William J. Salerno

This paper evaluates combining expression-based surrogate variables and genotype-based principal components in differential expression analysis, finding the combined approach improves replicability and biological recall in ALS datasets.

This study quantifies cancer risk and penetrance in CHEK2 heterozygotes using genomic data from two large biobanks, finding increased risks for several cancers and younger age of onset.

The paper compares the effectiveness of whole genome sequencing, whole exome sequencing with imputation, and array genotyping in detecting genetic associations across 100 complex traits in the UK Biobank, finding that WES+IMP provides similar signal yield to WGS with greater efficiency.

This paper presents the largest catalog of human protein-coding variation from 985,830 individuals, identifying rare variants and their functional implications for precision medicine.

The paper presents a comprehensive catalog of structural variants across 138,134 individuals, identifying novel variants and their associations with cardio-metabolic and hematologic traits.

xAtlas is a scalable variant caller for NGS data that provides faster and accurate SNV and indel detection compared to existing methods.

The paper genotypes and sequences 140,000 adults from the Mexico City Prospective Study, revealing ancestry diversity and developing imputation resources for genetic studies.

This study identifies 53 genetic loci associated with hearing loss, including 15 novel ones, using genome-wide and exome-sequencing data from multiple cohorts.

The paper examines genetic variation and natural selection at SARS-CoV-2 host genes in diverse populations and links selected variants to clinical phenotypes in COVID-19.

The paper identifies a rare variant that lowers ACE2 expression and reduces COVID-19 risk, and develops a genetic risk score predicting severe disease.

The paper identifies 51 known and 23 novel gene-disease associations using exome sequencing data from 200,000 UK Biobank participants, highlighting high-impact rare variants for 26 diseases and traits.

The paper describes exome sequencing of 200,643 UK Biobank participants, providing a rich resource of coding variants for genetic and drug discovery research.

SVCollector selects an optimal subset of individuals for long-read sequencing to maximize genetic diversity representation across subpopulations.

The paper defines an open-source, lossless read-mapping protocol for NGS data and demonstrates direct variant calling without base quality score recalibration.

The paper introduces spVCF, a compressed variant call format that reduces file size by over 10X with minimal information loss.

Multi-ethnic type 2 diabetes (T2D) meta-analysis of 228,499 cases and 1,178,783 controls finds 318 previously unreported loci, 804 expression-colocalized genes, and 13 SNP-by-T2D vascular-outcome interactions.

The paper catalogs structural variants across 19,652 genomes and identifies their associations with proteomic measurements and disease phenotypes.

Atlas-CNV identifies single-exon CNVs in targeted sequencing data with reduced false discovery rate using C-scores and ExonQC thresholds.

Exomes of 49,960 UK Biobank participants reveal 231,631 predicted loss-of-function variants (>10-fold more than imputed data); burden tests implicate PIEZO1, MEPE, and COL6A1 in disease traits.

The paper maps and characterizes structural variants in 17,795 human genomes, revealing their frequency, impact, and relationship to gene dosage and regulatory elements.

VCPA is a genomic variant calling pipeline and data management tool for Alzheimer’s Disease Sequencing Project, providing variant calling and job tracking for WGS/WES data on Amazon cloud.

Parliament2 combines multiple structural variant callers to improve accuracy and speed, offering a Docker-based solution for efficient variant calling.

GLnexus, a joint variant caller backed by an incrementally growable gVCF database, largely matched GATK on 50,000 exomes while keeping more rare indels and using 3.8–6.6-fold fewer core-hours.

SVCollector selects optimal samples for validating and long-read resequencing of structural variants to maximize discovery and validation accuracy.

The paper describes the quality control and integration of genotype calls from two pipelines for whole genome sequencing data in the Alzheimer’s Disease Sequencing Project, resulting in a high-quality consensus dataset.