TY  - JOUR
A1  - Nattestad, Maria
A1  - Goodwin, Sara
A1  - Ng, Karen
A1  - Baslan, Timour
A1  - Sedlazeck, Fritz
A1  - Rescheneder, Philipp
A1  - Garvin, Tyler
A1  - Fang, Han
A1  - Gurtowski, James
A1  - Hutton, Elizabeth
A1  - Tseng, Elizabeth
A1  - Chin, Jason
A1  - Beck, Timothy
A1  - Sundaravadanam, Yogi
A1  - Kramer, Melissa
A1  - Antoniou, Eric
A1  - McPherson, John
A1  - Hicks, James
A1  - McCombie, W. Richard
A1  - Schatz, Michael C
T1  - Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line
Y1  - 2018/06/28 
JF  - Genome Research 
JO  - Genome Research 
DO  - 10.1101/gr.231100.117 
SP  - gr.231100.117 
UR  - http://genome.cshlp.org/content/early/2018/06/28/gr.231100.117.abstract 
N2  - 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. 
ER  -