Home LiteratureArticle Details
PMID: 18711218 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Review

Tilting at quixotic trait loci (QTL): an evolutionary perspective on genetic causation.

Genetics ·Vol. 179 ·No. 4 ·2008-08-00 ·Pages 1741-56

Weiss KM

Abstract

Recent years have seen great advances in generating and analyzing data to identify the genetic architecture of biological traits. Human disease has understandably received intense research focus, and the genes responsible for most Mendelian diseases have successfully been identified. However, the same advances have shown a consistent if less satisfying pattern, in which complex traits are affected by variation in large numbers of genes, most of which have individually minor or statistically elusive effects, leaving the bulk of genetic etiology unaccounted for. This pattern applies to diverse and unrelated traits, not just disease, in basically all species, and is consistent with evolutionary expectations, raising challenging questions about the best way to approach and understand biological complexity.

MeSH Terms
Animals Chromosome Mapping Evolution, Molecular Genetic Variation Genetics, Population Humans Quantitative Trait Loci
Authors & Affiliations
1 authors, click to expand affiliations / ORCID
Weiss Kenneth M
Department of Anthropology and Integrated Biosciences Genetics Program, Pennsylvania State University, University Park, Pennsylvania 16802, USA. [email protected]
References (133)
133 references, click to expand
  1. Identification of epilepsy genes in human and mouse.
    Annu Rev Genet. 2001;35:567-88 PMID: 11700294
  2. Mapping determinants of human gene expression by regional and genome-wide association.
    Nature. 2005 Oct 27;437(7063):1365-9 PMID: 16251966
  3. Genome-wide association with select biomarker traits in the Framingham Heart Study.
    BMC Med Genet. 2007 Sep 19;8 Suppl 1:S11 PMID: 17903293
  4. 'Racial' differences in genetic effects for complex diseases.
    Nat Genet. 2004 Dec;36(12):1312-8 PMID: 15543147
  5. The distribution of fitness effects of new mutations.
    Nat Rev Genet. 2007 Aug;8(8):610-8 PMID: 17637733
  6. Genetics of gene expression and its effect on disease.
    Nature. 2008 Mar 27;452(7186):423-8 PMID: 18344981
  7. Genetics. Delivering new disease genes.
    Science. 2006 Dec 1;314(5804):1403-5 PMID: 17138888
  8. New susceptibility genes for ulcerative colitis.
    Nat Genet. 2008 Jun;40(6):686-8 PMID: 18509308
  9. A common CFH haplotype, with deletion of CFHR1 and CFHR3, is associated with lower risk of age-related macular degeneration.
    Nat Genet. 2006 Oct;38(10):1173-7 PMID: 16998489
  10. Construction of a genetic linkage map in man using restriction fragment length polymorphisms.
    Am J Hum Genet. 1980 May;32(3):314-31 PMID: 6247908
  11. The genetic architecture of quantitative traits.
    Annu Rev Genet. 2001;35:303-39 PMID: 11700286
  12. Analysis of genetically complex epilepsies.
    Epilepsia. 2005;46 Suppl 10:7-14 PMID: 16359464
  13. Cryptic causation of human disease: reading between the (germ) lines.
    Trends Genet. 2005 Feb;21(2):82-8 PMID: 15661353
  14. Multiple regions within 8q24 independently affect risk for prostate cancer.
    Nat Genet. 2007 May;39(5):638-44 PMID: 17401364
  15. Meta-analysis of genome-wide linkage studies of asthma and related traits.
    Respir Res. 2008 Apr 28;9:38 PMID: 18442398
  16. From Darwin's finches to canaries in the coal mine--mining the genome for new biology.
    N Engl J Med. 2008 Jun 26;358(26):2760-3 PMID: 18579810
  17. A critical appraisal of the scientific basis of commercial genomic profiles used to assess health risks and personalize health interventions.
    Am J Hum Genet. 2008 Mar;82(3):593-9 PMID: 18319070
  18. A common allele on chromosome 9 associated with coronary heart disease.
    Science. 2007 Jun 8;316(5830):1488-91 PMID: 17478681
  19. How to interpret a genome-wide association study.
    JAMA. 2008 Mar 19;299(11):1335-44 PMID: 18349094
  20. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
    Nature. 2007 Jun 14;447(7146):799-816 PMID: 17571346
  21. The eukaryotic genome as an RNA machine.
    Science. 2008 Mar 28;319(5871):1787-9 PMID: 18369136
  22. Characterization of BRCA1 and BRCA2 mutations in a large United States sample.
    J Clin Oncol. 2006 Feb 20;24(6):863-71 PMID: 16484695
  23. Gene mapping in the 20th and 21st centuries: statistical methods, data analysis, and experimental design.
    Hum Biol. 2000 Feb;72(1):63-132 PMID: 10721614
  24. Evolution in Mendelian Populations.
    Genetics. 1931 Mar;16(2):97-159 PMID: 17246615
  25. Diabetes mellitus: a "thrifty" genotype rendered detrimental by "progress"?
    Am J Hum Genet. 1962 Dec;14:353-62 PMID: 13937884
  26. HLA-B*5701 screening for hypersensitivity to abacavir.
    N Engl J Med. 2008 Feb 7;358(6):568-79 PMID: 18256392
  27. Progress in defining the molecular biology of age related macular degeneration.
    Hum Genet. 2007 Nov;122(3-4):219-36 PMID: 17659362
  28. Genetic analysis of genome-wide variation in human gene expression.
    Nature. 2004 Aug 12;430(7001):743-7 PMID: 15269782
  29. Non-replication and inconsistency in the genome-wide association setting.
    Hum Hered. 2007;64(4):203-13 PMID: 17551261
  30. Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes.
    Nat Genet. 2008 May;40(5):638-45 PMID: 18372903
  31. Lifespan depends on month of birth.
    Proc Natl Acad Sci U S A. 2001 Feb 27;98(5):2934-9 PMID: 11226344
  32. Frequency and carrier risk associated with common BRCA1 and BRCA2 mutations in Ashkenazi Jewish breast cancer patients.
    Am J Hum Genet. 1998 Jul;63(1):45-51 PMID: 9634504
  33. Genome-wide association: a promising start to a long race.
    Trends Genet. 2006 Jul;22(7):350-4 PMID: 16713652
  34. Renin-angiotensin system gene polymorphisms and coronary artery disease in a large angiographic cohort: detection of high order gene-gene interaction.
    Atherosclerosis. 2007 Nov;195(1):172-80 PMID: 17118372
  35. Dobzhansky-Muller incompatibilities in protein evolution.
    Proc Natl Acad Sci U S A. 2002 Nov 12;99(23):14878-83 PMID: 12403824
  36. Sequence-level population simulations over large genomic regions.
    Genetics. 2007 Nov;177(3):1725-31 PMID: 17947444
  37. Near-neutrality in evolution of genes and gene regulation.
    Proc Natl Acad Sci U S A. 2002 Dec 10;99(25):16134-7 PMID: 12461171
  38. Phenotypic and genetic heterogeneity in a genome-wide linkage study of asthma families.
    BMC Pulm Med. 2005 Jan 05;5:1 PMID: 15634351
  39. Evolution by phenotype: a biomedical perspective.
    Perspect Biol Med. 2003 Spring;46(2):159-82 PMID: 12721519
  40. Positive selection at the protein network periphery: evaluation in terms of structural constraints and cellular context.
    Proc Natl Acad Sci U S A. 2007 Dec 18;104(51):20274-9 PMID: 18077332
  41. Genetics. Was the Human Genome Project worth the effort?
    Science. 2005 Apr 15;308(5720):362-4 PMID: 15769856
  42. Monogenic traits are not simple: lessons from phenylketonuria.
    Trends Genet. 1999 Jul;15(7):267-72 PMID: 10390625
  43. Effect of in utero and early-life conditions on adult health and disease.
    N Engl J Med. 2008 Jul 3;359(1):61-73 PMID: 18596274
  44. Genomewide scans of complex human diseases: true linkage is hard to find.
    Am J Hum Genet. 2001 Nov;69(5):936-50 PMID: 11565063
  45. Dissecting complex disease: the quest for the Philosopher's Stone?
    Int J Epidemiol. 2006 Jun;35(3):562-71 PMID: 16540539
  46. Genomics: guilt by association.
    Nature. 2007 Jun 7;447(7145):645-6 PMID: 17554292
  47. Reduced body weight is a common effect of gene knockout in mice.
    BMC Genet. 2008 Jan 08;9:4 PMID: 18182103
  48. Widespread and subtle: alternative splicing at short-distance tandem sites.
    Trends Genet. 2008 May;24(5):246-55 PMID: 18394746
  49. Variations in DNA elucidate molecular networks that cause disease.
    Nature. 2008 Mar 27;452(7186):429-35 PMID: 18344982
  50. Confounding, ascertainment bias, and the blind quest for a genetic 'fountain of youth'.
    Ann Med. 2003;35(7):532-44 PMID: 14649335
  51. Toward a human epigenome.
    Nat Genet. 2006 Dec;38(12):1359-60 PMID: 17133218
  52. Localization and identification of human quantitative trait loci: king harvest has surely come.
    Curr Opin Genet Dev. 2004 Jun;14(3):233-40 PMID: 15172664
  53. On the allelic spectrum of human disease.
    Trends Genet. 2001 Sep;17(9):502-10 PMID: 11525833
  54. The consensus coding sequences of human breast and colorectal cancers.
    Science. 2006 Oct 13;314(5797):268-74 PMID: 16959974
  55. Gene expression, genetics, and genomics in epilepsy: some answers, more questions.
    Epilepsia. 2007;48 Suppl 2:42-50 PMID: 17571352
  56. Time to give up on a single explanation for autism.
    Nat Neurosci. 2006 Oct;9(10):1218-20 PMID: 17001340
  57. Unravelling the pathogenesis of inflammatory bowel disease.
    Nature. 2007 Jul 26;448(7152):427-34 PMID: 17653185
  58. Mapping, fine mapping, and molecular dissection of quantitative trait Loci in domestic animals.
    Annu Rev Genomics Hum Genet. 2007;8:131-62 PMID: 17477823
  59. Assessing the evolutionary impact of amino acid mutations in the human genome.
    PLoS Genet. 2008 May 30;4(5):e1000083 PMID: 18516229
  60. Connecting the dots between genes, biochemistry, and disease susceptibility: systems biology modeling in human genetics.
    Mol Genet Metab. 2005 Feb;84(2):104-11 PMID: 15670716
  61. Epigenetics and twins: three variations on the theme.
    Trends Genet. 2006 Jul;22(7):347-50 PMID: 16697072
  62. Joint inference of the distribution of fitness effects of deleterious mutations and population demography based on nucleotide polymorphism frequencies.
    Genetics. 2007 Dec;177(4):2251-61 PMID: 18073430
  63. Resolving the paradox of common, harmful, heritable mental disorders: which evolutionary genetic models work best?
    Behav Brain Sci. 2006 Aug;29(4):385-404; discussion 405-52 PMID: 17094843
  64. Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks.
    Nat Genet. 2008 Jul;40(7):854-61 PMID: 18552845
  65. Risk loci, biological candidates and biomarkers.
    Nat Genet. 2008 Mar;40(3):257 PMID: 18305468
  66. Common and rare variants in multifactorial susceptibility to common diseases.
    Nat Genet. 2008 Jun;40(6):695-701 PMID: 18509313
  67. Allele multiplicity in simple Mendelian disorders.
    Am J Hum Genet. 1982 Nov;34(6):866-73 PMID: 7180845
  68. Genetic architecture of common multifactorial diseases.
    Ciba Found Symp. 1996;197:211-29; discussion 229-32 PMID: 8827376
  69. Sizing up human height variation.
    Nat Genet. 2008 May;40(5):489-90 PMID: 18443579
  70. Traversing the conceptual divide between biological and statistical epistasis: systems biology and a more modern synthesis.
    Bioessays. 2005 Jun;27(6):637-46 PMID: 15892116
  71. Asthma genetics 2006: the long and winding road to gene discovery.
    Genes Immun. 2006 Mar;7(2):95-100 PMID: 16395390
  72. Polygenes, risk prediction, and targeted prevention of breast cancer.
    N Engl J Med. 2008 Jun 26;358(26):2796-803 PMID: 18579814
  73. Raising the estimate of functional human sequences.
    Genome Res. 2007 Sep;17(9):1245-53 PMID: 17690206
  74. CFH haplotypes without the Y402H coding variant show strong association with susceptibility to age-related macular degeneration.
    Nat Genet. 2006 Sep;38(9):1049-54 PMID: 16936733
  75. Linkage disequilibrium and the mapping of complex human traits.
    Trends Genet. 2002 Jan;18(1):19-24 PMID: 11750696
  76. Forward-time simulations of human populations with complex diseases.
    PLoS Genet. 2007 Mar 23;3(3):e47 PMID: 17381243
  77. A genome-wide association study of psoriasis and psoriatic arthritis identifies new disease loci.
    PLoS Genet. 2008 Mar 28;4(3):e1000041 PMID: 18369459
  78. ForSim: a tool for exploring the genetic architecture of complex traits with controlled truth.
    Bioinformatics. 2008 Aug 15;24(16):1821-2 PMID: 18565989
  79. Gene-testing firms face legal battle.
    Nature. 2008 Jun 26;453(7199):1148-9 PMID: 18580905
  80. Relative impact of nucleotide and copy number variation on gene expression phenotypes.
    Science. 2007 Feb 9;315(5813):848-53 PMID: 17289997
  81. Aspects of genetic susceptibility to human infectious diseases.
    Annu Rev Genet. 2006;40:469-86 PMID: 17094741
  82. A navigator for human genome epidemiology.
    Nat Genet. 2008 Feb;40(2):124-5 PMID: 18227866
  83. How many diseases does it take to map a gene with SNPs?
    Nat Genet. 2000 Oct;26(2):151-7 PMID: 11017069
  84. The human obesity gene map: the 2005 update.
    Obesity (Silver Spring). 2006 Apr;14(4):529-644 PMID: 16741264
  85. An overview of the genetic dissection of complex traits.
    Adv Genet. 2008;60:3-34 PMID: 18358314
  86. A treasure trove for lipoprotein biology.
    Nat Genet. 2008 Feb;40(2):129-30 PMID: 18227868
  87. Phenotypic differences in genetically identical organisms: the epigenetic perspective.
    Hum Mol Genet. 2005 Apr 15;14 Spec No 1:R11-8 PMID: 15809262
  88. The cooperative genome: organisms as social contracts.
    Int J Dev Biol. 2009;53(5-6):753-63 PMID: 19557681
  89. Psychiatric genetics: progress amid controversy.
    Nat Rev Genet. 2008 Jul;9(7):527-40 PMID: 18560438
  90. Reporting of systematic reviews: the challenge of genetic association studies.
    PLoS Med. 2007 Jun;4(6):e211 PMID: 17593896
  91. The Framingham Heart Study, on its way to becoming the gold standard for Cardiovascular Genetic Epidemiology?
    BMC Med Genet. 2007 Oct 04;8:63 PMID: 17916250
  92. Advances in autism genetics: on the threshold of a new neurobiology.
    Nat Rev Genet. 2008 May;9(5):341-55 PMID: 18414403
  93. Retinitis pigmentosa.
    Lancet. 2006 Nov 18;368(9549):1795-809 PMID: 17113430
  94. Population genetics--making sense out of sequence.
    Nat Genet. 1999 Jan;21(1 Suppl):56-60 PMID: 9915503
  95. MicroRNAs flex their muscles.
    Trends Genet. 2008 Apr;24(4):159-66 PMID: 18325627
  96. Association between microdeletion and microduplication at 16p11.2 and autism.
    N Engl J Med. 2008 Feb 14;358(7):667-75 PMID: 18184952
  97. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls.
    Nature. 2007 Jun 7;447(7145):661-78 PMID: 17554300
  98. Mitochondria as chi.
    Genetics. 2008 Jun;179(2):727-35 PMID: 18558648
  99. Genomics and public health research.
    JAMA. 2007 Jun 6;297(21):2347; author reply 2347-8 PMID: 17551127
  100. Bona fide genetic associations with bone mineral density.
    N Engl J Med. 2008 May 29;358(22):2403-5 PMID: 18445778
  101. Genome-wide mapping of human loci for essential hypertension.
    Lancet. 2003 Jun 21;361(9375):2118-23 PMID: 12826435
  102. Large upward bias in estimation of locus-specific effects from genomewide scans.
    Am J Hum Genet. 2001 Dec;69(6):1357-69 PMID: 11593451
  103. Genome scans and candidate gene approaches in the study of common diseases and variable drug responses.
    Trends Genet. 2003 Nov;19(11):615-22 PMID: 14585613
  104. Systematic meta-analyses and field synopsis of genetic association studies in schizophrenia: the SzGene database.
    Nat Genet. 2008 Jul;40(7):827-34 PMID: 18583979
  105. The functional consequences of alternative promoter use in mammalian genomes.
    Trends Genet. 2008 Apr;24(4):167-77 PMID: 18329129
  106. The frailty of adaptive hypotheses for the origins of organismal complexity.
    Proc Natl Acad Sci U S A. 2007 May 15;104 Suppl 1:8597-604 PMID: 17494740
  107. Inference of population structure using multilocus genotype data.
    Genetics. 2000 Jun;155(2):945-59 PMID: 10835412
  108. Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humans.
    Nat Genet. 2008 Feb;40(2):189-97 PMID: 18193044
  109. Overcoming the winner's curse: estimating penetrance parameters from case-control data.
    Am J Hum Genet. 2007 Apr;80(4):605-15 PMID: 17357068
  110. A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1.
    Science. 1994 Oct 7;266(5182):66-71 PMID: 7545954
  111. How malaria has affected the human genome and what human genetics can teach us about malaria.
    Am J Hum Genet. 2005 Aug;77(2):171-92 PMID: 16001361
  112. Mapping autism risk loci using genetic linkage and chromosomal rearrangements.
    Nat Genet. 2007 Mar;39(3):319-28 PMID: 17322880
  113. Reporting of human genome epidemiology (HuGE) association studies: an empirical assessment.
    BMC Med Res Methodol. 2008 May 20;8:31 PMID: 18492284
  114. A HapMap harvest of insights into the genetics of common disease.
    J Clin Invest. 2008 May;118(5):1590-605 PMID: 18451988
  115. Genetic and genomic analysis of a fat mass trait with complex inheritance reveals marked sex specificity.
    PLoS Genet. 2006 Feb;2(2):e15 PMID: 16462940
  116. Bringing age-related macular degeneration into focus.
    Nat Genet. 2008 Jul;40(7):820-1 PMID: 18583975
  117. On the use of familial aggregation in population-based case probands for calculating penetrance.
    J Natl Cancer Inst. 2002 Aug 21;94(16):1221-6 PMID: 12189225
  118. Generalized analysis of molecular variance.
    PLoS Genet. 2007 Apr 6;3(4):e51 PMID: 17411342
  119. Genetics of autism: complex aetiology for a heterogeneous disorder.
    Nat Rev Genet. 2001 Dec;2(12):943-55 PMID: 11733747
  120. Medicine. The future of personal genomics.
    Science. 2007 Sep 21;317(5845):1687 PMID: 17885116
  121. High-density association study and nomination of susceptibility genes for hypertension in the Japanese National Project.
    Hum Mol Genet. 2008 Feb 15;17(4):617-27 PMID: 18003638
  122. Replicating genotype-phenotype associations.
    Nature. 2007 Jun 7;447(7145):655-60 PMID: 17554299
  123. Genomics and biology come together to fight HIV.
    PLoS Biol. 2008 Mar 25;6(3):e76 PMID: 18366259
  124. Linkage of early-onset familial breast cancer to chromosome 17q21.
    Science. 1990 Dec 21;250(4988):1684-9 PMID: 2270482
  125. Breast and ovarian cancer risks due to inherited mutations in BRCA1 and BRCA2.
    Science. 2003 Oct 24;302(5645):643-6 PMID: 14576434
  126. Random monoallelic expression: making a choice.
    Trends Genet. 2008 Jun;24(6):257-9 PMID: 18450315
  127. Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes.
    Nat Genet. 2007 Jul;39(7):857-64 PMID: 17554260
  128. Mining gene expression profiles: expression signatures as cancer phenotypes.
    Nat Rev Genet. 2007 Aug;8(8):601-9 PMID: 17607306
  129. Letting the genome out of the bottle--will we get our wish?
    N Engl J Med. 2008 Jan 10;358(2):105-7 PMID: 18184955
  130. A gene expression network model of type 2 diabetes links cell cycle regulation in islets with diabetes susceptibility.
    Genome Res. 2008 May;18(5):706-16 PMID: 18347327
  131. The functional impact of structural variation in humans.
    Trends Genet. 2008 May;24(5):238-45 PMID: 18378036
  132. Methods for meta-analysis in genetic association studies: a review of their potential and pitfalls.
    Hum Genet. 2008 Feb;123(1):1-14 PMID: 18026754
  133. Phenotypically concordant and discordant monozygotic twins display different DNA copy-number-variation profiles.
    Am J Hum Genet. 2008 Mar;82(3):763-71 PMID: 18304490
Article Info
Journal
Genetics
Abbr.
Genetics
ISSN
0016-6731
Published
2008-08-00
Pages
1741-56
Language
English
Region
United States
NLM ID
0374636
PMCID
PMC2516055
Subset
IM
Grants
NIMH NIH HHS · R01 MH063749 · United States
NIMH NIH HHS · MH063749 · United States
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]