2026-10-11T11:29:52Z https://api.figshare.com/v2/oai

oai:figshare.com:article/32248455 2026-09-21T22:57:32Z category_24310 category_24205 item_type_3 month_year_09_2026

Data release for "Markedly divergent performance of variant annotation methods for gene-level association testing" Matthew Aguirre (10028699) Flaviyan Jerome Irudayanathan (23587929) Kipper Fletez-Brant (23587931) Genomics Translational and applied bioinformatics Variant Classification Genome-wide association study Rare variant association testing Gene burden test <p dir="ltr">This is the data release for "Markedly divergent performance of variant annotation methods for gene-level association testing" (<a href="https://doi.org/10.1186/s12864-026-13379-2" target="_blank" rel="noreferrer">Irudayanathan and Aguirre, et. al., 2026</a>). This release consists of four files in <code>.parquet</code> format, which we provide to the research community so as to enable (1) reproducibility of our work and (2) further analysis of these data.</p><p dir="ltr">One file (<code>.variants.parquet</code>) contains information on variants and their annotations, scores, and labels as computed using the machine-learning tools considered in our study.</p><p dir="ltr">The remaining files contain summary statistics from gene association tests, which were computed using variant labels and gene annotations from the variant file. The columns of these files are largely consistent with the output format of <a href="https://rgcgithub.github.io/regenie/" target="_blank" rel="noreferrer">REGENIE</a> (cf. <a href="https://doi.org/10.1038/s41588-021-00870-7" target="_blank" rel="noreferrer">Mbatchou et. al. 2021</a>), which was used to perform all of our genotype-phenotype analysis. One file (<code>.sumstats.parquet</code>) contains results from our primary analysis of data from the UK Biobank study (cf. <a href="https://doi.org/10.1038/s41586-018-0579-z" target="_blank" rel="noreferrer">Bycroft et. al., 2018</a>). We also provide files containing results from two additional analyses: one, sensitivity analysis of minor allele frequency thresholds (<code>.sumstats.af.parquet</code>) for gene burden tests in UK Biobank, and the other a replication study (<code>.sumstats.aou.parquet</code>) using data from the All of Us cohort (cf. <a href="https://www.nejm.org/doi/full/10.1056/NEJMsr1809937" target="_blank" rel="noreferrer">AllofUs Program, 2019</a>).</p><p dir="ltr">Examples on the use of these files can be found on the <a href="https://github.com/Genentech/ml-burden" target="_blank" rel="noreferrer">github repository</a> accompanying our publication.</p> 2026-09-21T22:57:32Z Dataset Dataset 10.6084/m9.figshare.32248455.v1 https://figshare.com/articles/dataset/Data_release_for_Markedly_divergent_performance_of_variant_annotation_methods_for_gene-level_association_testing_/32248455 CC BY 4.0