James Holt

This study tests hypotheses about ancient introgression and gene flow in Pacific salmonids, finding introgression between trout and salmon ancestors but not between trout lineages.

Portello improves variant calling accuracy in rare-disease whole genome sequencing by aligning de novo assembly contigs to a reference genome, reducing basecall errors and enabling better interpretation of complex loci.

SVTopo visualizes complex structural variants using high-accuracy long reads, providing clear figures to understand multi-breakpoint events in human genomes.

The paper creates a long-read benchmark for genetic variants using a large pedigree, improving variant calling performance and introducing new truth sets for tandem repeats and structural variants.

Sawfish improves long-read structural variant calling accuracy by modeling local haplotypes, outperforming existing tools in benchmark tests and joint-genotyping analyses.

StarPhase diplotypes 21 pharmacogenes using long-read sequencing with high accuracy, updating 26.2% of existing diplotypes and highlighting gaps in pharmacogenomic databases.

This work extends vcfdist to jointly benchmark SNPs, INDELs, and SVs, showing error reductions and improved accuracy over previous methods.

This study evaluates the diagnostic yield of long-read sequencing in pediatric sensorineural hearing loss, finding it detects structural variants missed by short-read sequencing.

The paper analyzes VUS rates in genetic testing and finds lower rates in exome/genome sequencing compared to multi-gene panels, suggesting improvements in variant reporting practices.

HiPhase jointly phases small and structural variants from HiFi sequencing, achieving improved phase block NG50 and gene phasing rates.

The paper introduces FMLRC2, a tool for polishing de novo nanopore assemblies, and demonstrates its effectiveness for bacterial and eukaryotic genomes.

This study uses machine learning to predict false positive variants in clinical genome sequencing, reducing the need for confirmatory Sanger testing by 78.22%.

This paper uses long-read genome sequencing to identify pathogenic variants in neurodevelopmental disorders, finding clinically relevant structural variants in two of six probands.

Genome sequencing for early-onset dementia identified genetic variants in 50% of patients, including pathogenic variants and moderate penetrance alleles, supporting an oligogenic model.

VarSight uses binary classification algorithms to prioritize clinically reported variants in rare disease patients, outperforming existing methods in identifying pathogenic variants.

This paper identifies pathogenic structural variants in rare disease patients using whole genome sequencing and reports their clinical relevance.

The paper develops a method to detect diploid-triploid mixoploidy using whole genome sequencing data and validates it with clinical cytogenetic testing.