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

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, researchers from Stanford University School of Medicine introduce Simul-seq, a technique for the production of high-quality whole-genome and transcriptome sequencing libraries from small quantities of cells or tissues. They 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, the researchers identify germline polymorphisms that are associated with response to cancer therapies. They further leverage this integrative data to uncover expressed mutations in several known cancer genes as well as a recurrent mutation in the motor domain of KIF3B that significantly affects kinesin-microtubule interactions. Simul-seq provides a new streamlined approach for generating comprehensive genome and transcriptome profiles from limited quantities of clinically relevant samples.

Simultaneous, single-tube sequencing of DNA and RNA

(a) Schematic of Simul-seq method. (b) Cross-species mapping rates for Simul-seq libraries produced from a mixture of yeast mRNA and human genomic DNA (n = 2) as well as yeast RNA-seq (n = 3) and human DNA-seq controls (n = 2). (c) Droplet digital PCR (ddPCR) assays on Simul-seq libraries (n = 3 technical replicates per library) with varying amounts of RNA-specific PCR amplification followed by an additional five cycles of PCR with primer sets for both RNA and DNA. (d) DNA and RNA library ratios measured by ddPCR (n = 3 technical replicates per library) are correlated with subsequent read ratios.