The genotyping services offered by the Genomics Core include the Illumina BeadArray technology for SNPs, and the ABI technology for resolution of fluorescently tagged PCR products encompassing STRPs or other genomic region(s) of interest. Both technologies are widely used by a large number of NHGRI investigators;16 investigators from five different branches used the Core services this year. The Core received 290 service requests in FY2012, nearly twice as many as last year (150 requests). This increase covers a 15-month period (June 11 - Aug 12), and when annualized, requests increased 55% from FY2011. The Core processed 13,140 DNA samples this year, over 2-fold increase from last year (6,400 samples), and a 65% increase for a comparable 12-month time period. For the past three years, there has been a steady increase in the number of service requests (108, 150, 290) and in number of samples (730, 6,400, 13,140) processed by the Core. SNP assays (and the arrays) used included GoldenGate (mouse1440) and Infinium (HumanOmni2.5, HumanOmniExpress, 370CNV, and Human 450K Methylation). The number of samples processed and the genotypes generated were for mouse genotype (758, 1M), human genotype (2,400, 1119M) and methylation (96, 36M) studies. As anticipated from the use of high-density SNP arrays, nearly all the genotypes generated this year (1156M) were from SNP technology, though the number of samples processed with SNP technology (3,254) accounted for a third of those processed with ABI technology (9,886). ABI technology is capable of separating fluorescently labeled PCR products at single-base resolution, and continues to accommodate novel applications. We established this capability to help develop an efficient screening strategy for mutagenesis efforts in zebrafish. This strategy helped find germline transmitting founder fish and determines the size of the insertion or deletion mutation generated by the ZFNs (zinc‐finger nucleases) and TALENs (transcription activator like effector nucleases) technologies. Zebrafish DNA samples (8,810) accounted for 90% of all the DNA processed with ABI technology this year (9,886), and doubled from last year (4,343). The Core continues to provide ABI-based STRP genotyping, and over 1000 DNA samples were genotyped for studies such as deletion mapping by MLPA, microsatellite instability, mouse speed congenics, sample characterization, and parent-of-origin studies. The Core uses genotyping to help investigators identify samples by fingerprinting DNA samples with a set of highly polymorphic STRP markers. We have now added a relatively high-density SNP chip at an affordable cost (192,000 SNPs;$39 per sample). The Core processed 1,680 DNA samples using these chips for NISC. These genotypes generated by the Core, in general, covered a variety of applications, such as linkage, association, scanning focus regions for fine mapping of linked loci, copy number variation, identification of deletion intervals, parent of origin of deletions, speed congenics, methylation/expression in cancer, variations introduced by the iPS technology, mosaicism, uniparental disomy, homozygosity mapping and nonclassical linkage analysis, among others. While genotyping was the main activity of the Core, limited physical mapping and sequencing services, as well as access to DNA panels were also offered. The Core also assists investigators with data analysis. In FY2010, the Core purchased and installed an Illumina iScan that allowed genotyping with higher density (2.5M) and higher throughput (OmniExpress) SNP chips. This has substantially extended our ability to process increased number of samples (this year, 3284 samples) and generate large number of genotypes (1156M).
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