Your browser doesn't support javascript.
loading
Tracing cancer evolution and heterogeneity using Hi-C.
Erdmann-Pham, Dan Daniel; Batra, Sanjit Singh; Turkalo, Timothy K; Durbin, James; Blanchette, Marco; Yeh, Iwei; Shain, Hunter; Bastian, Boris C; Song, Yun S; Rokhsar, Daniel S; Hockemeyer, Dirk.
Afiliación
  • Erdmann-Pham DD; Department of Mathematics, University of California, Berkeley, CA, 94720, USA.
  • Batra SS; Department of Statistics, Stanford University, Stanford, CA, 94305, USA.
  • Turkalo TK; Computer Science Division, University of California, Berkeley, CA, 94720, USA.
  • Durbin J; Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA.
  • Blanchette M; Dovetail Genomics, Enterprise Way, Scotts Valley, CA, 95066, USA.
  • Yeh I; Dovetail Genomics, Enterprise Way, Scotts Valley, CA, 95066, USA.
  • Shain H; Department of Dermatology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, 94143, USA.
  • Bastian BC; Department of Pathology, University of California, San Francisco, CA, 94143, USA.
  • Song YS; Department of Dermatology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, 94143, USA.
  • Rokhsar DS; Department of Dermatology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, 94143, USA.
  • Hockemeyer D; Department of Pathology, University of California, San Francisco, CA, 94143, USA.
Nat Commun ; 14(1): 7111, 2023 11 06.
Article en En | MEDLINE | ID: mdl-37932252
Chromosomal rearrangements can initiate and drive cancer progression, yet it has been challenging to evaluate their impact, especially in genetically heterogeneous solid cancers. To address this problem we developed HiDENSEC, a new computational framework for analyzing chromatin conformation capture in heterogeneous samples that can infer somatic copy number alterations, characterize large-scale chromosomal rearrangements, and estimate cancer cell fractions. After validating HiDENSEC with in silico and in vitro controls, we used it to characterize chromosome-scale evolution during melanoma progression in formalin-fixed tumor samples from three patients. The resulting comprehensive annotation of the genomic events includes copy number neutral translocations that disrupt tumor suppressor genes such as NF1, whole chromosome arm exchanges that result in loss of CDKN2A, and whole-arm copy-number neutral loss of homozygosity involving PTEN. These findings show that large-scale chromosomal rearrangements occur throughout cancer evolution and that characterizing these events yields insights into drivers of melanoma progression.
Asunto(s)
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Aberraciones Cromosómicas / Melanoma Límite: Humans Idioma: En Revista: Nat Commun Asunto de la revista: BIOLOGIA / CIENCIA Año: 2023 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Reino Unido
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Aberraciones Cromosómicas / Melanoma Límite: Humans Idioma: En Revista: Nat Commun Asunto de la revista: BIOLOGIA / CIENCIA Año: 2023 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Reino Unido