A Tutorial on Statistical Methods for Population Association Studies
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Linkage Disequilibrium
Linkage Disequilibrium Biostatistics 666 Logistics: Office Hours Office hours on Mondays at 4 pm. Room 4614 School of Public Health Tower Previously … Basic properties of a locus • Allele Frequencies • Genotype Frequencies Hardy-Weinberg Equilibrium • Relationship between allele and genotype frequencies that holds for most genetic markers Exact Tests for Hardy-Weinberg Equilibrium Today … We’ll consider properties of pairs of alleles Haplotype frequencies Linkage equilibrium Linkage disequilibrium Let’s consider the history of two neighboring alleles… Alleles that exist today arose through ancient mutation events… Before Mutation A C G T A A G T A C G T A C G T G T A C G A C G After Mutation A C G T A A G T A C G T A C G T G T A C G A C G A C G T A C G T A CMutation G T A C G T G T A C G A C G Alleles that exist today arose through ancient mutation events… Before Mutation A After Mutation A C Mutation One allele arose first, and then the other… Before Mutation A G C G After Mutation A G C G C C Mutation Recombination generates new arrangements for ancestral alleles Before Recombination A G C G C C After Recombination A G C G C C A C Recombinant Haplotype Linkage Disequilibrium Chromosomes are mosaics Ancestor Extent and conservation of mosaic pieces depends on Present-day • Recombination rate • Mutation rate • Population size • Natural selection Combinations of alleles at very close markers reflect ancestral haplotypes Why is linkage disequilibrium important for gene mapping? Association Studies and Linkage Disequilibrium -
Genetic, Epidemiological and Biological Analysis of Interleukin-10
Genes and Immunity (2009) 10, 174–180 & 2009 Macmillan Publishers Limited All rights reserved 1466-4879/09 $32.00 www.nature.com/gene ORIGINAL ARTICLE Genetic, epidemiological and biological analysis of interleukin-10 promoter single-nucleotide polymorphisms suggests a definitive role for À819C/T in leprosy susceptibility AC Pereira1,5, VN Brito-de-Souza1,5, CC Cardoso2, IMF Dias-Baptista1, FPC Parelli1,3, J Venturini1,3, FR Villani-Moreno1, AG Pacheco4 and MO Moraes2 1Instituto Lauro de Souza Lima, Bauru, Sa˜o Paulo, Brazil; 2Laborato´rio de Hansenı´ase, Departamento de Micobacterioses, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil; 3Tropical Diseases Area, Botucatu Medical School, Sao Paulo State University, UNESP, Botucatu, Sa˜o Paulo, Brazil and 4Departamento de Epidemiologia e Me´todos Quantitativos em Sau´de (DEMQS), Escola Nacional de Sau´de Pu´blica (ENSP)/PROCC, FIOCRUZ, Rio de Janeiro, Brazil Leprosy is a complex infectious disease influenced by genetic and environmental factors. The genetic contributing factors are considered heterogeneous and several genes have been consistently associated with susceptibility like PARK2, tumor necrosis factor (TNF), lymphotoxin-a (LTA) and vitamin-D receptor (VDR). Here, we combined a case–control study (374 patients and 380 controls), with meta-analysis (5 studies; 2702 individuals) and biological study to test the epidemiological and physiological relevance of the interleukin-10 (IL-10) genetic markers in leprosy. We observed that the À819T allele is associated with leprosy susceptibility either in the case–control or in the meta-analysis studies. Haplotypes combining promoter single-nucleotide polymorphisms also implicated a haplotype carrying the À819T allele in leprosy susceptibility (odds ratio (OR) ¼ 1.40; P ¼ 0.01). -
The Role of Haplotypes in Candidate Gene Studies
Genetic Epidemiology 27: 321–333 (2004) The Role of Haplotypes in Candidate Gene Studies Andrew G. Clarkn Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York Human geneticists working on systems for which it is possible to make a strong case for a set of candidate genes face the problem of whether it is necessary to consider the variation in those genes as phased haplotypes, or whether the one-SNP- at-a-time approach might perform as well. There are three reasons why the phased haplotype route should be an improvement. First, the protein products of the candidate genes occur in polypeptide chains whose folding and other properties may depend on particular combinations of amino acids. Second, population genetic principles show us that variation in populations is inherently structured into haplotypes. Third, the statistical power of association tests with phased data is likely to be improved because of the reduction in dimension. However, in reality it takes a great deal of extra work to obtain valid haplotype phase information, and inferred phase information may simply compound the errors. In addition, if the causal connection between SNPs and a phenotype is truly driven by just a single SNP, then the haplotype- based approach may perform worse than the one-SNP-at-a-time approach. Here we examine some of the factors that affect haplotype patterns in genes, how haplotypes may be inferred, and how haplotypes have been useful in the context of testing association between candidate genes and complex traits. Genet. Epidemiol. & 2004 Wiley-Liss, Inc. Key words: haplotype inference; haplotype association testing; candidate genes; linkage equilibrium Grant sponsor: NIH; Grant numbers: GM65509, HL072904. -
PLINK: a Toolset for Whole Genome Association and Population-Based Linkage Analyses
1 PLINK: a toolset for whole genome association and population-based linkage analyses Shaun Purcell1,2, Benjamin Neale1,2,3, Kathe Todd-Brown1, Lori Thomas1, Manuel A R Ferreira1, David Bender1,2, Julian Maller1,2, Paul I W de Bakker1,2, Mark J Daly1,2, Pak C Sham4 1 Center for Human Genetic Research, MGH, Boston, USA. 2 Broad Institute of Harvard and MIT, Cambridge, USA. 3 Institute of Psychiatry, University of London, London, UK. 4 Genome Research Center, University of Hong Kong, Pokfulam, Hong Kong. Correspondence: Shaun Purcell, Rm 6.254, CPZ-N, 185 Cambridge Street, Boston, MA, 02114, USA; Tel: 617-726-7642; Fax: 617-726-0830; [email protected] Keywords : Whole genome association studies, single nucleotide polymorphisms, identity-by-state, identity-by-descent, linkage analysis, computer software Abstract Whole-genome association studies (WGAS) bring new computational as well as analytic challenges to researchers. Many existing genetic analysis tools are not designed to handle such large datasets in a convenient manner and do not necessarily exploit the new opportunities that whole-genome data bring. To address these issues, we developed PLINK, an open source C/C++ WGAS toolset. Large datasets, comprising hundreds of thousands of markers geno- typed for thousands of individuals, can be rapidly manipulated and analyzed in their entirety. As well as providing tools to make the basic analytic steps computationally efficient, PLINK also supports some novel approaches to whole-genome data, that take advantage of whole-genome coverage. We in- troduce PLINK and describe the five main domains of function: data man- agement, summary statistics, population stratification, association analysis and identity-by-descent estimation. -
Basics in Genetics Analysis
Genetics and Diseases Basics in Genetics Analysis Heping Zhang Environment 9/24/2007 Dr. Doug Brutlag Lecture Syllabus “central paradigm” //www.s-star.org/ 2 Diseases Progression Known and Probable Risk Factors z Being a woman How does the Breast Cancer grows and spread? z Getting older z Having a personal history of BC or ovarian cancer z Having a family history of breast cancer z Having a previous biopsy showing carcinoma in situ z Having your first period before age 12 z Starting menopause after age 55 A malignant Malignant Cancer cells z Never having children tumor within tumors spread z Having your first child after age 30 the breast suppress z Having a mutation in the BRCA1 or BRCA2 genes normal ones z Drinking more than 1 alcoholic drink per day z Being overweight after menopause or gaining weight as an adult. 9/24/2007 3 9/24/2007 4 Genetic Epidemiology Terminology • How is a disease transmitted in families? ( Marker: a known DNA sequence that can be identified by a Inheritance patterns). simple assay e.g., D1S80, D4S43, D16S126 • What is the recurrence Allele: a viable DNA coding that occupies a given locus risk for relatives? (position) on a chromosome e.g., A, a; • Mendelian disorders Genotype: the observed alleles at a genetic locus for an • Autosomal or X-linked individual • Dominant or recessive e.g., AA, Aa, aa; 0 Homozygous: AA, aa 0 Heterozygous: Aa Phenotype: the expression of a particular genotype 0 Continuous: blood pressure 0 Dichotomous: Cancer, Hypertension 9/24/2007 Duke University Center of Human Genetics 5 9/24/2007 6 1 Mendel’s Laws DNA Polymorphism and Human Variation First Law Segregation of Characteristics: the sex cell of a plant or animal may contain one factor (allele) for different traits but not both factors needed to express the traits. -
Transferability of Tag Snps to Capture Common Genetic Variation in DNA Repair Genes Across Multiple Populations Paul I.W. De
Transferability of Tag SNPs to Capture Common Genetic Variation in DNA Repair Genes Across Multiple Populations Paul I.W. De Bakker, Robert R. Graham, David Altshuler, Brian E. Henderson, and Christopher A. Haiman Pacific Symposium on Biocomputing 11:478-486(2006) TRANSFERABILITY OF TAG SNPS TO CAPTURE COMMON GENETIC VARIATION IN DNA REPAIR GENES ACROSS MULTIPLE POPULATIONS PAUL I.W. DE BAKKER, ROBERT R. GRAHAM, DAVID ALTSHULER Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA BRIAN E. HENDERSON, CHRISTOPHER A. HAIMAN Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA Genetic association studies can be made more cost-effective by exploiting linkage disequilibrium patterns between nearby single-nucleotide polymorphisms (SNPs). The International HapMap Project now offers a dense SNP map across the human genome in four population samples. One question is how well tag SNPs chosen from a resource like HapMap can capture common variation in independent disease samples. To address the issue of tag SNP transferability, we genotyped 2,783 SNPs across 61 genes (with a total span of 6 Mb) involved in DNA repair in 466 individuals from multiple populations. We picked tag SNPs in samples with European ancestry from the Centre d’Etude du Polymorphisme Humain, and evaluated coverage of common variation in the other samples. Our comparative analysis shows that common variation in non- African samples can be captured robustly with only marginal loss in terms of the maximum r2. We also evaluated the transferability of specified multi-marker haplotypes as predictors for untyped SNPs, and demonstrate that they provide equivalent coverage compared to single-marker tests (pairwise tags) while requiring fewer SNPs for genotyping. -
Genetic Association Tests for Binary Traits with An
GENETIC ASSOCIATION TESTS FOR BINARY TRAITS WITH AN APPLICATION by SULGI KIM Submitted in partial fulfillment of the requirements For the degree of Doctor of Philosophy Dissertation Advisor: Dr. Robert C. Elston Department of Epidemiology and Biostatistics CASE WESTER RESERVE UNIVERSITY August, 2009 CASE WESTERN RESERVE UNIVERSITY SCHOOL OF GRADUATE STUDIES We hereby approved the dissertation of Sulgi Kim candidate for the Ph. D. degree*. (Signed) Robert C. Elston, Ph.D Department of Epidemiology and Biostatistics Chair of the committee Xiaofeng Zhu, Ph.D Department of Epidemiology and Biostatistics Courtney Gray-McGuire, Ph.D Department of Epidemiology and Biostatistics Jill S. Barnholtz-Sloan, Ph.D Case Comprehensive Cancer Center June 8, 2009 *We also certify that written approval has been obtained for any proprietary material therein. ii Table of Contents List of Tables .................................................................................................................... iv List of Figures .....................................................................................................................v Acknowledgements .......................................................................................................... vi Abstract ...............................................................................................................................1 Chapter 1. Introduction.....................................................................................................3 Chapter 2. Association Tests -
Efficient Design and Analysis of Genome-Wide
UNIVERSITY OF CALIFORNIA Los Angeles Efficient Design and Analysis of Genome-wide Association Studies A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Computer Science by Emrah Kostem 2013 c Copyright by Emrah Kostem 2013 ABSTRACT OF THE DISSERTATION Efficient Design and Analysis of Genome-wide Association Studies by Emrah Kostem Doctor of Philosophy in Computer Science University of California, Los Angeles, 2013 Professor Eleazar Eskin, Chair The recent advances in genomic technologies, have made it possible to collect large- scale information on genetic variation across a diverse biological landscape. This has resulted in an exponential influx of genetic information and the field of genetics has be- come data-rich in a relatively short amount of time. These developments have opened new avenues to elucidate the genetic basis of complex diseases, where the traditional disease study approaches had little success. In recent years, the genome-wide association study (GWAS) approach has gained widespread popularity for its ease of use and effectiveness, and is now the standard approach to study complex diseases. In GWAS, information on millions of single- nucleotide polymorphisms (SNPs) is collected from case and control individuals. SNP genotyping is cost-effective and due to their abundance in the genome, SNPs are cor- related to their neighboring genetic variation, which makes them tags for genomic regions. Typically, each SNP is statistically tested for association to disease, and the genomic regions tagged by the significant SNPs are believed to be harboring the func- tional variants contributing to disease. In order to reduce the cost of GWAS and the redundancy in the information col- ii lected, an informative subset of the SNPs, or tag SNPs, are genotyped. -
Design and Analysis of Genetic Association Studies
ection S ON Design and Analysis of Statistical Genetic Association G enetics Studies Hemant K Tiwari, Ph.D. Professor & Head Section on Statistical Genetics Department of Biostatistics School of Public Health Association Analysis • Linkage Analysis used to be the first step in gene mapping process • Closely located SNPs to disease locus may co- segregate due to linkage disequilibrium i.e. allelic association due to linkage. • The allelic association forms the theoretical basis for association mapping Linkage vs. Association • Linkage analysis is based on pedigree data (within family) • Association analysis is based on population data (across families) • Linkage analyses rely on recombination events • Association analyses rely on linkage disequilibrium • The statistic in linkage analysis is the count of the number of recombinants and non-recombinants • The statistical method for association analysis is “statistical correlation” between Allele at a locus with the trait Linkage Disequilibrium • Over time, meiotic events and ensuing recombination between loci should return alleles to equilibrium. • But, marker alleles initially close (genetically linked) to the disease allele will generally remain nearby for longer periods of time due to reduced recombination. • This is disequilibrium due to linkage, or “linkage disequilibrium” (LD). Linkage Disequilibrium (LD) • Chromosomes are mosaics Ancestor • Tightly linked markers Present-day – Alleles associated – Reflect ancestral haplotypes • Shaped by – Recombination history – Mutation, Drift Tishkoff -
Large-Scale Evolutionary Analysis of Polymorphic Inversions in the Human Genome
ADVERTIMENT. Lʼaccés als continguts dʼaquesta tesi queda condicionat a lʼacceptació de les condicions dʼús establertes per la següent llicència Creative Commons: http://cat.creativecommons.org/?page_id=184 ADVERTENCIA. El acceso a los contenidos de esta tesis queda condicionado a la aceptación de las condiciones de uso establecidas por la siguiente licencia Creative Commons: http://es.creativecommons.org/blog/licencias/ WARNING. The access to the contents of this doctoral thesis it is limited to the acceptance of the use conditions set by the following Creative Commons license: https://creativecommons.org/licenses/?lang=en Doctoral thesis Large-scale evolutionary analysis of polymorphic inversions in the human genome Author Carla Giner Delgado Director Mario Caceres´ Aguilar Departament de Gen`eticai de Microbiologia Facultat de Bioci`encies Universitat Aut`onomade Barcelona 2017 Large-scale evolutionary analysis of polymorphic inversions in the human genome Mem`oriapresentada per Carla Giner Delgado per a optar al grau de Doctora en Gen`etica per la Universitat Aut`onomade Barcelona Autora Director Carla Giner Delgado Mario Caceres´ Aguilar Bellaterra, 28 de Setembre de 2017 Abstract Chromosomal inversions are structural variants that invert a fragment of the genome without usually modifying its content, and their subtle but powerful effects in natural populations have fascinated evolutionary biologists for a long time. Discovered a century ago in fruit flies, their association with dif- ferent evolutionary processes, such as local adaptation and speciation, was soon evident in several species. However, in the current era of genomics and big data, inversions frequently escape the grasp of current technologies and remain largely overlooked in humans. -
Genome-Wide Association Studies: Understanding the Genetics of Common Disease the Academy of Medical Sciences | FORUM
The Academy of Medical Sciences | FORUM Genome-wide association studies: understanding the genetics of common disease Symposium report July 2009 The Academy of Medical Sciences The Academy of Medical Sciences promotes advances in medical science and campaigns to ensure these are converted into healthcare benefits for society. Our Fellows are the UK’s leading medical scientists from hospitals and general practice, academia, industry and the public service. The Academy seeks to play a pivotal role in determining the future of medical science in the UK, and the benefits that society will enjoy in years to come. We champion the UK’s strengths in medical science, promote careers and capacity building, encourage the implementation of new ideas and solutions – often through novel partnerships – and help to remove barriers to progress. The Academy’s FORUM with industry The Academy’s FORUM is an active network of scientists from industry and academia, with representation spanning the pharmaceutical, biotechnology and other health product sectors, as well as trade associations, Research Councils and other major charitable research funders. Through promoting interaction between these groups, the FORUM aims to take forward national discussions on scientific opportunities, technology trends and the associated strategic choices for healthcare and other life-science sectors. The FORUM builds on what is already distinctive about the Academy: its impartiality and independence, its focus on research excellence across the spectrum of clinical and basic sciences and its commitment to interdisciplinary working. Acknowledgements This report provides a summary of the discussion at the FORUM symposium on ‘Genome-wide association studies’ held in October 2008. -
Study of Genetic Association
Statistical Genomics and Bioinformatics Workshop 8/16/2013 Statistical Genomics and Bioinformatics Workshop: Genetic Association and RNA-Seq Studies Population Genetics and Genome‐wide Genetic Association Studies (GWAS) Brooke L. Fridley, PhD University of Kansas Medical Center 1 Study of Genetic Association Cases Controls Genetic association studies look at the frequency of genetic changes in a group of cases and controls to try to determine whether specific changes are associated with disease. 2 1 Statistical Genomics and Bioinformatics Workshop 8/16/2013 Genetic Analysis Strategies Linkage effect GWAS Association size Rare Variant Analysis allele frequency Ardlie, Kruglyak & Seielstad (2002) Nature Genetics Reviews Zondervan & Cardon (2004) Nature Genetics Reviews 3 Genetics of Complex Traits • Multiple genes / variants – Common and rare variants – Interactions, Haplotypes, Pathways • Environment – Gene‐Environment interaction 4 2 Statistical Genomics and Bioinformatics Workshop 8/16/2013 In reality, much more complex! 5 NIHGRI GWAS Catalog (8/11/2013) http://www.genome.gov/gwastudies/ 6 3 Statistical Genomics and Bioinformatics Workshop 8/16/2013 Population Genetics 7 Recombination A1 B1 D1 Before meioses A2 B2 D2 A1 B1 D2 Crossovers occur during meioses A2 B2 D1 D2 A1 B1 After recombination A2 B2 D1 8 4 Statistical Genomics and Bioinformatics Workshop 8/16/2013 Linkage Disequilibrium (LD) • Particular alleles at neighboring loci tend to be co-inherited. • For tightly linked loci, this co-inheritance might lead to associations between