Simul-seq: combined DNA and RNA sequencing for whole-genome and transcriptome profiling.

ABSTRACT: Paired DNA and RNA profiling is increasingly employed in genomics research to uncover molecular mechanisms of disease and to explore personal genotype and phenotype correlations. Here, we introduce Simul-seq, a technique for the production of high-quality whole-genome and transcriptome sequencing libraries from small quantities of cells or tissues. We apply the method to laser-capture-microdissected esophageal adenocarcinoma tissue, revealing a highly aneuploid tumor genome with extensive blocks of increased homozygosity and corresponding increases in allele-specific expression. Among this widespread allele-specific expression, we identify germline polymorphisms that are associated with response to cancer therapies. We further leverage this integrative data to uncover expressed mutations i

SUBMITTER: Reuter JA 

PROVIDER: S-EPMC5734913 | biostudies-literature | 2016 Nov

REPOSITORIES: biostudies-literature