NHGRI/DIR Genomics Core

National Human Genome Research Institute

Investigators

Linked publications, trials & patents

Abstract

Both Illumina and ABI technologies are widely used by many investigators. This year, FY2022, in addition to two programs (NISC and UDP), a total of eight NHGRI investigators, representing seven branches/offices, used the Core genotyping services. Outside of NHGRI, three investigators from other institutes (NHLBI, NIAID and NIDCR) also utilized the Cores services this year. Over the past four years, FY2019-FY2022, the number of DNA samples processed by the Core were 13,262 and 6,407, 7556 and 8243 respectively. The Core generated 4.55 billion (B) genotypes in FY2022, higher than the 3.25B in FY2021. Please note, in addition to STRPs, this number represents the total number of SNPs on a given array times the number of samples for which that array was run (e.g., a one million SNP array run on 10 samples represents 10 million genotypes) and data was tracked. The genotyping data is used for studies related to Diamond-Blackfan anemia, Fanconi anemia, cancer, inherited bone marrow failure syndromes, Smith-Magenis syndrome, acute myeloid leukemia, ADHD, congenital heart disease, kidney disease, oculocutaneous albinism, and genochondromatosis, etc. The data are 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, the Core has large SNP-based projects. Over the last three years (FY2020-FY2022), the number of samples the Core processed for NISC were 1,920, 1824 and 2,688. The genotyping samples processed for NISC belong to multiple investigators from other institutes, demonstrating that the Genomics Core serves a larger scientific community than just NHGRI. In FY2018, two large SNP genotyping projects consisting of 5,056 and 4,118 DNA samples were completed. In FY2022, single large projects included sample sizes of 529, 561, 1,570, and 1,920. We anticipate the Core will process several large projects of similar size in the coming year. Samples run on SNP arrays (5,032 samples) represent about 61% of the total 8,243 DNA samples processed by the Core this year, which is a higher percentage than the last two years (47% and 55%). The remaining 39% of samples were processed using ABI technology. This reflects an increase in the human DNA samples we receive for SNP genotyping, and a decrease in the number of zebrafish samples received in the recent years. 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, 3,137, 95 and 768) for the past ten years (FY2012-2021), and the number for FY2022 was 999. The fact that the efforts of investigators are now focused on characterization of these mutants, and the fact that some labs as well as the Zebrafish Core are now performing some of their own genotyping likely explains the decrease of recent years. Also, 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 also assists investigators with data analysis and access to software/tools, such as GoldenHelix, Nexus, and GenomeStudio. The Core helps researchers take advantage of learning and using these tools, and helps with the handling, collection, evaluation, and processing of SNP and other data sets. The Core has provided significant data analysis support over the past four years (FY2019-FY2022). In addition, the Core also helps with troubleshooting and problem solving issues investigators may have in handling their data and performing QC assessments. This service is of huge value to investigators with small projects, as are most users of the Core, who lack the required tools or expertise for the analysis of large data sets.