NHGRI/DIR Genomics Core

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The Genomics Core primarily offers genotyping services to the NHGRI investigators. To a limited extent, services related to physical mapping, sequencing and access to DNA panels are also available. Genotyping is performed using either of two technologies, Illumina BeadArray for SNPs or ABI capillary electrophoretic sizing of fluorescently tagged PCR products encompassing STRPs or other genomic region(s) of interest. Both Illumina and ABI technologies are widely used by a large number of NHGRI investigators. This year, 18 investigators and three adjuncts representing all nine branches and two programs (NISC and UDP) used Core genotyping services. Over the past four years (FY2012-FY2015), there has been a steady increase in service requests received (353, 583, 707 and 853) and the number of DNA samples processed (9895, 17608, 40350, and 42466). Human SNP genotyping was carried out on eight different BeadArray types using Illumina Infinium technology. We processed 6,188 human DNA samples and generated >3 billion genotypes. In addition, 96 samples were processed using methylation arrays. The genotyping data is used for studies such as linkage, association, copy number variation, deletion intervals, methylation status, variations introduced by the iPS technology, parent-of-origin of deletions, mosaicism, uniparental disomy, and to generate haplotypes for discovering variants from sequence data. In addition to numerous small projects, we do have some large SNP projects. Over the last four years (FY2012-FY2015), we processed 1152, 1536, 2256 and 4032 samples for SNP genotyping for NISC. Since NISC genotypes all samples received for whole exome and targeted sequencing, the sample numbers are likely to increase in the future. Further, a large SNP genotyping project (3,000) samples for an MCIDB lab was started recently. Investigators requesting SNP genotyping bear a portion of the cost by using their own budgets to purchase the SNP chip kits, which include SNP chips and reagents. Samples run on SNP and methylation arrays (6,284 samples) represent only about 15% of the total 42,466 DNA samples processed by the Core this year. The remaining samples (36,182) were processed using ABI technology, which has the capability to separate fluorescently labeled PCR products at single-base resolution. In 2010, we developed an efficient screening strategy for zebrafish mutagenesis, which led to identification of germline transmitting founder fish and the size of insertion/deletion mutations generated by ZFNs and TALENs. Recent introduction of CRISPR/Cas technology for targeted mutagenesis resulted in a huge surge in the number of zebrafish DNA samples processed (5492, 14619, 35539, 28986 for FY2012-2015, respectively). The CRISPR technology is being extended to mouse genome as well. In fact, for the past three years (FY2013-FY2015) the number of mouse (8, 612, 6211) and human (493, 500, 985) samples processed has been steadily increasing. While genotyping was the main activity of the Core, requests for human, mouse, and zebrafish BAC clones were also processed (56, 93, 26 and 2 BAC clones were provided during FY2012-2015). Requests for aliquots of DNA panels (eight, nine, three and two) were also processed during the FY2012-2015 period. We will continue to provide access to BAC libraries and DNA panels, and running sequencing reactions for NHGRI investigators. Since FY2010, the Core has assisted investigators with data analysis and access to software/tools, such as GoldenHelix, Nexus, and GenomeStudio. The Core provided training on Illuminas GenomeStudio, and several researchers at NHGRI are using this software on their own computers. While an earlier purchase of unlimited licenses for GenomeStudio made this possible, the yearly renewal expense of Nexus and GoldenHelix limits their availability to only one computer in the Core. Core helps researchers to take advantage of learning and using these tools, and also helps with the handling, collection, evaluation, and processing of SNP and other data sets. The Core has provided significant data analysis support for 11 investigators over the past three years on different projects, covering copy number variation, linkage disequilibrium analysis, population stratification, and association studies. Analyses for detecting deletions, duplications, loss of heterozygosity, and regions portraying signs of chromosomal mosaicism in DNA samples from patients diagnosed with Fanconi anemia and head and neck cancer were also performed. Other studies include changes associated with the processing of iPS, Acute myeloid leukemia, Smith-Magenis syndrome, Febrile Infection-Related Epilepsy Syndrome, population stratification and variant frequency ranking of the African-American Ancestral SNPs, and eye diseases Coloboma and Leber Congenital Amaurosis (LCA). This service is of huge value to investigators with small projects, as are most users of the Core, who do not have the required tools or expertise for the analysis of large data sets.