Somatic mosaicism is increasingly recognized as a fundamental feature of human biology, yet the detection of somatic mutations remains challenging. The Somatic Mosaicism across Human Tissues (SMaHT) Network conducted large-scale benchmarking experiments involving cell lines and donor tissues to evaluate sequencing tech...
A. Abyzov, Abhiram Natu, Adam Voshall et al.· Cell· 1 citation
Summary African genomes are marked by extensive complexity in the number and distribution of variants yet remain under-represented in genetic databases and the human reference genome. This gap in representation limits the broad application of genomic medicine. Sickle cell disease (SCD)—one of the most common monogenic...
Pamela D. Lurie, M. Mahmoud, Aparna Haldipur et al.· HGG advances· 0 citations
Long-read RNA sequencing has revealed extensive transcript diversity, but newly observed isoforms remain difficult to interpret beyond their classification as known or novel. Here, we present IsoAtlas, an interactive multispecies database for visual exploration and population-scale interpretation of transcript isoforms...
Xin-Chang Zheng, F. Sedlazeck· bioRxiv· 0 citations
The Genome in a Bottle (GIAB) Consortium’s HG002 v5.0q benchmark set is presented, a more comprehensive variant benchmark derived from a fully phased, highly curated, and accurate diploid assembly of HG002 to provide confident small- and structural-variant calls across previously inaccessible regions.
Nathan D. Olson, Nathan Dwarshuis, Nancy F. Hansen et al.· bioRxiv· 1 citation
Isocall, a scalable and deterministic computational method for jointly calling transcripts from multiple PacBio long-read RNA sequencing samples, converts aligned full-length non-concatemer reads into compact per-sample transcript profiles, merges these profiles across samples, and jointly identifies known and novel tr...
E. Dolzhenko, Megan D. Schertzer, Ryan Gossart et al.· bioRxiv· 1 citation
The first integrated analysis of the Somatic Mosaicism across Human Tissues (SMaHT) Network’s production resource is presented, profiling up to 20 tissues from 25 donors using short- and long-read, duplex, single-cell, transcriptomic, and epigenomic sequencing, alongside donor-specific near-telomere-to-telomere assembl...
F. Sedlazeck, Tim H. H. Coorens, Peter J. Park et al.· bioRxiv· 2 citations
This Primer outlines the computational foundations of long-read whole-genome analysis in human genomics, spanning read processing, mapping, de novo assembly, multi-class variant detection, haplotype phasing, repeat analysis and epigenetic profiling, and highlights key analytical trade-offs between mapping-based and ass...
Xin-Chang Zheng, P. Sanio, Rui-Bang Luo et al.· Nature Reviews Methods Prime...· 0 citations
An integrated wet-lab and computational platform designed to overcome barriers to population-scale long-read RNA sequencing, providing a scalable, community-ready framework for isoform-resolved transcriptomics in neurodegeneration, aging, and complex brain disease.
C. Kouam, Jackson Mingle, Pilar Álvarez Jerez et al.· bioRxiv· 0 citations
A telomere-to-telomere genome benchmark with near-perfect accuracy across 99.4% of the diploid HG002 genome is presented, expanding the reach of genomic medicine to the entire genome and enabling a new era of personalized genomics.
Nancy F. Hansen, Nathan Dwarshuis, Hyun Joo Ji et al.· Cell· 8 citations
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