Journal
GENOME RESEARCH
Volume 28, Issue 8, Pages 1126-1135Publisher
COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT
DOI: 10.1101/gr.231100.117
Keywords
-
Categories
Funding
- National Science Foundation [DBI-1350041]
- National Institutes of Health [R01-HG006677, UM1-HG008898]
- Cold Spring Harbor Laboratory (CSHL) Cancer Center [5P30CA045508]
- Watson School of Biological Sciences at CSHL from the US National Institutes of Health [5T32GM065094]
- Pacific Biosciences
- William C. and Joyce C. O'Neil Charitable Trust, Memorial Sloan Kettering Single Cell Sequencing Initiative
- NATIONAL CANCER INSTITUTE [P30CA045508] Funding Source: NIH RePORTER
- NATIONAL HUMAN GENOME RESEARCH INSTITUTE [R01HG006677, UM1HG008898] Funding Source: NIH RePORTER
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [T32GM065094] Funding Source: NIH RePORTER
Ask authors/readers for more resources
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.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available