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Articles by Asher Bryant
Proof-of-concept study for the detection of somatic structural variant driver alterations using HiFi long-read sequencing in a pediatric leukemia cohort
Abstract Gene fusions are common primary drivers of pediatric leukemias and are the result of underlying structural variants (SVs). Current clinical workflows to detect such alterations rely on a multimodal approach, which often increases analysis time and overall cost of testing. In this study, we used long-read sequencing (lrSeq) as a proof-of-concept to determine whether clinically relevant (cr) SVs could be detected within a small (n = 17) pediatric leukemia cohort.
Accurate somatic small variant discovery for multiple sequencing technologies with DeepSomatic - Nature Biotechnology
Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair - Scientific Data
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Abstract The Genome in a Bottle Consortium (GIAB), hosted by the National Institute of Standards and Technology (NIST), is developing new matched tumor-normal samples, the first explicitly consented for public dissemination of genomic data and cell lines.
By Jennifer McDaniel, Vaidehi Patel, Nathan Olson, Hua-Jun He, Zhiyong He, Kristin Sikkink, Fritz J Sedlazeck, Harsha V. Doddapaneni, Shalini N. Jhangiani, Marie-Claude Gingras, Heer H. Mehta, Sairam Behera, Luis F. Paulin, Victor Weigman, Isai Salas-Gonzalez, Miten Jain, Giuseppe Narzisi, Catherine Reeves, Aaron M. Wenger, Ian McLaughlin, Benedict Paten, Jimin Park, Karen H Miga, Joshua Gardner, Gail Rosen, Rajiv C. McCoy, Francesco Brundu, Konrad Scheffler, Sean Truong, Severine Catreux, Lesley Hannah, Nika Iremadze, Mikhail Kolmogorov, Ayse G. Keskus, Asher Bryant, Christopher Mason, Justin P. Wagner, Andrew Liss, Alison Rojas, Mitch Sudkamp, Erfan Sayyari, Chunlin Xiao
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Nature
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Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing - Nature Biotechnology
Abstract For the detection of somatic structural variation (SV) in cancer genomes, long-read sequencing is advantageous over short-read sequencing with respect to mappability and variant phasing. However, most current long-read SV detection methods are not developed for the analysis of tumor genomes characterized by complex rearrangements and heterogeneity. Here, we present Severus, a breakpoint graph-based algorithm for somatic SV calling from long-read cancer sequencing.
Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads
Abstract Most current studies rely on short-read sequencing to detect somatic structural variation (SV) in cancer genomes. Long-read sequencing offers the advantage of better mappability and long-range phasing, which results in substantial improvements in germline SV detection. However, current long-read SV detection methods do not generalize well to the analysis of somatic SVs in tumor genomes with complex rearrangements, heterogeneity, and aneuploidy.
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