NHGRI/DIR Genomics Core

National Human Genome Research Institute

Investigators

Linked publications, trials & patents

Abstract

Genotyping services utilizing both Illumina and ABI technologies are used by investigators. This year, FY2025, in addition to two programs (NISC and UDP), four NHGRI investigators, representing four branches/offices, used the Core genotyping services. Outside of NHGRI, six investigators from other institutes (NCI, NIAID, NICHD, NHLBI, NIAMS, and NIMH) also utilized the Core’s services this year. Over the past three years, FY2023-FY2025, the number of DNA samples processed by the Core were 5,425, 5,941, and 3,569, respectively. The total number of genotypes generated during these three years were 3.93 billion (B), 3.40 B, and 1.15 B. 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. Over the years the genotyping data has been used for studies related to cancer, inherited bone marrow failure syndromes (Diamond-Blackfan anemia, Fanconi anemia, Dyskeratosis congenita), Smith-Magenis syndrome, acute myeloid leukemia, ADHD, congenital heart disease, kidney disease, oculocutaneous albinism, and genochondromatosis, among others. In the past year, the services were requested for projects that included, head and neck cancer, islet cell biology, mouse methylation, diabetes, and hematological disorders. The data are analyzed for identity by descent, copy number variation, deletion intervals, methylation status, parent-of-origin of deletions, detection and quantitation of chromosomal mosaic events, and to generate haplotypes for discovering variants from sequence data. In addition to many small projects, we do have some large SNP projects. Over the last three years (FY2023-FY2025), the number of samples the Core processed for NISC were 2,112, 3,120, and 2,544. The samples genotyped for NISC belong to multiple investigators from other institutes, indicating the Genomics Core serves a larger scientific community than just NHGRI. In. We anticipate the Core to process several more similar projects in the coming year. Samples run on SNP arrays (3,387 samples) represent about 95% of the total 3569 DNA samples processed by the Core this year, which is a higher percentage than the last two years (68% and 86%). The remaining 5% of samples (182) were processed using ABI and Taqman technology. This reflects the increase in human DNA samples we receive for SNP genotyping, and a decrease in the number of mouse/zebrafish samples we received in the recent years. 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 helps with the handling, collection, processing, evaluation, and analysis of SNP data generated by the Core and also for genotype data generated outside of the Core. In addition to SNP genotype/methylation data, the Core has contributed bioinformatics support for sequencing projects generated by Miseq, panel sequencing, and whole exome sequencing. The services are related to copy number variation analysis, 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, Diamond-Blackfan 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, Gaucher disease, differential methylation among long covid, congenital heart disease, oculocutaneous albinism, and breast and colorectal cancers. 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.