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Floris P. Barthel

As seen in: Nature, Cell Press
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Articles

Accurate somatic small variant discovery for multiple sequencing technologies with DeepSomatic - Nature Biotechnology

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By Pi-Chuan Chang, Ayse G. Keskus, Asher Bryant, Yongmei Zhao, Giuseppe Narzisi, Irina Pushel, Tomi Pastinen, T. Rhyker Ranallo-Benavidez, Christine Brown, Nicolas Robine, Floris P. Barthel, Midhat S. Farooqi, Karen H Miga, Andrew Carroll, Mikhail Kolmogorov, Benedict Paten, Lisa A. Lansdon
| Nature Verified
Abstract Somatic variant detection is an integral part of cancer genomics analysis. While most methods have focused on short-read sequencing, long-read technologies offer potential advantages in repeat mapping and variant phasing. We present DeepSomatic, a deep-learning method for detecting somatic small nucleotide variations and insertions and deletions from both short-read and long-read data.
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Longitudinal molecular trajectories of diffuse glioma in adults

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By Floris P. Barthel, Kevin Johnson, Frederick S. Varn, Anzhela D. Moskalik
| Nature Verified
Abstract The evolutionary processes that drive universal therapeutic resistance in adult patients with diffuse glioma remain unclear1,2. Here we analysed temporally separated DNA-sequencing data and matched clinical annotation from 222 adult patients with glioma.
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The Tandem Duplicator Phenotype Is a Prevalent Genome-Wide Cancer Configuration Driven by Distinct Gene Mutations

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By Francesca Menghi, , Floris P. Barthel, Vinod Yadav
| Cell Press Verified
The tandem duplicator phenotype (TDP) is a genome-wide instability configuration primarily observed in breast, ovarian, and endometrial carcinomas. Here, we stratify TDP tumors by classifying their tandem duplications (TDs) into three span intervals, with modal values of 11 kb, 231 kb, and 1.7 Mb, respectively. TDPs with ∼11 kb TDs feature loss of TP53 and BRCA1. TDPs with ∼231 kb and ∼1.7 Mb TDs associate with CCNE1 pathway activation and CDK12 disruptions, respectively.
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