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Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line.
Nattestad, Maria; Goodwin, Sara; Ng, Karen; Baslan, Timour; Sedlazeck, Fritz J; Rescheneder, Philipp; Garvin, Tyler; Fang, Han; Gurtowski, James; Hutton, Elizabeth; Tseng, Elizabeth; Chin, Chen-Shan; Beck, Timothy; Sundaravadanam, Yogi; Kramer, Melissa; Antoniou, Eric; McPherson, John D; Hicks, James; McCombie, W Richard; Schatz, Michael C.
Afiliación
  • Nattestad M; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
  • Goodwin S; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
  • Ng K; Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada.
  • Baslan T; Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.
  • Sedlazeck FJ; Johns Hopkins University, Baltimore, Maryland 21211, USA.
  • Rescheneder P; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.
  • Garvin T; Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, A-1030 Wien, Austria.
  • Fang H; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
  • Gurtowski J; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
  • Hutton E; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
  • Tseng E; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
  • Chin CS; Pacific Biosciences, Menlo Park, California 94025, USA.
  • Beck T; Pacific Biosciences, Menlo Park, California 94025, USA.
  • Sundaravadanam Y; Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada.
  • Kramer M; Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada.
  • Antoniou E; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
  • McPherson JD; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
  • Hicks J; UC Davis Comprehensive Cancer Center, Sacramento, California 95817, USA.
  • McCombie WR; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
  • Schatz MC; Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.
Genome Res ; 28(8): 1126-1135, 2018 08.
Article en En | MEDLINE | ID: mdl-29954844
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.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Oncogenes / Neoplasias de la Mama / Reordenamiento Génico / Amplificación de Genes Límite: Female / Humans Idioma: En Revista: Genome Res Asunto de la revista: BIOLOGIA MOLECULAR / GENETICA Año: 2018 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Estados Unidos
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Oncogenes / Neoplasias de la Mama / Reordenamiento Génico / Amplificación de Genes Límite: Female / Humans Idioma: En Revista: Genome Res Asunto de la revista: BIOLOGIA MOLECULAR / GENETICA Año: 2018 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Estados Unidos