Mark Fleharty

A complete diploid human genome benchmark for personalized genomics

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.

Whole-Genome Sequencing is a Viable Replacement for Chromosomal Microarray and Fragile X PCR Testing

This study shows that whole-genome sequencing can replace chromosomal microarray and Fragile X testing with higher accuracy and broader coverage for genetic disorders.

Neptune: An environment for the delivery of genomic medicine

Neptune delivers structured genomic data to EHR systems through customizable reports and variant reanalysis, supporting over 15,000 clinical reports.

Best Practices for Benchmarking Germline Small Variant Calls in Human Genomes

The paper develops standardized tools and best practices for benchmarking germline small variant calls in human genomes using truth sets and performance metrics.

New synthetic-diploid benchmark for accurate variant calling evaluation

The paper introduces a new synthetic-diploid benchmark for variant calling accuracy, derived from de novo PacBio assemblies of homozygous human cell lines to reduce bias in error rate estimation.

Characterization and remediation of sample index swaps by non-redundant dual indexing on massively parallel sequencing platforms

The paper characterizes index swapping on Illumina sequencers and proposes dual indexing to mitigate its effects, showing varying swap rates across methods and sequencers.

Landscape of X chromosome inactivation across human tissues

This paper systematically surveys X chromosome inactivation across human tissues using transcriptomic and genomic data, finding that XCI is generally uniform but shows heterogeneity and identifies new escape genes with sex-biased expression.