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Completing the map of human genetic variation

A plan to identify and integrate normal structural variation into the human genome sequence.

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Figure 1: Paired-end sequence approach.
Figure 2: Sequencing structural variation.

References

  1. IHGSC. Initial sequencing and analysis of the human genome. Nature 409, 860– 921 (2001).

  2. Venter, J. C. et al. The sequence of the human genome. Science 291, 1304– 1351 (2001).

    ArticleΒ  ADSΒ  CASΒ  Google ScholarΒ 

  3. Collins, F. S., Green, E. D., Guttmacher, A. E. & Guyer, M. S. A vision for the future of genomics research. Nature 422, 835– 847 (2003).

    ArticleΒ  ADSΒ  CASΒ  Google ScholarΒ 

  4. IHMC. A haplotype map of the human genome. Nature 437, 1299– 1320 (2005).

  5. Hinds, D. A. et al. Whole-genome patterns of common DNA variation in three human populations. Science 307, 1072– 1079 (2005).

    ArticleΒ  ADSΒ  CASΒ  Google ScholarΒ 

  6. Weber, J. L. et al. Human diallelic insertion/deletion polymorphisms. Am. J. Hum. Genet. 71, 854– 862 (2002).

    ArticleΒ  Google ScholarΒ 

  7. Bhangale, T. R., Rieder, M. J., Livingston, R. J. & Nickerson, D. A. Comprehensive identification and characterization of diallelic insertion–deletion polymorphisms in 330 human candidate genes. Hum. Mol. Genet. 14, 59– 69 (2005).

    ArticleΒ  CASΒ  Google ScholarΒ 

  8. Mills, R. E. et al. An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res. 16, 1182– 1190 (2006).

    ArticleΒ  CASΒ  Google ScholarΒ 

  9. Feuk, L., Carson, A. R. & Scherer, S. W. Structural variation in the human genome. Nature Rev. Genet. 7, 85– 97 (2006).

    ArticleΒ  CASΒ  Google ScholarΒ 

  10. Freeman, J. L. et al. Copy number variation: new insights in genome diversity. Genome Res. 16, 949– 961 (2006).

    ArticleΒ  CASΒ  Google ScholarΒ 

  11. Sharp, A. J., Cheng, Z. & Eichler, E. E. Structural variation of the human genome. Annu. Rev. Genom. Hum. Genet. 7, 407– 442 (2006).

    ArticleΒ  CASΒ  Google ScholarΒ 

  12. Iafrate, A. J. et al. Detection of large-scale variation in the human genome. Nature Genet. 36, 949– 951 (2004).

    ArticleΒ  CASΒ  Google ScholarΒ 

  13. Sebat, J. et al. Large-scale copy number polymorphism in the human genome. Science 305, 525– 528 (2004).

    ArticleΒ  ADSΒ  CASΒ  Google ScholarΒ 

  14. Tuzun, E. et al. Fine-scale structural variation of the human genome. Nature Genet. 37, 727– 732 (2005).

    ArticleΒ  CASΒ  Google ScholarΒ 

  15. Hinds, D. A., Kloek, A. P., Jen, M., Chen, X. & Frazer, K. A. Common deletions and SNPs are in linkage disequilibrium in the human genome. Nature Genet. 38, 82– 85 (2006).

    ArticleΒ  CASΒ  Google ScholarΒ 

  16. Conrad, D. F., Andrews, T. D., Carter, N. P., Hurles, M. E. & Pritchard, J. K. A high-resolution survey of deletion polymorphisms in the human genome. Nature Genet. 38, 75– 81 (2006).

    ArticleΒ  CASΒ  Google ScholarΒ 

  17. McCarroll, S. A. et al. Common deletion polymorphisms in the human genome. Nature Genet. 38, 86– 92 (2006).

    ArticleΒ  CASΒ  Google ScholarΒ 

  18. Redon, R. et al. Global variation in copy number in the human genome. Nature 444, 444– 454 (2006).

    ArticleΒ  ADSΒ  CASΒ  Google ScholarΒ 

  19. Khaja, R. et al. Genome assembly comparison identifies structural variants in the human genome. Nature Genet. 38, 1413– 1418 (2006).

    ArticleΒ  CASΒ  Google ScholarΒ 

  20. Wilson, E. B. The sex chromosomes. Arch. Mikrosk. Anat. Entwicklungsmech 77, 249– 271 (1911).

    ArticleΒ  Google ScholarΒ 

  21. Cooley, T. B. & Lee, P. A series of cases of splenomegaly in children with anemia and peculiar bone changes. Trans. Am. Pediatr. Soc. 37, 29 (1925).

    Google ScholarΒ 

  22. Levine, P., Katzin, E. M. & Burnham, L. Isoimmunization in pregnancy: its possible bearing on the etiology of erythroblastosis foetalis. J. Am. Med. Assoc. 116, 825– 827 (1941).

    ArticleΒ  Google ScholarΒ 

  23. Deeb, S. S. The molecular basis of variation in human color vision. Clin. Genet. 67, 369– 377 (2005).

    ArticleΒ  CASΒ  Google ScholarΒ 

  24. Wagner, F. F. & Flegel, W. A. The molecular basis of the Rh blood group phenotypes. Immunohematol. 20, 23– 36 (2004).

    CASΒ  Google ScholarΒ 

  25. Fucharoen, S. & Winichagoon, P. Thalassemia and abnormal hemoglobin. Int. J. Hematol. 76 (Suppl. 2), 83– 89 (2002).

    ArticleΒ  Google ScholarΒ 

  26. Lupski, J. R. Genomic disorders: structural features of the genome can lead to DNA rearrangements and human disease traits. Trends Genet. 14, 417– 422 (1998).

    ArticleΒ  CASΒ  Google ScholarΒ 

  27. Stankiewicz, P. & Lupski, J. R. Genomic architecture, rearrangements and genomic disorders. Trends Genet. 18, 74– 82 (2002).

    ArticleΒ  CASΒ  Google ScholarΒ 

  28. Lupski, J. R. & Stankiewicz, P. Genomic disorders: molecular mechanisms for rearrangements and conveyed phenotypes. PLoS Genet. 1, e49 (2005).

    ArticleΒ  Google ScholarΒ 

  29. Duncan, I. W. Transvection effects in Drosophila. Annu. Rev. Genet. 36, 521– 556 (2002).

    ArticleΒ  CASΒ  Google ScholarΒ 

  30. Jakobsson, J. et al. Large differences in testosterone excretion in Korean and Swedish men are strongly associated with a UDP-glucuronosyl transferase 2B17 polymorphism. J. Clin. Endocrinol. Metab. 91, 687– 693 (2006).

    ArticleΒ  CASΒ  Google ScholarΒ 

  31. Park, J. et al. Deletion polymorphism of UDP-glucuronosyltransferase 2B17 and risk of prostate cancer in African American and Caucasian men. Cancer Epidemiol. Biomarkers Prev. 15, 1473– 1478 (2006).

    ArticleΒ  CASΒ  Google ScholarΒ 

  32. Gonzalez, E. et al. The Influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility. Science 307, 1434– 1440 (2005).

    ArticleΒ  ADSΒ  CASΒ  Google ScholarΒ 

  33. Fellermann, K. et al. A chromosome 8 gene-cluster polymorphism with low human beta-defensin 2 gene copy number predisposes to Crohn disease of the colon. Am. J. Hum. Genet. 79, 439– 448 (2006).

    ArticleΒ  CASΒ  Google ScholarΒ 

  34. Aitman, T. J. et al. Copy number polymorphism in Fcgr3 predisposes to glomerulonephritis in rats and humans. Nature 439, 851– 855 (2006).

    ArticleΒ  ADSΒ  CASΒ  Google ScholarΒ 

  35. Buckland, P. R. Polymorphically duplicated genes: their relevance to phenotypic variation in humans. Ann. Med. 35, 308– 315 (2003).

    ArticleΒ  CASΒ  Google ScholarΒ 

  36. Lupski, J. R. et al. DNA duplication associated with Charcot–Marie–Tooth disease type 1A. Cell 66, 219– 232 (1991).

    ArticleΒ  CASΒ  Google ScholarΒ 

  37. Locke, D. P. et al. Linkage disequilibrium and heritability of copy-number polymorphisms within duplicated regions of the human genome. Am. J. Hum. Genet. 79, 275– 290 (2006).

    ArticleΒ  CASΒ  Google ScholarΒ 

  38. Wirtenberger, M., Hemminki, K. & Burwinkel, B. Identification of frequent chromosome copy-number polymorphisms by use of high-resolution single-nucleotide-polymorphism arrays. Am. J. Hum. Genet. 78, 520– 522 (2006).

    ArticleΒ  CASΒ  Google ScholarΒ 

  39. Sharp, A. J. et al. Segmental duplications and copy-number variation in the human genome. Am. J. Hum. Genet. 77, 78– 88 (2005).

    ArticleΒ  CASΒ  Google ScholarΒ 

  40. Rozen, S. et al. Abundant gene conversion between arms of massive palindromes in human and ape Y chromosomes. Nature 423, 873– 876 (2003).

    ArticleΒ  ADSΒ  CASΒ  Google ScholarΒ 

  41. Repping, S. et al. High mutation rates have driven extensive structural polymorphism among human Y chromosomes. Nature Genet. 38, 463– 467 (2006).

    ArticleΒ  CASΒ  Google ScholarΒ 

  42. Schmutz, J. et al. The DNA sequence and comparative analysis of human chromosome 5. Nature 431, 268– 274 (2004).

    ArticleΒ  ADSΒ  CASΒ  Google ScholarΒ 

  43. Eichler, E. E. Widening the spectrum of human genetic variation. Nature Genet. 38, 9– 11 (2006).

    ArticleΒ  CASΒ  Google ScholarΒ 

  44. Bentley, D. R. Whole-genome re-sequencing. Curr. Opin. Genet. Dev. 16, 545– 552 (2006).

    ArticleΒ  CASΒ  Google ScholarΒ 

  45. Lackner, C., Cohen, J. C. & Hobbs, H. H. Molecular definition of the extreme size polymorphism in apolipoprotein(a). Hum. Mol. Genet. 2, 933– 940 (1993).

    ArticleΒ  CASΒ  Google ScholarΒ 

  46. Rao, Y. et al. Duplications and defects in the CYP2A6 gene: identification, genotyping, and in vivo effects on smoking. Mol. Pharmacol. 58, 747– 755 (2000).

    ArticleΒ  CASΒ  Google ScholarΒ 

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Acknowledgements

We thank R. Spielman and three anonymous reviewers for helpful comments.

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Reprints and permissions information is available at www.nature.com/reprints. Correspondence and requests for materials should be addressed to E.E.E. (eee@gs.washington.edu).

Author Contributions E.E.E., D.A.N., D.A., A.F., J.R.L. and S.T.S. wrote the manuscript. A.M.B, L.D.B., N.P.C., D.M.C., M.G., C.L., J.C.M., J.K.P., J.S., D.S., D.V. and R.H.W. contributed to the plan design and provided comments and suggestions during preparation of the manuscript.

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The Human Genome Structural Variation Working Group. Completing the map of human genetic variation. Nature 447, 161–165 (2007). https://doi.org/10.1038/447161a

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