New genetic association datasets
With its latest release, the MSK-KP now includes the largest GWAS for osteoarthritis (OA) to date, from the Genetics of Osteoarthritis (GO) Consortium. Published by Boer et al., 2021, the study includes associations for 11 OA-related phenotypes, including OA in hip, knee, spine, finger, thumb, and hand, and having had joint replacement surgery. Associations were analyzed in main and sex-specific analyses, and a separate analysis generated associations for early-onset OA. Summary statistic files for these datasets are available from the Downloads page of the MSK-KP. The Boer et al. study included a list of predicted effector genes for OA, and we are working to make that list available in the MSK-KP.
Several other datasets for non-musculoskeletal associations have also been added to the MSK-KP:
- The MAGIC 2021 glycemic traits GWAS datasets add associations for fasting glucose, fasting insulin, two-hour glucose, and HbA1c (all adjusted for BMI). 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.
- Datasets from the latest Trans-Omics for Precision Medicine (TOPMed) study of sleep-disordered breathing (Cade et al., 2021) include associations for five different measures of apnea 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.
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.
Nature Reviews: Rheumatology review on the MSK-KP
A new review article in Nature Reviews: Rheumatology by Jennifer Westendorf et al. summarizes the current state of the MSK-KP and its future directions. Please give it a read, and consider whether you might have results to share in the MSK-KP!