Common genetic variation and human disease.

The landscape of human genetics has changed remarkably in a relatively short space of time. The field has progressed from comparatively small studies of rare genetic diseases to vast consortia based efforts that target the inherited components of common complex diseases and which typically involve thousands of individual samples. In particular, genome wide association studies have become possible as a result of a new generation of genotyping platforms. At the time of writing, these have led to the discovery of more than 150 novel susceptibility loci across a broad spectrum of diseases, a few in genes with high biological plausibility but the majority in others that had not been considered candidates. Here, we provide an overview of the field of complex disease genetics pertaining to mapping by association and consider the many pitfalls and caveats that have arisen.

[1]  Jacqueline K. Wittke-Thompson,et al.  Rational inferences about departures from Hardy-Weinberg equilibrium. , 2005, American journal of human genetics.

[2]  J. Lykke-Andersen,et al.  mRNA quality control: Marking the message for life or death , 2001, Current Biology.

[3]  C. Carlson,et al.  Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. , 2004, American journal of human genetics.

[4]  Theodore R Holford,et al.  Genetic variation in TNF and IL10 and risk of non-Hodgkin lymphoma: a report from the InterLymph Consortium. , 2006, The Lancet. Oncology.

[5]  K. Frazer,et al.  Common deletions and SNPs are in linkage disequilibrium in the human genome , 2006, Nature Genetics.

[6]  N. Malats,et al.  NAT2 slow acetylation, GSTM1 null genotype, and risk of bladder cancer: results from the Spanish Bladder Cancer Study and meta-analyses , 2005, The Lancet.

[7]  S Beck,et al.  Characterization of recombination in the HLA class II region. , 1997, American journal of human genetics.

[8]  Richard A Koup,et al.  Homozygous Defect in HIV-1 Coreceptor Accounts for Resistance of Some Multiply-Exposed Individuals to HIV-1 Infection , 1996, Cell.

[9]  Hugues Sicotte,et al.  SNP500Cancer: a public resource for sequence validation, assay development, and frequency analysis for genetic variation in candidate genes , 2005, Nucleic Acids Res..

[10]  Terrence S. Furey,et al.  The UCSC Genome Browser Database: update 2006 , 2005, Nucleic Acids Res..

[11]  P. Stenson,et al.  Human Gene Mutation Database (HGMD , 2003 .

[12]  J. Gilbert,et al.  Complement Factor H Variant Increases the Risk of Age-Related Macular Degeneration , 2005, Science.

[13]  J. Gulcher,et al.  The gene encoding 5-lipoxygenase activating protein confers risk of myocardial infarction and stroke , 2004, Nature Genetics.

[14]  E. Lander,et al.  Meta-analysis of genetic association studies supports a contribution of common variants to susceptibility to common disease , 2003, Nature Genetics.

[15]  Stephen Chanock,et al.  Candidate Genes and Single Nucleotide Polymorphisms (SNPs) in the Study of Human Disease , 2002, Disease markers.

[16]  Clive Brown,et al.  Toward the $1000 human genome , 2005 .

[17]  J. Pritchard,et al.  Use of unlinked genetic markers to detect population stratification in association studies. , 1999, American journal of human genetics.

[18]  Carlos Bustamante,et al.  Genomic scans for selective sweeps using SNP data. , 2005, Genome research.

[19]  F. Collins,et al.  Shattuck lecture--medical and societal consequences of the Human Genome Project. , 1999, The New England journal of medicine.

[20]  Lon R Cardon,et al.  Evaluating coverage of genome-wide association studies , 2006, Nature Genetics.

[21]  N. Morton,et al.  Toward positional cloning with SNPs. , 2002, Current opinion in molecular therapeutics.

[22]  Michael P Epstein,et al.  A simple and improved correction for population stratification in case-control studies. , 2007, American journal of human genetics.

[23]  Patricio Yankilevich,et al.  Evaluating HapMap SNP data transferability in a large-scale genotyping project involving 175 cancer-associated genes , 2006, Human Genetics.

[24]  P. Vineis,et al.  Current smoking, occupation, N-acetyltransferase-2 and bladder cancer: a pooled analysis of genotype-based studies. , 2001, Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology.

[25]  T. Manolio,et al.  How to Interpret a Genome-wide Association Study Topic Collections , 2022 .

[26]  J. Ioannidis,et al.  Association of GSTM1, GSTT1, and GSTP1 gene polymorphisms with the risk of prostate cancer: a meta-analysis. , 2005, Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology.

[27]  M. Maitland,et al.  TPMT, UGT1A1 and DPYD: genotyping to ensure safer cancer therapy? , 2006, Trends in pharmacological sciences.

[28]  D. Conrad,et al.  A worldwide survey of haplotype variation and linkage disequilibrium in the human genome , 2006, Nature Genetics.

[29]  K. Gunderson,et al.  A genome-wide scalable SNP genotyping assay using microarray technology , 2005, Nature Genetics.

[30]  P. O'dwyer,et al.  Uridine diphosphate glucuronosyltransferase (UGT) 1A1 and irinotecan: practical pharmacogenomics arrives in cancer therapy. , 2006, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[31]  Daniel O Stram,et al.  Software for tag single nucleotide polymorphism selection , 2005, Human Genomics.

[32]  Richard C Trembath,et al.  A synonymous SNP of the corneodesmosin gene leads to increased mRNA stability and demonstrates association with psoriasis across diverse ethnic groups. , 2004, Human molecular genetics.

[33]  P. Stenson,et al.  Human Gene Mutation Database (HGMD®): 2003 update , 2003, Human mutation.

[34]  D. Clayton,et al.  Population structure, differential bias and genomic control in a large-scale, case-control association study , 2005, Nature Genetics.

[35]  Francis S Collins,et al.  A HapMap harvest of insights into the genetics of common disease. , 2008, The Journal of clinical investigation.

[36]  N. Scrimshaw,et al.  The acceptability of milk and milk products in populations with a high prevalence of lactose intolerance. , 1988, The American journal of clinical nutrition.

[37]  P. Deloukas,et al.  The portability of tagSNPs across populations: a worldwide survey. , 2006, Genome research.

[38]  D. Gudbjartsson,et al.  Common variants on chromosomes 2q35 and 16q12 confer susceptibility to estrogen receptor–positive breast cancer , 2007, Nature Genetics.

[39]  S. Gabriel,et al.  Efficiency and power in genetic association studies , 2005, Nature Genetics.

[40]  Eric E. Smith,et al.  Variants conferring risk of atrial fibrillation on chromosome 4q25 , 2007, Nature.

[41]  Kenny Q. Ye,et al.  Large-Scale Copy Number Polymorphism in the Human Genome , 2004, Science.

[42]  Nunzio Bottini,et al.  A functional variant of lymphoid tyrosine phosphatase is associated with type I diabetes , 2004, Nature Genetics.

[43]  J. Ott Methods of analysis and resources available for genetic trait mapping. , 1999, The Journal of heredity.

[44]  A. Whittemore,et al.  Multiple regions within 8q24 independently affect risk for prostate cancer , 2007, Nature Genetics.

[45]  W. Willett,et al.  A genome-wide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer , 2007, Nature Genetics.

[46]  J J Goedert,et al.  Contrasting genetic influence of CCR2 and CCR5 variants on HIV-1 infection and disease progression. Hemophilia Growth and Development Study (HGDS), Multicenter AIDS Cohort Study (MACS), Multicenter Hemophilia Cohort Study (MHCS), San Francisco City Cohort (SFCC), ALIVE Study. , 1997, Science.

[47]  J. Ott,et al.  Complement Factor H Polymorphism in Age-Related Macular Degeneration , 2005, Science.

[48]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[49]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[50]  N. Risch Searching for genetic determinants in the new millennium , 2000, Nature.

[51]  P. Reitsma,et al.  A common genetic variation in the 3'-untranslated region of the prothrombin gene is associated with elevated plasma prothrombin levels and an increase in venous thrombosis. , 1996, Blood.

[52]  Gonçalo R. Abecasis,et al.  Genetic variants regulating ORMDL3 expression contribute to the risk of childhood asthma , 2007, Nature.

[53]  Jonathan P. Bollback,et al.  The Use of Coded PCR Primers Enables High-Throughput Sequencing of Multiple Homolog Amplification Products by 454 Parallel Sequencing , 2007, PloS one.

[54]  A. Clark,et al.  Inference of haplotypes from PCR-amplified samples of diploid populations. , 1990, Molecular biology and evolution.

[55]  A. Gylfason,et al.  A common variant associated with prostate cancer in European and African populations , 2006, Nature Genetics.

[56]  S. P. Fodor,et al.  Large-scale genotyping of complex DNA , 2003, Nature Biotechnology.

[57]  Timothy B. Stockwell,et al.  The Sequence of the Human Genome , 2001, Science.

[58]  J. Ware The limitations of risk factors as prognostic tools. , 2006, The New England journal of medicine.

[59]  N Risch,et al.  The Future of Genetic Studies of Complex Human Diseases , 1996, Science.

[60]  Paola Sebastiani,et al.  Minimal haplotype tagging , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[61]  M. Munafo,et al.  Meta-analysis of genetic association studies. , 2004, Trends in genetics : TIG.

[62]  W. Willett,et al.  Multiple loci identified in a genome-wide association study of prostate cancer , 2008, Nature Genetics.

[63]  H. Trowell Dietary fiber definitions. , 1988, The American journal of clinical nutrition.

[64]  L. Tsui,et al.  Erratum: Identification of the Cystic Fibrosis Gene: Genetic Analysis , 1989, Science.

[65]  R C Elston,et al.  Linkage and association to genetic markers. , 1995, Experimental and clinical immunogenetics.

[66]  T. Rebbeck,et al.  Glutathione S-transferases M1, T1, and P1 and breast cancer: a pooled analysis. , 2004, Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology.

[67]  D. Nickerson,et al.  Variation is the spice of life , 2001, Nature Genetics.

[68]  Evan E Eichler,et al.  Widening the spectrum of human genetic variation , 2006, Nature Genetics.

[69]  Vilmundur Gudnason,et al.  A variant of the gene encoding leukotriene A4 hydrolase confers ethnicity-specific risk of myocardial infarction , 2006, Nature Genetics.

[70]  N. Risch,et al.  A comparison of linkage disequilibrium measures for fine-scale mapping. , 1995, Genomics.

[71]  L. Hurst,et al.  Hearing silence: non-neutral evolution at synonymous sites in mammals , 2006, Nature Reviews Genetics.

[72]  Jonathan C. Cohen,et al.  Multiple rare variants in NPC1L1 associated with reduced sterol absorption and plasma low-density lipoprotein levels. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[73]  J. Pritchard,et al.  The allelic architecture of human disease genes: common disease-common variant...or not? , 2002, Human molecular genetics.

[74]  Jianping Xu Extracting haplotypes from diploid organisms. , 2006, Current issues in molecular biology.

[75]  D. Altshuler,et al.  Completing the map of human genetic variation , 2007, Nature.

[76]  P. Donnelly,et al.  A Fine-Scale Map of Recombination Rates and Hotspots Across the Human Genome , 2005, Science.

[77]  P. McKeigue,et al.  Problems of reporting genetic associations with complex outcomes , 2003, The Lancet.

[78]  M. McCarthy,et al.  Genome-wide association studies for complex traits: consensus, uncertainty and challenges , 2008, Nature Reviews Genetics.

[79]  J. Barrett,et al.  Genetic linkage studies , 2005, The Lancet.

[80]  P. Donnelly,et al.  A new statistical method for haplotype reconstruction from population data. , 2001, American journal of human genetics.

[81]  A. Clark,et al.  The role of haplotypes in candidate gene studies , 2004, Genetic epidemiology.

[82]  J. Robert,et al.  Pharmacogenetics of human carboxylesterase 2, an enzyme involved in the activation of irinotecan into SN‐38 , 2004, Clinical pharmacology and therapeutics.

[83]  Pardis C Sabeti,et al.  Genetic signatures of strong recent positive selection at the lactase gene. , 2004, American journal of human genetics.

[84]  Bernice R. Packer,et al.  High level of functional polymorphism indicates a unique role of natural selection at human immune system loci , 2005, Immunogenetics.

[85]  Bernice R. Packer,et al.  Widespread purifying selection at polymorphic sites in human protein-coding loci , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[86]  Alan F. Scott,et al.  Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders , 2004, Nucleic Acids Res..

[87]  Adrian Vella,et al.  Localization of a type 1 diabetes locus in the IL2RA/CD25 region by use of tag single-nucleotide polymorphisms. , 2005, American journal of human genetics.

[88]  D. Reich,et al.  Principal components analysis corrects for stratification in genome-wide association studies , 2006, Nature Genetics.

[89]  E. Lander,et al.  On the allelic spectrum of human disease. , 2001, Trends in genetics : TIG.

[90]  Jing Huang,et al.  Parallel genotyping of over 10,000 SNPs using a one-primer assay on a high-density oligonucleotide array. , 2004, Genome research.

[91]  Zhaohui S. Qin,et al.  A comparison of phasing algorithms for trios and unrelated individuals. , 2006, American journal of human genetics.

[92]  M. Daly,et al.  Transferability of tag SNPs in genetic association studies in multiple populations , 2006, Nature Genetics.

[93]  J. Pritchard Are rare variants responsible for susceptibility to complex diseases? , 2001, American journal of human genetics.

[94]  E Lai,et al.  A 4-Mb high-density single nucleotide polymorphism-based map around human APOE. , 1998, Genomics.

[95]  Geoffrey B. Nilsen,et al.  Whole-Genome Patterns of Common DNA Variation in Three Human Populations , 2005, Science.

[96]  Simon C. Potter,et al.  Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls , 2007, Nature.

[97]  J. Pritchard,et al.  Linkage disequilibrium in humans: models and data. , 2001, American journal of human genetics.

[98]  K. Roeder,et al.  Genomic Control for Association Studies , 1999, Biometrics.

[99]  Nathaniel Rothman,et al.  Assessing the Probability That a Positive Report is False: An Approach for Molecular Epidemiology Studies , 2004 .

[100]  D. Haussler,et al.  Ultraconserved Elements in the Human Genome , 2004, Science.

[101]  S. Antonarakis,et al.  Moderately severe hemophilia A resulting from Glu----Gly substitution in exon 7 of the factor VIII gene. , 1988, American journal of human genetics.

[102]  R. N. Hoover,et al.  Scanning the horizon: What is the future of genome-wide association studies in accelerating discoveries in cancer etiology and prevention? , 2007, Cancer Causes & Control.

[103]  Frank Dudbridge,et al.  Haplotype tagging for the identification of common disease genes , 2001, Nature Genetics.

[104]  Lior Pachter,et al.  VISTA: computational tools for comparative genomics , 2004, Nucleic Acids Res..

[105]  Paul J. Harrison,et al.  Neuregulin 1 transcripts are differentially expressed in schizophrenia and regulated by 5' SNPs associated with the disease. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[106]  Samuel H. Wilson,et al.  The Environmental Genome Project: phase I and beyond. , 2004, Molecular interventions.

[107]  Steven Henikoff,et al.  SIFT: predicting amino acid changes that affect protein function , 2003, Nucleic Acids Res..

[108]  D. Hunter Gene–environment interactions in human diseases , 2005, Nature Reviews Genetics.

[109]  Y. Hasegawa,et al.  Clinical Pharmacogenetics of Irinotecan (CPT-11) , 2005, Drug metabolism reviews.

[110]  Jennifer Wessel,et al.  A comprehensive literature review of haplotyping software and methods for use with unrelated individuals , 2005, Human Genomics.

[111]  Andrew D. Johnson,et al.  Multidrug resistance polypeptide 1 (MDR1, ABCB1) variant 3435C>T affects mRNA stability , 2005, Pharmacogenetics and genomics.

[112]  Rui Mei,et al.  Large-scale SNP analysis reveals clustered and continuous patterns of human genetic variation , 2005, Human Genomics.

[113]  M. Ratain,et al.  Genetic predisposition to the metabolism of irinotecan (CPT-11). Role of uridine diphosphate glucuronosyltransferase isoform 1A1 in the glucuronidation of its active metabolite (SN-38) in human liver microsomes. , 1998, The Journal of clinical investigation.

[114]  N. Orr,et al.  Neovascular Age-Related Macular Degeneration Risk Based on CFH, LOC387715/HTRA1, and Smoking , 2007, PLoS medicine.

[115]  M. Olivier,et al.  Comparison of linkage disequilibrium patterns between the HapMap CEPH samples and a family-based cohort of Northern European descent. , 2006, Genomics.

[116]  P. Donnelly,et al.  Replicating genotype–phenotype associations , 2007, Nature.

[117]  Pieter H. Reitsma,et al.  Mutation in blood coagulation factor V associated with resistance to activated protein C , 1994, Nature.

[118]  K. Offit Genomic profiles for disease risk: predictive or premature? , 2008, JAMA.

[119]  R. Richards,et al.  Fragile X syndrome unstable element, p(CCG)n, and other simple tandem repeat sequences are binding sites for specific nuclear proteins. , 1993, Human molecular genetics.

[120]  Stephen J O'Brien,et al.  Human genes that limit AIDS , 2004, Nature Genetics.

[121]  N. Rothman,et al.  Population stratification in epidemiologic studies of common genetic variants and cancer: quantification of bias. , 2000, Journal of the National Cancer Institute.

[122]  D. Haussler,et al.  Computational screening of conserved genomic DNA in search of functional noncoding elements , 2005, Nature Methods.

[123]  L. Excoffier,et al.  Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. , 1995, Molecular biology and evolution.

[124]  Pardis C Sabeti,et al.  Linkage disequilibrium in the human genome , 2001, Nature.

[125]  D. Gudbjartsson,et al.  Genome-wide association study identifies a second prostate cancer susceptibility variant at 8q24 , 2007, Nature Genetics.

[126]  Paolo Vineis,et al.  A road map for efficient and reliable human genome epidemiology , 2006, Nature Genetics.

[127]  Randall Pruim,et al.  Tag SNP selection for Finnish individuals based on the CEPH Utah HapMap database , 2006, Genetic epidemiology.

[128]  K. Buetow,et al.  The use of common genetic polymorphisms to enhance the epidemiologic study of environmental carcinogens. , 2001, Biochimica et biophysica acta.

[129]  J. Hirschhorn,et al.  A comprehensive review of genetic association studies , 2002, Genetics in Medicine.

[130]  Eric Boerwinkle,et al.  Population-based resequencing of ANGPTL4 uncovers variations that reduce triglycerides and increase HDL , 2007, Nature Genetics.

[131]  Tom H. Pringle,et al.  The human genome browser at UCSC. , 2002, Genome research.

[132]  Wing-Kin Sung,et al.  Association mapping via regularized regression analysis of single-nucleotide-polymorphism haplotypes in variable-sized sliding windows. , 2007, American journal of human genetics.

[133]  Adrian Vella,et al.  Replication of an association between the lymphoid tyrosine phosphatase locus (LYP/PTPN22) with type 1 diabetes, and evidence for its role as a general autoimmunity locus. , 2004, Diabetes.

[134]  N. Orr,et al.  A common CFH haplotype, with deletion of CFHR1 and CFHR3, is associated with lower risk of age-related macular degeneration , 2006, Nature Genetics.

[135]  P. Bork,et al.  Human non-synonymous SNPs: server and survey. , 2002, Nucleic acids research.

[136]  N. Risch Developments in gene mapping with linkage methods. , 1991, Current opinion in genetics & development.

[137]  M. Daly,et al.  Methods for high-density admixture mapping of disease genes. , 2004, American journal of human genetics.

[138]  M. Daly,et al.  A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms , 2001, Nature.

[139]  James R. Knight,et al.  Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.

[140]  Muin J. Khoury,et al.  Letting the genome out of the bottle--will we get our wish? , 2008, The New England journal of medicine.

[141]  Weihua Chang,et al.  Whole-genome genotyping with the single-base extension assay , 2005, Nature Methods.

[142]  S. Nagar,et al.  Pharmacogenetics of Uridine Diphosphoglucuronosyltransferase (UGT) 1A Family Members and its Role in Patient Response to Irinotecan , 2006, Drug metabolism reviews.

[143]  B. Rovin,et al.  The Influence of CCL 3 L 1 Gene – Containing Segmental Duplications on HIV-1 / AIDS Susceptibility , 2009 .

[144]  S. Gabriel,et al.  Assessing the impact of population stratification on genetic association studies , 2004, Nature Genetics.

[145]  M. Olivier A haplotype map of the human genome , 2003, Nature.

[146]  J. Witte,et al.  8q24 and prostate cancer: association with advanced disease and meta-analysis , 2008, European Journal of Human Genetics.

[147]  P Donnelly,et al.  Coalescents and genealogical structure under neutrality. , 1995, Annual review of genetics.

[148]  P. Fearnhead,et al.  Genome-wide association study of prostate cancer identifies a second risk locus at 8q24 , 2007, Nature Genetics.

[149]  A. Monaco,et al.  Cloning the gene for an inherited human disorder—chronic granulomatous disease—on the basis of its chromosomal location , 1986, Nature.

[150]  R. Grantham Amino Acid Difference Formula to Help Explain Protein Evolution , 1974, Science.

[151]  M. Daly,et al.  Evaluating and improving power in whole-genome association studies using fixed marker sets , 2006, Nature Genetics.

[152]  Pardis C Sabeti,et al.  Common deletion polymorphisms in the human genome , 2006, Nature Genetics.

[153]  Elizabeth M. Smigielski,et al.  dbSNP: the NCBI database of genetic variation , 2001, Nucleic Acids Res..

[154]  M. D. Topal,et al.  Complementary base pairing and the origin of substitution mutations , 1976, Nature.

[155]  A. Whittemore,et al.  Admixture mapping identifies 8q24 as a prostate cancer risk locus in African-American men , 2006, Proceedings of the National Academy of Sciences.

[156]  S. P. Fodor,et al.  Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays , 2004, Nature Methods.

[157]  Eric S. Lander,et al.  Human genome sequence variation and the influence of gene history, mutation and recombination , 2002, Nature Genetics.

[158]  L. Feuk,et al.  Detection of large-scale variation in the human genome , 2004, Nature Genetics.