Long insert whole genome sequencing for copy number variant and translocation detection

Nucleic Acids Research

Volumn 42, Issue 2, 2014, Pages

  Liang, Winnie S ^a   Aldrich, Jessica ^a   Tembe, Waibhav ^a   Kurdoglu, Ahmet ^a   Cherni, Irene ^a   Phillips, Lori ^a   Reiman, Rebecca ^a   Baker, Angela ^a   Weiss, Glen J ^a,b   Carpten, John D ^a   Craig, David W ^a  

^a TRANSLATIONAL GENOMICS RESEARCH INSTITUTE   (United States)

^b CANCER TREATMENT CENTERS OF AMERICA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; RNA; TRANSCRIPTOME;

ARTICLE; BIOINFORMATICS; COPY NUMBER VARIATION; COST EFFECTIVENESS ANALYSIS; GENE INSERTION; GENE SEQUENCE; GENE TRANSLOCATION; HETEROZYGOSITY; HUMAN; HUMAN GENOME; PRIORITY JOURNAL; RNA SEQUENCE; TUMOR GENE; DNA SEQUENCE; EVALUATION STUDY; GENE LIBRARY; GENETICS; GENOMICS; HIGH THROUGHPUT SEQUENCING; METHODOLOGY; NEOPLASM;

DNA COPY NUMBER VARIATIONS; GENE LIBRARY; GENOME, HUMAN; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; NEOPLASMS; SEQUENCE ANALYSIS, DNA; TRANSLOCATION, GENETIC;

EID: 84893298543     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt865     Document Type: Article

References (16)

1. Meyerson, M., Gabriel, S. and Getz, G. (2010) Advances in understanding cancer genomes through second-generation sequencing. Nat. Rev. Genet., 11, 685-696.
2. Tran, B., Dancey, J.E., Kamel-Reid, S., McPherson, J.D., Bedard, P.L., Brown, A.M., Zhang, T., Shaw, P., Onetto, N., Stein, L. et al. (2012) Cancer genomics: technology, discovery, and translation. J. Clin. Oncol., 30, 647-660.
3. Roychowdhury, S., Iyer, M.K., Robinson, D.R., Lonigro, R.J., Wu, Y.M., Cao, X., Kalyana-Sundaram, S., Sam, L., Balbin, O.A., Quist, M.J. et al. (2011) Personalized oncology through integrative high-throughput sequencing: a pilot study. Sci. Transl. Med., 3, 111ra121.
4. Yao, F., Ariyaratne, P.N., Hillmer, A.M., Lee, W.H., Li, G., Teo, A.S., Woo, X.Y., Zhang, Z., Chen, J.P., Poh, W.T. et al. (2012) Long span DNA paired-end-tag (DNA-PET) sequencing strategy for the interrogation of genomic structural mutations and fusion-point-guided reconstruction of amplicons. PLoS One, 7, e46152.
5. Lander, E.S. and Waterman, M.S. (1988) Genomic mapping by fingerprinting random clones: a mathematical analysis. Genomics, 2, 231-239.
6. Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
7. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G. and Durbin, R. (2009) The sequence alignment/map format and SAMtools. Bioinformatics, 25, 2078-2079.
8. McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M. et al. (1297) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res., 20, 1297-1303.
9. Ju, J., Kim, D.H., Bi, L., Meng, Q., Bai, X., Li, Z., Li, X., Marma, M.S., Shi, S., Wu, J. et al. (2006) Four-color DNA sequencing by synthesis using cleavable fluorescent nucleotide reversible terminators. Proc. Natl Acad. Sci. USA, 103, 19635-19640.
10. Forbes, S.A., Bhamra, G., Bamford, S., Dawson, E., Kok, C., Clements, J., Menzies, A., Teague, J.W., Futreal, P.A. and Stratton, M.R. (2008) The Catalogue of Somatic Mutations in Cancer (COSMIC). Curr. Protoc. Hum. Genet., Chapter 10, Unit 10.11.
11. Wu, J., Grzeda, K.R., Stewart, C., Grubert, F., Urban, A.E., Snyder, M.P. and Marth, G.T. (2012) Copy Number Variation detection from 1000 Genomes Project exon capture sequencing data. BMC Bioinformatics, 13, 305.
12. Rausch, T., Zichner, T., Schlattl, A., Stutz, A.M., Benes, V. and Korbel, J.O. (2012) DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics, 28, i333-i339.
13. Wang, J., Mullighan, C.G., Easton, J., Roberts, S., Heatley, S.L., Ma, J., Rusch, M.C., Chen, K., Harris, C.C., Ding, L. et al. (2011) CREST maps somatic structural variation in cancer genomes with base-pair resolution. Nat. Methods, 8, 652-654.
14. Chen, K., Wallis, J.W., McLellan, M.D., Larson, D.E., Kalicki, J.M., Pohl, C.S., McGrath, S.D., Wendl, M.C., Zhang, Q., Locke, D.P. et al. (2009) BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat. Methods, 6, 677-681.
15. Suzuki, S., Yasuda, T., Shiraishi, Y., Miyano, S. and Nagasaki, M. (2011) ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information. BMC Bioinformatics, 12, S7.
16. Hormozdiari, F., Alkan, C., Eichler, E.E. and Sahinalp, S.C. (2009) Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes. Genome Res., 19, 1270-1278.