In: Twin research and human genetics: the official journal of the International Society for Twin Studies (ISTS) and the Human Genetics Society of Australasia, Band 17, Heft 3, S. 143-150
With the dramatic technological developments of genome-wide association single-nucleotide polymorphism (SNP) chips and next generation sequencing, human geneticists now have the ability to assay genetic variation at ever-rarer allele frequencies. To fully understand the impact of these rare variants on common, complex diseases, we must be able to accurately assess their statistical significance. However, it is well established that classical association tests are not appropriate for the analysis of low-frequency variation, giving spurious findings when observed counts are too few. To further our understanding of the asymptotic properties of traditional association tests, we conducted a range of simulations of a typical rare variant (~1%) under the null hypothesis and tested the allelic χ2, Cochran–Armitage trend, Wald, and Fisher's exact tests. We demonstrate that rare variation shows marked deviation from the expected distributional behavior for each test, with fewer minor alleles corresponding to a greater degree of test statistics deflation. The effect becomes more pronounced at progressively smaller α levels. We also show that the Wald test is particularly deflated at α levels consistent with genome-wide association significance, much more so than the other association tests considered. In general, these classical association tests are inappropriate for the analysis of variants for which the minor allele is observed fewer than 80 times, largely irrespective of sample size.
In: Twin research and human genetics: the official journal of the International Society for Twin Studies (ISTS) and the Human Genetics Society of Australasia, Band 8, Heft 2, S. 101-107
In: Twin research and human genetics: the official journal of the International Society for Twin Studies (ISTS) and the Human Genetics Society of Australasia, Band 23, Heft 2, S. 87-89
AbstractDr Nick Martin has made enormous contributions to the field of behavior genetics over the past 50 years. Of his many seminal papers that have had a profound impact, we focus on his early work on the power of twin studies. He was among the first to recognize the importance of sample size calculation before conducting a study to ensure sufficient power to detect the effects of interest. The elegant approach he developed, based on the noncentral chi-squared distribution, has been adopted by subsequent researchers for other genetic study designs, and today remains a standard tool for power calculations in structural equation modeling and other areas of statistical analysis. The present brief article discusses the main aspects of his seminal paper, and how it led to subsequent developments, by him and others, as the field of behavior genetics evolved into the present era.
In: Twin research and human genetics: the official journal of the International Society for Twin Studies (ISTS) and the Human Genetics Society of Australasia, Band 20, Heft 2, S. 108-118
Sequence-based association studies are at a critical inflexion point with the increasing availability of exome-sequencing data. A popular test of association is the sequence kernel association test (SKAT). Weights are embedded within SKAT to reflect the hypothesized contribution of the variants to the trait variance. Because the true weights are generally unknown, and so are subject to misspecification, we examined the efficiency of a data-driven weighting scheme. We propose the use of a set of theoretically defensible weighting schemes, of which, we assume, the one that gives the largest test statistic is likely to capture best the allele frequency–functional effect relationship. We show that the use of alternative weights obviates the need to impose arbitrary frequency thresholds. As both the score test and the likelihood ratio test (LRT) may be used in this context, and may differ in power, we characterize the behavior of both tests. The two tests have equal power, if the weights in the set included weights resembling the correct ones. However, if the weights are badly specified, the LRT shows superior power (due to its robustness to misspecification). With this data-driven weighting procedure the LRT detected significant signal in genes located in regions already confirmed as associated with schizophrenia — thePRRC2A(p= 1.020e-06) and theVARS2(p= 2.383e-06) — in the Swedish schizophrenia case-control cohort of 11,040 individuals with exome-sequencing data. The score test is currently preferred for its computational efficiency and power. Indeed, assuming correct specification, in some circumstances, the score test is the most powerful test. However, LRT has the advantageous properties of being generally more robust and more powerful under weight misspecification. This is an important result given that, arguably, misspecified models are likely to be the rule rather than the exception in weighting-based approaches.
The Million Veteran Program (MVP) was established in 2011 as a national research initiative to determine how genetic variation influences the health of U.S. military veterans. We genotyped 312,571 MVP participants using a custom biobank array and linked the genetic data to laboratory and clinical phenotypes extracted from electronic health records covering a median of 10.0 years of follow-up. Among 297,626 veterans with at least 1 blood lipid measurement including 57,332 blacks and 24,743 Hispanics, we tested up to ~32 million variants for association with lipid levels and identified 118 novel genome-wide significant loci after meta-analysis with data from the Global Lipids Genetics Consortium (total N > 600,000). Through a focus on mutations predicted to result in a loss of gene function and a phenome-wide association study, we propose novel indications for pharmaceutical inhibitors targeting PCSK9 (abdominal aortic aneurysm), ANGPTL4 (type 2 diabetes), and PDE3B (triglycerides and coronary disease).
Publisher's version (útgefin grein) ; Polycystic ovary syndrome (PCOS) is a disorder characterized by hyperandrogenism, ovulatory dysfunction and polycystic ovarian morphology. Affected women frequently have metabolic disturbances including insulin resistance and dysregulation of glucose homeostasis. PCOS is diagnosed with two different sets of diagnostic criteria, resulting in a phenotypic spectrum of PCOS cases. The genetic similarities between cases diagnosed based on the two criteria have been largely unknown. Previous studies in Chinese and European subjects have identified 16 loci associated with risk of PCOS. We report a fixed-effect, inverse-weighted-variance meta-analysis from 10,074 PCOS cases and 103,164 controls of European ancestry and characterisation of PCOS related traits. We identified 3 novel loci (near PLGRKT, ZBTB16 and MAPRE1), and provide replication of 11 previously reported loci. Only one locus differed significantly in its association by diagnostic criteria; otherwise the genetic architecture was similar between PCOS diagnosed by self-report and PCOS diagnosed by NIH or non-NIH Rotterdam criteria across common variants at 13 loci. Identified variants were associated with hyperandrogenism, gonadotropin regulation and testosterone levels in affected women. Linkage disequilibrium score regression analysis revealed genetic correlations with obesity, fasting insulin, type 2 diabetes, lipid levels and coronary artery disease, indicating shared genetic architecture between metabolic traits and PCOS. Mendelian randomization analyses suggested variants associated with body mass index, fasting insulin, menopause timing, depression and male-pattern balding play a causal role in PCOS. The data thus demonstrate 3 novel loci associated with PCOS and similar genetic architecture for all diagnostic criteria. The data also provide the first genetic evidence for a male phenotype for PCOS and a causal link to depression, a previously hypothesized comorbid disease. Thus, the genetics provide a comprehensive view of PCOS that encompasses multiple diagnostic criteria, gender, reproductive potential and mental health. ; This work has been supported by MRC grant MC_U106179472 (FD, KO, JRBP), Samuel Oschin Comprehensive Cancer Institute Developmental Funds, Center for Bioinformatics and Functional Genomics and Department of Biomedical Sciences Developmental Funds (MRJ), NCI P30CA177558 (CH), NCI UM1CA186107 (PK), European Regional Development Fund (Project No. 2014-2020.4.01.15-0012) and the European Union's Horizon 2020 research and innovation program under grant agreements No 692065 (TL, RM, AS) and 692145 (RM), NICHD R01HD065029 (RS), Estonian Ministry of Education and Research (grant IUT34-16 to TL), NICHD R01HD057450 (MU), NICHD P50HD044405 (AD), NICHD R01HD057223 (AD), R01HD085227 (MGH, AD), deCode Genetics (GT, UT, KS, US), Raine Medical Research Foundation Priming Grant (BHM), SCGOPHCG RAC 2015-16/034 (SGW, BGAS), 2016-17/018 (BGAS), NIHR BRC, Wellcome Trust, MRC (TDS), Eris M. Field Chair in Diabetes Research (MOG), NIDDK P30 DK063491 (MOG), NIDDK U01DK094431, U01DK048381 (DE), NICHD U10HD38992 (RL), Estonian Ministry of Education and Research (grant IUT34-16), Enterprise Estonia (grant EU48695); the EU-FP7 Marie Curie Industry-Academia Partnerships and Pathways (IAPP, grant SARM, EU324509 to AS), Wellcome (090532, 098381, 203141); European Commission (ENGAGE: HEALTH-F4-2007-201413 to MIM), MRC G0802782, MR/M012638/1 (SF), Li Ka Shing Foundation, WT-SSI/John Fell Funds, NIHR Biomedical Research Centre, Oxford, Widenlife and NICHD 5P50HD028138-27 (CML), NICHD R01HD065029, ADA 1-10-CT-57, Harvard Clinical and Translational Science Center, from the National Center for Research Resources 1UL1 RR025758 (CKW). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. ; Peer Reviewed
To access publisher's full text version of this article, please click on the hyperlink in Additional Links field or click on the hyperlink at the top of the page marked Files. This article is open access. ; Protein-truncating variants protective against human disease provide in vivo validation of therapeutic targets. Here we used targeted sequencing to conduct a search for protein-truncating variants conferring protection against inflammatory bowel disease exploiting knowledge of common variants associated with the same disease. Through replication genotyping and imputation we found that a predicted protein-truncating variant (rs36095412, p.R179X, genotyped in 11,148 ulcerative colitis patients and 295,446 controls, MAF=up to 0.78%) in RNF186, a single-exon ring finger E3 ligase with strong colonic expression, protects against ulcerative colitis (overall P=6.89 × 10(-7), odds ratio=0.30). We further demonstrate that the truncated protein exhibits reduced expression and altered subcellular localization, suggesting the protective mechanism may reside in the loss of an interaction or function via mislocalization and/or loss of an essential transmembrane domain. ; National Institute of Diabetes and Digestive and Kidney Disease (NIDDK) DK064869 DK062432 National Human Genome Research Institute (NHGRI) DK064869 DK043351 HG005923 Crohns and Colitis Foundation 3765 Leona M. & Harry B. Helmsley Charitable Trust 2015PG-IBD001 Amgen 2013583217 CCFA 3765 Cedars-Sinai F. Widjaja Foundation, info:eu-repo/grantAgreement/EC/FP7/305479, European Union DK062413 AI067068 U54DE023789-01 Leona M. and Harry B. Helmsley Charitable Trust Crohn's and Colitis Foundation of America NIH DK062431 U01 DK062429 U01 DK062422 R01 DK092235 U01 DK062420 Medical Research Council, UK MR/J00314X/1 Wellcome Trust WT091310 098051 Inflammatory Bowel Disease Genetic Research Chair at the University of Pittsburgh PO1DK046763
The direct estimation of heritability from genome-wide common variant data as implemented in the program Genome-wide Complex Trait Analysis (GCTA) has provided a means to quantify heritability attributable to all interrogated variants. We have quantified the variance in liability to disease explained by all SNPs for two phenotypically-related neurobehavioral disorders, obsessive-compulsive disorder (OCD) and Tourette Syndrome (TS), using GCTA. Our analysis yielded a heritability point estimate of 0.58 (se = 0.09, p = 5.64e-12) for TS, and 0.37 (se = 0.07, p = 1.5e-07) for OCD. in addition, we conducted multiple genomic partitioning analyses to identify genomic elements that concentrate this heritability. We examined genomic architectures of TS and OCD by chromosome, MAF bin, and functional annotations. in addition, we assessed heritability for early onset and adult onset OCD. Among other notable results, we found that SNPs with a minor allele frequency of less than 5% accounted for 21% of the TS heritability and 0% of the OCD heritability. Additionally, we identified a significant contribution to TS and OCD heritability by variants significantly associated with gene expression in two regions of the brain (parietal cortex and cerebellum) for which we had available expression quantitative trait loci (eQTLs). Finally we analyzed the genetic correlation between TS and OCD, revealing a genetic correlation of 0.41 (se = 0.15, p = 0.002). These results are very close to previous heritability estimates for TS and OCD based on twin and family studies, suggesting that very little, if any, heritability is truly missing (i.e., unassayed) from TS and OCD GWAS studies of common variation. the results also indicate that there is some genetic overlap between these two phenotypically-related neuropsychiatric disorders, but suggest that the two disorders have distinct genetic architectures. ; Judah Foundation ; NIH ; Tourette Syndrome Association International Consortium for Genetics (TSAICG) ; New Jersey Center for Tourette Syndrome and Associated Disorders ; NIMH ; Obsessive Compulsive Foundation ; Ontario Mental Health Foundation ; Tourette Syndrome Association ; American Academy of Child and Adolescent Psychiatry (AACAP) ; Anxiety Disorders Association of America (ADAA) ; University of British Columbia ; Michael Smith Foundation ; American Recovery and Re-investment Act (ARRA) ; Australian Research Council ; Australian National Health and Medical Research Council ; German Research Foundation ; NIH Genes, Environment and Health Initiative [GEI] ; Gene Environment Association Studies (GENEVA) under GEI ; NIH GEI ; National Institute on Alcohol Abuse and Alcoholism ; National Institute on Drug Abuse ; Univ Chicago, Dept Med, Med Genet Sect, Chicago, IL 60637 USA ; Harvard Univ, Massachusetts Gen Hosp, Dept Psychiat,Sch Med, Psychiat & Neurodev Genet Unit,Ctr Human Genet Re, Boston, MA USA ; Broad Inst Harvard & MIT, Stanley Ctr Psychiat Res, Cambridge, MA USA ; Univ Chicago, Dept Med, Chicago, IL 60637 USA ; Univ Chicago, Dept Human Genet, Chicago, IL 60637 USA ; Univ Amsterdam, Acad Med Ctr, Dept Psychiat, NL-1105 AZ Amsterdam, Netherlands ; Massachusetts Gen Hosp, Analyt & Translat Genet Unit, Boston, MA 02114 USA ; Univ Queensland, Diamantina Inst, Brisbane, Qld 4072, Australia ; Univ Queensland, Queensland Brain Inst, Brisbane, Qld 4072, Australia ; Univ Hlth Network, Toronto Western Res Inst, Toronto, ON, Canada ; Hosp Sick Children, Toronto, ON M5G 1X8, Canada ; Univ Vita Salute San Raffaele, Milan, Italy ; Hadassah Hebrew Univ Med Ctr, Herman Dana Div Child & Adolescent Psychiat, Jerusalem, Israel ; Univ Pontificia Bolivariana, Univ Antioquia, Medellin, Colombia ; Johns Hopkins Univ, Sch Med, Dept Psychiat & Behav Sci, Baltimore, MD 21205 USA ; Yale Univ, Dept Psychiat, New Haven, CT 06520 USA ; Yale Univ, Sch Med, Ctr Child Study, New Haven, CT 06510 USA ; North Shore Long Isl Jewish Med Ctr, Manhasset, NY USA ; NYU Med Ctr, New York, NY 10016 USA ; North Shore Long Isl Jewish Hlth Syst, Manhasset, NY USA ; Hofstra Univ, Sch Med, Hempstead, NY 11550 USA ; Inst Nacl Psiquiatria Ramon de la Fuente Muniz, Mexico City, DF, Mexico ; UCL, London, England ; Univ Hong Kong, Dept Psychiat, Hong Kong, Hong Kong, Peoples R China ; Univ São Paulo, Sch Med, Dept Psychiat, São Paulo, Brazil ; Vrije Univ Amsterdam, Med Ctr, Dept Psychiat, Amsterdam, Netherlands ; Univ Utrecht, Dept Clin & Hlth Psychol, Utrecht, Netherlands ; Altrecht Acad Anxiety Ctr, Utrecht, Netherlands ; Univ Milan, Osped San Raffaele, I-20127 Milan, Italy ; Univ Calif Los Angeles, Dept Psychol, Los Angeles, CA 90024 USA ; Univ Calif San Diego, Dept Psychiat, La Jolla, CA 92093 USA ; Univ Montreal, Montreal, PQ, Canada ; Univ Calif Los Angeles, Keck Sch Med, Div Biostat, Dept Preventat Med, Los Angeles, CA USA ; Univ Illinois, Dept Psychiat, Inst Juvenile Res, Chicago, IL 60612 USA ; Univ Ghent, Lab Pharmaceut Biotechnol, B-9000 Ghent, Belgium ; Inst Pasteur, Paris, France ; French Natl Sci Fdn, Fondat Fondamental, Creteil, France ; Hop Robert Debre, AP HP, Dept Child & Adolescent Psychiat, F-75019 Paris, France ; Univ Montreal, Dept Psychiat, Montreal, PQ H3C 3J7, Canada ; Univ Wurzburg, Dept Child & Adolescent Psychiat Psychosomat & Ps, D-97070 Wurzburg, Germany ; Univ Munich, Dept Psychiat & Psychotherapy, Munich, Germany ; Yale Univ, Sch Med, Dept Psychiat, New Haven, CT USA ; Harvard Univ, Sch Med, Dept Psychiat, Massachusetts Gen Hosp,OCD Program, Boston, MA 02115 USA ; Univ Med Greifswald, Helios Hosp Stralsund, Dept Psychiat & Psychotherapy, Greifswald, Germany ; Butler Hosp, Brown Med Sch, Dept Psychiat & Human Behav, Providence, RI 02906 USA ; Shaare Zedek Med Ctr, Neuropediatr Unit, Jerusalem, Israel ; Rutgers State Univ, Dept Genet, Human Genet Inst New Jersey, Piscataway, NJ USA ; Univ Stellenbosch, Dept Psychiat, ZA-7600 Stellenbosch, South Africa ; Univ São Paulo, Fac Med, Dept Psychiat, BR-05508 São Paulo, Brazil ; Baylor Coll Med, Dept Neurol, Parkinsons Dis Ctr, Houston, TX 77030 USA ; Baylor Coll Med, Dept Neurol, Movement Disorders Clin, Houston, TX 77030 USA ; Massachusetts Gen Hosp, Dept Psychiat, Boston, MA 02114 USA ; Ctr Addict & Mental Hlth, Neurogenet Sect, Toronto, ON, Canada ; Univ Toronto, Dept Psychiat, Toronto, ON, Canada ; Yale Univ, Sch Med, Dept Genet, Yale Child Study Ctr, New Haven, CT 06510 USA ; Overlook Hosp, Atlantic Neurosci Inst, Summit, NJ USA ; Carracci Med Grp, Mexico City, DF, Mexico ; Inst Mondor Rech Biomed, Creteil, France ; Yale Univ, Ctr Child Study, New Haven, CT 06520 USA ; Univ Bonn, Dept Psychiat & Psychotherapy, Bonn, Germany ; Univ Illinois, Dept Psychiat, Inst Human Genet, Chicago, IL 60612 USA ; Univ Stellenbosch, Dept Psychiat, MRC Unit Anxiety & Stress Disorders, ZA-7600 Stellenbosch, South Africa ; Univ Calif San Francisco, Dept Psychiat, San Francisco, CA USA ; UCI, Sch Med, Dept Psychiat & Human Behav, Irvine, CA USA ; Univ Utah, Salt Lake City, UT USA ; NIMH Intramural Res Program, Clin Sci Lab, Bethesda, MD USA ; Med City Dallas Hosp, Dept Clin Res, Dallas, TX USA ; Univ Med Ctr, Rudolf Magnus Inst Neurosci, Dept Psychiat, Utrecht, Netherlands ; Univ Calif Los Angeles, Semel Inst Neurosci & Human Behav, Ctr Neurobehav Genet, Los Angeles, CA 90024 USA ; Yale Univ, Sch Med, Dept Genet, New Haven, CT 06510 USA ; Univ So Calif, Keck Sch Med, Zilkha Neurogenet Inst, Dept Psychiat & Behav Sci, Los Angeles, CA 90033 USA ; Univ Calif Los Angeles, David Geffen Sch Med, Dept Psychiat & Biobehav Sci, Los Angeles, CA 90095 USA ; Yale Univ, Dept Psychol, New Haven, CT 06520 USA ; Partners Psychiat & McLean Hosp, Boston, MA USA ; Sunnybrook Hlth Sci Ctr, Frederick W Thompson Anxiety Disorders Ctr, Toronto, ON M4N 3M5, Canada ; St George Hosp, London, England ; Sch Med, London, England ; Hosp Nacl Ninos Dr Carlos Saenz Herrera, San Jose, Costa Rica ; Universidade Federal de São Paulo, Dept Psychiat, Child & Adolescent Psychiat Unit UPIA, São Paulo, Brazil ; Wayne State Univ, Dept Psychiat & Behav Neurosci, Detroit, MI 48207 USA ; Detroit Med Ctr, Detroit, MI USA ; McGill Univ, Montreal Neurol Inst, Montreal, PQ, Canada ; Univ Cologne, Dept Psychiat & Psychotherapy, D-50931 Cologne, Germany ; Univ Fed Bahia, Univ Hlth Care Serv SMURB, Salvador, BA, Brazil ; Youthdale Treatment Ctr, Toronto, ON, Canada ; Johns Hopkins Univ Sch Med, Baltimore, MD USA ; Univ Cape Town, ZA-7925 Cape Town, South Africa ; Univ Med Ctr Utrecht, Dept Med Genet, Utrecht, Netherlands ; Vanderbilt Univ, Kennedy Ctr Res Human Dev, Dept Psychiat, Nashville, TN 37235 USA ; Vanderbilt Univ, Kennedy Ctr Res Human Dev, Dept Pediat & Pharmacol, Nashville, TN 37235 USA ; Vanderbilt Univ, Inst Brain, Nashville, TN 37235 USA ; Univ Zurich, Dept Child & Adolescent Psychiat, Zurich, Switzerland ; Univ Wurzburg, Dept Child & Adolescent Psychiat, D-97070 Wurzburg, Germany ; Univ Amsterdam, Acad Med Ctr, Ctr Psychiat, NL-1105 BC Amsterdam, Netherlands ; Inst Royal Netherlands Acad Arts & Sci NIN KNAW, Netherlands Inst Neurosci, Amsterdam, Netherlands ; NIMH Intramural Res Program, Unit Stat Genom, Bethesda, MD USA ; Univ Utah, Dept Psychiat, Salt Lake City, UT USA ; Natl Inst Genom Med SAP, Carracci Med Grp, Mexico City, DF, Mexico ; Vrije Univ Amsterdam, Ctr Neurogen & Cognit Res, Dept Funct Genom, Amsterdam, Netherlands ; Vrije Univ Amsterdam Med Ctr, Dept Clin Genet, Amsterdam, Netherlands ; Erasmus Univ, Med Ctr, Dept Child & Adolescent Psychiat, Rotterdam, Netherlands ; Univ Michigan, Dept Psychiat, Ann Arbor, MI 48109 USA ; Vrije Univ Amsterdam, Med Ctr, Dept Clin Genet, Sect Med Genom, Amsterdam, Netherlands ; German Ctr Neurodegenerat Dis, Tubingen, Germany ; Hosp Sick Children, Program Genet & Genome Biol, Toronto, ON M5G 1X8, Canada ; Erasmus MC, Dept Clin Genet, Rotterdam, Netherlands ; Univ British Columbia, British Columbia Mental Hlth & Addict Res Inst, Vancouver, BC V5Z 1M9, Canada ; Brigham & Womens Hosp, Div Cognit & Behav Neurol, Boston, MA 02115 USA ; Massachusetts Gen Hosp, Dept Neurol, Boston, MA 02114 USA ; Universidade Federal de São Paulo, Dept Psychiat, Child & Adolescent Psychiat Unit UPIA, São Paulo, Brazil ; NIH: NS40024 ; NIH: NS16648 ; NIH: MH079489 ; NIH: MH073250 ; NIH: NS037484 ; NIH: 1R01MH079487-01A1 ; NIH: K20 MH01065 ; NIH: R01 MH58376 ; NIH: MH085057 ; NIH: MH079494 ; NIH: HHSN268200782096C ; NIMH: R01MH092293 ; American Recovery and Re-investment Act (ARRA): NS40024-07S1 ; American Recovery and Re-investment Act (ARRA): NS16648-29S1 ; Australian Research Council: FT0991360 ; Australian Research Council: DE130100614 ; Australian National Health and Medical Research Council: 1047956 ; Australian National Health and Medical Research Council: 1052684 ; German Research Foundation: DFG GR 1912/1-1 ; NIH Genes, Environment and Health Initiative [GEI]: U01 HG004422 ; NIH GEI: U01HG004438 ; : R01 MH090937 ; : P50MH094267 ; Web of Science