The paper identifies somatic and germline genetic variations in brain tissue from children with epilepsy-associated developmental lesions, highlighting new candidate genes and structural variations.

Epilepsia · Jun 10, 2022Peer-reviewedGenetic & Genomic Medicine

Discovery of Clinically Relevant Fusions in Pediatric Cancer

Stephanie LaHaye, James Fitch, Kyle Voytovich, Adam Herman, Benjamin Kelly, Grant Lammi, Jeremy A. Arbesfeld, Saranga Wijeratne, Samuel J. Franklin, Kathleen M. Schieffer, Natalie Bir, Sean D McGrath, Anthony R. Miller, Amy N. Wetzel, Katherine E. Miller, , Peter White

The paper develops an ensemble fusion-calling pipeline to improve the detection of clinically relevant gene fusions in pediatric cancer, identifying 67 fusions with a 29.3% diagnostic yield.

BMC Genomics · Dec 1, 2021Peer-reviewedGenomics

Samovar: Single-sample mosaic SNV calling with linked reads

Charlotte A. Darby, James Fitch, Patrick Joseph Brennan, Benjamin Kelly, Natalie Bir, Vincent J. Magrini, Jeffrey Leonard, Catherine E. Cottrell, Julie M. Gastier, Richard K. Wilson, Elaine R. Mardis, Peter White, Ben Langmead, Michael C. Schatz

Samovar calls mosaic SNVs in single samples using linked-read data with accuracy comparable to trio or tumor/normal pair analyses.

iScience · May 29, 2019Peer-reviewedGenomics

The prognostic effects of somatic mutations in ER-positive breast cancer

Obi L. Griffith, Nicholas C. Spies, Meenakshi Anurag, Malachi Griffith, Jingqin Rosy Luo, Dongsheng Tu, Belinda Jane Yeo, Jason Kunisaki, Christopher A. Miller, Kilannin Krysiak, Jasreet Hundal, Benjamin J. Ainscough, Zachary L. Skidmore, Katie Marie Campbell, Runjun D. Kumar, , Matthew J. Ellis

The paper identifies somatic mutations with prognostic effects in ER+ breast cancer using genomic data from multiple cohorts.

Nature Communications · Aug 22, 2018Peer-reviewedGenomics