Inter- and Intra-Species Comparative Sequencing

National Human Genome Research Institute

Investigators

Linked publications, trials & patents

Abstract

Over the last year, NISC operated the following suite of production sequencing machines: 1 PacBio Sequel 2, 1 NextSeq 550, 1 NovaSeq 6000, and 3 MiSeqs. Using these platforms, we have generated over 1,773 billion reads in the past year. 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. The NovaSeq 6000 allows NISC to effectively meet the rising interest in studying whole genome sequence datasets, with over 948 human genomes sequenced and analyzed in the past year. The adoption of many new sequencing protocols in production created the commensurate need for dramatic changes to sample tracking, flow control and primary analysis pipelines, as well as project management and cost accounting. Rapid design, development and implementation of new Laboratory Information Management System (LIMS) by a dedicated NISC team has met the initial challenges and continues to evolve quickly to adapt to a continuous flow of changes in sequencing technologies. A combination of talented IT staff and bioinformaticians have met the challenges of extremely large and complex data sets by implementing and continuously adapting pipeline programs to support rapidly evolving software associated with each of the sequencing platforms. Beyond primary analysis that results in DNA basecalls and quality scores, NISC has worked closely with members of other NHGRI research groups to implement and support high-throughput production of biologically relevant secondary analysis. One shining example of these efforts is the production scale processing of Whole Genome Sequencing (WGS) data for all of our clients, using a newly implemented GPU accelerated GATK4 best practices pipeline. With these new sequence alignment and genetic variant calling systems in place, we can analyze WGS datasets at a rate of one per hour, matching our maximum throughput of the NovaSeq 6000. Publications for fiscal-year 2021 span a wide range of projects, and are summarized as follows: 1) WES projects (n = 6) (Beck, Ferrada et al. 2020, Currin, Erdos et al. 2021, Dudley, Hong et al. 2021, Schnappauf, Zhou et al. 2020, Zhou, Sood et al. 2021, Pitsava, Feldkamp et al. 2021) 2) Whole Genome Sequencing (n = 3) (Manion, Dulanto Chiang et al. 2020, Proctor, Dangana et al. 2021, Schnappauf, Zhou et al. 2020) 3) RNAseq,(n = 3) (Currin, Erdos et al. 2021, Rodriguez-Gil, Baxter et al. 2021, Schnappauf, Zhou et al. 2020 4) ATACseq (n = 1) (Currin, Erdos et al. 2021) 5) Microbiome study (n = 3) (Manion, Dulanto Chiang et al. 2020, Proctor, Dangana et al. 2021, Huang, Welsh et al. 2021) 6) Custom Capture (n = 2) (Loftus, Lundh et al. 2021, Schnappauf, Sampaio Moura et al. 2020) 7) PacBio Amplicon Seq (n = 2) (Schnappauf, Zhou et al. 2020, Zhou, Sood et al. 2021) The NISC team worked with two PIs at NIH related to COVID-19 and SARS-CoV-2. In collaboration with Dr. Cliff Lane at NIAID we have generated 389 SARS-CoV-2 genomes from patients in Clinical Trials. In collaboration with Dr. Lothar Hennighausen at NIDDK, we have generated 320 RNA-seq datasets on a cohort of people from Ischgl Austria who experienced a SARS-CoV-2 superspreading event early in the pandemic. See PMC7895922 for analysis results for some of these RNA-seq datasets. In the foreseeable future, NISC is well positioned to provide next-gen sequence data for a multitude of investigators across NIH. We also expect increasing access to sequencing by the NIH Clinical Center with our CLIA exome test and continuing our sequencing support for Intramural NHGRI investigators for their most promising projects. Our focus is to increase operational efficiencies of the next-gen pipeline, 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. We have also added a PromethION to our suite of sequencing instruments and once this is fully integrated into our production pipeline, super high-quality and contiguous genome assemblies will be 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 .