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Deep whole-genome sequencing of 3 cancer cell lines on 2 sequencing platforms.
Arora, Kanika; Shah, Minita; Johnson, Molly; Sanghvi, Rashesh; Shelton, Jennifer; Nagulapalli, Kshithija; Oschwald, Dayna M; Zody, Michael C; Germer, Soren; Jobanputra, Vaidehi; Carter, Jade; Robine, Nicolas.
Afiliação
  • Arora K; New York Genome Center, New York, NY, 10013, USA.
  • Shah M; New York Genome Center, New York, NY, 10013, USA.
  • Johnson M; New York Genome Center, New York, NY, 10013, USA.
  • Sanghvi R; New York Genome Center, New York, NY, 10013, USA.
  • Shelton J; New York Genome Center, New York, NY, 10013, USA.
  • Nagulapalli K; New York Genome Center, New York, NY, 10013, USA.
  • Oschwald DM; New York Genome Center, New York, NY, 10013, USA.
  • Zody MC; New York Genome Center, New York, NY, 10013, USA.
  • Germer S; New York Genome Center, New York, NY, 10013, USA.
  • Jobanputra V; New York Genome Center, New York, NY, 10013, USA.
  • Carter J; New York Genome Center, New York, NY, 10013, USA.
  • Robine N; New York Genome Center, New York, NY, 10013, USA. nrobine@nygenome.org.
Sci Rep ; 9(1): 19123, 2019 12 13.
Article em En | MEDLINE | ID: mdl-31836783
ABSTRACT
To test the performance of a new sequencing platform, develop an updated somatic calling pipeline and establish a reference for future benchmarking experiments, we performed whole-genome sequencing of 3 common cancer cell lines (COLO-829, HCC-1143 and HCC-1187) along with their matched normal cell lines to great sequencing depths (up to 278x coverage) on both Illumina HiSeqX and NovaSeq sequencing instruments. Somatic calling was generally consistent between the two platforms despite minor differences at the read level. We designed and implemented a novel pipeline for the analysis of tumor-normal samples, using multiple variant callers. We show that coupled with a high-confidence filtering strategy, the use of combination of tools improves the accuracy of somatic variant calling. We also demonstrate the utility of the dataset by creating an artificial purity ladder to evaluate the somatic pipeline and benchmark methods for estimating purity and ploidy from tumor-normal pairs. The data and results of the pipeline are made accessible to the cancer genomics community.
Assuntos

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Perfilação da Expressão Gênica / Sequenciamento Completo do Genoma / Neoplasias Limite: Humans Idioma: En Ano de publicação: 2019 Tipo de documento: Article

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Perfilação da Expressão Gênica / Sequenciamento Completo do Genoma / Neoplasias Limite: Humans Idioma: En Ano de publicação: 2019 Tipo de documento: Article