona, Spain
| | - Emilija Lazarova
- Ss. Cyril and Methodius University in Skopje, Medical Faculty, University Clinic of Radiotherapy and Oncology, Skopje, Republic of North Macedonia
| | - Flavio Lejbkowicz
- Clalit National Cancer Control Center, Carmel Medical Center and Technion Faculty of Medicine, Haifa, Israel
| | - Goska Leslie
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | | | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, M. Sklodowska-Curie Cancer Center, Oncology Institute, Warsaw, Poland
| | - Wing-Yee Lo
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
| | - Jennifer T Loud
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Alicja Lukomska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Robert J MacInnis
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Arto Mannermaa
- Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | | | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Sara Margolin
- Department of Oncology, Södersjukhuset, Stockholm, Sweden
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Maria Elena Martinez
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
- Department of Family Medicine and Public Health, University of California, San Diego, La Jolla, CA, USA
| | - Laura Matricardi
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology (IOV)-IRCCS, Padua, Italy
| | - Lesley McGuffog
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Catriona McLean
- Department of Anatomical Pathology, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Noura Mebirouk
- Genetic Epidemiology of Cancer Team, INSERM U900, Institut Curie, PSL University, Mines ParisTech, Paris, France
| | - Alfons Meindl
- Department of Gynecology and Obstetrics, Ludwig Maximilian University of Munich, Munich, Germany
| | - Usha Menon
- MRC Clinical Trials Unit at UCL, Institute of Clinical Trials and Methodology, University College London, London, UK
| | - Austin Miller
- NRG Oncology, Statistics and Data Management Center, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Elvira Mingazheva
- Department of Genetics and Fundamental Medicine, Bashkir State Medical University, Ufa, Russia
| | - Marco Montagna
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology (IOV)-IRCCS, Padua, Italy
| | - Anna Marie Mulligan
- Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Claire Mulot
- Université Paris Sorbonne Cité, INSERM UMR-S1147, Paris, France
| | - Taru A Muranen
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Katherine L Nathanson
- Department of Medicine, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Patrick Neven
- Leuven Multidisciplinary Breast Center, Department of Oncology, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - William G Newman
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester NIHR Biomedical Research Centre, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
- Division of Evolution and Genomic Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Finn C Nielsen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Jesse Nodora
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
- Department of Family Medicine and Public Health, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kenneth Offit
- Clinical Genetics Research Laboratory, Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Edith Olah
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
| | - Olufunmilayo I Olopade
- Center for Clinical Cancer Genetics, The University of Chicago, Chicago, IL, USA
- Department of Clinical Pathology, University of Melbourne, Melbourne, Victoria, Australia
| | - Håkan Olsson
- Department of Cancer Epidemiology, Clinical Sciences, Lund University, Lund, Sweden
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nick Orr
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Laura Papi
- Unit of Medical Genetics, Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Florence, Italy
| | - Janos Papp
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
| | | | - Michael T Parsons
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Bernard Peissel
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Ana Peixoto
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
| | - Beth Peshkin
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Paolo Peterlongo
- Genome Diagnostics Program, IFOM, FIRC Institute of Molecular Oncology, Milan, Italy
| | - Julian Peto
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Kelly-Anne Phillips
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
- Peter MacCallum Cancer Center, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Marion Piedmonte
- NRG Oncology, Statistics and Data Management Center, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Dijana Plaseska-Karanfilska
- Research Centre for Genetic Engineering and Biotechnology 'Georgi D. Efremov', Macedonian Academy of Sciences and Arts, Skopje, Republic of Macedonia
| | - Karolina Prajzendanc
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Ross Prentice
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Darya Prokofyeva
- Department of Genetics and Fundamental Medicine, Bashkir State Medical University, Ufa, Russia
| | - Brigitte Rack
- Department of Gynaecology and Obstetrics, University Hospital Ulm, Ulm, Germany
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Research, INT, Milan, Italy
| | - Susan J Ramus
- Adult Cancer Program, Lowy Cancer Research Centre, University of NSW Sydney, Sydney, New South Wales, Australia
- School of Women's and Children's Health, Faculty of Medicine, University of NSW Sydney, Sydney, New South Wales, Australia
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | | | - Muhammad U Rashid
- Molecular Genetics of Breast Cancer, DKFZ, Heidelberg, Germany
- Department of Basic Sciences, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), Lahore, Pakistan
| | - Gad Rennert
- Clalit National Cancer Control Center, Carmel Medical Center and Technion Faculty of Medicine, Haifa, Israel
| | - Hedy S Rennert
- Clalit National Cancer Control Center, Carmel Medical Center and Technion Faculty of Medicine, Haifa, Israel
| | - Harvey A Risch
- Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, USA
| | - Atocha Romero
- Medical Oncology Department, Hospital Universitario Puerta de Hierro, Madrid, Spain
- Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
| | - Matti A Rookus
- Department of Epidemiology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Matthias Rübner
- Department of Gynaecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center ER-EMN, Erlangen, Germany
| | - Thomas Rüdiger
- Institute of Pathology, Staedtisches Klinikum Karlsruhe, Karlsruhe, Germany
| | | | - Sarah Sampson
- Prevent Breast Cancer Centre and Nightingale Breast Screening Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Durham, NC, USA
| | - Elinor J Sawyer
- Research Oncology, Guy's Hospital, King's College London, London, UK
| | - Maren T Scheuner
- Cancer Genetics and Prevention Program, University of California, San Francisco, San Francisco, CA, USA
| | - Rita K Schmutzler
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Andreas Schneeweiss
- Molecular Biology of Breast Cancer, University Women's Clinic Heidelberg, University of Heidelberg, Heidelberg, Germany
- NCT, University Hospital and DKFZ, Heidelberg, Germany
| | - Minouk J Schoemaker
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Ben Schöttker
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Peter Schürmann
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Leigha Senter
- Clinical Cancer Genetics Program, Division of Human Genetics, Department of Internal Medicine, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Priyanka Sharma
- Department of Internal Medicine, Division of Oncology, University of Kansas Medical Center, Westwood, Kansas City, KS, USA
| | - Mark E Sherman
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Jacksonville, FL, USA
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Christian F Singer
- Department of Obstetrics and Gynecology and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Snezhana Smichkoska
- Ss. Cyril and Methodius University in Skopje, Medical Faculty, University Clinic of Radiotherapy and Oncology, Skopje, Republic of North Macedonia
| | - Penny Soucy
- Genomics Center, Centre Hospitalier Universitaire de Québec-Université Laval Research Center, Québec City, Québec, Canada
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, Victoria, Australia
| | - John J Spinelli
- Population Oncology, BC Cancer, Vancouver, British Columbia, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jennifer Stone
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
- Curtin UWA Centre for Genetic Origins of Health and Disease, Curtin University and University of Western Australia, Perth, Western Australia, Australia
| | - Dominique Stoppa-Lyonnet
- Department of Genetics, INSERM U830, Institut Curie, Paris Descartes Sorbonne-Paris Cité University, Paris, France
| | - Anthony J Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Csilla I Szabo
- National Human Genome Research Institute, National Cancer Institute, Bethesda, MD, USA
| | - Rulla M Tamimi
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - Jack A Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Durham, NC, USA
- Epigenetic and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Durham, NC, USA
| | - Manuel R Teixeira
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
- Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
| | - MaryBeth Terry
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Darcy L Thull
- Department of Medicine, Magee-Womens Hospital, School of Medicine, University of Pittsburgh , Pittsburgh, PA, USA
| | - Marc Tischkowitz
- Program in Cancer Genetics, Departments of Human Genetics and Oncology, McGill University, Montréal, Québec, Canada
- Department of Medical Genetics, National Institute for Health Research, Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Amanda E Toland
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
| | - Rob A E M Tollenaar
- Department of Surgery, Leiden University Medical Center, Leiden, the Netherlands
| | - Ian Tomlinson
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Wellcome Trust Centre for Human Genetics and Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Diana Torres
- Molecular Genetics of Breast Cancer, DKFZ, Heidelberg, Germany
- Institute of Human Genetics, Pontificia Universidad Javeriana, Bogota, Colombia
| | - Melissa A Troester
- Department of Epidemiology, Gillings School of Global Public Health and UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Thérèse Truong
- Cancer and Environment Group, Center for Research in Epidemiology and Population Health (CESP), INSERM, University Paris-Sud, University of Paris-Saclay, Paris, France
| | - Nadine Tung
- Department of Medical Oncology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Michael Untch
- Department of Gynecology and Obstetrics, Helios Clinics Berlin-Buch, Berlin, Germany
| | - Celine M Vachon
- Department of Health Science Research, Division of Epidemiology, Mayo Clinic, Rochester, MN, USA
| | | | - Lizet E van der Kolk
- Family Cancer Clinic, The Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Elke M van Veen
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester NIHR Biomedical Research Centre, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
- Division of Evolution and Genomic Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | | | - Ana Vega
- Molecular Medicine Unit, Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, Servicio Galego de Saude (SERGAS), Santiago de Compostela, Spain
- CIBERER, Santiago de Compostela, Spain
| | - Barbara Wappenschmidt
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Clarice R Weinberg
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, NIH, Durham, NC, USA
| | | | - Hans Wildiers
- Leuven Multidisciplinary Breast Center, Department of Oncology, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit, Biocenter Oulu, University of Oulu, Oulu, Finland
- Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre Oulu, Oulu, Finland
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Alicja Wolk
- Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University, Szczecin, Poland
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Xiaohong R Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Department of Health and Human Services, Bethesda, MD, USA
| | - Drakoulis Yannoukakos
- Molecular Diagnostics Laboratory, INRASTES, National Centre for Scientific Research 'Demokritos', Athens, Greece
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Kristin K Zorn
- Magee-Womens Hospital, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, Victoria, Australia
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jacques Simard
- Genomics Center, Centre Hospitalier Universitaire de Québec-Université Laval Research Center, Québec City, Québec, Canada
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Marjanka K Schmidt
- Division of Molecular Pathology, The Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Nilanjan Chatterjee
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
| | - Montserrat García-Closas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Department of Health and Human Services, Bethesda, MD, USA
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14
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Tsekmekidou X, Tsetsos F, Koufakis T, Karras SN, Georgitsi M, Papanas N, Papazoglou D, Roumeliotis A, Panagoutsos S, Thodis E, Theodoridis M, Pasadakis P, Maltezos E, Paschou P, Kotsa K. Association between CUBN gene variants, type 2 diabetes and vitamin D concentrations in an elderly Greek population. J Steroid Biochem Mol Biol 2020; 198:105549. [PMID: 31770575 DOI: 10.1016/j.jsbmb.2019.105549] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 11/03/2019] [Accepted: 11/20/2019] [Indexed: 12/14/2022]
Abstract
Accumulating evidence suggests a potential implication of vitamin D biological network in the pathogenesis of diabetes mellitus. The megalin-cubilin endocytotic system constitutes a key transport structure, with a modulating role in vitamin D metabolism. We aimed to assess the contribution of variants in the CUBN gene to the genetic risk of Type 2 Diabetes Mellitus (T2DM). 95 polymorphisms within CUBN were genotyped in 716 patients with T2DM and 542 controls of Greek origin. Samples were analyzed on Illumina Human PsychArray. Permutation test analysis was implemented to determine statistical significance. Twenty-five-hydroxy-vitamin-D [25(OH)D)] levels were measured in a sub-group of participants (n = 276). Permutation analysis associated rs11254375_G/T (pemp = 0.00049, OR = 1.482), rs6602175_G/T (pemp = 0.016, OR = 0.822), rs1801224_G/T (pemp = 0.025, OR = 0.830), rs4366393_A/G (pemp = 0.028, OR = 0.829) and rs7071576_A/G (pemp = 0.04, OR = 1.219) with T2DM. Mean 25(OH)D concentrations were significantly lower in patients with T2DM compared to controls (16.70 ± 6.69 ng/ml vs 18.51 ± 6.71 ng/ml, p < 0.001), although both groups were vitamin D deficient. In a further quantitative analysis, rs41301097 was strongly associated with higher 25(OH)D concentrations (p = 5.233e-6, beta = 15.95). Our results indicate a potential role of CUBN gene in T2DM genetic susceptibility in the Greek population. These findings may also denote an indirect effect of vitamin D metabolism dysregulation on the pathogenesis of T2DM. Further studies are required to replicate our findings and clarify the complex underlying mechanisms.
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Affiliation(s)
- Xanthippi Tsekmekidou
- Division of Endocrinology and Metabolism and Diabetes Center, First Department of Internal Medicine, Medical School, Aristotle University of Thessaloniki, AHEPA University Hospital, Thessaloniki, Greece
| | - Fotis Tsetsos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Theocharis Koufakis
- Division of Endocrinology and Metabolism and Diabetes Center, First Department of Internal Medicine, Medical School, Aristotle University of Thessaloniki, AHEPA University Hospital, Thessaloniki, Greece
| | - Spyridon N Karras
- Division of Endocrinology and Metabolism and Diabetes Center, First Department of Internal Medicine, Medical School, Aristotle University of Thessaloniki, AHEPA University Hospital, Thessaloniki, Greece
| | - Marianthi Georgitsi
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece; Laboratory of General Biology-Genetics, Department of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Nikolaos Papanas
- Diabetes Centre, Second Department of Internal Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Dimitrios Papazoglou
- Diabetes Centre, Second Department of Internal Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | | | | | - Elias Thodis
- Department of Nephrology, Democritus University of Thrace, Alexandroupolis, Greece
| | - Marios Theodoridis
- Department of Nephrology, Democritus University of Thrace, Alexandroupolis, Greece
| | - Ploumis Pasadakis
- Department of Nephrology, Democritus University of Thrace, Alexandroupolis, Greece
| | - Eustratios Maltezos
- Diabetes Centre, Second Department of Internal Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Peristera Paschou
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Kalliopi Kotsa
- Division of Endocrinology and Metabolism and Diabetes Center, First Department of Internal Medicine, Medical School, Aristotle University of Thessaloniki, AHEPA University Hospital, Thessaloniki, Greece.
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15
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Zhou Z, Lunetta KL, Smith AK, Wolf EJ, Stone A, Schichman SA, McGlinchey RE, Milberg WP, Miller MW, Logue MW. Correction for multiple testing in candidate-gene methylation studies. Epigenomics 2019; 11:1089-1105. [PMID: 31240951 PMCID: PMC7132638 DOI: 10.2217/epi-2018-0204] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 05/15/2019] [Indexed: 01/02/2023] Open
Abstract
Aim: We compared the performance of multiple testing corrections for candidate gene methylation studies, namely Sidak (accurate Bonferroni), false-discovery rate and three adjustments that incorporate the correlation between CpGs: extreme tail theory (ETT), Gao et al. (GEA), and Li and Ji methods. Materials & methods: The experiment-wide type 1 error rate was examined in simulations based on Illumina EPIC and 450K data. Results: For high-correlation genes, Sidak and false-discovery rate corrections were conservative while the Li and Ji method was liberal. The GEA method tended to be conservative unless a threshold parameter was adjusted. The ETT yielded an appropriate type 1 error rate. Conclusion: For genes with substantial correlation across measured CpGs, GEA and ETT can appropriately correct for multiple testing in candidate gene methylation studies.
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Affiliation(s)
- Zhenwei Zhou
- National Center for PTSD, VA Boston Healthcare System, Boston, MA 02130, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Alicia K Smith
- Department of Gynecology & Obstetrics, Emory University, Atlanta, GA 30322, USA
- Department of Psychiatry & Behavioral Sciences, Emory University, Atlanta, GA 30329, USA
| | - Erika J Wolf
- National Center for PTSD, VA Boston Healthcare System, Boston, MA 02130, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Annjanette Stone
- Pharmacogenomics Analysis Laboratory, Research Service, Central Arkansas Veterans Healthcare System, Little Rock, AR 72205, USA
| | - Steven A Schichman
- Pharmacogenomics Analysis Laboratory, Research Service, Central Arkansas Veterans Healthcare System, Little Rock, AR 72205, USA
| | - Regina E McGlinchey
- Geriatric Research Educational & Clinical Center & Translational Research Center for TBI & Stress Disorders, VA Boston Healthcare System, Boston, MA 02130, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA 02215, USA
| | - William P Milberg
- Department of Psychiatry, Harvard Medical School, Boston, MA 02215, USA
- Department of Psychiatry, Boston University, Boston, MA 02118, USA
| | - Mark W Miller
- National Center for PTSD, VA Boston Healthcare System, Boston, MA 02130, USA
- Department of Psychiatry, Boston University, Boston, MA 02118, USA
| | - Mark W Logue
- National Center for PTSD, VA Boston Healthcare System, Boston, MA 02130, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
- Department of Psychiatry, Boston University, Boston, MA 02118, USA
- Biomedical Genetics, Boston University School of Medicine, Boston, MA 02118, USA
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16
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Jiang J, Cole JB, Freebern E, Da Y, VanRaden PM, Ma L. Functional annotation and Bayesian fine-mapping reveals candidate genes for important agronomic traits in Holstein bulls. Commun Biol 2019; 2:212. [PMID: 31240250 PMCID: PMC6582147 DOI: 10.1038/s42003-019-0454-y] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 04/29/2019] [Indexed: 12/19/2022] Open
Abstract
A hundred years of data collection in dairy cattle can facilitate powerful studies of complex traits. Cattle GWAS have identified many associated genomic regions. With increasing numbers of cattle sequenced, fine-mapping of causal variants is becoming possible. Here we imputed selected sequence variants to 27,214 Holstein bulls that have highly reliable phenotypes for 35 production, reproduction, and body conformation traits. We performed single-marker scans for the 35 traits and multi-trait tests of the three trait groups, revealing 282 candidate QTL for fine-mapping. We developed a Bayesian Fine-MAPping approach (BFMAP) to integrate fine-mapping with functional enrichment analysis. Our fine-mapping identified 69 promising candidate genes, including ABCC9, VPS13B, MGST1, SCD, MKL1, CSN1S1 for production, CHEK2, GC, KALRN for reproduction, and TMTC2, ARRDC3, ZNF613, CCND2, FGF6 for conformation traits. Collectively, these results demonstrated the utility of BFMAP, identified candidate genes, and enhanced our understanding of the genetic basis of cattle complex traits.
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Affiliation(s)
- Jicai Jiang
- 1Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742 USA
| | - John B Cole
- 2Animal Genomics and Improvement Laboratory, USDA, Building 5, Beltsville, MD 20705 USA
| | - Ellen Freebern
- 1Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742 USA
| | - Yang Da
- 3Department of Animal Science, University of Minnesota, St Paul, MN 55108 USA
| | - Paul M VanRaden
- 2Animal Genomics and Improvement Laboratory, USDA, Building 5, Beltsville, MD 20705 USA
| | - Li Ma
- 1Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742 USA
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17
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Genetic Predisposition to Symptomatic Lumbar Disk Herniation in Pediatric and Young Adult Patients. Spine (Phila Pa 1976) 2019; 44:E640-E649. [PMID: 30475332 DOI: 10.1097/brs.0000000000002949] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
STUDY DESIGN Case-control whole-genome sequencing analysis of a highly select, young cohort with symptomatic lumbar disk herniation (LDH) compared with the standard variation in a large reference population. OBJECTIVE To assess genetic influences predisposing pediatric and young adult patients to symptomatic LDH. SUMMARY OF BACKGROUND DATA LDH has traditionally been attributed to natural weakening or mechanical insult, but recent literature supports a potential genetic influence. METHODS Young patients with symptomatic, clinically confirmed LDH who underwent surgical treatment were included. Patients were younger than the average age of presentation, limiting the influence of environmental risks. DNA collected from these patients was compared with a reference genome (1000 Genomes Project). A genome-wide association study using whole-genome sequencing was used to characterize genetic mutations potentially associated with LDH. RESULTS Among the 61 candidate genes flagged, 20 had missense mutations in 2 or more LDH cases. Missense mutations in collagen-encoding genes were observed in 12 of 15 patients (80%). A potential association with clinical presentation was indicated by odds ratios of key single-nucleotide polymorphism (SNP) variants in genes that encode collagen. Relative to the reference population, the LDH cohort demonstrated two statistically significant SNP variants in the gene encoding for aggrecan, a protein that facilitates load-bearing properties in the cartilaginous end plate. Aggrecan genes SNPs rs3817428 and rs11638262 were significantly associated with decreased odds of symptomatic LDH: odds ratio 0.05 (0.02-0.11) and 0.04 (0-0.26), respectively (P < 1 × 10 for both). CONCLUSION These results suggest that collagen-encoding variants may be a genetic risk factor for LDH. They also shed new light on the role of variants that impact aggrecan, which sustains the cartilaginous end plate. Genetic predisposition to LDH may therefore be related to a multimodal combination of mutations that affect the nucleus pulposus, annulus fibrosus, and the cartilaginous end plates. LEVEL OF EVIDENCE 4.
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18
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Choi S, Lee S, Kim Y, Hwang H, Park T. HisCoM-GGI: Hierarchical structural component analysis of gene-gene interactions. J Bioinform Comput Biol 2018; 16:1840026. [PMID: 30567476 DOI: 10.1142/s0219720018400267] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Although genome-wide association studies (GWAS) have successfully identified thousands of single nucleotide polymorphisms (SNPs) associated with common diseases, these observations are limited for fully explaining "missing heritability". Determining gene-gene interactions (GGI) are one possible avenue for addressing the missing heritability problem. While many statistical approaches have been proposed to detect GGI, most of these focus primarily on SNP-to-SNP interactions. While there are many advantages of gene-based GGI analyses, such as reducing the burden of multiple-testing correction, and increasing power by aggregating multiple causal signals across SNPs in specific genes, only a few methods are available. In this study, we proposed a new statistical approach for gene-based GGI analysis, "Hierarchical structural CoMponent analysis of Gene-Gene Interactions" (HisCoM-GGI). HisCoM-GGI is based on generalized structured component analysis, and can consider hierarchical structural relationships between genes and SNPs. For a pair of genes, HisCoM-GGI first effectively summarizes all possible pairwise SNP-SNP interactions into a latent variable, from which it then performs GGI analysis. HisCoM-GGI can evaluate both gene-level and SNP-level interactions. Through simulation studies, HisCoM-GGI demonstrated higher statistical power than existing gene-based GGI methods, in analyzing a GWAS of a Korean population for identifying GGI associated with body mass index. Resultantly, HisCoM-GGI successfully identified 14 potential GGI, two of which, (NCOR2 <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mo>×</mml:mo></mml:math> SPOCK1) and (LINGO2 <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mo>×</mml:mo></mml:math> ZNF385D) were successfully replicated in independent datasets. We conclude that HisCoM-GGI method may be a valuable tool for genome to identify GGI in missing heritability, allowing us to better understand the biological genetic mechanisms of complex traits. We conclude that HisCoM-GGI method may be a valuable tool for genome to identify GGI in missing heritability, allowing us to better understand biological genetic mechanisms of complex traits. An implementation of HisCoM-GGI can be downloaded from the website ( http://statgen.snu.ac.kr/software/hiscom-ggi ).
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Affiliation(s)
- Sungkyoung Choi
- Department of Pharmacology, Yonsei University College of Medicine, 50-1 Yonsei-ro Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Sungyoung Lee
- Center for Precision Medicine, Seoul National University Hospital, 71 Daehak-ro Jongno-gu, Seoul 03082, Republic of Korea
| | - Yongkang Kim
- Department of Statistics, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul 08826, Republic of Korea.,Department of Psychology, McGill University, 2001 Avenue McGill College, Montreal, Quebec H3A 1G1, Canada
| | - Heungsun Hwang
- Department of Psychology, McGill University, 2001 Avenue McGill College, Montreal, Quebec H3A 1G1, Canada
| | - Taesung Park
- Department of Statistics, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul 08826, Republic of Korea.,Interdisciplinary Program in Bioinformatics, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul 08826, Republic of Korea
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19
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Machine learning identifies interacting genetic variants contributing to breast cancer risk: A case study in Finnish cases and controls. Sci Rep 2018; 8:13149. [PMID: 30177847 PMCID: PMC6120908 DOI: 10.1038/s41598-018-31573-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 08/22/2018] [Indexed: 01/01/2023] Open
Abstract
We propose an effective machine learning approach to identify group of interacting single nucleotide polymorphisms (SNPs), which contribute most to the breast cancer (BC) risk by assuming dependencies among BCAC iCOGS SNPs. We adopt a gradient tree boosting method followed by an adaptive iterative SNP search to capture complex non-linear SNP-SNP interactions and consequently, obtain group of interacting SNPs with high BC risk-predictive potential. We also propose a support vector machine formed by the identified SNPs to classify BC cases and controls. Our approach achieves mean average precision (mAP) of 72.66, 67.24 and 69.25 in discriminating BC cases and controls in KBCP, OBCS and merged KBCP-OBCS sample sets, respectively. These results are better than the mAP of 70.08, 63.61 and 66.41 obtained by using a polygenic risk score model derived from 51 known BC-associated SNPs, respectively, in KBCP, OBCS and merged KBCP-OBCS sample sets. BC subtype analysis further reveals that the 200 identified KBCP SNPs from the proposed method performs favorably in classifying estrogen receptor positive (ER+) and negative (ER-) BC cases both in KBCP and OBCS data. Further, a biological analysis of the identified SNPs reveals genes related to important BC-related mechanisms, estrogen metabolism and apoptosis.
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20
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Zhu Q, Yan L, Liu Q, Zhang C, Wei L, Hu Q, Preus L, Clay-Gilmour AI, Onel K, Stram DO, Pooler L, Sheng X, Haiman CA, Zhu X, Spellman SR, Pasquini M, McCarthy PL, Liu S, Hahn T, Sucheston-Campbell LE. Exome chip analyses identify genes affecting mortality after HLA-matched unrelated-donor blood and marrow transplantation. Blood 2018; 131:2490-2499. [PMID: 29610366 PMCID: PMC5981168 DOI: 10.1182/blood-2017-11-817973] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 03/20/2018] [Indexed: 02/07/2023] Open
Abstract
Although survival outcomes have significantly improved, up to 40% of patients die within 1 year of HLA-matched unrelated-donor blood and marrow transplantation (BMT). To identify non-HLA genetic contributors to mortality after BMT, we performed the first exome-wide association study in the DISCOVeRY-BMT cohorts using the Illumina HumanExome BeadChip. This study includes 2473 patients with acute myeloid leukemia, acute lymphoblastic leukemia, or myelodysplastic syndrome and 2221 10/10 HLA-matched donors treated from 2000 to 2011. Single-variant and gene-level analyses were performed on overall survival (OS), transplantation-related mortality (TRM), and disease-related mortality (DRM). Genotype mismatches between recipients and donors in a rare nonsynonymous variant of testis-expressed gene TEX38 significantly increased risk of TRM, which was more dramatic when either the recipient or donor was female. Using the SKAT-O test to evaluate gene-level effects, variant genotypes of OR51D1 in recipients were significantly associated with OS and TRM. In donors, 4 (ALPP, EMID1, SLC44A5, LRP1), 1 (HHAT), and 2 genes (LYZL4, NT5E) were significantly associated with OS, TRM, and DRM, respectively. Inspection of NT5E crystal structures showed 4 of the associated variants affected the enzyme structure and likely decreased the catalytic efficiency of the enzyme. Further confirmation of these findings and additional functional studies may provide individualized risk prediction and prognosis, as well as alternative donor selection strategies.
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Affiliation(s)
- Qianqian Zhu
- Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY
| | - Li Yan
- Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY
| | - Qian Liu
- Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY
| | - Chi Zhang
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE
| | - Lei Wei
- Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY
| | - Qiang Hu
- Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY
| | - Leah Preus
- College of Pharmacy, The Ohio State University, Columbus, OH
| | | | - Kenan Onel
- Department of Pediatric Hematology/Oncology, Cohen Children's Medical Center, Northwell Health, Manhasset, NY
| | - Daniel O Stram
- Preventive Medicine, University of Southern California, Los Angeles, CA
| | - Loreall Pooler
- Preventive Medicine, University of Southern California, Los Angeles, CA
| | - Xin Sheng
- Preventive Medicine, University of Southern California, Los Angeles, CA
| | | | - Xiaochun Zhu
- Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, WI
| | - Stephen R Spellman
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program/Be The Match, Minneapolis, MN
| | - Marcelo Pasquini
- Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, WI
| | - Philip L McCarthy
- Blood and Marrow Transplant Program, Department of Medicine, Roswell Park Cancer Institute, Buffalo, NY; and
| | - Song Liu
- Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY
| | - Theresa Hahn
- Blood and Marrow Transplant Program, Department of Medicine, Roswell Park Cancer Institute, Buffalo, NY; and
| | - Lara E Sucheston-Campbell
- College of Pharmacy, The Ohio State University, Columbus, OH
- College of Veterinary Medicine, The Ohio State University, Columbus, OH
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21
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Catalano C, da Silva Filho MI, Frank C, Jiraskova K, Vymetalkova V, Levy M, Liska V, Vycital O, Naccarati A, Vodickova L, Hemminki K, Vodicka P, Weber ANR, Försti A. Investigation of single and synergic effects of NLRC5 and PD-L1 variants on the risk of colorectal cancer. PLoS One 2018; 13:e0192385. [PMID: 29408916 PMCID: PMC5800657 DOI: 10.1371/journal.pone.0192385] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 01/20/2018] [Indexed: 12/31/2022] Open
Abstract
Constitutive activation of interferon signaling pathways has been reported in colorectal cancer (CRC), leading to a strong CD8+ T cell response through stimulation of NLRC5 expression. Primed CD8+ T cell expansion, however, may be negatively regulated by PD-L1 expression. Additionally, aberrant PD-L1 expression enables cancer cells to escape the immune attack. Our study aimed to select potential regulatory variants in the NLRC5 and PD-L1 genes by using several online in silico tools, such as UCSC browser, HaploReg, Regulome DB, Gtex Portal, microRNA and transcription factor binding site prediction tools and to investigate their influence on CRC risk in a Czech cohort of 1424 CRC patients and 1114 healthy controls. Logistic regression analysis adjusted for age and gender reported a moderate association between rectal cancer risk and two NLRC5 SNPs, rs1684575 T>G (OR: 1.60, 95% CI: 1.13-2.27, recessive model) and rs3751710 (OR: 0.70, 95% CI: 0.51-0.96, dominant model). Given that a combination of genetic variants, rather than a single polymorphism, may explain better the genetic etiology of CRC, we studied the interplay between the variants within NLRC5, PD-L1 and the previously genotyped IFNGR1 and IFNGR2 variants, to evaluate their involvement in the risk of CRC development. Overall we obtained 18 pair-wise interactions within and between the NLRC5 ad PD-L1 genes and 6 more when IFNGR variants were added. Thirteen out of the 24 interactions were below the threshold for the FDR calculated and controlled at an arbitrary level q*<0.10. Furthermore, the interaction IFNGR2 rs1059293 C>T-NLRC5 rs289747 G>A (P<0.0001) remained statistically significant even after Bonferroni correction. Our data suggest that not only a single genetic variant but also an interaction between two or more variants within genes involved in immune regulation may play important roles in the onset of CRC, providing therefore novel biological information, which could eventually improve CRC risk management but also PD-1-based immunotherapy in CRC.
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Affiliation(s)
- Calogerina Catalano
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Christoph Frank
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Katerina Jiraskova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, 1 Medical Faculty, Charles University, Prague, Czech Republic
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, 1 Medical Faculty, Charles University, Prague, Czech Republic
| | - Miroslav Levy
- Department of Surgery, First Medical Faculty, Charles University and Thomayer Hospital, Prague, Czech Republic
| | - Vaclav Liska
- Department of Surgery, First Medical Faculty, Charles University and Thomayer Hospital, Prague, Czech Republic
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University Prague, Pilsen, Czech Republic
| | - Ondrej Vycital
- Department of Surgery, First Medical Faculty, Charles University and Thomayer Hospital, Prague, Czech Republic
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University Prague, Pilsen, Czech Republic
| | - Alessio Naccarati
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Molecular and Genetic Epidemiology, Italian Institute for Genomic Medicine (IIGM), Turin, Italy
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, 1 Medical Faculty, Charles University, Prague, Czech Republic
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University Prague, Pilsen, Czech Republic
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Center for Primary Health Care Research, Clinical Research Center, Lund University, Malmö, Sweden
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, 1 Medical Faculty, Charles University, Prague, Czech Republic
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University Prague, Pilsen, Czech Republic
| | - Alexander N. R. Weber
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Asta Försti
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Center for Primary Health Care Research, Clinical Research Center, Lund University, Malmö, Sweden
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22
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Ryu E, Nassan M, Jenkins GD, Armasu SM, Andreazza A, McElroy SL, Vawter MP, Frye MA, Biernacka JM. A Genome-Wide Search for Bipolar Disorder Risk Loci Modified by Mitochondrial Genome Variation. MOLECULAR NEUROPSYCHIATRY 2017; 3:125-134. [PMID: 29594131 DOI: 10.1159/000464444] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 02/22/2017] [Indexed: 12/13/2022]
Abstract
Mitochondrial DNA mutations have been reported to be associated with bipolar disorder (BD). In this study, we performed genome-wide analyses to assess mitochondrial single-nucleotide polymorphism (mtSNP) effects on BD risk and early-onset BD (EOBD) among BD patients, focusing on interaction effects between nuclear SNPs (nSNPs) and mtSNPs. Common nSNP and mtSNP data from European American BD cases (n = 1,001) and controls (n = 1,034) from the Genetic Association Information Network BD study were analyzed to assess the joint effect of nSNP and nSNP-mtSNP interaction on the risk of BD and EOBD. The effect of nSNP-mtSNP interactions was also assessed. For BD risk, the strongest evidence of an association was obtained for nSNP rs1880924 in MGAM and mtSNP rs3088309 in CytB (pjoint = 8.2 × 10-8, pint = 1.4 × 10-4). Our results also suggest that the minor allele of the nSNP rs583990 in CTNNA2 increases the risk of EOBD among carriers of the mtSNP rs3088309 minor allele, while the nSNP has no effect among those carrying the mtSNP major allele (OR = 4.53 vs. 1.05, pjoint = 2.1 × 10-7, pint = 1.16 × 10-6). While our results are not statistically significant after multiple testing correction and a large-sample replication is required, our exploratory study demonstrates the potential importance of considering the mitochondrial genome for identifying genetic factors associated with BD.
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Affiliation(s)
- Euijung Ryu
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Malik Nassan
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | - Gregory D Jenkins
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | | | - Ana Andreazza
- Department of Department of Psychiatry and Pharmacology, University of Toronto, Toronto, ON, Canada
| | - Susan L McElroy
- Department of Lindner Center of HOPE, Mason, OH, USA.,Department of University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Marquis P Vawter
- Department of Psychiatry and Human Behavior, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Mark A Frye
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | - Joanna M Biernacka
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA.,Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
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23
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McGinnis R, Steinthorsdottir V, Williams NO, Thorleifsson G, Shooter S, Hjartardottir S, Bumpstead S, Stefansdottir L, Hildyard L, Sigurdsson JK, Kemp JP, Silva GB, Thomsen LCV, Jääskeläinen T, Kajantie E, Chappell S, Kalsheker N, Moffett A, Hiby S, Lee WK, Padmanabhan S, Simpson NAB, Dolby VA, Staines-Urias E, Engel SM, Haugan A, Trogstad L, Svyatova G, Zakhidova N, Najmutdinova D, Dominiczak AF, Gjessing HK, Casas JP, Dudbridge F, Walker JJ, Pipkin FB, Thorsteinsdottir U, Geirsson RT, Lawlor DA, Iversen AC, Magnus P, Laivuori H, Stefansson K, Morgan L. Variants in the fetal genome near FLT1 are associated with risk of preeclampsia. Nat Genet 2017. [PMID: 28628106 DOI: 10.1038/ng.3895] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Preeclampsia, which affects approximately 5% of pregnancies, is a leading cause of maternal and perinatal death. The causes of preeclampsia remain unclear, but there is evidence for inherited susceptibility. Genome-wide association studies (GWAS) have not identified maternal sequence variants of genome-wide significance that replicate in independent data sets. We report the first GWAS of offspring from preeclamptic pregnancies and discovery of the first genome-wide significant susceptibility locus (rs4769613; P = 5.4 × 10-11) in 4,380 cases and 310,238 controls. This locus is near the FLT1 gene encoding Fms-like tyrosine kinase 1, providing biological support, as a placental isoform of this protein (sFlt-1) is implicated in the pathology of preeclampsia. The association was strongest in offspring from pregnancies in which preeclampsia developed during late gestation and offspring birth weights exceeded the tenth centile. An additional nearby variant, rs12050029, associated with preeclampsia independently of rs4769613. The newly discovered locus may enhance understanding of the pathophysiology of preeclampsia and its subtypes.
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Affiliation(s)
| | | | | | | | | | - Sigrun Hjartardottir
- Department of Obstetrics and Gynecology, Landspitali University Hospital, Reykjavik, Iceland
| | | | | | | | | | - John P Kemp
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK.,University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
| | - Gabriela B Silva
- Centre of Molecular Inflammation Research (CEMIR) and Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.,St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Liv Cecilie V Thomsen
- Centre of Molecular Inflammation Research (CEMIR) and Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway
| | - Tiina Jääskeläinen
- Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Eero Kajantie
- National Institute for Health and Welfare, Helsinki, Finland.,Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,PEDEGO Research Unit, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Sally Chappell
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Noor Kalsheker
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Ashley Moffett
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Susan Hiby
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Wai Kwong Lee
- BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Sandosh Padmanabhan
- BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Nigel A B Simpson
- Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Leeds, UK
| | - Vivien A Dolby
- Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Leeds, UK
| | - Eleonora Staines-Urias
- Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK.,Nuffield Department of Obstetrics &Gynaecology, University of Oxford, Oxford, UK
| | - Stephanie M Engel
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Anita Haugan
- Norwegian Institute of Public Health, Oslo, Norway
| | | | - Gulnara Svyatova
- Scientific Center of Obstetrics, Gynecology and Perinatology, Almaty, Kazakhstan
| | - Nodira Zakhidova
- Institute of Immunology, Uzbek Academy of Sciences, Tashkent, Uzbekistan
| | - Dilbar Najmutdinova
- Republic Specialized Scientific Practical Medical Centre of Obstetrics and Gynecology, Tashkent, Uzbekistan
| | | | | | - Anna F Dominiczak
- BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Håkon K Gjessing
- Norwegian Institute of Public Health, Oslo, Norway.,Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Juan P Casas
- Farr Institute of Health Informatics, University College London, London, UK
| | - Frank Dudbridge
- Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - James J Walker
- Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Leeds, UK
| | | | - Unnur Thorsteinsdottir
- deCODE Genetics/Amgen, Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Reynir T Geirsson
- Department of Obstetrics and Gynecology, Landspitali University Hospital, Reykjavik, Iceland
| | - Debbie A Lawlor
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK.,School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Ann-Charlotte Iversen
- Centre of Molecular Inflammation Research (CEMIR) and Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Per Magnus
- Norwegian Institute of Public Health, Oslo, Norway
| | - Hannele Laivuori
- Medical and Clinical Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.,Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Kari Stefansson
- deCODE Genetics/Amgen, Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Linda Morgan
- School of Life Sciences, University of Nottingham, Nottingham, UK
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24
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A systematic review on the association between inflammatory genes and cognitive decline in non-demented elderly individuals. Eur Neuropsychopharmacol 2017; 27:568-588. [PMID: 26718789 DOI: 10.1016/j.euroneuro.2015.12.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 10/27/2015] [Accepted: 12/01/2015] [Indexed: 01/15/2023]
Abstract
Cognitive impairment, or decline, is not only a feature of Alzheimer׳s disease and other forms of dementia but also normal ageing. Abundant evidence from epidemiological studies points towards perturbed inflammatory mechanisms in aged individuals, though the cause-effect nature of this apparent relationship is difficult to establish. Genetic association studies focusing on polymorphism in and around inflammatory genes represent a viable approach to establish whether inflammatory mechanisms might play a causal role in cognitive decline, whilst also enabling the identification of specific genes potentially influencing specific cognitive facets. Thus, here we provide a review of published genetic association studies investigating inflammatory genes in the context of cognitive decline in elderly, non-demented, samples. Numerous candidate gene association studies have been performed to date, focusing almost exclusively on genes encoding major cytokines. Some of these studies report significant cognitive domain-specific associations implicating Interleukin 1β (IL1β) (rs16944), Tumour Necrosis Factor α (TNFα) (rs1800629) and C-reactive protein (CRP) in various domains of cognitive function. However, the majority of these studies are lacking in statistical power and have other methodological limitations, suggesting some of them may have yielded false positive results. Genome-wide association studies have implicated less direct and less obvious regulators of inflammatory processes (i.e., PDE7A, HS3ST4, SPOCK3), indicating that a shift away from the major cytokine-encoding genes in future studies will be important. Furthermore, better cohesion across studies with regards to the cognitive test batteries administered to participants along with the continued application of longitudinal designs will be vital.
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25
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Larson NB, McDonnell S, Cannon Albright L, Teerlink C, Stanford J, Ostrander EA, Isaacs WB, Xu J, Cooney KA, Lange E, Schleutker J, Carpten JD, Powell I, Bailey-Wilson JE, Cussenot O, Cancel-Tassin G, Giles GG, MacInnis RJ, Maier C, Whittemore AS, Hsieh CL, Wiklund F, Catalona WJ, Foulkes W, Mandal D, Eeles R, Kote-Jarai Z, Ackerman MJ, Olson TM, Klein CJ, Thibodeau SN, Schaid DJ. gsSKAT: Rapid gene set analysis and multiple testing correction for rare-variant association studies using weighted linear kernels. Genet Epidemiol 2017; 41:297-308. [PMID: 28211093 DOI: 10.1002/gepi.22036] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 11/16/2016] [Accepted: 12/09/2016] [Indexed: 01/28/2023]
Abstract
Next-generation sequencing technologies have afforded unprecedented characterization of low-frequency and rare genetic variation. Due to low power for single-variant testing, aggregative methods are commonly used to combine observed rare variation within a single gene. Causal variation may also aggregate across multiple genes within relevant biomolecular pathways. Kernel-machine regression and adaptive testing methods for aggregative rare-variant association testing have been demonstrated to be powerful approaches for pathway-level analysis, although these methods tend to be computationally intensive at high-variant dimensionality and require access to complete data. An additional analytical issue in scans of large pathway definition sets is multiple testing correction. Gene set definitions may exhibit substantial genic overlap, and the impact of the resultant correlation in test statistics on Type I error rate control for large agnostic gene set scans has not been fully explored. Herein, we first outline a statistical strategy for aggregative rare-variant analysis using component gene-level linear kernel score test summary statistics as well as derive simple estimators of the effective number of tests for family-wise error rate control. We then conduct extensive simulation studies to characterize the behavior of our approach relative to direct application of kernel and adaptive methods under a variety of conditions. We also apply our method to two case-control studies, respectively, evaluating rare variation in hereditary prostate cancer and schizophrenia. Finally, we provide open-source R code for public use to facilitate easy application of our methods to existing rare-variant analysis results.
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Affiliation(s)
- Nicholas B Larson
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Shannon McDonnell
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Lisa Cannon Albright
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Craig Teerlink
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Janet Stanford
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Elaine A Ostrander
- National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - William B Isaacs
- Brady Urological Institute, School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Jianfeng Xu
- NorthShore University HealthSystem Research Institute, Chicago, Illinois, United States of America
| | - Kathleen A Cooney
- Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States of America.,Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America.,Department of Urology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Ethan Lange
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Johanna Schleutker
- Department of Medical Biochemistry and Genetics, Institute of Biomedicine, University of Turku, Turku, Finland
| | - John D Carpten
- Department of Translational Genomics, University of Southern California, Los Angeles, California, United States of America
| | - Isaac Powell
- Department of Urology, Wayne State University, Detroit, Michigan, United States of America
| | - Joan E Bailey-Wilson
- Statistical Genetics Section, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | | | | | - Graham G Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia.,Centre for Epidemiology and Biostatistics, School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | - Robert J MacInnis
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia.,Centre for Epidemiology and Biostatistics, School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | | | - Alice S Whittemore
- Department of Health Research and Policy, Stanford University, Stanford, California, United States of America
| | - Chih-Lin Hsieh
- Department of Urology, University of Southern California, Los Angeles, California, United States of America
| | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - William J Catalona
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - William Foulkes
- Department of Oncology, Montreal General Hospital, Montreal, Quebec, Canada.,Department of Human Genetics, Montreal General Hospital, Montreal, Quebec, Canada
| | - Diptasri Mandal
- Department of Genetics, LSU Health Sciences Center, New Orleans, Louisiana, United States of America
| | | | - Zsofia Kote-Jarai
- The Institute of Cancer Research, London, UK.,The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London
| | - Michael J Ackerman
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Timothy M Olson
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Christopher J Klein
- Department of Neurology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Stephen N Thibodeau
- Department of Laboratory Medicine/Pathology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Daniel J Schaid
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
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26
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Hampras SS, Sucheston-Campbell LE, Cannioto R, Chang-Claude J, Modugno F, Dörk T, Hillemanns P, Preus L, Knutson KL, Wallace PK, Hong CC, Friel G, Davis W, Nesline M, Pearce CL, Kelemen LE, Goodman MT, Bandera EV, Terry KL, Schoof N, Eng KH, Clay A, Singh PK, Joseph JM, Aben KK, Anton-Culver H, Antonenkova N, Baker H, Bean Y, Beckmann MW, Bisogna M, Bjorge L, Bogdanova N, Brinton LA, Brooks-Wilson A, Bruinsma F, Butzow R, Campbell IG, Carty K, Cook LS, Cramer DW, Cybulski C, Dansonka-Mieszkowska A, Dennis J, Despierre E, Dicks E, Doherty JA, du Bois A, Dürst M, Easton D, Eccles D, Edwards RP, Ekici AB, Fasching PA, Fridley BL, Gao YT, Gentry-Maharaj A, Giles GG, Glasspool R, Gronwald J, Harrington P, Harter P, Hasmad HN, Hein A, Heitz F, Hildebrandt MA, Hogdall C, Hogdall E, Hosono S, Iversen ES, Jakubowska A, Jensen A, Ji BT, Karlan BY, Kellar M, Kelley JL, Kiemeney LA, Klapdor R, Kolomeyevskaya N, Krakstad C, Kjaer SK, Kruszka B, Kupryjanczyk J, Lambrechts D, Lambrechts S, Le ND, Lee AW, Lele S, Leminen A, Lester J, Levine DA, Liang D, Lissowska J, Liu S, Lu K, Lubinski J, Lundvall L, Massuger LF, Matsuo K, McGuire V, McLaughlin JR, McNeish I, Menon U, Moes-Sosnowska J, Narod SA, Nedergaard L, Nevanlinna H, Nickels S, Olson SH, Orlow I, Weber RP, Paul J, Pejovic T, Pelttari LM, Perkins B, Permuth-Wey J, Pike MC, Plisiecka-Halasa J, Poole EM, Risch HA, Rossing MA, Rothstein JH, Rudolph A, Runnebaum IB, Rzepecka IK, Salvesen HB, Schernhammer E, Schmitt K, Schwaab I, Shu XO, Shvetsov YB, Siddiqui N, Sieh W, Song H, Southey MC, Tangen IL, Teo SH, Thompson PJ, Timorek A, Tsai YY, Tworoger SS, Tyrer J, van Altena AM, Vergote I, Vierkant RA, Walsh C, Wang-Gohrke S, Wentzensen N, Whittemore AS, Wicklund KG, Wilkens LR, Wu AH, Wu X, Woo YL, Yang H, Zheng W, Ziogas A, Gayther SA, Ramus SJ, Sellers TA, Schildkraut JM, Phelan CM, Berchuck A, Chenevix-Trench G, Cunningham JM, Pharoah PP, Ness RB, Odunsi K, Goode EL, Moysich KB. Assessment of variation in immunosuppressive pathway genes reveals TGFBR2 to be associated with risk of clear cell ovarian cancer. Oncotarget 2016; 7:69097-69110. [PMID: 27533245 PMCID: PMC5340115 DOI: 10.18632/oncotarget.10215] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/1969] [Accepted: 12/31/1969] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Regulatory T (Treg) cells, a subset of CD4+ T lymphocytes, are mediators of immunosuppression in cancer, and, thus, variants in genes encoding Treg cell immune molecules could be associated with ovarian cancer. METHODS In a population of 15,596 epithelial ovarian cancer (EOC) cases and 23,236 controls, we measured genetic associations of 1,351 SNPs in Treg cell pathway genes with odds of ovarian cancer and tested pathway and gene-level associations, overall and by histotype, for the 25 genes, using the admixture likelihood (AML) method. The most significant single SNP associations were tested for correlation with expression levels in 44 ovarian cancer patients. RESULTS The most significant global associations for all genes in the pathway were seen in endometrioid ( p = 0.082) and clear cell ( p = 0.083), with the most significant gene level association seen with TGFBR2 ( p = 0.001) and clear cell EOC. Gene associations with histotypes at p < 0.05 included: IL12 ( p = 0.005 and p = 0.008, serous and high-grade serous, respectively), IL8RA ( p = 0.035, endometrioid and mucinous), LGALS1 ( p = 0.03, mucinous), STAT5B ( p = 0.022, clear cell), TGFBR1 ( p = 0.021 endometrioid) and TGFBR2 ( p = 0.017 and p = 0.025, endometrioid and mucinous, respectively). CONCLUSIONS Common inherited gene variation in Treg cell pathways shows some evidence of germline genetic contribution to odds of EOC that varies by histologic subtype and may be associated with mRNA expression of immune-complex receptor in EOC patients.
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MESH Headings
- Adenocarcinoma, Clear Cell/genetics
- Adenocarcinoma, Clear Cell/immunology
- Adult
- Aged
- Carcinoma, Ovarian Epithelial
- Female
- Gene Expression Regulation, Neoplastic
- Gene Frequency
- Genetic Predisposition to Disease/genetics
- Genotype
- Humans
- Middle Aged
- Neoplasms, Glandular and Epithelial/genetics
- Neoplasms, Glandular and Epithelial/immunology
- Ovarian Neoplasms/genetics
- Ovarian Neoplasms/immunology
- Polymorphism, Single Nucleotide
- Protein Serine-Threonine Kinases/genetics
- Receptor, Transforming Growth Factor-beta Type II
- Receptors, Transforming Growth Factor beta/genetics
- Risk Factors
- T-Lymphocytes, Regulatory/immunology
- T-Lymphocytes, Regulatory/metabolism
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Affiliation(s)
- Shalaka S. Hampras
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida, USA
| | - Lara E. Sucheston-Campbell
- College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Rikki Cannioto
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Jenny Chang-Claude
- German Cancer Research Center (DKFZ), Division of Cancer Epidemiology, Heidelberg, Germany
| | - Francesmary Modugno
- Department of Epidemiology and Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Women's Cancer Research Program, Magee-Women's Research Institute and University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, USA
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Peter Hillemanns
- Clinics of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
| | - Leah Preus
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Keith L. Knutson
- Department of Immunology, Mayo Clinic, Rochester, Minnesota, USA
| | - Paul K. Wallace
- Department of Flow & Image Cytometry, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Chi-Chen Hong
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Grace Friel
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Warren Davis
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Mary Nesline
- Center for Personalized Medicine, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Celeste L. Pearce
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California, USA
| | - Linda E. Kelemen
- Alberta Health Services-Cancer Care, Department of Population Health Research, Calgary, Alberta, Canada
| | - Marc T. Goodman
- Cancer Prevention and Control, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Elisa V. Bandera
- Cancer Prevention and Control, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | - Kathryn L. Terry
- Obstetrics and Gynecology Center, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Nils Schoof
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Kevin H. Eng
- Department of Biostatistics & Bioinformatics, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Alyssa Clay
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Prashant K. Singh
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Janine M. Joseph
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Katja K.H. Aben
- Department for Health Evidence, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Hoda Anton-Culver
- Department of Epidemiology and School of Medicine, University of California Irvine, Irvine, California, USA
| | - Natalia Antonenkova
- Byelorussian Institute for Oncology and Medical Radiology Aleksandrov N.N., Minsk, Belarus
| | - Helen Baker
- Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Yukie Bean
- Department of Obstetrics & Gynecology and Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Matthias W. Beckmann
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Maria Bisogna
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Line Bjorge
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
| | - Natalia Bogdanova
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Louise A. Brinton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Angela Brooks-Wilson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Fiona Bruinsma
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
| | - Ralf Butzow
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Ian G. Campbell
- Cancer Genetics Laboratory, Research Division, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, Australia
| | - Karen Carty
- Cancer Research UK Clinical Trials Unit, The Beatson West of Scotland Cancer Centre, University of Glasgow, Glasgow, UK
| | - Linda S. Cook
- Division of Epidemiology and Biostatistics, Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico, USA
| | - Daniel W. Cramer
- Obstetrics and Gynecology Center, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Cezary Cybulski
- International Hereditary Cancer Center, Department of Genetics and Pathology, Clinic of Opthalmology, Pomeranian Medical University, Szczecin, Poland
| | - Agnieszka Dansonka-Mieszkowska
- Department of Pathology and Labolatory Diagnostic, The Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Joe Dennis
- Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Evelyn Despierre
- Division of Gynecological Oncology, Department of Oncology, University Hospitals Leuven, Belgium
| | - Ed Dicks
- Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Jennifer A. Doherty
- Department of Community and Family Medicine, Section of Biostatistics & Epidemiology, The Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Andreas du Bois
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte/Evang. Huyssens-Stiftung/Knappschaft GmbH, Essen, Germany
| | - Matthias Dürst
- Department of Gynecology, Jena University Hospital - Friedrich Schiller University, Jena, Germany
| | - Doug Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Diana Eccles
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
| | - Robert P. Edwards
- Department of Obstetrics, Gynecology & Reproductive Sciences and Ovarian Cancer Center of Excellence, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Arif B. Ekici
- Institute of Human Genetics, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Peter A. Fasching
- Department of Medicine, Division of Hematology and Oncology, University of California at Los Angeles, Los Angeles, California, USA
| | - Brooke L. Fridley
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, Kansas, USA
| | | | - Aleksandra Gentry-Maharaj
- Institute for Women's Health, Population Health Sciences, University College - London, London, United Kingdom
| | - Graham G. Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia
| | - Rosalind Glasspool
- Cancer Research UK Clinical Trials Unit, The Beatson West of Scotland Cancer Centre, University of Glasgow, Glasgow, UK
| | - Jacek Gronwald
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Patricia Harrington
- Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Philipp Harter
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte/Evang. Huyssens-Stiftung/Knappschaft GmbH, Essen, Germany
| | - Hanis Nazihah Hasmad
- Cancer Research Initiatives Foundation, Sime Darby Medical Center, Subang Jaya, Malaysia
| | - Alexander Hein
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Florian Heitz
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte/Evang. Huyssens-Stiftung/Knappschaft GmbH, Essen, Germany
| | | | - Claus Hogdall
- Department of Gynaecology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Estrid Hogdall
- Institute of Cancer Epidemiology, Danish Cancer Society, Copenhagen, Denmark
| | - Satoyo Hosono
- Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Aichi, Japan
| | - Edwin S. Iversen
- Department of Statistical Science, Duke University, Durham, North Carolina, USA
| | - Anna Jakubowska
- International Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Allan Jensen
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Bu-Tian Ji
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Beth Y. Karlan
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Melissa Kellar
- Department of Obstetrics & Gynecology and Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Joseph L. Kelley
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Lambertus A. Kiemeney
- Department for Health Evidence, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Rüdiger Klapdor
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Nonna Kolomeyevskaya
- Division of Gynecologic Oncology, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Camilla Krakstad
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
| | - Susanne K. Kjaer
- Department of Gynaecology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Bridget Kruszka
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Jolanta Kupryjanczyk
- Department of Pathology and Labolatory Diagnostic, The Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Diether Lambrechts
- Vesalius Research Center, VIB, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Oncology, University of Leuven, Belgium
| | - Sandrina Lambrechts
- Division of Gynecological Oncology, Department of Oncology, University Hospitals Leuven, Belgium
| | - Nhu D. Le
- Cancer Control Research, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Alice W. Lee
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California, USA
| | - Shashikant Lele
- Division of Gynecologic Oncology, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Arto Leminen
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Jenny Lester
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Douglas A. Levine
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Dong Liang
- College of Pharmacy and Health Sciences, Texas Southern University, Houston, Texas, USA
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, M. Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Song Liu
- Department of Biostatistics & Bioinformatics, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Karen Lu
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jan Lubinski
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia
| | - Lene Lundvall
- Department of Gynaecology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Leon F.A.G. Massuger
- Department of Gynaecology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Keitaro Matsuo
- Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Aichi, Japan
| | - Valeria McGuire
- Department of Health Research and Policy - Epidemiology, Stanford University School of Medicine, Stanford, California, USA
| | - John R. McLaughlin
- Prosserman Centre for Health Research, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Ian McNeish
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Usha Menon
- Women's Cancer, UCL EGA Institute for Women's Health, London, UK
| | - Joanna Moes-Sosnowska
- Department of Pathology and Labolatory Diagnostic, The Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Steven A. Narod
- Women's College Research Institute, Toronto, Ontario, Canada
| | - Lotte Nedergaard
- Department of Pathology, Rigshospitalet, University of Copenhagen, Denmark
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Stefan Nickels
- German Cancer Research Center (DKFZ), Division of Cancer Epidemiology, Heidelberg, Germany
| | - Sara H. Olson
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Irene Orlow
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Rachel Palmieri Weber
- Department of Community and Family Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - James Paul
- Cancer Research UK Clinical Trials Unit, The Beatson West of Scotland Cancer Centre, University of Glasgow, Glasgow, UK
| | - Tanja Pejovic
- Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Liisa M. Pelttari
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Barbara Perkins
- Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Jenny Permuth-Wey
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida, USA
| | - Malcolm C. Pike
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Joanna Plisiecka-Halasa
- Department of Pathology and Labolatory Diagnostic, The Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Elizabeth M. Poole
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Harvey A. Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, Connecticut, USA
| | - Mary Anne Rossing
- Program in Epidemiology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Joseph H. Rothstein
- Department of Health Research and Policy - Epidemiology, Stanford University School of Medicine, Stanford, California, USA
| | - Anja Rudolph
- German Cancer Research Center (DKFZ), Division of Cancer Epidemiology, Heidelberg, Germany
| | - Ingo B. Runnebaum
- Department of Gynecology, Jena University Hospital - Friedrich Schiller University, Jena, Germany
| | - Iwona K. Rzepecka
- Department of Pathology and Labolatory Diagnostic, The Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Helga B. Salvesen
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
| | - Eva Schernhammer
- Department of Community and Family Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Kristina Schmitt
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Ira Schwaab
- Institut für Humangenetik Wiesbaden, Wiesbaden, Germany
| | - Xiao-Ou Shu
- Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Yurii B Shvetsov
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Hawaii, USA
| | - Nadeem Siddiqui
- Department of Gynaecological Oncology, Glasgow Royal Infirmary, Glasgow, Scotland, UK
| | - Weiva Sieh
- Department of Health Research and Policy - Epidemiology, Stanford University School of Medicine, Stanford, California, USA
| | - Honglin Song
- Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Melissa C. Southey
- Department of Pathology, The University of Melbourne, Melbourne, Australia
| | - Ingvild L. Tangen
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
| | - Soo-Hwang Teo
- Cancer Research Initiatives Foundation, Sime Darby Medical Center, Subang Jaya, Malaysia
| | - Pamela J. Thompson
- Cancer Prevention and Control, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Agnieszka Timorek
- Department of Obstetrics, Gynecology and Oncology, Warsaw Medical University and Brodnowski Hospital, Warsaw, Poland
| | - Ya-Yu Tsai
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida, USA
| | - Shelley S. Tworoger
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Jonathan Tyrer
- Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Anna M. van Altena
- Department of Gynaecology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Ignace Vergote
- Division of Gynecological Oncology, Department of Oncology, University Hospitals Leuven, Belgium
| | - Robert A. Vierkant
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
| | - Christine Walsh
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Shan Wang-Gohrke
- German Cancer Research Center (DKFZ), Division of Cancer Epidemiology, Heidelberg, Germany
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Alice S. Whittemore
- Department of Health Research and Policy - Epidemiology, Stanford University School of Medicine, Stanford, California, USA
| | - Kristine G. Wicklund
- Program in Epidemiology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Lynne R. Wilkens
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Hawaii, USA
| | - Anna H. Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California, USA
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yin-Ling Woo
- Department of Obstetrics and Gynaecology, Affiliated with UM Cancer Research Institute, Faculty of Medicine, University of Malaya, Malaysia
| | - Hannah Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Wei Zheng
- Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Argyrios Ziogas
- Department of Epidemiology and School of Medicine, University of California Irvine, Irvine, California, USA
| | - Simon A. Gayther
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California, USA
| | - Susan J. Ramus
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California, USA
| | - Thomas A. Sellers
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida, USA
| | - Joellen M. Schildkraut
- Department of Community and Family Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Catherine M. Phelan
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida, USA
| | - Andrew Berchuck
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina, USA
| | - Georgia Chenevix-Trench
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- On behalf of the Australian Ovarian Cancer Study Group
| | - Julie M. Cunningham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Paul P. Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Roberta B. Ness
- School of Public Health, The University of Texas, Houston, Texas, USA
| | - Kunle Odunsi
- Division of Gynecologic Oncology, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Ellen L. Goode
- Department of Health Science Research, Division of Epidemiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Kirsten B. Moysich
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York, USA
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Hoffmann TJ, Keats BJ, Yoshikawa N, Schaefer C, Risch N, Lustig LR. A Large Genome-Wide Association Study of Age-Related Hearing Impairment Using Electronic Health Records. PLoS Genet 2016; 12:e1006371. [PMID: 27764096 PMCID: PMC5072625 DOI: 10.1371/journal.pgen.1006371] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 09/16/2016] [Indexed: 01/22/2023] Open
Abstract
Age-related hearing impairment (ARHI), one of the most common sensory disorders, can be mitigated, but not cured or eliminated. To identify genetic influences underlying ARHI, we conducted a genome-wide association study of ARHI in 6,527 cases and 45,882 controls among the non-Hispanic whites from the Genetic Epidemiology Research on Adult Health and Aging (GERA) cohort. We identified two novel genome-wide significant SNPs: rs4932196 (odds ratio = 1.185, p = 4.0x10-11), 52Kb 3’ of ISG20, which replicated in a meta-analysis of the other GERA race/ethnicity groups (1,025 cases, 12,388 controls, p = 0.00094) and in a UK Biobank case-control analysis (30,802 self-reported cases, 78,586 controls, p = 0.015); and rs58389158 (odds ratio = 1.132, p = 1.8x10-9), which replicated in the UK Biobank (p = 0.00021). The latter SNP lies just outside exon 8 and is highly correlated (r2 = 0.96) with the missense SNP rs5756795 in exon 7 of TRIOBP, a gene previously associated with prelingual nonsyndromic hearing loss. We further tested these SNPs in phenotypes from audiologist notes available on a subset of GERA (4,903 individuals), stratified by case/control status, to construct an independent replication test, and found a significant effect of rs58389158 on speech reception threshold (SRT; overall GERA meta-analysis p = 1.9x10-6). We also tested variants within exons of 132 other previously-identified hearing loss genes, and identified two common additional significant SNPs: rs2877561 (synonymous change in ILDR1, p = 6.2x10-5), which replicated in the UK Biobank (p = 0.00057), and had a significant GERA SRT (p = 0.00019) and speech discrimination score (SDS; p = 0.0019); and rs9493627 (missense change in EYA4, p = 0.00011) which replicated in the UK Biobank (p = 0.0095), other GERA groups (p = 0.0080), and had a consistent significant result for SRT (p = 0.041) and suggestive result for SDS (p = 0.081). Large cohorts with GWAS data and electronic health records may be a useful method to characterize the genetic architecture of ARHI. Age-related hearing impairment (ARHI) is one of the most common sensory disorders. While ARHI effects can be mitigated with current technologies, it cannot be cured or eliminated. It is thus hoped that identification of genetic influences on ARHI may one day lead to curative therapies. Towards this goal, the current study utilized electronic health record data from non-Hispanic whites in the Genetic Epidemiology Research on Adult Health and Aging (GERA) cohort to conduct a genome-wide association study of ARHI, and tested the significant variants for replication in other GERA race/ethnicity groups, independent GERA phenotypes, and self-reported ARHI from the UK Biobank. We discovered two genome-wide significant SNPs. The first was novel and near ISG20. The second was in TRIOBP, a gene previously associated with prelingual nonsyndromic hearing loss. Motivated by our TRIOBP results, we also looked at exons in known hearing loss genes, and identified two additional SNPs, rs2877561 in ILDR1 and rs9493672 in EYA4 (at a significance threshold adjusted for number of SNPs in those regions). These results suggest that large cohorts with GWAS data and electronic health records may be a useful method to characterize the genetic architecture of ARHI.
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Affiliation(s)
- Thomas J. Hoffmann
- Department of Epidemiology and Biostatistics, and Institute for Human Genetics, University of California San Francisco, San Francisco, United States of America
- * E-mail:
| | - Bronya J. Keats
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, United States of America
| | - Noriko Yoshikawa
- Department of Head and Neck Surgery, Kaiser Permanente Medical Center, Oakland, United States of America
| | - Catherine Schaefer
- Kaiser Permanente Northern California Division of Research, Oakland, United States of America
| | - Neil Risch
- Department of Epidemiology and Biostatistics, and Institute for Human Genetics, University of California San Francisco, San Francisco, United States of America
- Kaiser Permanente Northern California Division of Research, Oakland, United States of America
| | - Lawrence R. Lustig
- Department of Otolaryngology—Head and Neck Surgery, Columbia University Medical Center, Columbia, United States of America
- New York Presbyterian Hospital, New York, United States of America
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Wiuf C, Schaumburg-Müller Pallesen J, Foldager L, Grove J. LandScape: a simple method to aggregate p-values and other stochastic variables without a priori grouping. Stat Appl Genet Mol Biol 2016; 15:349-61. [PMID: 27269897 DOI: 10.1515/sagmb-2015-0085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In many areas of science it is custom to perform many, potentially millions, of tests simultaneously. To gain statistical power it is common to group tests based on a priori criteria such as predefined regions or by sliding windows. However, it is not straightforward to choose grouping criteria and the results might depend on the chosen criteria. Methods that summarize, or aggregate, test statistics or p-values, without relying on a priori criteria, are therefore desirable. We present a simple method to aggregate a sequence of stochastic variables, such as test statistics or p-values, into fewer variables without assuming a priori defined groups. We provide different ways to evaluate the significance of the aggregated variables based on theoretical considerations and resampling techniques, and show that under certain assumptions the FWER is controlled in the strong sense. Validity of the method was demonstrated using simulations and real data analyses. Our method may be a useful supplement to standard procedures relying on evaluation of test statistics individually. Moreover, by being agnostic and not relying on predefined selected regions, it might be a practical alternative to conventionally used methods of aggregation of p-values over regions. The method is implemented in Python and freely available online (through GitHub, see the Supplementary information).
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He L, Pitkäniemi J, Heikkilä K, Chou YL, Madden PAF, Korhonen T, Sarin AP, Ripatti S, Kaprio J, Loukola A. Genome-wide time-to-event analysis on smoking progression stages in a family-based study. Brain Behav 2016; 6:e00462. [PMID: 27134767 PMCID: PMC4842934 DOI: 10.1002/brb3.462] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 02/19/2016] [Accepted: 02/28/2016] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Various pivotal stages in smoking behavior can be identified, including initiation, conversion from experimenting to established use, development of tolerance, and cessation. Previous studies have shown high heritability for age of smoking initiation and cessation; however, time-to-event genome-wide association studies aiming to identify underpinning genes that accelerate or delay these transitions are missing to date. METHODS We investigated which single nucleotide polymorphisms (SNPs) across the whole genome contribute to the hazard ratio of transition between different stages of smoking behavior by performing time-to-event analyses within a large Finnish twin family cohort (N = 1962), and further conducted mediation analyses of plausible intermediate traits for significant SNPs. RESULTS Genome-wide significant signals were detected for three of the four transitions: (1) for smoking cessation on 10p14 (P = 4.47e-08 for rs72779075 flanked by RP11-575N15 and GATA3), (2) for tolerance on 11p13 (P = 1.29e-08 for rs11031684 in RP1-65P5.1), mediated by smoking quantity, and on 9q34.12 (P = 3.81e-08 for rs2304808 in FUBP3), independent of smoking quantity, and (3) for smoking initiation on 19q13.33 (P = 3.37e-08 for rs73050610 flanked by TRPM4 and SLC6A16) in analysis adjusted for first time sensations. Although our top SNPs did not replicate, another SNP in the TRPM4-SLC6A16 gene region showed statistically significant association after region-based multiple testing correction in an independent Australian twin family sample. CONCLUSION Our results suggest that the functional effect of the TRPM4-SLC6A16 gene region deserves further investigation, and that complex neurotransmitter networks including dopamine and glutamate may play a critical role in smoking initiation. Moreover, comparison of these results implies that genetic contributions to the complex smoking behavioral phenotypes vary among the transitions.
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Affiliation(s)
- Liang He
- Department of Public Health University of Helsinki Helsinki Finland
| | - Janne Pitkäniemi
- Department of Public Health University of Helsinki Helsinki Finland; Finnish Cancer Registry Institute for Statistical and Epidemiological Cancer Research Helsinki Finland
| | - Kauko Heikkilä
- Department of Public Health University of Helsinki Helsinki Finland; Institute for Molecular Medicine Finland (FIMM) University of Helsinki Helsinki Finland
| | - Yi-Ling Chou
- Washington University School of Medicine Department of Psychiatry St. Louis Missouri
| | - Pamela A F Madden
- Washington University School of Medicine Department of Psychiatry St. Louis Missouri
| | - Tellervo Korhonen
- Department of Public Health University of Helsinki Helsinki Finland; National Institute for Health and Welfare Helsinki Finland; Institute of Public Health and Clinical Nutrition University of Eastern Finland Kuopio Finland
| | - Antti-Pekka Sarin
- Institute for Molecular Medicine Finland (FIMM)University of Helsinki Helsinki Finland; National Institute for Health and Welfare Helsinki Finland
| | - Samuli Ripatti
- Department of Public Health University of Helsinki Helsinki Finland; Institute for Molecular Medicine Finland (FIMM) University of Helsinki Helsinki Finland; Wellcome Trust Sanger Institute Hinxton Cambridge UK
| | - Jaakko Kaprio
- Department of Public Health University of Helsinki Helsinki Finland; Institute for Molecular Medicine Finland (FIMM) University of Helsinki Helsinki Finland; National Institute for Health and Welfare Helsinki Finland
| | - Anu Loukola
- Department of Public Health University of Helsinki Helsinki Finland; Institute for Molecular Medicine Finland (FIMM) University of Helsinki Helsinki Finland
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Ramos GB, Salomão H, Francio AS, Fava VM, Werneck RI, Mira MT. Association Analysis Suggests SOD2 as a Newly Identified Candidate Gene Associated With Leprosy Susceptibility. J Infect Dis 2016; 214:475-8. [PMID: 27132285 DOI: 10.1093/infdis/jiw170] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 04/21/2016] [Indexed: 11/14/2022] Open
Abstract
Genetic studies have identified several genes and genomic regions contributing to the control of host susceptibility to leprosy. Here, we test variants of the positional and functional candidate gene SOD2 for association with leprosy in 2 independent population samples. Family-based analysis revealed an association between leprosy and allele G of marker rs295340 (P = .042) and borderline evidence of an association between leprosy and alleles C and A of markers rs4880 (P = .077) and rs5746136 (P = .071), respectively. Findings were validated in an independent case-control sample for markers rs295340 (P = .049) and rs4880 (P = .038). These results suggest SOD2 as a newly identified gene conferring susceptibility to leprosy.
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Affiliation(s)
| | | | | | - Vinícius Medeiros Fava
- Program in Infectious Diseases and Immunity in Global Health, Research Institute of the McGill University Health Centre McGill International TB Centre Department of Human Genetics Department of Medicine, McGill University, Montreal, Canada
| | - Renata Iani Werneck
- Graduate Program in Health Sciences, School of Medicine School of Life Sciences, Pontifícia Universidade Católica do Paraná, Curitiba, Brazil
| | - Marcelo Távora Mira
- Graduate Program in Health Sciences, School of Medicine School of Life Sciences, Pontifícia Universidade Católica do Paraná, Curitiba, Brazil
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Sesar A, Cacheiro P, López-López M, Camiña-Tato M, Quintáns B, Monroy-Jaramillo N, Alonso-Vilatela ME, Cebrián E, Yescas-Gómez P, Ares B, Rivas MT, Castro A, Carracedo A, Sobrido MJ. Synaptotagmin XI in Parkinson's disease: New evidence from an association study in Spain and Mexico. J Neurol Sci 2016; 362:321-5. [PMID: 26944171 DOI: 10.1016/j.jns.2016.02.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 01/10/2016] [Accepted: 02/07/2016] [Indexed: 01/29/2023]
Abstract
INTRODUCTION The pathophysiology of PD (Parkinson's disease) has been related to the ubiquitin proteasome system and oxidative stress. Parkin acts as ubiquitin ligase on several substrates. Because genetic variants often have different frequencies across populations, population specific analyses are necessary to complement and validate results from genome-wide association studies. METHODS We carried out an association study with genes coding for parkin substrates and cellular stress components in the Galician population (Northern Spain). SNCA and MAPT SNPs were also analyzed. We studied 75 SNPs in a discovery sample of 268 PD patients and 265 controls from Galicia. A replication sample of 271 patients and 260 controls was recruited from Mexico City. RESULTS We observed significant association between PD and SNPs in MAPT. Nominal p-values<0.05 were obtained in the Galician cohort for SNPs in SYT11, coding for synaptotagmin XI. These results were replicated in the Mexican sample. DISCUSSION The associated markers lie within a ~140kb strong linkage disequilibrium segment that harbors several candidate genes, including SYT11. SNPs from the GBA-SYT11-RAB25 region have been previously associated with PD, however the functionally relevant variants remain unknown. Our data support a likely role of genetic factors within 1q22 in PD susceptibility.
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Affiliation(s)
- Angel Sesar
- Department of Neurology, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain; Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain.
| | - Pilar Cacheiro
- Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain; Grupo de Medicina Xenómica, Fundación Pública Galega de Medicina Xenómica-SERGAS, Santiago de Compostela, Spain
| | - Marisol López-López
- Biological Systems Department, Universidad Autónoma Metropolitana, Campus Xochimilco, Mexico City, Mexico
| | - Montserrat Camiña-Tato
- Grupo de Medicina Xenómica, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Beatriz Quintáns
- Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain; Grupo de Medicina Xenómica, Fundación Pública Galega de Medicina Xenómica-SERGAS, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Institute of Health Carlos III, Spain
| | - Nancy Monroy-Jaramillo
- Neurogenetics Department, Instituto Nacional de Neurología y Neurocirugía "Manuel Velasco Suárez", Mexico City, Mexico
| | - María-Elisa Alonso-Vilatela
- Neurogenetics Department, Instituto Nacional de Neurología y Neurocirugía "Manuel Velasco Suárez", Mexico City, Mexico
| | - Ernesto Cebrián
- Department of Neurology, Complejo Hospitalario Universitario de Pontevedra, Pontevedra, Spain
| | - Petra Yescas-Gómez
- Neurogenetics Department, Instituto Nacional de Neurología y Neurocirugía "Manuel Velasco Suárez", Mexico City, Mexico
| | - Begoña Ares
- Department of Neurology, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain; Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
| | - María-Teresa Rivas
- Department of Neurology, Complejo Hospitalario Universitario de Coruña, La Coruña, Spain
| | - Alfonso Castro
- Department of Neurology, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain; Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
| | - Angel Carracedo
- Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain; Grupo de Medicina Xenómica, Fundación Pública Galega de Medicina Xenómica-SERGAS, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Institute of Health Carlos III, Spain
| | - María-Jesús Sobrido
- Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain; Grupo de Medicina Xenómica, Fundación Pública Galega de Medicina Xenómica-SERGAS, Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Institute of Health Carlos III, Spain
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Emily M. AGGrEGATOr: A Gene-based GEne-Gene interActTiOn test for case-control association studies. Stat Appl Genet Mol Biol 2016; 15:151-71. [DOI: 10.1515/sagmb-2015-0074] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractAmong the large of number of statistical methods that have been proposed to identify gene-gene interactions in case-control genome-wide association studies (GWAS), gene-based methods have recently grown in popularity as they confer advantage in both statistical power and biological interpretation. All of the gene-based methods jointly model the distribution of single nucleotide polymorphisms (SNPs) sets prior to the statistical test, leading to a limited power to detect sums of SNP-SNP signals. In this paper, we instead propose a gene-based method that first performs SNP-SNP interaction tests before aggregating the obtained
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Babron MC, Etcheto A, Dizier MH. A New Correction for Multiple Testing in Gene-Gene Interaction Studies. Ann Hum Genet 2015; 79:380-384. [PMID: 25912889 DOI: 10.1111/ahg.12113] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 02/26/2015] [Indexed: 11/30/2022]
Abstract
A major problem in gene-gene interaction studies in large marker panels is how to correct for multiple testing while accounting for the dependence between marker pairs due to the presence of linkage disequilibrium. The "gold standard" approach is to perform permutations of case/control labels. However, this is often not feasible in practice, due to computational demands. Here, we propose a correction based on the effective number of independent tests of interaction between marker pairs. This number depends on the effective number of independent single-marker tests. We tested its validity using simulated samples, as well as that of another correction of marker pair tests. We showed that our approach was valid while the other correction strongly underestimated the effective number of independent tests. Our method provides estimates of the effective number of independent tests close to those reported in the literature for a Genome-Wide Interaction Study on a 550K chip. Our correction method is quick and simple, and can be applied whatever the marker panel and the underlying linkage disequilibrium pattern.
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Affiliation(s)
- Marie-Claude Babron
- Inserm, UMR946, Genetic variation and Human diseases, F-75010, Paris, France.,Université Paris-Diderot, Sorbonne Paris-Cité, UMR946, F-75010, Paris, France
| | - Adrien Etcheto
- Inserm, UMR946, Genetic variation and Human diseases, F-75010, Paris, France.,Université de Nantes, Nantes, F-44000, France
| | - Marie-Helene Dizier
- Inserm, UMR946, Genetic variation and Human diseases, F-75010, Paris, France.,Université Paris-Diderot, Sorbonne Paris-Cité, UMR946, F-75010, Paris, France
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McDaneld TG, Kuehn LA, Thomas MG, Snelling WM, Smith TPL, Pollak EJ, Cole JB, Keele JW. Genomewide association study of reproductive efficiency in female cattle. J Anim Sci 2015; 92:1945-57. [PMID: 24782394 DOI: 10.2527/jas.2012-6807] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Reproductive efficiency is of economic importance in commercial beef cattle production, as failure to achieve pregnancy reduces the number of calves marketed per cow exposed. Identification of genetic markers with predictive merit for reproductive success would facilitate early selection of sires with daughters having improved reproductive rate without increasing generation intervals. To identify regions of the genome harboring variation affecting reproductive success, we applied a genomewide association study (GWAS) approach based on the >700,000 SNP marker assay, using a procedure based on genotyping multianimal pools of DNA to increase the number of animals that could be genotyped with available resources. Cows from several populations were classified according to reproductive efficiency, and DNA was pooled within population and phenotype prior to genotyping. Populations evaluated included a research population at the U.S. Meat Animal Research Center, 2 large commercial ranch populations, and a number of smaller populations (<100 head) across the United States. We detected 2 SNP with significant genomewide association (P ≤ 1.49 × 10(-7)), on BTA21 and BTA29, 3 SNP with suggestive associations (P ≤ 2.91 × 10(-6)) on BTA5, and 1 SNP with suggestive association each on BTA1 and BTA25. In addition to our novel findings, we confirmed previously published associations for SNP on BTA-X and all autosomes except 3 (BTA21, BTA22, and BTA28) encompassing substantial breed diversity including Bos indicus and Bos taurus breeds. The study identified regions of the genome associated with reproductive efficiency, which are being targeted for further analysis to develop robust marker systems, and demonstrated that DNA pooling can be used to substantially reduce the cost of GWAS in cattle.
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Affiliation(s)
- T G McDaneld
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933
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