Clinical implications of human population differences in genome-wide rates of functional genotypes

Frontiers in Genetics

Volumn 3, Issue NOV, 2012, Pages

  Torkamani, Ali ^a,b,c   Pham, Phillip ^a,b   Libiger, Ondrej ^a,c   Bansal, Vikas ^a,b   Zhang, Guangfa ^a,c   Zeeland, Ashley A Scott Van ^a,b   Tewhey, Ryan ^a,c   Topol, Eric J ^a,b,c   Schork, Nicholas J ^a,b,c  

^a Scripps Translational Sciences Institute   (United States)

^b SCRIPPS HEALTH   (United States)

^c SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

Clinical sequencing; Congenital disease; Population genetics; Whole genome sequencing

Indexed keywords

EID: 84876081745     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2012.00211     Document Type: Article

References (53)

1. Adzhubei, I. A., Schmidt, S., Peshkin, L., Ramensky, V. E., Gerasimova, A., Bork, P., et al. (2010). A method and server for predicting damaging missense mutations. Nat. Methods 7, 248-249.
2. Bainbridge, M. N., Wiszniewski, W., Murdock, D. R., Friedman, J., Gonzaga-Jauregui, C., Newsham, I., et al. (2011). Whole-genome sequencing for optimized patient management. Sci. Transl. Med. 3, 87re3.
3. Balasubramanian, S., Habegger, L., Frankish, A., Macarthur, D. G., Harte, R., Tyler-Smith, C., et al. (2011). Gene inactivation and its implications for annotation in the era of personal genomics. Genes Dev. 25,1-10.
4. Bansal, V., Libiger, O., Torkamani, A., and Schork, N. J. (2010). Statistical analysis strategies for association studies involving rare variants. Nat. Rev. Genet. 11,773-785.
5. Biesecker, L. G., Mullikin, J. C., Facio, F. M., Turner, C., Cherukuri, P. F., Blakesley, R. W., et al. (2009). The Clinseq Project: piloting large-scale genome sequencing for research in genomic medicine. Genome Res. 19, 1665-1674.
6. Boyko, A. R., Williamson, S. H., Indap, A. R., Degenhardt, J. D., Hernandez, R. D., et al. (2008). Assessing the evolutionary impact of amino acid mutations in the human genome. PLoS Genet. 4, e1000083. doi:10.1371/journal.pgen.1000083
7. Braun, H. I. (ed.). (1994). The Collected Works Of John W. Tukey. New York: Chapman and Hall.
8. Bustamante, C. D., Burchard, E. G., and De La Vega, F. M. (2011). Genomics for the world. Nature 475,163-165.
9. Casto, A. M., and Feldman, M. W. (2011). Genome-wide association study SNPs in the human genome diversity project populations: does selection affect unlinked SNPs with shared trait associations? PLoS Genet. 7, e1001266. doi:10.1371/journal.pgen.1001266
10. Chiaromonte, F., Yap, V. B., and Miller, W. (2002). Scoringpairwise genomic sequence alignments. Pac. Symp. Biocomput. 7, 115-126.
11. Conrad, D. F., Jakobsson, M., Coop, G., Wen, X., Wall, J. D., Rosenberg, N. A., et al. (2006). A worldwide survey of haplotype variation and linkage disequilibrium in the human genome. Nat. Genet. 38, 1251-1260.
12. Consortium, G. P. (2010). A map of human genome variation from population-scale sequencing. Nature 467, 1061-1073.
13. Consortium, T. I. H. (2005). A haplotype map of the human genome. Nature 437, 1299-1320.
14. Day, I. N. (2010). dbSNP in the detail and copy number complexities. Hum. Mutat. 31, 2-4.
15. Drmanac, R., Sparks, A. B., Callow, M. J., Halpern, A. L., Burns, N. L., Kermani, B. G., et al. (2010). Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science 327,78-81.
16. Evans, P. D., Gilbert, S. L., Mekel-Bobrov, N., Vallender, E. J., Anderson, J. R., Vaez-Azizi, L. M., et al. (2005). Microcephalin, a gene regulating brain size, continues to evolve adaptively in humans. Science 309, 1717-1720.
17. Frazer, K. A., Ballinger, D. G., Cox, D. R., Hinds, D. A., Stuve, L. L., Gibbs, R. A., et al. (2007). A second generation human haplotype map of over 3.1 million SNPs. Nature 449, 851-861.
18. Fujita, P. A., Rhead, B., Zweig, A. S., Hinrichs, A. S., Karolchik, D., Cline, M. S., et al. (2011). The UCSC genome browser database: update 2011. Nucleic Acids Res. 39, D876-D882.
19. Gonzaga-Jauregui, C., Lupski, J. R., and Gibbs, R. A. (2012). Human genome sequencing in health and disease. Annu. Rev. Med. 63, 35-61.
20. Gravel, S., Henn, B. M., Gutenkunst, R. N., Indap, A. R., Marth, G. T., Clark, A. G., et al. (2011). Demographic history and rare allele sharing among human populations. Proc. Natl. Acad. Sci. U.S.A. 108, 11983-11988.
21. Harismendy, O., Ng, P. C., Strausberg, R. L., Wang, X., Stockwell, T. B., Beeson, K. Y., et al. (2009). Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol. 10, R32.
22. Hernandez, R. D., Williamson, S. H., and Bustamante, C. D. (2007). Context dependence, ancestral misidentification, and spurious signatures of natural selection. Mol. Biol. Evol. 24, 1792-1800.
23. Ionita-Laza, I., Makarov, V., Yoon, S., Raby, B., Buxbaum, J., Nicolae, D. L., et al. (2011). Finding disease variants in mendelian disorders by using sequence data: methods and applications. Am. J. Hum. Genet. 89, 701-712.
24. Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D. (2003). Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc. Natl. Acad. Sci. U.S.A. 100, 11484-11489.
25. Kumar, P., Henikoff, S., and Ng, P. C. (2009). Predicting the effects of coding non-synonymous variants on protein function using the sift algorithm. Nat. Protoc. 4, 1073-1081.
26. Lam, H. Y., Clark, M. J., Chen, R., Natsoulis, G., O'Huallachain, M., Dewey, F. E., et al. (2012). Performance comparison of whole-genome sequencing platforms. Nat. Biotechnol. 30, 78-82.
27. Li, J. Z., Absher, D. M., Tang, H., Southwick, A. M., Casto, A.M., Ramachandran, S., et al. (2008). Worldwide human relationships inferred from genome-wide patterns of variation. Science 319,1100-1104.
28. Lohmueller, K. E., Indap, A. R., Schmidt, S., Boyko, A. R., Hernandez, R. D., Hubisz, M. J., et al. (2008). Proportionally more deleterious genetic variation in european than in african populations. Nature 451, 994-997.
29. Lupski, J. R., Reid, J. G., Gonzaga-Jauregui, C., Rio Deiros, D., Chen, D. C., Nazareth, L., et al. (2010). Whole-genome sequencing in a patient with charcot-marie-tooth neuropathy. N. Engl. J. Med. 362,1181-1191.
30. Lyon, G. J., and Wang, K. (2012). Identifying disease mutations in genomic medicine settings: current challenges and how to accelerate progress. Genome Med. 4, 58.
31. MacArthur, D. G., Balasubramanian, S., Frankish, A., Huang, N., Morris, J., Walter, K., et al. (2012). A systematic survey of loss-of-function variants in human protein-coding genes. Science 335, 823-828.
32. Mangan, M. E., Williams, J. M., Kuhn, R. M., and Lathe, W. C. III. (2009). The UCSC genome browser: what every molecular biologist should know. Curr. Protoc. Mol. Biol. Chapter 19, Unit19.9.
33. Moore, B., Hu, H., Singleton, M., Reese, M. G., De La Vega, E M., and Yandell, M. (2011). Global analysis of disease-related DNA sequence variation in 10 healthy individuals: implications for whole genome-based clinical diagnostics. Genet. Med. 13, 210-217.
34. Nelson, M. R., Wegmann, D., Ehm, M. G., Kessner, D., St Jean, P., Verzilli, C., et al. (2012). An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people. Science 337, 100-104.
35. Ng, P. C., and Henikoff, S. (2003). Sift: predicting amino acid changes that affect protein function. Nucleic Acids Res. 31,3812-3814.
36. Nielsen, R., Hellmann, I., Hubisz, M., Bustamante, C., and Clark, A. G. (2007). Recent and ongoing selection in the human genome. Nat. Rev. Genet. 8, 857-868.
37. Nievergelt, C. M., Libiger, O., and Schork, N. J. (2007). Generalized analysis of molecular variance. PLoS Genet. 3, e51. doi:10.1371/journal.pgen.0030051
38. Pelak, K., Shianna, K. V., Ge, D., Maia, J. M., Zhu, M., Smith, J. P., et al. (2010). The characterization of twenty sequenced human genomes. PLoS Genet. 6, e1001111. doi:10.1371/journal.pgen.1001111
39. Pickrell, J. K., Coop, G., Novembre, J., Kudaravalli, S., Li, J. Z., Absher, D., et al. (2009). Signals of recent positive selection in a worldwide sample of human populations. Genome Res. 19, 826-837.
40. Plumpton, M., and Barnes, M. R. (2007). "Predictive functional analysis of polymorphisms: an overview," in Bioinformatics for Geneticists, ed. M. R. Barnes (New York: John Wiley And Sons, Ltd), 249-280.
41. Ramensky, V., Bork, P., and Sunyaev, S. (2002). Human non-synonymous SNPs: server and survey. Nucleic Acids Res. 30, 3894-3900.
42. Reich, D., Price, A. L., and Patterson, N. (2008). Principal component analysis of genetic data. Nat. Genet. 40, 491-492.
43. Roach, J. C., Glusman, G., Smit, A. F., Huff, C. D., Hubley, R., Shannon, P. T., et al. (2010). Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science 328,636-639.
44. Rope, A. F., Wang, K., Evjenth, R., Xing, J., Johnston, J. J., Swensen, J. J., et al. (2011). Using VAAST to identify an X-linked disorder resulting in lethality in male infants due to N-terminal acetyltransferase deficiency. Am. J. Hum. Genet. 89, 28-43.
45. Rosenberg, N. A., Pritchard, J. K., Weber, J. L., Cann, H. M., Kidd, K. K., Zhivotovsky, L. A., et al. (2002). Genetic structure of human populations. Science 298, 2381-23
46. Schwartz, S., Kent, W. J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R. C., et al. (2003). Human-mouse alignments with BLASTZ. Genome Res. 13, 103-107.
47. Stephens, J. C., Reich, D. E., Goldstein, D. B., Shin, H. D., Smith, M. W., Car-rington, M., et al. (1998). Dating the origin of the CCR5-Delta32 AIDS-resistance allele by the coalescence of haplotypes. Am. J. Hum. Genet. 62, 1507-1515.
48. Sunyaev, S., Ramensky, V., Koch, I., Lathe, W III, Kondrashov, A. S., and Bork, P. (2001). Prediction of deleterious human alleles. Hum. Mol. Genet. 10,591-597.
49. Tennessen, J. A., Bigham, A. W., O'Connor, T. D., Fu, W., Kenny, E. E., Gravel, S., et al. (2012). Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science 337, 64-69.
50. Tewhey, R., Bansal, V., Torkamani, A., Topol, E. J., and Schork, N. J. (2011). The importance of phase information for human genomics. Nat. Rev. Genet. 12,215-223.
51. Torkamani, A., Scott-Van Zeeland, A. A., Topol, E. J., and Schork, N. J. (2011). Annotating individ ual human genomes. Genomics 98, 233-241.
52. Worthey, E. A., Mayer, A. N., Syverson, G. D., Helbling, D., Bonacci, B. B., Decker, B., et al. (2011). Making a definitive diagnosis: suc cessful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease. Genet. Med. 13, 255-262.
53. Yandell, M., Huff, C., Hu, H., Singleton, M., Moore, B., Xing, J., et al. (2011). A probabilistic disease-gene finder for personal genomes. Genome Res. 21, 1529-1542.