Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line
- Maria Nattestad1,
- Sara Goodwin1,
- Karen Ng2,
- Timour Baslan3,
- Fritz J. Sedlazeck4,5,
- Philipp Rescheneder6,
- Tyler Garvin1,
- Han Fang1,
- James Gurtowski1,
- Elizabeth Hutton1,
- Elizabeth Tseng7,
- Chen-Shan Chin7,
- Timothy Beck2,
- Yogi Sundaravadanam2,
- Melissa Kramer1,
- Eric Antoniou1,
- John D. McPherson8,
- James Hicks1,
- W. Richard McCombie1 and
- Michael C. Schatz1,4
- 1Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;
- 2Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada;
- 3Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA;
- 4Johns Hopkins University, Baltimore, Maryland 21211, USA;
- 5Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA;
- 6Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, A-1030 Wien, Austria;
- 7Pacific Biosciences, Menlo Park, California 94025, USA;
- 8UC Davis Comprehensive Cancer Center, Sacramento, California 95817, USA
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.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.231100.117.
- Received October 9, 2017.
- Accepted June 27, 2018.
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