TIARA: A database for accurate analysis of multiple personal genomes based on cross-technology

Nucleic Acids Research

Volumn 39, Issue SUPPL. 1, 2011, Pages

  Hong, Dongwan ^a   Park, Sung Soo ^a   Ju, Young Seok ^a,c,d   Kim, Sheehyun ^a,d   Shin, Jong Yeon ^a,b   Kim, Sujung ^b   Yu, Saet Byeol ^b   Lee, Won Chul ^b   Lee, Seungbok ^a   Park, Hansoo ^e   Kim, Jong Il ^a,b   Seo, Jeong Sun ^a,b,c,d  

^a Seoul National University   (South Korea)

^b Psoma Therapeutics Inc   (South Korea)

^c Seoul National University College of Medicine   (South Korea)

^d Macrogen Inc   (South Korea)

^e BRIGHAM AND WOMEN S HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPARATIVE GENOMIC HYBRIDIZATION; COMPUTER INTERFACE; COPY NUMBER VARIATION; FILE TRANSFER PROTOCOL; GENE SEQUENCE; GENE TECHNOLOGY; GENETIC DATABASE; GENETIC VARIABILITY; GENOME ANALYSIS; HIGH THROUGHPUT SCREENING; HUMAN; INDEL MUTATION; INFORMATION RETRIEVAL; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; TOTAL INTEGRATED ARCHIVE OF SHORT READ AND ARRAY DATABASE; WEB BROWSER;

DATABASES, NUCLEIC ACID; GENETIC VARIATION; GENOME, HUMAN; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; NUCLEIC ACID HYBRIDIZATION; SEQUENCE ANALYSIS, DNA; USER-COMPUTER INTERFACE;

EID: 78651325928     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq1101     Document Type: Article

References (26)

1. Levy, S., Sutton, G., Ng, P.C., Feuk, L., Halpern, A.L., Walenz, B.P., Axelrod, N., Huang, J., Kirkness, E.F., Denisov, G. et al. (2007) The diploid genome sequence of an individual human. PLoS Biol., 5, e254.
2. Wheeler, D.A., Srinivasan, M., Egholm, M., Shen, Y., Chen, L., McGuire, A., He, W., Chen, Y.J., Makhijani, V., Roth, G.T. et al. (2008) The complete genome of an individual by massively parallel DNA sequencing. Nature, 452, 872-876.
3. Wang, J., Wang, W., Li, R., Li, Y., Tian, G., Goodman, L., Fan, W., Zhang, J., Li, J., Guo, Y. et al. (2008) The diploid genome sequence of an Asian individual. Nature, 456, 60-65.
4. Bentley, D.R., Balasubramanian, S., Swerdlow, H.P., Smith, G.P., Milton, J., Brown, C.G., Hall, K.P., Evers, D.J., Barnes, C.L., Bignell, H.R. et al. (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature, 456, 53-59.
5. McKernan, K.J., Peckham, H.E., Costa, G.L., McLaughlin, S.F., Fu, Y., Tsung, E.F., Clouser, C.R., Duncan, C., Ichikawa, J.K., Lee, C.C. et al. (2009) Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res., 19, 1527-1541.
6. Kim, J.I., Ju, Y.S., Park, H., Kim, S., Lee, S., Yi, J.H., Mudge, J., Miller, N.A., Hong, D., Bell, C.J. et al. (2009) A highly annotated whole-genome sequence of a Korean individual. Nature, 460, 1011-1015.
7. Pushkarev, D., Neff, N.F.and Quake, S.R. (2009) Single-molecule sequencing of an individual human genome. Nat. Biotechnol., 27, 847-852.
8. Drmanac, R., Sparks, A.B., Callow, M.J., Halpern, A.L., Burns, N.L., Kermani, B.G., Carnevali, P., Nazarenko, I., Nilsen, G.B., Yeung, G. et al. (2010) Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science, 327, 78-81.
9. Snyder, M., Du, J.and Gerstein, M. (2010) Personal genome sequencing: Current approaches and challenges. Genes Dev., 24, 423-431.
10. Ju, Y.S., Hong, D., Kim, S., Park, S.S., Lee, S., Park, H., Kim, J.I.and Seo, J.S. (2010) Reference-unbiased copy number variant analysis using CGH microarrays. Nucleic Acids Res., doi:10.1093/ nar/gkq730.
11. Iafrate, A.J., Feuk, L., Rivera, M.N., Listewnik, M.L., Donahoe, P.K., Qi, Y., Scherer, S.W.and Lee, C. (2004) Detection of large-scale variation in the human genome. Nat. Genet., 36, 949-951.
12. Redon, R., Ishikawa, S., Fitch, K.R., Feuk, L., Perry, G.H., Andrews, T.D., Fiegler, H., Shapero, M.H., Carson, A.R., Chen, W. et al. (2006) Global variation in copy number in the human genome. Nature, 444, 444-454. (Pubitemid 44809057)
13. McCarroll, S.A.and Altshuler, D.M. (2007) Copy-number variation and association studies of human disease. Nat. Genet., 39, S37-S42.
14. Perry, G.H., Ben-Dor, A., Tsalenko, A., Sampas, N., Rodriguez-Revenga, L., Tran, C.W., Scheffer, A., Steinfeld, I., Tsang, P., Yamada, N.A. et al. (2008) The fine-scale and complex architecture of human copy-number variation. Am. J. Hum. Genet., 82, 685-695.
15. Conrad, D.F., Pinto, D., Redon, R., Feuk, L., Gokcumen, O., Zhang, Y., Aerts, J., Andrews, T.D., Barnes, C., Campbell, P. et al. (2010) Origins and functional impact of copy number variation in the human genome. Nature, 464, 704-712.
16. Park, H., Kim, J.I., Ju, Y.S., Gokcumen, O., Mills, R.E., Kim, S., Lee, S., Suh, D., Hong, D., Kang, H.P. et al. (2010) Discovery of common Asian copy number variants using integrated high-resolution array CGH and massively parallel DNA sequencing. Nat. Genet., 42, 400-405.
17. Korbel, J.O., Urban, A.E., Affourtit, J.P., Godwin, B., Grubert, F., Simons, J.F., Kim, P.M., Palejev, D., Carriero, N.J., Du, L. et al. (2007) Paired-end mapping reveals extensive structural variation in the human genome. Science, 318, 420-426.
18. Yoon, S., Xuan, Z., Makarov, V., Ye, K.and Sebat, J. (2009) Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Res., 19, 1586-1592.
19. Chiang, D.Y., Getz, G., Jaffe, D.B., O'Kelly, M.J., Zhao, X., Carter, S.L., Russ, C., Nusbaum, C., Meyerson, M.and Lander, E.S. (2009) High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat. Methods, 6, 99-103.
20. Rhead, B., Karolchik, D., Kuhn, R.M., Hinrichs, A.S., Zweig, A.S., Fujita, P.A., Diekhans, M., Smith, K.E., Rosenbloom, K.R., Raney, B.J. et al. (2010) The UCSC Genome Browser database: Update 2010. Nucleic Acids Res., 38, D613-D619.
21. Li, G., Ma, L., Song, C., Yang, Z., Wang, X., Huang, H., Li, Y., Li, R., Zhang, X., Yang, H. et al. (2009) The YH database: The first Asian diploid genome database. Nucleic Acids Res., 37, D1025-D1028.
22. Axelrod, N., Lin, Y., Ng, P.C., Stockwell, T.B., Crabtree, J., Huang, J., Kirkness, E., Strausberg, R.L., Frazier, M.E., Venter, J.C. et al. (2009) The HuRef Browser: a web resource for individual human genomics. Nucleic Acids Res., 37, D1018-D1024.
23. Shumway, M., Cochrane, G.and Sugawara, H. (2010) Archiving next generation sequencing data. Nucleic Acids Res., 38, D870-D871.
24. Kersey, P.J., Lawson, D., Birney, E., Derwent, P.S., Haimel, M., Herrero, J., Keenan, S., Kerhornou, A., Koscielny, G., Kahari, A. et al. (2010) Ensembl Genomes: Extending Ensembl across the taxonomic space. Nucleic Acids Res., 38, D563-D569.
25. Wu, T.D.and Nacu, S. (2010) Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics, 26, 873-881.
26. Lipson, D., Aumann, Y., Ben-Dor, A., Linial, N.and Yakhini, Z. (2006) Efficient calculation of interval scores for DNA copy number data analysis. J. Comput. Biol., 13, 215-228.