David I. Benjamin

Himito: a Graph-based Toolkit for Mitochondrial Genome Analysis using Long Reads

Himito is a graph-based toolkit for analyzing mitochondrial genomes using long reads, achieving superior performance in assembly and variant calling and revealing age-related patterns in the All of Us dataset.

Exploring penetrance of clinically relevant variants in over 800,000 humans from the Genome Aggregation Database

The paper analyzes over 800,000 human genomes to assess penetrance of clinically relevant variants, finding that 95% of pLoF variants in severe diseases have explanations for lack of disease manifestation.

A genome-wide mutational constraint map quantified from variation in 76,156 human genomes

Rare-variant depletion in 1kb windows of 76,156 gnomAD genomes, versus feature-adjusted mutation expectations, marks regulatory elements and outperforms seven alternative scores at flagging functional non-coding variants.

Inferring compound heterozygosity from large-scale exome sequencing data

The paper develops a method to infer compound heterozygosity from exome sequencing data, achieving high accuracy in phasing rare variants for recessive disease diagnosis.

GATK-gCNV: A Rare Copy Number Variant Discovery Algorithm and Its Application to Exome Sequencing in the UK Biobank

GATK-gCNV detects rare copy number variants from exome sequencing data, achieving high recall in benchmarking and generating a reference catalog of rare coding CNVs in the UK Biobank.

Mitochondrial DNA variation across 56,434 individuals in gnomAD

The paper presents a pipeline to call mitochondrial DNA variants in gnomAD, reporting population frequencies for 10,850 unique mtDNA variants across 56,434 individuals.

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.