Inter- and Intra-Species Comparative Sequencing

National Human Genome Research Institute

Investigators

Linked publications & trials

Abstract

Over the last year, NISC sequenced more than 10,000 samples in support of the NIH Intramural Research Program for 52 investigators from 14 NIH Institutes or Centers. Specifically, NISC provides NIH Intramural scientists access to the latest DNA and RNA sequencing technologies: Pacific Biosciences Revio, Illumina NovaSeq X Plus and MiSeq (n = 4), and Oxford Nanopore Technology P24 PromethION. Though we remain consistently at a level of a mid-scale genome sequencing center, we have maintained advantageous economies of scale while remaining relatively agile. NISC’s current portfolio of sequencers can accommodate a wide range of project scales, sample types and output requirements. These project types include: counting experiments (such as ChIP-seq, RNA-seq, single-cell multiomics), and genome or targeted sequencing for small variant detection on our short read sequencing platforms, or direct RNA, full-length transcript, base modification detection, large amplicon and genome sequencing and assembly with our long read technologies. In the past year NISC also began to offer a CLIA certified Genome Sequencing with Secondary Findings test for Clinical Center protocols. NISC also continues to apply our expertise in generating high-quality ultra-long read data sets used in telomere-to -telomere (T2T) genome assemblies of humans and other animals. Publications for fiscal-year 2025 span a wide range of projects and are summarized as follows: 1) Exome and targeted sequencing projects (n = 2)(Alvarez Jerez et al., 2024 and Carter et al.,2025) 2) Whole genome sequencing, assembly and analysis (n = 3) (de Lima et al., 2024; Schnitzler et al., 2024 and Yoo et al., 2025) 3) Skin microbiome studies (n = 4) (Popowitch et al., 2024; Che et al., 2025; Er et al., 2025 and Proctor et al., 2025) 4) Transcriptomics (n = 2) (Nath et al., 2024 and Palmer et al., 2025) In the foreseeable future, NISC is well positioned to provide DNA and RNA sequence data for investigators within NHGRI and across the NIH Intramural Program. We also expect increased usage of our CLIA Genome Sequencing with Secondary Findings test for patients enrolled in clinical protocols and and continued sequencing support for intramural NHGRI investigators and their most promising projects. Our focus is to increase operational efficiencies, refine existing protocols, implement additional protocols as new sample/experimental types are requested from researchers, and continue to expand the value-added data analysis packages available. With long-read technologies now fully integrated into our production pipeline, state-of-the-art contiguous T2T genome assemblies are available to NIH intramural researchers. In summary, we will continue to monitor developments in the rapidly evolving sequencing and informatics technologies, implementing those we deem most appropriate for our collaborating investigators.