Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line

Nattestad, M., Goodwin, S., Ng, K., Baslan, T., Sedlazeck, F., Rescheneder, P., Garvin, T., Fang, H., Gurtowski, J., Hutton, E., Tseng, E., Chin, J., Beck, T., Sundaravadanam, Y., Kramer, M., Antoniou, E., McPherson, J., Hicks, J., McCombie, W. R., Schatz, M. C. (August 2018) Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line. Genome Res, 28 (8). pp. 1126-1135. ISSN 1088-9051

Abstract

The SK-BR-3 cell line is one of the most important models for HER2+ breast cancers, which affect one in five breast cancer patients. SK-BR-3 is known to be highly rearranged although much of the variation is in complex and repetitive regions that may be underreported. Addressing this, we sequenced SK-BR-3 using long-read single molecule sequencing from Pacific Biosciences, and develop one of the most detailed maps of structural variations (SVs) in a cancer genome available with nearly 20,000 variants present, most of which were missed by short read sequencing. Surrounding the important ERBB2 oncogene (also known as HER2), we discover a complex sequence of nested duplications and translocations, suggesting a punctuated progression. Full-length transcriptome sequencing further revealed several novel gene fusions within the nested genomic variants. Combining long-read genome and transcriptome sequencing enables an in-depth analysis of how SVs disrupt the genome and sheds new light on the complex mechanisms involved in cancer genome evolution.

Item Type:	Paper
Subjects:	diseases & disorders > cancer > cancer types > breast cancer bioinformatics > genomics and proteomics > genetics & nucleic acid processing > transcriptomes Investigative techniques and equipment > assays > whole genome sequencing
CSHL Authors:	Nattestad, Maria Goodwin, Sara Baslan, Timour Garvin, Tyler Fang, Han Gurtowski, James Kramer, Melissa R. Antoniou, Eric Hicks, James B. McCombie, W. Richard Schatz, Michael C. Hutton, Elizabeth
Communities:	CSHL labs > Hicks lab CSHL labs > McCombie lab CSHL labs > Schatz lab School of Biological Sciences > Publications CSHL Cancer Center Program > Cancer Genetics and Genomics Program
Depositing User:	Matthew Dunn
Date:	August 2018
Date Deposited:	15 Aug 2018 15:48
Last Modified:	05 Nov 2020 14:53
PMCID:	PMC6071638
Related URLs:	Publisher
URI:	https://repository.cshl.edu/id/eprint/37109

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