A genome-wide comparison of the functional properties of rare and common genetic variants in humans

American Journal of Human Genetics

Volumn 88, Issue 4, 2011, Pages 458-468

  Zhu, Qianqian ^a   Ge, Dongliang ^a   Maia, Jessica M ^a   Zhu, Mingfu ^a   Petrovski, Slave ^a,b   Dickson, Samuel P ^a   Heinzen, Erin L ^a   Shianna, Kevin V ^a   Goldstein, David B ^a  

^a DUKE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF MELBOURNE   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; CLINICAL ARTICLE; EUROPE; EXOME; FUNCTIONAL GENOMICS; GENE FREQUENCY; GENE FUNCTION; GENE LOCATION; GENE MUTATION; GENE SEQUENCE; GENE STRUCTURE; GENETIC CODE; GENETIC VARIABILITY; GENOME; GENOTYPE; HUMAN; NONHUMAN; PHENOTYPE; POPULATION; PRIORITY JOURNAL; RANDOMIZATION; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM;

ALLELES; CONSERVED SEQUENCE; EUROPEAN CONTINENTAL ANCESTRY GROUP; EVOLUTION, MOLECULAR; GENE FREQUENCY; GENES, REGULATOR; GENETIC VARIATION; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MODELS, GENETIC; MUTATION; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; SELECTION, GENETIC;

EID: 79953673289     PISSN: 00029297     EISSN: 15376605     Source Type: Journal    
DOI: 10.1016/j.ajhg.2011.03.008     Document Type: Article

References (46)

1. T.A. Manolio, F.S. Collins, N.J. Cox, D.B. Goldstein, L.A. Hindorff, D.J. Hunter, M.I. McCarthy, E.M. Ramos, L.R. Cardon, and A. Chakravarti Finding the missing heritability of complex diseases Nature 461 2009 747 753
2. E.T. Cirulli, and D.B. Goldstein Uncovering the roles of rare variants in common disease through whole-genome sequencing Nat. Rev. Genet. 11 2010 415 425
3. J. McClellan, and M.C. King Genetic heterogeneity in human disease Cell 141 2010 210 217
4. R.P. Alexander, G. Fang, J. Rozowsky, M. Snyder, and M.B. Gerstein Annotating non-coding regions of the genome Nat. Rev. Genet. 11 2010 559 571
5. E. Birney, J.A. Stamatoyannopoulos, A. Dutta, R. Guigó, T.R. Gingeras, E.H. Margulies, Z. Weng, M. Snyder, E.T. Dermitzakis, R.E. Thurman ENCODE Project Consortium NISC Comparative Sequencing Program Baylor College of Medicine Human Genome Sequencing Center Washington University Genome Sequencing Center Broad Institute Children's Hospital Oakland Research Institute Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project Nature 447 2007 799 816 (Pubitemid 46920138)
6. M.K. Halushka, J.-B. Fan, K. Bentley, L. Hsie, N. Shen, A. Weder, R. Cooper, R. Lipshutz, and A. Chakravarti Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis Nat. Genet. 22 1999 239 247 (Pubitemid 29297249)
7. G.V. Kryukov, L.A. Pennacchio, and S.R. Sunyaev Most rare missense alleles are deleterious in humans: implications for complex disease and association studies Am. J. Hum. Genet. 80 2007 727 739 (Pubitemid 46564409)
8. S.B. Ng, E.H. Turner, P.D. Robertson, S.D. Flygare, A.W. Bigham, C. Lee, T. Shaffer, M. Wong, A. Bhattacharjee, and E.E. Eichler Targeted capture and massively parallel sequencing of 12 human exomes Nature 461 2009 272 276
9. I.P. Gorlov, O.Y. Gorlova, S.R. Sunyaev, M.R. Spitz, and C.I. Amos Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms Am. J. Hum. Genet. 82 2008 100 112 (Pubitemid 351726083)
10. Y. Li, N. Vinckenbosch, G. Tian, E. Huerta-Sanchez, T. Jiang, H. Jiang, A. Albrechtsen, G. Andersen, H. Cao, and T. Korneliussen Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants Nat. Genet. 42 2010 969 972
11. D.G. Torgerson, A.R. Boyko, R.D. Hernandez, A. Indap, X. Hu, T.J. White, J.J. Sninsky, M. Cargill, M.D. Adams, C.D. Bustamante, and A.G. Clark Evolutionary processes acting on candidate cis-regulatory regions in humans inferred from patterns of polymorphism and divergence PLoS Genet. 5 2009 e1000592
12. S. Katzman, A.D. Kern, G. Bejerano, G. Fewell, L. Fulton, R.K. Wilson, S.R. Salama, and D. Haussler Human genome ultraconserved elements are ultraselected Science 317 2007 915 (Pubitemid 47301312)
13. S. Asthana, M. Roytberg, J. Stamatoyannopoulos, and S. Sunyaev Analysis of sequence conservation at nucleotide resolution PLoS Comput. Biol. 3 2007 e254
14. J.A. Drake, C. Bird, J. Nemesh, D.J. Thomas, C. Newton-Cheh, A. Reymond, L. Excoffier, H. Attar, S.E. Antonarakis, E.T. Dermitzakis, and J.N. Hirschhorn Conserved noncoding sequences are selectively constrained and not mutation cold spots Nat. Genet. 38 2006 223 227 (Pubitemid 43177238)
15. A.R. Boyko, S.H. Williamson, A.R. Indap, J.D. Degenhardt, R.D. Hernandez, K.E. Lohmueller, M.D. Adams, S. Schmidt, J.J. Sninsky, and S.R. Sunyaev Assessing the evolutionary impact of amino acid mutations in the human genome PLoS Genet. 4 2008 e1000083
16. S. Asthana, W.S. Noble, G. Kryukov, C.E. Grant, S. Sunyaev, and J.A. Stamatoyannopoulos Widely distributed noncoding purifying selection in the human genome Proc. Natl. Acad. Sci. USA 104 2007 12410 12415 (Pubitemid 47206151)
17. D.L. Goode, G.M. Cooper, J. Schmutz, M. Dickson, E. Gonzales, M. Tsai, K. Karra, E. Davydov, S. Batzoglou, R.M. Myers, and A. Sidow Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes Genome Res. 20 2010 301 310
18. G.M. Cooper, D.L. Goode, S.B. Ng, A. Sidow, M.J. Bamshad, J. Shendure, and D.A. Nickerson Single-nucleotide evolutionary constraint scores highlight disease-causing mutations Nat. Methods 7 2010 250 251
19. R.M. Durbin, G.R. Abecasis, D.L. Altshuler, A. Auton, L.D. Brooks, R.M. Durbin, R.A. Gibbs, M.E. Hurles, G.A. McVean 1000 Genomes Project Consortium A map of human genome variation from population-scale sequencing Nature 467 2010 1061 1073
20. H. Li, and R. Durbin Fast and accurate short read alignment with Burrows-Wheeler transform Bioinformatics 25 2009 1754 1760
21. H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, R. Durbin 1000 Genome Project Data Processing Subgroup The Sequence Alignment/Map format and SAMtools Bioinformatics 25 2009 2078 2079
22. G. Benson Tandem repeats finder: a program to analyze DNA sequences Nucleic Acids Res. 27 1999 573 580 (Pubitemid 29210025)
23. R. Redon, S. Ishikawa, K.R. Fitch, L. Feuk, G.H. Perry, T.D. Andrews, H. Fiegler, M.H. Shapero, A.R. Carson, and W. Chen Global variation in copy number in the human genome Nature 444 2006 444 454 (Pubitemid 44809057)
24. Zhu, M., and Goldstein, D. (2010). Estimation by Read Depth with SNVs (ERDS). http://www.duke.edu/∼mz34/erds.htm.
25. J.A. Bailey, A.M. Yavor, H.F. Massa, B.J. Trask, and E.E. Eichler Segmental duplications: organization and impact within the current human genome project assembly Genome Res. 11 2001 1005 1017 (Pubitemid 32834546)
26. R. Khaja, J. Zhang, J.R. MacDonald, Y. He, A.M. Joseph-George, J. Wei, M.A. Rafiq, C. Qian, M. Shago, and L. Pantano Genome assembly comparison identifies structural variants in the human genome Nat. Genet. 38 2006 1413 1418 (Pubitemid 44837563)
27. A. Visel, S. Prabhakar, J.A. Akiyama, M. Shoukry, K.D. Lewis, A. Holt, I. Plajzer-Frick, V. Afzal, E.M. Rubin, and L.A. Pennacchio Ultraconservation identifies a small subset of extremely constrained developmental enhancers Nat. Genet. 40 2008 158 160 (Pubitemid 351171389)
28. Gumby website. http://pga.jgi-psf.org/gumby/.
29. G.V. Kryukov, A. Shpunt, J.A. Stamatoyannopoulos, and S.R. Sunyaev Power of deep, all-exon resequencing for discovery of human trait genes Proc. Natl. Acad. Sci. USA 106 2009 3871 3876
30. R.D. Hernandez A flexible forward simulator for populations subject to selection and demography Bioinformatics 24 2008 2786 2787 (Pubitemid 352722628)
31. A. Siepel, G. Bejerano, J.S. Pedersen, A.S. Hinrichs, M. Hou, K. Rosenbloom, H. Clawson, J. Spieth, L.W. Hillier, and S. Richards Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes Genome Res. 15 2005 1034 1050 (Pubitemid 41126859)
32. K.S. Pollard, M.J. Hubisz, K.R. Rosenbloom, and A. Siepel Detection of nonneutral substitution rates on mammalian phylogenies Genome Res. 20 2010 110 121
33. W.J. Kent, C.W. Sugnet, T.S. Furey, K.M. Roskin, T.H. Pringle, A.M. Zahler, and D. Haussler The human genome browser at UCSC Genome Res. 12 2002 996 1006 (Pubitemid 34662293)
34. ENCODE Project Consortium The ENCODE (ENCyclopedia Of DNA Elements) Project Science 306 2004 636 640
35. N.D. Heintzman, R.K. Stuart, G. Hon, Y. Fu, C.W. Ching, R.D. Hawkins, L.O. Barrera, S. Van Calcar, C. Qu, and K.A. Ching Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome Nat. Genet. 39 2007 311 318 (Pubitemid 46328487)
36. N.D. Heintzman, G.C. Hon, R.D. Hawkins, P. Kheradpour, A. Stark, L.F. Harp, Z. Ye, L.K. Lee, R.K. Stuart, and C.W. Ching Histone modifications at human enhancers reflect global cell-type-specific gene expression Nature 459 2009 108 112
37. G. Bejerano, M. Pheasant, I. Makunin, S. Stephen, W.J. Kent, J.S. Mattick, and D. Haussler Ultraconserved elements in the human genome Science 304 2004 1321 1325 (Pubitemid 38697428)
38. K.E. Lohmueller, A.R. Indap, S. Schmidt, A.R. Boyko, R.D. Hernandez, M.J. Hubisz, J.J. Sninsky, T.J. White, S.R. Sunyaev, and R. Nielsen Proportionally more deleterious genetic variation in European than in African populations Nature 451 2008 994 997 (Pubitemid 351301732)
39. A. Eyre-Walker, M. Woolfit, and T. Phelps The distribution of fitness effects of new deleterious amino acid mutations in humans Genetics 173 2006 891 900 (Pubitemid 43945904)
40. S. Subramanian High proportions of deleterious polymorphisms in constrained human genes Mol. Biol. Evol. 28 2011 49 52
41. S.H. Williamson, R. Hernandez, A. Fledel-Alon, L. Zhu, R. Nielsen, and C.D. Bustamante Simultaneous inference of selection and population growth from patterns of variation in the human genome Proc. Natl. Acad. Sci. USA 102 2005 7882 7887 (Pubitemid 40781032)
42. R.D. Hernandez, J.L. Kelley, E. Elyashiv, S.C. Melton, A. Auton, G. McVean, G. Sella, M. Przeworski 1000 Genomes Project Classic selective sweeps were rare in recent human evolution Science 331 2011 920 924
43. J.K. Pritchard Are rare variants responsible for susceptibility to complex diseases? Am. J. Hum. Genet. 69 2001 124 137 (Pubitemid 32614025)
44. A. Eyre-Walker Evolution in health and medicine Sackler colloquium: Genetic architecture of a complex trait and its implications for fitness and genome-wide association studies Proc. Natl. Acad. Sci. USA 107 Suppl 1 2010 1752 1756
45. M. Nei, Y. Suzuki, and M. Nozawa The neutral theory of molecular evolution in the genomic era Annu. Rev. Genomics Hum. Genet. 11 2010 265 289
46. B. Woolf On estimating the relation between blood group and disease Ann. Hum. Genet. 19 1955 251 253