Adam C. English

The paper analyzes genetic variation, ancestry, and DNA methylation in Hispanic/Latino participants using long-read sequencing, identifying novel variants and phenotype associations.

SniffCell assigns somatic variants to cell types using DNA methylation from bulk long-read sequencing, revealing cell-type-specific mutations in human tissues.

T2T-HG002v1.1, a complete diploid HG002 assembly lacking detectable errors over 99.4% of its length, enables genome-based benchmarking of assemblies, sequencing reads, and phased variant calls.

This paper presents near-complete, haplotype-resolved assemblies of a pancreatic cancer genome and normal tissue, identifying extensive somatic variants and epigenetic changes in previously excluded regions.

The paper introduces a computational model to quantify tandem repeat instability using long-read sequencing data and applies it to identify unstable alleles in 256 HPRC cell lines.

TBAS enables cost-effective long-read sequencing of rare-disease trios with high variant detection accuracy and a 77% potential solve rate.

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.

The paper benchmarks somatic structural variant detection at ultra-low allele fractions using synthetic data and evaluates 12 pipelines, finding long-read sequencing provides higher accuracy than short-read methods.

This paper introduces a method called kanpig for accurately genotyping structural variants using long-read alignment pileups, achieving higher concordance than existing tools.

The paper introduces a new TR catalog, TRExplorer v1.0, containing 4.86 million loci, designed for both short-read and long-read analyses and includes variation clusters identified using long-read HiFi data.

DRAGEN provides fast and accurate genome analysis across 3,202 genomes, outperforming existing methods in variant detection speed and accuracy for various types including SNV, indel, STR, SV, and CNV.

The paper benchmarks small and large variants in tandem repeats across 86 samples, creating a benchmark dataset and comparison method for TR variant calling.

The paper introduces TRGT, a tool for tandem repeat genotyping, and a database of 937,122 TRs across 100 genomes, achieving high concordance and detecting repeat expansions, methylation, and mosaicism.

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.

Truvari improves structural variant comparison by preserving allelic diversity, reducing allele frequency inflation compared to other methods.

The paper introduces a structural variant calling pipeline called BioGraph, which achieves higher sensitivity for detecting SVs compared to existing pipelines, though with lower precision.

Genome in a Bottle benchmark of 12745 sequence-resolved insertions and deletions of 50 bp or more, integrating 19 calling methods, scores false negatives and false positives alike.

The paper defines functional equivalence standards for genome sequencing pipelines to enable harmonized variant calling across diverse datasets with minimal batch effects.

The paper manually curates gene models in the Asian citrus psyllid genome to improve annotation for HLB control research.