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Demonstrating paths for unlocking the value of cloud genomics through cross cohort analysis.

ABSTRACT: Recently, large scale genomic projects such as All of Us and the UK Biobank have introduced a new research paradigm where data are stored centrally in cloud-based Trusted Research Environments (TREs). To characterize the advantages and drawbacks of different TRE attributes in facilitating cross-cohort analysis, we conduct a Genome-Wide Association Study of standard lipid measures using two approaches: meta-analysis and pooled analysis. Comparison of full summary data from both approaches with an external study shows strong correlation of known loci with lipid levels (R² ~ 83-97%). Importantly, 90 variants meet the significance threshold only in the meta-analysis and 64 variants are significant only in pooled analysis, with approximately 20% of variants in each of those groups being most prevalent in non-European, non-Asian ancestry individuals. These findings have important implications, as technical and policy choices lead to cross-cohort analyses generating similar, but not identical results, particularly for non-European ancestral populations.

SUBMITTER: Deflaux N

PROVIDER: S-EPMC10480504 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature

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Demonstrating paths for unlocking the value of cloud genomics through cross cohort analysis.

Deflaux Nicole N Selvaraj Margaret Sunitha MS Condon Henry Robert HR Mayo Kelsey K Haidermota Sara S Basford Melissa A MA Lunt Chris C Philippakis Anthony A AA Roden Dan M DM Denny Joshua C JC Musick Anjene A Collins Rory R Allen Naomi N Effingham Mark M Glazer David D Natarajan Pradeep P Bick Alexander G AG

Nature communications 20230905 1

Recently, large scale genomic projects such as All of Us and the UK Biobank have introduced a new research paradigm where data are stored centrally in cloud-based Trusted Research Environments (TREs). To characterize the advantages and drawbacks of different TRE attributes in facilitating cross-cohort analysis, we conduct a Genome-Wide Association Study of standard lipid measures using two approaches: meta-analysis and pooled analysis. Comparison of full summary data from both approaches with an ...[more]

PMID: 37669985

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Demonstrating paths for unlocking the value of cloud genomics through cross cohort analysis.

Publications

Demonstrating paths for unlocking the value of cloud genomics through cross cohort analysis.

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