Workshop: Beyond genetic associations: using the Association to Function Knowledge Portal to prioritize potential effector genes for complex diseases

Genome-wide association studies (GWAS) have now identified thousands of associated loci for complex diseases and related traits. But despite this success, in only a handful of cases so far have association data been translated to knowledge of causal variants, effector transcripts, biological networks, and potential therapeutic targets. Accelerating progress in this area requires 1) the large-scale integration of genetic association data with detailed, cell type-specific annotation of the epigenome, transcriptome, and proteome, and 2) open-access resources that make these integrated results easily interpretable for research scientists worldwide. 

In this workshop we will present one such resource, the Association to Function Knowledge Portal (A2FKP). Supported by NHGRI as a Genomic Community Resource, the A2FKP integrates high quality genetic and genomic datasets, bioinformatic method results, and expert-curated knowledge for multiple classes of disease, including metabolic, cardiovascular, immunological, pulmonary, musculoskeletal, and neurodegenerative disorders. The A2FKP is being developed in collaboration with the research communities in each of these disease areas. Epigenomic and functional results in the A2FKP are aggregated in collaboration with a sister resource, the Common Metabolic Diseases Genome Atlas (CMDGA). 

Attendees of this workshop will get an overview of the data underlying the A2FKP, will learn how to query the A2FKP both via the web interface and programmatically, and will practice using its interactive tools to form and test hypotheses about loci and genes of interest. Hands-on exercises will provide instruction in using the A2FKP to answer questions such as:

  • Do current genetic and genomic data support the involvement of my favorite gene in a particular disease or trait?
  • Which gene in a genetically associated locus is most likely to be causal for the associated trait?
  • What is the overall genetic architecture of a particular complex disease? 
  • For a variant of interest, what is the range of phenotypes with which it is associated? Does it lie within a region that has a potential tissue-specific regulatory role?
  • How can I programmatically access the results in the A2FKP?

Attendees are also welcome to bring specific questions from their own research.

Maria Costanzo, PhD

Creative Lead for the Knowledge Portal Network

Broad Institute of MIT and Harvard

Maria Costanzo, Ph.D., is the Creative Lead for the Knowledge Portal Network at the Broad Institute of MIT and Harvard. Costanzo earned her Ph.D. in molecular biology at Harvard University and holds a B.A. degree in microbiology from the University of Pennsylvania. Costanzo’s role on the Portal team is to spread awareness of the resources and to facilitate use of the Knowledge Portals, by writing clear documentation and participating in tool and interface development. Prior to joining the Broad Institute in 2015, Costanzo was a biocuration scientist with the Saccharomyces, Candida, and Aspergillus Genome Databases at Stanford University. She was also employed by Proteome, Inc. and Incyte Genomics, and performed basic research on the genetics and molecular biology of the model organism Saccharomyces cerevisiae (brewer’s/baker’s yeast) at Cornell University.

Noël Burtt

Director of Operations and Development of the Diabetes Research & Knowledge Portals

Medical and Population Genetics Program and Metabolism Program at the Broad Institute of MIT and Harvard

Noël Burtt is the director of operations and development of the Diabetes Research & Knowledge Portals in the Medical and Population Genetics Program and Metabolism Program at the Broad Institute of MIT and Harvard. Burtt received her B.S. from the University of New Hampshire in molecular biology and human genetics. Burtt’s work centers on the operational and organizational leadership of large-scale, international genetics consortia and public/private partnerships for human genetics studies, with a focus on type 2 diabetes and cardiometabolic diseases. Prior to her work at the Broad, Burtt joined the Whitehead Center for Genome Research in 1999 to help develop and scale technologies for genotyping and sequencing, tools that were used in some of the first genome-wide association studies (GWAS). Burtt has also managed two public-private partnerships with Novartis and Pfizer as part of the effort to use human genetics to develop better therapies for diabetes. She has contributed to more than 126 publications of genomic studies of diabetes, obesity, cancer, cardiovascular disease, and other disorders.

Jason Flannick

Assistant Professor of Pediatrics

Harvard Medical School and the Division of Genetics and Genomics at Boston Children’s Hospital

Jason Flannick is an assistant professor of pediatrics at Harvard Medical School and the Division of Genetics and Genomics at Boston Children’s Hospital, and an associate member of the Broad Institute of MIT and Harvard. Flannick received his B.A. in computer science, mathematics, and physics from Cornell University. Flannick later earned his M.S. and Ph.D. in computer science from Stanford University, writing his thesis on approaches to compare protein interaction networks across different species. He spent four years as a postdoctoral fellow in statistical and computational genetics in David Altshuler’s laboratory at Massachusetts General Hospital and the Broad Institute. The Flannick Lab develops computational approaches to use human genetic and broader genomic data to understand or better treat human diseases, with a current focus on diabetes.

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Workshop: Beyond genetic associations: using the Association to Function Knowledge Portal to prioritize potential effector genes for complex diseases
11/16/2022 at 3:00 PM (EST)  |  Recorded On: 11/17/2022
11/16/2022 at 3:00 PM (EST)  |  Recorded On: 11/17/2022
A2FKP Quick Reference Guide
Open to download resource.
Open to download resource.