Whole genome sequence analysis of BT-474 using complete Genomics’ standard and long fragment read technologies

Serban Ciotlos1, Qing Mao1, Rebecca Yu Zhang1, Zhenyu Li2, Robert Chin1, Natali Gulbahce1, Sophie Jia Liu1, Radoje Drmanac1,2, Brock A. Peters1,2
1Complete Genomics, Inc., 2071 Stierlin Court, Mountain View, CA 94043, USA
2BGI-Shenzhen, Shenzhen 518083, China

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Lasfargues EY, Coutinho WG, Redfield ES. Isolation of two human tumor epithelial cell lines from solid breast carcinomas. J Natl Cancer Inst. 1978;61(4):967–78.

Rondon-Lagos M, Verdun Di Cantogno L, Marchio C, Rangel N, Payan-Gomez C, Gugliotta P, et al. Differences and homologies of chromosomal alterations within and between breast cancer cell lines: a clustering analysis. Mol Cytogenet. 2014;7(1):8. doi: 10.1186/1755-8166-7-8 .

Peters BA, Kermani BG, Sparks AB, Alferov O, Hong P, Alexeev A, et al. Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells. Nature. 2012;487(7406):190–5. doi: 10.1038/nature11236 .

Peters BA, Kermani BG, Alferov O, Agarwal MR, McElwain MA, Gulbahce N, et al. Detection and phasing of single base de novo mutations in biopsies from human in vitro fertilized embryos by advanced whole-genome sequencing. Genome Res. 2015;25(3):426–34. doi: 10.1101/gr.181255.114 .

Drmanac R, Sparks AB, Callow MJ, Halpern AL, Burns NL, Kermani BG, et al. Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science. 2010;327(5961):78–81. doi: 10.1126/science.1181498 .

Carnevali P, Baccash J, Halpern AL, Nazarenko I, Nilsen GB, Pant KP, et al. Computational techniques for human genome resequencing using mated gapped reads. J Comput Biol. 2012;19(3):279–92. doi: 10.1089/cmb.2011.0201 .

Edgren H, Murumagi A, Kangaspeska S, Nicorici D, Hongisto V, Kleivi K, et al. Identification of fusion genes in breast cancer by paired-end RNA-sequencing. Genome Biol. 2011;12(1):R6. doi: 10.1186/gb-2011-12-1-r6 .

Kangaspeska S, Hultsch S, Edgren H, Nicorici D, Murumagi A, Kallioniemi O. Reanalysis of RNA-sequencing data reveals several additional fusion genes with multiple isoforms. PLoS One. 2012;7(10):e48745. doi: 10.1371/journal.pone.0048745 .

Zook JM, Chapman B, Wang J, Mittelman D, Hofmann O, Hide W, et al. Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls. Nat Biotechnol. 2014;32(3):246–51. doi: 10.1038/nbt.2835 .

Lawrence MS, Stojanov P, Mermel CH, Robinson JT, Garraway LA, Golub TR, et al. Discovery and saturation analysis of cancer genes across 21 tumour types. Nature. 2014;505(7484):495–501. doi: 10.1038/nature12912 .

Vogelstein B, Papadopoulos N, Velculescu VE, Zhou S, Diaz Jr LA, Kinzler KW. Cancer genome landscapes. Science. 2013;339(6127):1546–58. doi: 10.1126/science.1235122 .

COSMIC. http://cancer.sanger.ac.uk/cosmic . Accessed 10/01/2015.

Landrum MJ, Lee JM, Riley GR, Jang W, Rubinstein WS, Church DM, et al. ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res. 2014;42(Database issue):D980–5. doi: 10.1093/nar/gkt1113 .

Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S, et al. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature. 2012;483(7391):603–7. doi: 10.1038/nature11003 .

Complete Genomics. http://www.completegenomics.com/customer-support/documentation/100357139-2/ .

Serban Ciotlos; Qing Mao; Rebecca Yu Zhang; Zhenyu Li; Robert Chin; Natali Gulbahce; Sophie Jia Liu; Radoje Drmanac; Brock A Peters (2016): Supporting materials for “Whole genome sequence analysis of BT-474 using Complete Genomics’ standard and Long Fragment Read technologies”. GigaScience Database. doi.org/ 10.5524/100188