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 regions of interest. The Core adopted ABI technology to find indels generated initially by zinc finger nuclease (ZFN) technology, and later by CRISPR/Cas mutagenesis approach. The Core processed over the last five years 95,000 PCR fragments for zebrafish mutagenesis projects for multiple investigators and the Zebrafish Core. CRISPR/Cas technology is now used increasingly for targeted mutagenesis in mouse and, to some extent, in human cell lines. Currently, services include human and mouse SNP genotyping, mouse, zebrafish and human primer testing and (CRISPR/Cas) mutation screening, mouse speed congenics, human and mouse STRPs, MLPA (Multiplex ligation-dependent probe amplification) for deletions, and fragment analysis for a variety of other applications. Both Illumina and ABI technologies are widely used by a large number of NHGRI investigators. This year, in addition to two programs (NISC and UDP), a total of 14 investigators representing six branches used the Core genotyping services. Human SNP genotyping was carried out on different BeadArray types using Illumina technology and the Core generated 3.5 billion genotypes in FY2019. The genotyping data is used for studies related to Diamond-Blackfan anemia, Fanconi anemia, cancer, inherited bone marrow failure syndromes, Smith-Magenis syndrome, cardiovascular diseases, scleroderma, diabetes, kidney disease, Gaucher disease/Parkinson's disease, Congenital Heart Disease study, Turner syndrome, ADHD, eye diseases, deafness, and microsatellite instability, among others. The data was analyzed for identity by descent, copy number variation, deletion intervals, methylation status, parent-of-origin of deletions, mosaicism, 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 five years (FY2015-FY2019), the number of samples we processed for NISC were 4,032, 2,256, 2,712, 2,688, and 1,728. The genotyping samples processed for NISC belong to multiple investigators from other institutes, indicating the Genomics Core serves a larger scientific community than just NHGRI. In FY2018, two large SNP genotyping projects were completed: 5,056 DNA samples genotyped for cardiovascular disease studies from the Rotimi lab, and 4,118 DNA samples were processed for the scleroderma studies from the Kastner lab. A kidney disease project involving 768 DNA samples was also completed in FY2019. Samples run on SNP and methylation arrays (4,256 samples) represent about 32% of the total 13,262 DNA samples processed by the Core this year, which is slightly higher to that of last year (27%). The remaining 68% of samples were processed using ABI technology. The Genomics Core has processed a large number of zebrafish DNA samples (5,492, 14,619, 35,539, 28,986, 34,714, 20,198, 7,593, and 3,137) for the past eight years (FY2012-2019). Since the realization of the efficacy of CRISPR/Cas technology around 2012, there was a surge in the processing of zebrafish samples while a huge number of mutants were being generated. The fact that the efforts of investigators are focused now on characterization of these mutants, and that the Burgess lab and the Zebrafish Core are performing some of their own genotyping, probably explains the decrease in samples processed by the Genomics Core this year. However, The Zebrafish Core has initiated newer projects, and it is anticipated that the Genomics Core will receive more samples in the coming months. Also, the CRISPR technology is being extended to an increasing number of mouse mutagenesis projects, and the genotyping of the founder mice will be performed at the Genomics Core. The Core has been assisting investigators with data analysis and access to software/tools, such as GoldenHelix, Nexus, and GenomeStudio. The 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 been providing significant data analysis support over the years. The services are related to 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 iPSC, 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), ADHD, Congenital Heart Disease, Holoprosencephaly, diabetes, kidney disease, Turner syndrome, and Fanconi anemia. In addition to performing analysis, the core also helps with troubleshooting or problem solving any issues investigators may have in handling their data. 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.
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