Lee Lichtenstein

Multi-omics in the All Of Us Research Program expands mapping genetic mechanisms in health and disease

The paper reports on the All of Us multi-omics cohort, identifying 182,246 QTLs and demonstrating rare variant effects across proteomic and transcriptomic data.

A 515,579-Genome Reference Panel Improves Rare-Variant Imputation Across Multiple Underrepresented Populations

The paper presents a large reference panel of 515,579 genomes to improve rare-variant imputation across underrepresented populations, enhancing accuracy for variants with frequencies as low as 0.002%.

Systematic common and rare variant association testing in 392,030 whole genomes in All of Us

The paper performs large-scale GWAS and RVAS on 392,030 whole genomes from All of Us, identifying 49,863 associations and 193 novel pLoF gene-phenotype links through meta-analysis with UK Biobank.

Population-scale Long-read Sequencing in the All of Us Research Program

The paper analyzes long-read sequencing data from the All of Us Research Program to identify structural variants and their associations with diseases in a large cohort of Black or African American participants.

A common flanking variant is associated with enhanced meiotic stability of the FGF14-SCA27B locus

The paper identifies a common flanking variant linked to increased meiotic stability at the FGF14-SCA27B repeat locus.

The frequency of pathogenic variation in the All of Us cohort reveals ancestry-driven disparities

The paper analyzes pathogenic variant frequencies in the All of Us cohort by ancestry, revealing disparities and potential biases in genomic data.

Calling Somatic SNVs and Indels with Mutect2

Mutect2 calls somatic SNVs and indels via local haplotype assembly, Bayesian genotyping and F-score-optimised filtering, with roughly one false call per 5 Mb in exome replicate-versus-replicate tests.

Somatic Truth Data from Cell Lineage

The paper introduces a benchmark dataset of validated somatic mutations derived from cell lineage, providing a large collection of true somatic variation for use in mutation discovery pipelines.