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

By Maria Nattestad, Sara Goodwin, Karen Ng, Timour Baslan, Fritz J Sedlazeck, Philipp Rescheneder, Tyler Garvin, Han Fang, James Gurtowski, Elizabeth Hutton, Elizabeth Tseng, Chen-Shan Chin, Timothy Beck, Yogi Sundaravadanam, Melissa Kramer, Eric Antoniou, John D. McPherson, James Hicks, W. Richard McCombie, Michael C. Schatz

Posted 10 Aug 2017
bioRxiv DOI: 10.1101/174938 (published DOI: 10.1101/gr.231100.117)

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 prior efforts. Surrounding the important HER2 locus, 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 transcriptome and sheds new light on the complexity of cancer progression.

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