The phenotype-genotype reference map: Improving biobank data science through replication.

Lisa Bastarache; Sarah Delozier; Anita Pandit; Jing He; Adam Lewis; Aubrey C Annis; Jonathon LeFaive; Joshua C Denny; Robert J Carroll; Russ B Altman; Jacob J Hughey; Matthew Zawistowski; Josh F Peterson

doi:10.1016/j.ajhg.2023.07.012

PubMed · 37607538

The phenotype-genotype reference map: Improving biobank data science through replication.

Lisa Bastarache·Sarah Delozier·Anita Pandit·Jing He·Adam Lewis·Aubrey C Annis·Jonathon LeFaive·Joshua C Denny·Robert J Carroll·Russ B Altman·Jacob J Hughey·Matthew Zawistowski·Josh F Peterson

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Abstract

Population-scale biobanks linked to electronic health record data provide vast opportunities to extend our knowledge of human genetics and discover new phenotype-genotype associations. Given their dense phenotype data, biobanks can also facilitate replication studies on a phenome-wide scale. Here, we introduce the phenotype-genotype reference map (PGRM), a set of 5,879 genetic associations from 523 GWAS publications that can be used for high-throughput replication experiments. PGRM phenotypes are standardized as phecodes, ensuring interoperability between biobanks. We applied the PGRM to five ancestry-specific cohorts from four independent biobanks and found evidence of robust replications across a wide array of phenotypes. We show how the PGRM can be used to detect data corruption and to empirically assess parameters for phenome-wide studies. Finally, we use the PGRM to explore factors associated with replicability of GWAS results.

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Humans Biological Specimen Banks Data Science Phenomics Phenotype Genotype GWAS PheWAS biobanks data quality electronic health records phecodes phenotyping replication Journal Article Research Support, N.I.H., Extramural

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Lisa Bastarache, Sarah Delozier, Anita Pandit, Jing He, Adam Lewis, Aubrey C Annis, Jonathon LeFaive, Joshua C Denny, Robert J Carroll, Russ B Altman, Jacob J Hughey, Matthew Zawistowski, Josh F Peterson. 2023-08-21. The phenotype-genotype reference map: Improving biobank data science through replication.. https://doi.org/10.1016/j.ajhg.2023.07.012

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