Sean R. McGee

Benchmarking long-read variant sensitivity across ONT and PacBio platforms using known clinically reported variants in a cohort of critically ill newborns

Short-Read Sequencing Benchmarking with Donor-Specific Assemblies

This study benchmarks nine short-read sequencing chemistries across seven sequencers using donor-specific assemblies to measure sequencing errors against sample-matched references, revealing platform-specific error profiles and highlighting the importance of donor-specific references for unbiased comparison.

MitoScope: a comprehensive mitochondrial genome analysis workflow for long-read sequencing data

MitoScope is a long-read sequencing workflow for mitochondrial genome analysis that improves sensitivity and precision in variant detection and NUMT profiling.

Donor-specific assemblies enhance somatic structural variant detection in complex genomic regions

This study benchmarks donor-specific assemblies for improved detection of somatic structural variants in a melanoma cell line, finding they identify more variants, especially in repeat-rich regions.

The Platinum Pedigree: A long-read benchmark for genetic variants

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.

A familial, telomere-to-telomere reference for human de novo mutation and recombination from a four-generation pedigree

The paper uses a four-generation family to systematically assess de novo mutations and recombination, finding high mutation rates and paternal bias, along with a detailed recombination map.

Frequency of pharmacogenomic variation and medication exposures among All of Us Participants

The paper assesses pharmacogenomic variation and medication exposures in a diverse cohort using whole genome sequencing and EHR data, finding high prevalence of actionable variants and previously unreported alleles.

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.