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 20 investigators from seven different branches (CGCGB, GDRB, GMBB, MCIDGB, MGMGB MGB, and TFGB) used the Core genotyping and other services. Table 1 lists the investigators and their use of the major services offered by the Core. The Core received 707 service requests in FY2014, a 20% increase from last year (583 requests). More importantly, the 42,515 DNA samples processed this year is nearly 2.5 times as many as last year (17,872 DNAs). Looking back over the past four years, there has been a steady increase in service requests received (217, 353, 583, and 707) and in DNA samples processed (6,611, 10,975, 17,872, and 42,515) by the Core. Human SNP genotyping was carried out on a variety of BeadArrays using Illumina Infinium technology including HumanCore, HumanExome, HumanCoreExome, Methylation450K, HumanOmniExpress and HumanOmniExpressExome. The Core has the capability to process any type of new BeadArrays that is supported by the Illumina SNP technology. We processed 5,268 human DNA samples, and generated over 2 billion SNP genotypes, and 144 samples using methylation arrays. The samples run on SNP and methylation arrays (5412 samples) represent only about 13% of the total 42, 515 DNA samples processed by the Core this year. The remaining 87% of the samples (37,103) were processed using ABI technology. The capability of ABI technology to separate fluorescently labeled PCR products at single-base resolution has been adopted for a variety of applications at the Core. In 2010, we developed an efficient screening strategy for zebrafish mutagenesis conducted at the Zebrafish Core. This strategy identified germline transmitting founder fish and determined the size of insertion/deletion mutations generated by ZFNs and TALENs, the engineered nuclease mutagenesis technologies. Screening requests (15, 57, 121 and 239) and the number of zebrafish DNA samples processed (829, 4,593, 6,552, and 14,891) steadily increased from FY10 through FY13. However, introduction of CRISPR a recent addition of ease of design, low-cost and a more efficient technology for targeted mutagenesis, resulted in a huge surge in the number of projects and of zebrafish DNA samples processed by the Core. This year, the Genomics Core processed 35,911 DNA samples, nearly 2.5 times that of last year (14,891). We learned from the Zebrafish Core mutations in 15 genes are being evaluated, and mutagenesis for ten other genes is underway. In addition, Burgess and UDP (Undiagnosed Disease Program) groups are generating mutants in >100 genes, and thus the anticipated use of the Genomics Core for mutation screening is going to be huge in the coming years. The consistent use of the ABI technology for human (484 samples) and mouse genome (708 samples) for a variety of applications persisted this year. The popularity of CRISPR technology is being extended to the mouse genome as well and many more investigators are anticipated to use this service in the coming year. Genotypes and fragment size data for human DNA samples, in general, are used for a variety of applications, such as linkage, association, scanning focus regions for fine mapping of linked loci, copy number variation, identification of deletion intervals, methylation/expression in cancer, variations introduced by the iPS technology, deletion mapping by MLPA, parent-of-origin of deletions, mosaicism, uniparental disomy, homozygosity mapping, among others. In addition to numerous small SNP projects, two large SNP projects included 576 DNA samples processed for UDP, and 3216 samples for NISC. Compared to last year of 240 for UPD and 1584 for NISC, this represents a 2- to 3-fold increase. Since NISC intends to genotype all the samples received for WES and targeted sequencing, the sample numbers are likely to increase in the future. New users of SNP genotyping services included investigators from SBRB, where a relatively larger size project for genotyping/methylation analysis has just begun. While genotyping was the main activity of the Core, requests for human (23) and mouse (3) BAC clones were processed by the Core. Requests for aliquots of DNA from three panels were also processed this year. We will continue to provide access to BAC libraries and DNA panels for NHGRI investigators. Every 3-4 years, I visit Branch meetings and presented resources and services offered by the Core, and this activity was performed this year. Our presentations were productive and helped initiate utilization of the Cores technologies for novel applications. Each year the Genomics Core continues to adapt to the changing requirements of NHGRI researchers. The Core 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. Core helps researchers to take advantage of learning and using these tools as well, and also helps with issues in handling SNP data, collection, evaluation, processing for porting the dataset and such. The Core has provided significant data analysis support for 11 different projects this year, covering Copy Number Variation, Linkage Disequilibrium Analysis, Population Stratification, and association studies. This service is of huge value to investigators with small projects, as most users of the Core are, who do not have the required tools or expertize for analysis of large data sets. One of the ongoing projects is analysis for deletions, duplications, loss of heterozygosity, and regions portraying signs of chromosomal mosaicism in DNA samples from patients with Fanconi anemia. This effort has been very rewarding in understanding the disease process. The Core also is analyzing data for studies on head and neck cancer, genomic changes in bone marrow and peripheral blood DNA samples, changes associated with processing of iPS, Acute myeloid leukemia, Smith-Magenis syndrome, Febrile Infection-Related Epilepsy Syndrome, Population Stratification and Variant frequency ranking in the African-American Ancestral SNP analysis, eye diseases Coloboma and Leber Congenital Amaurosis (LCA).
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