The Staudt laboratory at NCI performs a number of different genomics methodologies to discover oncogenic mechanisms in lymphoma, all of which require high-throughput DNA sequencing. Specifically, the laboratory developed loss-of-function genetic screens to discover new molecular targets in cancer using libraries of small hairpin RNAs (shRNAs) that mediate RNA interference (RNAi).
The laboratory utilizes whole genome, whole exome and whole transcriptome cancer gene resequencing as a useful adjunct to RNAi screening, often identifying recurrent somatic mutations that account for the addiction of cancer cells to particular regulatory pathways. The laboratory developed an analytic pipeline to discover mutations using high-throughput RNA resequencing (RNA-seq), exome sequencing and whole genome sequencing.
The NCI has extensive experience conducting high-throughput sequencing experiments using Illumina platforms. The laboratory has completed over 500 RNA-seq samples, 300 ChIP-seq samples and 266 exome-seq samples. To date, these analyses have been performed in a sequencing core using the Illumina HiSeq platform. To facilitate and accelerate this type of research in the future, the NCI requires an Illumina NextSeq 500 machine to increase the turnaround time compared to the Illumina HiSeq 2000 platform. The NextSeq platform delivers sequences in one day versus six days for the HiSeq 2000 platform.