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
Somatic mosaicism is widespread in human biology and disease, yet robust benchmarks are scarce. The Somatic Mosaicism across Human Tissues (SMaHT) Consortium mixed six HapMap cell lines to create artificial somatic variants spanning 0.25%-16.5% variant allele fractions. We developed a technology-agnostic method that bu...
Nahyun Kong, Zi-Tian Tang, Andrew Ruttenberg et al.· Cell Genomics· 1 citation
This work establishes a framework and best practices for reliably detecting low-VAF mutations in non-cancer tissues and provides a valuable resource for the community.
Y.-J. Ha, Dominika Maziec, J. Markowski et al.· Cell Genomics· 2 citations
Transposable elements are a major source of gene-regulatory functions. Yet this contribution is understood largely from ancient insertions already fixed in the genome: the successes, seen long after the fact. The polymorphic phase before fixation or loss remains poorly resolved because such alleles could be scored only...
Juan Jiang, X. Zhuo, Rong-Han Li et al.· bioRxiv· 0 citations
The human pangenome captures genetic diversity beyond a single linear reference, yet conventional DNA methylome maps largely assume that the underlying CpG substrate is fixed. Here we present a first draft of the human panepigenome on DNA methylation, generated from 440 haplotype-resolved long-read methylomes spanning...
Zheng Dong, Juan F. Macias-Velasco, X. Zhuo et al.· bioRxiv· 0 citations
Toxicants in the environment can significantly impact physiology. Environmental chemical exposures during early developmental stages disturb normal embryonic development and programming, and dramatically impact long-term health as individuals age. Female and male animals show distinct phenotypes when responding to a gi...
The Vertebrate Regulatory MOdule Detector (VRMOD) provides a universal coordinate reference system for regulatory sequences across 309 vertebrate genomes and enables genome-wide annotation of non-coding regulatory elements in any vertebrate species using genomic sequence alone.
Tássia Mangetti Gonçalves, Casey L. Stewart, Samantha D. Baxley et al.· NAR Genomics and Bioinformat...· 0 citations
The Human Pangenome Reference Consortium’s (HPRC) Release 2 (HPRC2) is presented, an openly available, second phase pangenome that is an approximately fivefold expansion in genome number over HPRC Release 1 (HPRC1) and measurable improvement in genome completeness, contiguity, and accuracy.
Julian K. Lucas, Prajna Hebbar, Wen-Wei Liao et al.· bioRxiv· 6 citations
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