NHGRI/DIR Genomics Core

National Human Genome Research Institute

Investigators

Linked publications, trials & patents

Abstract

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 in zebrafish, and later by CRISPR/Cas mutagenesis approach. 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 13 investigators representing seven branches used the Core genotyping services. Two investigators from other institutes (NHLBI and NIMH), also utilized the Cores services this year. Human SNP genotyping was carried out on different BeadArray types using Illumina technology and the Core generated 3.25 billion genotypes in FY2021. 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 accommodate some large SNP projects, and in FY2021 there were four such projects: Shaw lab (864 samples), Rotimi lab (576), Chandra lab (550), and NISC (1,824). NISC also submitted 1,920 samples in FY2020, and 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. Samples run on SNP and methylation arrays (4,168 samples) represent about 55% of the total 7,556 DNA samples processed by the Core this year, which is higher than last year (47%). The remaining 45% of samples were processed using ABI technology. Over the years, the ABI technology was used for processing a large number of PCR fragments for zebrafish mutagenesis projects generated by the CRISPR technology, and the number of samples processed in FY2021 was 768. The CRISPR mutagenesis technology is now being extended to an increasing number of mouse mutagenesis projects, and the genotyping of the founder mice are performed at the Genomics Core. This year, the number of mouse DNA samples processed by the Core was 2,299. 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, eye diseases coloboma and Leber Congenital Amaurosis (LCA), ADHD, Congenital Heart Disease, Holoprosencephaly, kidney disease, Turner syndrome, Oculocutaneous albinism, breast and colorectal cancers, 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. The Core has recently acquired a QuantStudio Real-Time PCR system that will enable the genotyping of a smaller number of SNPs in a large number of samples, a service that was previously unavailable in the Core.