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, FY2023, 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, four investigators from other institutes (NCI, NHLBI and NIMH) also utilized the Cores services this year. Over the past four years, FY2020-FY2023, the number of DNA samples processed by the Core were 6,407, 7,556, 8,243 and 5,425 respectively. The Core generated 3.93 billion (B) genotypes in FY2023, compared to 3.25 B and 4.55 B in FY2021 and FY2022, respectively. Please note, in addition to STRPs, this number represents the total number of SNPs on a given array multiplied by 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 (FY2021 - FY2023), the number of samples the Core processed for NISC were 1,824, 2,688, and 2,112 respectively. 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. Samples run on SNP arrays (3,744 samples) represent about 69% of the total 5,425 DNA samples processed by the Core this year, which is a higher percentage than the last two years (55% and 61%). This reflects continued interest in the use of SNP genotyping technologies. The remaining 31% of samples were processed using ABI technology, primarily mouse DNA samples. The CRISPR mutagenesis technology is being extended to an increasing number of mouse mutagenesis projects. 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 any relevant open-source software, and helps with the handling, collection, evaluation, and processing of SNP and other data sets. 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. In addition, significant data analysis support is given for several studies. As an example, in an effort to molecularly diagnose a cohort of 352 OCA patients and compile a comprehensive catalog of OCA-causing variants, DNA samples collected from individuals diagnosed with oculocutaneous albinism type 1B were analyzed by genome-wide SNP array for chromosomal copy number variations. Three individuals were found to have deletions of TYR (Loftus et al., Haplotype-based analysis resolves missing heritability in oculocutaneous albinism type 1B. American Journal of Human Genetics 2023).