New genetic association datasets
With our October release we added genetic associations for multiple phenotypes, spanning diverse ancestries, to the Common Metabolic Diseases Knowledge Portal, its disease-specific component portals, and the Musculoskeletal Knowledge Portal.
The MAGIC 2021 glycemic traits GWAS datasets add associations for fasting glucose, fasting insulin, two-hour glucose, and HbA1c (all adjusted for BMI) to the portals. These results, from the Meta-Analyses of Glucose and Insulin-related traits Consortium (MAGIC), were recently published by Chen, Spracklen, Marenne, Varshney, Corbin, et al. Results are integrated into the portals in five single-ancestry datasets, for African Americans, sub-Saharan Africans, East Asians, Europeans, Hispanics, and South Asians.
This release also includes several datasets from the latest Trans-Omics for Precision Medicine (TOPMed) study of sleep-disordered breathing (Cade et al., 2021). Associations for five different measures of apnea are available in an overall analysis, TOPMed Sleep Apnea WGS, plus stratified subsets for females, males, European ancestry individuals, European ancestry females, and European ancestry males. Summary statistic files for these datasets are available from the Downloads pages of the CMDKP and the SDKP.
The largest GWAS for osteoarthritis to date, from the Genetics of Osteoarthritis (GO) Consortium, is now included in the Musculoskeletal Knowledge Portal. Published by Boer et al., 2021, the study includes associations for 11 osteoarthritis-related phenotypes in main and sex-specific analyses and an analysis of early-onset osteoarthritis. Summary statistic files for these datasets are available from the Downloads page of the MSK-KP.
Target gene predictions now available in GEM
GEM, the Genomic Region Miner tool available on Region pages of the Knowledge Portals, aligns genetic associations with epigenomic annotations to help researchers understand the regulatory potential of specific regions of the genome. Epigenomic datasets are first incorporated into the Common Metabolic Diseases Genome Atlas (CMDGA; cmdga.org) and then transferred to the CMDKP, where they are analyzed for tissue-specific enrichment of genetic associations and then displayed in GEM. A new type of epigenomic annotation is now available in GEM: target gene predictions, which make connections between regulatory regions and their target genes. The predictions, listed here in CMDGA, include those made using the ABC (Fulco, Nasser, et al. 2019); CHiCAGO (Miguel-Escalada et al. 2019), and Cicero (Chiou, Zeng, et al. 2021) methods. To see an example of their representation in GEM, go to the PCSK9 Region page and select "Liver" tissue in the GEM "Add tissue loop track" menu.
New information available on Gene pages
To provide more insight into the functions and biological roles of gene products, Gene pages of the Portals (see an example) now include Gene Ontology and pathway annotations, obtained from MyGene.info. The annotations are accessible via tabs in the Functional associations section at the top of the page.
The Gene page now also includes the HuGE (human genetic evidence) score for a gene, calculated with the experimental Human Genetic Evidence Calculator. The score is meant to quantify the support from available genetic evidence for the involvement of a gene product in a trait or disease. The HuGE score for the most significantly associated phenotype in the region is shown by default, and the phenotype may be changed to see other scores. Click the "View evidence in HuGE calculator" link to navigate to the stand-alone interface, where you can modify other parameters.