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Analysis of case–control association studies with known risk variants

Noah Zaitlen, Bogdan Paşaniuc, Nick Patterson, Samuela Pollack, Benjamin Voight, Leif Groop, David Altshuler, Brian E. Henderson, Laurence N. Kolonel, Loic Le Marchand, Kevin Waters, Christopher A. Haiman (+4 others)
2012 Computer applications in the biosciences : CABIOS  
Motivation: The question of how to best use information from known associated variants when conducting disease association studies has yet to be answered.  ...  Our approach may substantially improve disease gene discovery for diseases with many known risk variants. Availability: LTSOFT software is available online  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/bts259 pmid:22556366 pmcid:PMC3381970 fatcat:5seuhk64lvgbxbf24bpgnnj2la

A targeted genetic association study of epithelial ovarian cancer susceptibility

Madalene Earp, Stacey J. Winham, Nicholas Larson, Jennifer B. Permuth, Hugues Sicotte, Jeremy Chien, Hoda Anton-Culver, Elisa V. Bandera, Andrew Berchuck, Linda S. Cook, Daniel Cramer, Jennifer A. Doherty (+42 others)
2016 OncoTarget  
with risk than previously reported variants.  ...  Beyond known susceptibility regions, no variants were found to be associated with EOC risk at genome-wide statistical significance (p <5x10 -8 ), nor were any significant after Bonferroni correction for  ...  Here, we sought to identify additional EOC susceptibility variants through direct genotyping and analysis of EOC cases and controls from 13 independent studies.  ... 
doi:10.18632/oncotarget.7121 pmid:26848776 pmcid:PMC4884925 fatcat:cmrdv5zohbcfxhdfbnrgm54jmu

Stratifying Type 2 Diabetes Cases by BMI Identifies Genetic Risk Variants in LAMA1 and Enrichment for Risk Variants in Lean Compared to Obese Cases

John R. B. Perry, Benjamin F. Voight, Loïc Yengo, Najaf Amin, Josée Dupuis, Martha Ganser, Harald Grallert, Pau Navarro, Man Li, Lu Qi, Valgerdur Steinthorsdottir, Robert A. Scott (+64 others)
2012 PLoS Genetics  
This study provides evidence that stratification of type 2 diabetes cases by BMI may help identify additional risk variants and that lean cases may have a stronger genetic predisposition to type 2 diabetes  ...  A variant (rs8090011) in the LAMA1 gene was associated with type 2 diabetes in lean cases (P = 8.4610 29 , OR = 1.13 [95% CI 1.09-1.18]), and this association was stronger than that in obese cases (P =  ...  Acknowledgments Full study acknowledgments are available in Text S1. Author Contributions  ... 
doi:10.1371/journal.pgen.1002741 pmid:22693455 pmcid:PMC3364960 fatcat:zddy46ci7bevdersgsibro7mxa

Gene variants influencing measures of inflammation or predisposing to autoimmune and inflammatory diseases are not associated with the risk of type 2 diabetes

S. Rafiq, D. Melzer, M. N. Weedon, H. Lango, R. Saxena, L. J. Scott, C. N. A. Palmer, A. D. Morris, M. I. McCarthy, L. Ferrucci, A. T. Hattersley, E. Zeggini (+1 others)
2008 Diabetologia  
We tested the associations of these variants with type 2 diabetes using a meta-analysis of 4,107 cases and 5,187 controls from the Wellcome Trust Case Control Diabetologia (  ...  We tested the hypothesis that common gene variants known to alter circulating levels of inflammatory proteins, or known to alter autoimmune-related disease risk, influence type 2 diabetes risk.  ...  Duality of interest The authors declare that there is no duality of interest associated with this manuscript.  ... 
doi:10.1007/s00125-008-1160-3 pmid:18853133 pmcid:PMC2662689 fatcat:tdp7odjnpvefxmeywi7kk3ej64

A Genome-wide Association Study of Prostate Cancer in Latinos

Zhaohui Du, Hannah Hopp, Sue Ann Ingles, Chad Huff, Xin Sheng, Brandi Weaver, Mariana Stern, Thomas J. Hoffmann, Esther M. John, Stephen K. Van Den Eeden, Sara Strom, Robin J. Leach (+4 others)
2019 International Journal of Cancer  
In the present study, we performed a GWAS of prostate cancer (PrCa) in 2,820 Latino PrCa cases and 5,293 controls to search for novel PrCa risk loci and to examine the generalizability of known PrCa risk  ...  Genome-wide significant associations were observed with 84 variants all located at the known PrCa risk regions at 8q24 (128.484-128.548) and 10q11.22 (MSMB gene).  ...  associated with PrCa risk, even after excluding the outlier study MDA with Mexican American controls but a more diverse representation of Latino cases.  ... 
doi:10.1002/ijc.32525 pmid:31226226 pmcid:PMC7028127 fatcat:ilukew6yijbvjfx2zosb3k6u5u

Rare, Low-Frequency, and Common Variants in the Protein-Coding Sequence of Biological Candidate Genes from GWASs Contribute to Risk of Rheumatoid Arthritis

Dorothée Diogo, Fina Kurreeman, Eli A. Stahl, Katherine P. Liao, Namrata Gupta, Jeffrey D. Greenberg, Manuel A. Rivas, Brendan Hickey, Jason Flannick, Brian Thomson, Candace Guiducci, Stephan Ripke (+16 others)
2013 American Journal of Human Genetics  
First, we assessed the contribution of rare coding variants in the 25 genes to the risk of RA in a pooled sequencing study of 500 RA cases and 650 controls of European ancestry.  ...  We observed a strong enrichment of coding variants with a nominal signal of association with RA (p < 0.05) after adjusting for the best signal of association at the loci (p(enrichment) = 6.4 × 10(-4)).  ...  To test these 47 coding variants for association with RA risk, we performed a meta-analysis of all data combined and compared the association p values with meta-analysis results after 1,000 case-controls  ... 
doi:10.1016/j.ajhg.2012.11.012 pmid:23261300 pmcid:PMC3542467 fatcat:khrczla325babebsqgimjic7ru

Whole exome sequencing of extreme age-related macular degeneration phenotypes

Rebecca J Sardell, Jessica N Cooke Bailey, Monique D Courtenay, Patrice Whitehead, Reneé A Laux, Larry D Adams, Jorge A Fortun, Milam A Brantley, Jaclyn L Kovach, Stephen G Schwartz, Anita Agarwal, William K Scott (+2 others)
2016 Molecular Vision  
To identify AMD risk variants and generate hypotheses for future studies, we performed whole exome sequencing for 75 individuals whose phenotype was not well predicted by their genotype at known risk loci  ...  We hypothesized that these phenotypically extreme individuals were more likely to carry rare risk or protective variants with large effect sizes.  ...  ACKNOWLEDGMENTS We thank all the participants of this study. We thank Drs. Michael Hauser and Eric Postel for their assistance ascertaining participants.  ... 
pmid:27625572 pmcid:PMC5007100 fatcat:tmsnn3luvjbhroi5b65eunudny

Large-Scale Gene-Centric Analysis Identifies Novel Variants for Coronary Artery Disease

Peter M. Visscher
2011 PLoS Genetics  
In our replication study of 24 promising common variants, we identified novel associations of variants in or near LIPA, IL5, TRIB1, and ABCG5/ABCG8, with per-allele odds ratios for CAD risk with each of  ...  To complement genome-wide association (GWA) studies, we conducted a large and systematic candidate gene study of CAD susceptibility, including analysis of many uncommon and functional variants.  ...  Acknowledgments The authors would like to thank the DIAGRAM Consortium, the Global Lipids Consortium, and the GlobalBPGen Consortium for providing information on associations of SNPs with cardiovascular  ... 
doi:10.1371/journal.pgen.1002260 pmid:21966275 pmcid:PMC3178591 fatcat:53fdbof63vgl3dn2vwu45vbcvq

Genetic compendium of 1511 human brains available through the UK Medical Research Council Brain Banks Network Resource

Michael J. Keogh, Wei Wei, Ian Wilson, Jon Coxhead, Sarah Ryan, Sara Rollinson, Helen Griffin, Marzena Kurzawa-Akanbi, Mauro Santibanez-Koref, Kevin Talbot, Martin R. Turner, Chris-Anne McKenzie (+9 others)
2016 Genome Research  
Known risk-factor associations at the gene level were then tested through case burden testing using Sequence Kernel Association Test (SKAT-O) (Wu et al. 2011 ) against a group of control cases aged 55  ...  Variants in GRN were associated with DLB (P = 0.005), with eight variants seen in 12.1% of patients and only 3.2% of controls, though no single allele was significantly associated with disease (Supplemental  ... 
doi:10.1101/gr.210609.116 pmid:28003435 pmcid:PMC5204341 fatcat:4vma5xjtv5bhretozmhdah3vx4

Examination of Candidate Exonic Variants for Association to Alzheimer Disease in the Amish

Laura N. D'Aoust, Anna C. Cummings, Renee Laux, Denise Fuzzell, Laura Caywood, Lori Reinhart-Mercer, William K. Scott, Margaret A. Pericak-Vance, Jonathan L. Haines, Yi-Hsiang Hsu
2015 PLoS ONE  
We determined that Amish AD cases harbored a significantly higher burden of the known risk alleles compared to Amish cognitively normal controls, but a significantly lower burden when compared to cases  ...  By then genotyping the top candidate variants from the known AD genes and from linkage regions implicated previous studies in the full dataset, new associations could be confirmed.  ...  Jackson for all of his contributions to our studies of the Amish over the past 20 years.  ... 
doi:10.1371/journal.pone.0118043 pmid:25668194 pmcid:PMC4323242 fatcat:2bdnwv3twzgnxjolvjpcdiik4m

Pooled Sequencing of 531 Genes in Inflammatory Bowel Disease Identifies an Associated Rare Variant in BTNL2 and Implicates Other Immune Related Genes

Natalie J. Prescott, Benjamin Lehne, Kristina Stone, James C. Lee, Kirstin Taylor, Jo Knight, Efterpi Papouli, Muddassar M. Mirza, Michael A. Simpson, Sarah L. Spain, Grace Lu, Franca Fraternali (+18 others)
2015 PLoS Genetics  
The top 5 disease associated variants were genotyped in an extension panel of 3,662 IBD cases and 3,639 controls, and tested for association in a combined analysis of 10,147 IBD cases and 7,008 controls  ...  panels from 474 cases of Crohn's disease and 480 controls. 80 variants with evidence of association in the sequencing experiment or with potential functional significance were selected for follow up genotyping  ...  Gene selection criteria Table 2 . 2 Combined case-control association analysis of 5 sequence variants from the phase III extension study in 10,147 IBD cases and 7,008 controls from phases I-III.  ... 
doi:10.1371/journal.pgen.1004955 pmid:25671699 pmcid:PMC4335459 fatcat:dfxckizk3vauhemv4qqnhmwiv4

Large-Scale Gene-Centric Meta-Analysis across 39 Studies Identifies Type 2 Diabetes Loci

Richa Saxena, Clara C. Elbers, Yiran Guo, Inga Peter, Tom R. Gaunt, Jessica L. Mega, Matthew B. Lanktree, Archana Tare, Berta Almoguera Castillo, Yun R. Li, Toby Johnson, Marcel Bruinenberg (+143 others)
2012 American Journal of Human Genetics  
Fourth, a multiethnic meta-analysis of all 39 studies identified T2D-associated variants in BCL2 (p ¼ 2.1 3 10 À8 ).  ...  In silico follow-up analysis of putative association signals found in independent genome-wide association studies (including 8,130 cases and 38,987 controls) performed by the DIAGRAM consortium identified  ...  Dorn, II, 79 Acknowledgments The CARe Consortium wishes to acknowledge the support of the National Heart, Lung, and Blood Institute and the contributions of the research institutions, study investigators  ... 
doi:10.1016/j.ajhg.2011.12.022 pmid:22325160 pmcid:PMC3309185 fatcat:p43ttjqtdbdk3ccyrotebvo5ry

An integrated genome and phenome-wide association study approach to understanding Alzheimer's disease predisposition [article]

Archita Khaire, Courtney E Wimberly, Eleanor C Semmes, Jillian H Hurst, Kyle M Walsh
2022 medRxiv   pre-print
Traits enriched for association with LOAD SNPs were ascertained and used to identify trait-associated candidate SNPs to be tested for association with LOAD risk (17,008 cases; 37,154 controls).  ...  We recently published an analytic approach to integrate GWAS and phenome-wide association study (PheWAS) data, enabling identification of candidate traits and trait-associated variants impacting disease  ...  for association with known LOAD risk variants.  ... 
doi:10.1101/2022.01.03.22268705 fatcat:tdbklhqovbf7zky4jeezjob3sm

Frequency of Pathogenic Germline Variants in CDH1, BRCA2, CHEK2, PALB2, BRCA1, and TP53 in Sporadic Lobular Breast Cancer

Christos Petridis, Iteeka Arora, Vandna Shah, Charlotte L. Moss, Anca Mera, Angela Clifford, Cheryl Gillett, Sarah E. Pinder, Ian Tomlinson, Rebecca Roylance, Michael A. Simpson, Elinor J. Sawyer
2019 Cancer Epidemiology, Biomarkers and Prevention  
The aim of this study was to assess the frequency of germline variants in CDH1, BRCA2, BRCA1, CHEK2, PALB2, and TP53 in sporadic ILC and LCIS diagnosed in women ages ≤60 years.  ...  Invasive lobular breast cancer (ILC) accounts for approximately 15% of invasive breast carcinomas and is commonly associated with lobular carcinoma in situ (LCIS).  ...  The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked advertisement in accordance with 18 U.S.C.  ... 
doi:10.1158/1055-9965.epi-18-1102 pmid:31263054 fatcat:4puopr3ajraxxl56ojrs2hvmya

Rare Variation in TET2 Is Associated with Clinically Relevant Prostate Carcinoma in African Americans

D. C. Koboldt, K. L. Kanchi, B. Gui, D. E. Larson, R. S. Fulton, W. B. Isaacs, A. Kraja, I. B. Borecki, L. Jia, R. K. Wilson, E. R. Mardis, A. S. Kibel
2016 Cancer Epidemiology, Biomarkers and Prevention  
Results: TET2 in African Americans was associated with aggressive disease, with 24.4% of cases harboring a rare deleterious variant compared with 9.6% of controls (FET P ¼ 1.84 Â 10 À5 , OR ¼ 3.0; SKAT-O  ...  Common variants have been associated with prostate cancer risk. Unfortunately, few are reproducibly linked to aggressive disease, the phenotype of greatest clinical relevance.  ...  Eeles and colleagues examined 1,854 prostate cancer cases and in 1,894 controls and identified 7 novel variants associated with prostate cancer risk, one of which was in close proximity to TET2.  ... 
doi:10.1158/1055-9965.epi-16-0373 pmid:27486019 pmcid:PMC5093030 fatcat:nlznqziai5g2bpmrooa23eiavu
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