Resources

Data sets

Summary statistics from genetic association analyses conducted by our group are available from the GWAS Catalog and/or data.broadinstitute.org/lohlab, and individual-level derived data have been returned to data providers when possible. These data sets are summarized below; details are provided in each publication.

• Tang et al. 2026 Nat Genet: Anonymized WGS-based mosaic chromosomal alteration calls in UK Biobank; summary statistics for GWAS, burden, and allelic shift association tests of CN-LOH mutations in cis; WGS read-depth PCs and REF-bias estimates.
• Kamitaki et al. 2026b Nature: Viral DNA load GWAS summary statistics for UK Biobank and All of Us v8; individual-level viral load phenotypes for AoU participants.
• Kamitaki et al. 2026a Nature: Oral microbial abundance and composition GWAS summary statistics for SPARK (WGS1-5); individual-level quantifications of microbial abundances in SPARK saliva samples.
• Hujoel et al. 2026 Nature: Somatic repeat-expansion GWAS and PheWAS summary statistics for UK Biobank.
• Hujoel et al. 2024 Nat Genet: Coding CNV-phenotype association statistics for WES-derived CNV calls with 57 quantitative phenotypes in UK Biobank.
• Mukamel*, Handsaker* et al. 2023 Cell: VNTR-phenotype association statistics for WGS-imputed VNTRs with 668 phenotypes in UK Biobank.
• Hujoel et al. 2022 Cell: CNV-phenotype association statistics for SNP-array-derived CNVs with 56 quantitative phenotypes in UK Biobank.
• Mukamel*, Handsaker* et al. 2021 Science: Coding VNTR-phenotype association statistics for WES-imputed VNTRs with 787 phenotypes in UK Biobank.
• Barton et al. 2021 Nat Genet: Rare coding variant associations for WES-imputed variants with 54 quantitative traits in UK Biobank.
• Sherman et al. 2021 Nat Neurosci: Mosaic chromosomal alterations detected from SNP-array data for SSC and SPARK.
• Loh, Genovese, McCarroll 2020 Nature: Individual-level SNP-array-based mosaic chromosomal alteration calls in UK Biobank.
• Terao et al. 2020 Nature: Individual-level SNP-array-based mosaic chromosomal alteration calls in BioBank Japan.
• Loh et al. 2018 Nat Genet: GWAS summary statistics for 46 phenotypes in UK Biobank.

Software

• mCAs_WGS pipeline for calling mosaic chromosomal alterations from WGS data (Tang et al. 2026 Nat Genet).
• extractLongSTRs tool for efficiently extracting sequencing reads with high repeat content from WGS cram/bam files; other STR analysis pipelines used in Hujoel et al. 2026 Nature at https://github.com/mhujoel/STRs.
• HI-CNV software for calling CNVs from SNP-array genotyping probe intensity data using a haplotype-informed approach in large cohorts (Hujoel et al. 2022 Cell).
• Eagle software for estimating haplotype phase either using a phased reference panel or within a genotyped cohort (Loh et al. 2016b Nat Genet + Loh et al. 2016a Nat Genet).
• BOLT-LMM software for linear mixed model (LMM) association testing (Loh et al. 2015a Nat Genet + Loh et al. 2018 Nat Genet), heritability estimation (BOLT-REML; Loh et al. 2015b Nat Genet), and phenotype prediction.
• ALDER software for computing weighted linkage disequilibrium (LD) curves, which can be used to infer admixture parameters including dates, mixture proportions, and phylogeny (Loh, Lipson et al. 2013 Genetics).
• MixMapper software for analyzing allele frequency correlations among multiple populations simultaneously to build a tree (or “admixture graph”) of population relationships that incorporates the possibility of mixture (Lipson, Loh et al. 2013 Mol Biol Evol).