NISC currently operates the following suite of production sequencing machines: 1 PacBio RS II, 4 HiSeq2500s, and 3 MiSeqs. Using these platforms, we have generated over 520 billion reads in the past year alone. 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. In keeping with the Comparative Sequencing interests, several years ago NISC implemented an amplicon-based Sanger sequencing pipeline designed to focus on intra-species variation. Numerous clinically relevant projects were designed to amplify and sequence specific genes and regions of interest in small groups of human subjects, yielding great insights into disease related genotype/phenotype combinations. As an early model for application of genome sequence data to medical research our flagship ClinSeq Project greatly advanced the study of atherosclerosis by providing sequence data for 250 genes in over 500 volunteers (www.genome.gov/20519355). While this approach was extremely productive, we evaluated and then adopted the NextGen sequencing platform to more efficiently and rapidly collect whole exome data for the ClinSeq Project, followed by many other medically relevant projects. As a consequence of these advances, NISC no longer offers Sanger-based amplicon targeted sequencing in production mode. Two publications related to our earlier Sanger-based efforts are listed in the publications section of this report (de Filippo, Key et al. 2016),(Justice, Bishop et al. 2016). 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 Exome Sequencing (WES) data to all of our clients, the end product of which is distilled sets of variants of interest that are accessible in user-friendly fashion by the use of the in-house developed VarSifter program. The success of these programs has led to an increasing number of projects from a growing number of investigators. In 2014 we added a CLIA compliant pipeline for WES of samples originating from the NIH Clinical Center through the Clinical Center Genomics Opportunity program (www.genome.gov/27558725) and have completed sequencing of over 600 samples. The implementation of improved project management tools is helping to address the challenges associated with our continued growth, which is now yielding results as publications for custom capture and WES projects (n = 10) (Beck, Mullikin et al. 2016), (Boyden, Desai et al. 2016), (Cherukuri, Maduro et al. 2015), (Kruszka, Uwineza et al. 2015), (Maglic, Stephen et al. 2016), (Malicdan, Vilboux et al. 2015), (Ng, Hong et al. 2016), (O'Brien, Lozier et al. 2016), (Vilboux, Malicdan et al. 2016), (Zhou, Wang et al. 2016), Whole Genome Sequencing, Assembly and/or Annotation (n = 3) (Conlan, Park et al 2016). (Dotson, NISC et al. 2016), (Maduro, Pusey et al. 2016), RNAseq and micro RNA (n = 2) (Baran-Gale, Kurtz et al. 2015), (Hartley, Coon et al. 2015), ChIPseq (n = 1)(Lee , Beggs et al. 2015), microbiome studies (n = 3) (Oh, Byrd et al. 2016), (Jo, Deming et al. 2016), (Tsai, Conlan et al. 2016), methylation sequencing (n = 1) (Margolin , Petrykowska et al. 2016), Pacific Biosciences amplicon sequencing (n = 1)(Kane, Davids et al. 2016), and HIV and influenza antibody studies (n=4) (Bonsignori, Zhou et al. 2016), (Gorman, Soto et al. 2015), (Joyce, Wheatley et al. 2016), (Soto, Ofek et al. 2016). In the foreseeable future, NISC is well positioned to provide next-gen sequence data for several large, multi-year projects, for example, the Skin Microbiome Project, and Mouse Methylome Project, a collaboration with NIEHS, as well as expanding the access to sequencing by the NIH Clinical Center with our CLIA exome test and for Intramural NHGRI investigators through continued sequencing support of 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. Furthermore, we will continue to monitor developments in the rapidly evolving sequencing and informatics technologies, implementing those we deem most appropriate for the sequence data we produce for collaborating investigators.
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