Knowledge Portal Network Fall 2021 Newsletter

Contents

• New genetic association datasets in the Knowledge Portals
• DGA is now CMDGA
• Target gene predictions now available in GEM
• HuGeAMP platform will be extended to more disease areas
• AMP-CMD^® news
• Successful ancillary session held at ASHG 2021
• New informational resources
• Upcoming webinars

New genetic association datasets in the Knowledge Portals

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 (MSK-KP):

• MAGIC 2021 glycemic traits GWAS: associations for 4 glycemic traits in single-ancestry datasets for African Americans, sub-Saharan Africans, East Asians, Europeans, Hispanics, and South Asians, from Chen, Spracklen, Marenne, Varshney, Corbin et al., 2021.
• TOPMed sleep apnea whole genome sequence analysis: associations for 5 sleep-disordered breathing phenotypes from Cade et al., 2021, as an overall analysis plus stratified subsets for females, males, European ancestry individuals, European ancestry females, and European ancestry males. The full summary statistics are also available for download.
• Genetics of Osteoarthritis (GO) Consortium GWAS: associations for 11 osteoarthritis-related phenotypes, as published by Boer et al., 2021, in main and sex-specific analyses and an analysis of early-onset osteoarthritis. The full summary statistics are available for download from the MSK-KP, and the list of predicted osteoarthritis effector genes from this study will also be represented in the MSK-KP in the future.

DGA is now CMDGA

In keeping with the evolution of the Accelerating Medicines Partnership^® Type 2 Diabetes into AMP^® Common Metabolic Diseases, the Diabetes Epigenome Atlas has now become the Common Metabolic Diseases Genome Atlas (CMDGA; cmdga.org). It's much more than just a name change: CMDGA now incorporates epigenomic datasets relevant to many diseases beyond diabetes (see a list of recently added datasets). Several new data types have been added to CMDGA, including single cell embeddings, gene perturbations, statistical models, and pipelines. New tools are also available for exploring the data, including a Single Cell Browser and a Gene Expression Browser with dot plot and heat map views.

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. 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.

HuGeAMP platform will be extended to more disease areas

Our team at the Broad Institute has received funding from the National Human Genome Research Institute (NHGRI) to create an Association to Function Knowledge Portal (A2FKP). This project will build upon the work we've done to create and refine the CMDKP and its disease-specific sub-portals. In the A2FKP project, we will work with additional disease research communities to aggregate and analyze information that will help researchers mine insights from genetic and genomic information across many new disease areas.

AMP-CMD^® news

Did you know that the funding for AMP-CMD includes $500,000 annually for an Opportunity Pool (OP) to support research aligned with the consortium's goals? This funding opportunity is open to applicants both within and outside of the AMP-CMD consortium, and researchers who receive OP support become members of AMP-CMD. Review of proposals for years 1 and 2 of the award is now in progress, and the call for applications for the next round of funding will go out in early 2022. Watch the CMDKP home page for announcements!

Successful ancillary session held at ASHG 2021

The Knowledge Portal Network organized a well-attended ancillary session at the 2021 American Society of Human Genetics meeting: "Genetic, epigenomic, and functional approaches to identifying effector genes for complex diseases". The talks, from Drs. Anna Gloyn, Brent Richards, Krishna Aragam, and Jason Flannick, described a variety of strategies for synthesizing genetic and genomic data to predict and verify the genes that are causal for complex diseases. If you missed it, you can catch the recording on YouTube!

New informational resources

• A new publication in Nature Reviews Rheumatology (Westendorf JJ et al., 2021) describes the current state of the Musculoskeletal Knowledge Portal
• Webinar video (Sept. 23): Introducing the Common Metabolic Diseases Genome Atlas
• Webinar video (Oct. 28): Insights from the CARDIoGRAMplusC4D Consortium
• ASHG ancillary session: Genetic, epigenomic, and functional approaches to identifying effector genes for complex diseases

Upcoming webinars

• December 9, 2021: How to build your own Research Portal using tools available at the Knowledge Portal Network
• February 10, 2022: topic TBD
• April 14, 2022: topic TBD

Stay in touch!

Contact us with questions or suggestions; sign up for our mailing list; follow us on Twitter; join our LinkedIn group; or watch our videos on our HuGeAMP Knowledge Portals YouTube channel.