An initial map of insertion and deletion (INDEL) variation in the human genome

Genome Research

Volumn 16, Issue 9, 2006, Pages 1182-1190

  Mills, Ryan E ^a   Luttig, Christopher T ^a   Larkins, Christine E ^a   Beauchamp, Adam ^a   Tsui, Circe ^a   Pittard, W Stephen ^a   Devine, Scott E ^a  

^a EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BASE PAIRING; CHIMPANZEE; CHROMOSOME ANALYSIS; CONTROLLED STUDY; DENSITY FUNCTIONAL THEORY; EXON; GENE DELETION; GENE FUNCTION; GENE IDENTIFICATION; GENE INSERTION; GENE LOCATION; GENE MAPPING; GENETIC VARIABILITY; HUMAN; INTERMETHOD COMPARISON; INTRON; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; TRANSPOSON;

ANIMALS; COMPUTATIONAL BIOLOGY; GENOME, HUMAN; HUMANS; PAN TROGLODYTES; POLYMORPHISM, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE DELETION;

PAN TROGLODYTES;

EID: 33748271469     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.4565806     Document Type: Article

References (33)

1. Altshuler, D., Pollara, V.J., Cowles, C.R., Van Etten, W.J., Baldwin, J., Linton, L., and Lander, E.S. 2000. An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature 407: 513-516.
2. Bailey, J.A., Gu, Z., Clark, R.A., Reinert, K., Samonte, R.V., Schwartz, S., Adams, M.D., Myers, E.W., Li, P.W., and Eichler, E.E. 2002. Recent segmental duplications in the human genome. Science 297: 1003-1007.
3. Bennett, E.A., Coleman, L.E., Tsui, C., Pittard, W.S., and Devine, S.E. 2004. Natural genetic variation caused by transposable elements in humans. Genetics 168: 933-951.
4. Berger, J., Suzuki, T., Senti, K.A., Stubbs, J., Schaffner, G., and Dickson, B.J. 2001. Genetic mapping with SNP markers in Drosophila. Nat. Genet. 29: 475-481.
5. Bhangale, T.R., Rieder, M.J., Livingston, R.J., and Nickerson, D.A. 2005. Comprehensive identification and characterization of diallelic insertion-deletion polymorphisms in 330 human candidate genes. Hum. Mol. Genet. 14: 59-69.
6. Collins, F.S., Drumm, M.L., Cole, J.L., Lockwood, W.K., Vande Woude, G.F., and Iannuzzi, M.C. 1987. Construction of a general human chromosome jumping library, with application to cystic fibrosis. Science 235: 1046-1049.
7. Collins, F.S., Brooks, L.D., and Chakravarti, A. 1999. A DNA polymorphism discovery resource for research on human genetic variation. Genome Res. 8: 1229-1231.
8. Conrad, D.F., Andrews, T.D., Carter, N.P., Hurles, M.E., and Pritchard, J.K. 2006. A high resolution survey of deletion polymorphism in the human genome. Nat. Genet. 38: 75-81.
9. Daly, M.J., Rioux, J.D., Schaffner, S.F., Hudson, T.J., and Lander, E.S. 2001. High-resolution haplotype structure in the human genome. Nat. Genet. 29: 229-232.
10. Dawson, E., Chen, Y., Hunt, S., Smink, L.J., Hunt, A., Rice, K., Livingston, S., Bumpstead, S., Bruskiewich, R., Sham, P., et al. 2001. A SNP resource for human chromosome 22: Extracting dense clusters of SNPs from the genomic sequence. Genome Res. 11: 170-178.
11. Ewing, B. and Green, P. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8: 186-194.
12. Gabriel, S.B., Schaffner, S.F., Nguyen, H., Moore, J.M., Roy, J., Blumenstiel, B., Higgins, J., DeFelice, M., Lochner, A., Faggart, M., et al. 2002. The structure of haplotype blocks in the human genome. Science 296: 2225-2229.
13. The International HapMap Consortium. 2003. The International HapMap Project. Nature 426: 789-796.
14. _. 2005. A haplotype map of the human genome. Nature 437: 1299-1320.
15. The International SNP Map Working Group. 2001. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409: 928-933.
16. Judson, R., Salisbury, B., Schneider, J., Windemuth, A., and Stephens, J.C. 2002. How many SNPs does a genome-wide haplotype map require? Pharmacogenomics 3: 379-391.
17. Jurka, J. 2000. Repbase update: A database and an electronic journal of repetitive elements. Trends Genet. 16: 418-420.
18. Kent, W.J., Sugnet, C.W., Furey, T.S., Roskin, K.M., Pringle, T.H., Zahler, A.M., and Hausler, D. 2002. The human genome browser at UCSC. Genome Res. 12: 996-1006.
19. McCarroll, S.A., Hadnott, T.N., Perry, G.H., Sabeti, P.C., Zody, M.C., Barrett, J.C., Dallaire, S., Gabriel, S.B., Lee, C., Daly, M.J., et al. 2006. Common deletion polymorphisms in the human genome. Nat. Genet. 38: 86-92.
20. Mullikin, J.C., Hunt, S.E., Cole, C.G., Mortimore, B.J., Rice, C.M., Burton, J., Matthews, L.H., Pavitt, R., Plumb, R.W., Sims, S.K., et al. 2000. An SNP map of human chromosome 22. Nature 407: 516-520.
21. Nickerson, D.A., Taylor, S.L., Weiss, K.M., Clark, A.G., Hutchinson, R.G., Stengard, J., Saloma, V., Vartianen, E., Boerwinkle, E., and Sing, C.F. 1998. DNA sequence diversity in a 9.7-kb region of the human lipoprotein lipase gene. Nat. Genet. 19: 216-217.
22. Ostertag, E.M. and Kazazian, H.H. 2001. Biology of mammalian L1 retrotransposons. Annu. Rev. Genet. 35: 501-538.
23. Patil, N., Berno, A.J., Hinds, D.A., Barrett, W.A., Doshi, J.M., Hacker, C.R., Kautzer, C.R., Lee, D.H., Marjoribanks, C., McDonough, D.P., et al. 2001. Blocks of limited haplotype diversity revealed by high resolution scanning of human chromosome 21. Science 294: 1719-1723.
24. Rieder, M.J., Taylor, S.L., Clark, A.G., and Nickerson, D.A. 1999. Sequence variation in the human angiotensin converting enzyme. Nat. Genet. 22: 59-62.
25. Stenson, P.D., Ball, E.V., Mort, M., Phillips, A.D., Shiel, J.A., Thomas, N.S., Abeysinghe, S., Krawczak, M., and Cooper, D.N. 2003. Human Gene Mutation Database (HGMD): 2003 update. Hum. Mutat. 21: 577-581.
26. Stephens, J.C., Schneider, J.A., Tanguay, D.A., Choi, J., Acharya, T., Stanley, S.E., Jiang, R., Messer, C.J., Chew, A., Han, J.H., et al. 2001. Haplotype variation and linkage disequilibrium in 313 human genes. Science 293: 489-493.
27. Storey, J.D. and Tibshirani, R. 2003. Statistical significance for genome-wide experiments. Proc. Natl. Acad. Sci. 100: 9440-9445.
28. Taillon-Miller, P. and Kwok, P.Y. 2000. A high-density single-nucleotide polymorphism map of Xq25-q28. Genomics 65: 195-202.
29. Taillon-Miller, P., Piernot, E.E., and Kwok, P.Y. 1999. Efficient approach to unique single-nucleotide polymorphism discovery. Genome Res. 9: 499-505.
30. Tsui, C., Coleman, L.E., Griffith, J.L., Bennett, E.A., Goodson, S.G., Scott, J.D., Pittard, W.S., and Devine, S.E. 2003. Single nucleotide polymorphisms (SNPs) that map to gaps in the human SNP map. Nucleic Acids Res. 31: 4910-4916.
31. Warren, S.T., Zhang, F., Licameli, G.R., and Peters, J.F. 1987. The fragile X sites in somatic cell hybrids: An approach for molecular cloning of fragile sites. Science 237: 420-423.
32. Weber, J.L., David, D., Heil, J., Fan, Y., Zhao, C., and Marth, G. 2002. Human diallelic insertion/deletion polymorphisms. Am. J. Hum. Genet. 71: 854-862.
33. Wicks, S.R., Yeh, R.T., Gish, W.R., Waterston, R.H., and Plasterk, R.H.A. 2001. Rapid gene mapping in Caenorhabditis elegans using a high density polymorphism map. Nat. Genet. 28: 160-164.