The paper provides a uniformly processed compendium of alternative splicing profiles from pediatric cancer and non-diseased tissues, enabling large-scale analysis of splicing aberrations in pediatric cancers.

bioRxiv · Sep 21, 2026 · PreprintBioinformatics

A novel splice site variant in DEGS1 leads to aberrant splicing and loss of DEGS1 enzyme activity, a VUS resolved

Holly C. Beale, Victor Tse, J.Y. Lee, Jon Akutagawa, Yusuph Mavura, Brandon Saint-John, Allison R. Cheney, Dennis Mulligan, Guillermo Chacaltana, Martin E Gutierrez, Jessica Tenney, Joseph T.C. Shieh, Pierre‐Marie Martin, Tiffany Yip, Uğur Hodoğlugil, , Anne Michele Slavotinek

The paper identifies a pathogenic splice site variant in DEGS1 causing aberrant splicing and loss of enzyme activity in individuals with HLD18.

Human Genetics · May 6, 2026Peer-reviewedGenetic & Genomic Medicine

Comparative analysis of RNA expression in a single institution cohort of pediatric cancer patients

Yvonne A. Vasquez, Holly C. Beale, Lauren Sanders, A. Geoffrey Lyle, Ellen Towle Kephart, Katrina Learned, Drew Thompson, Jennifer Peralez, Amy Li, Min Huang, Kimberly A. Pyke‐Grimm, Sofie R. Salama, David H. Haussler, Isabel Bjork, L. Spunt Sheri, Olena M. Vaske

The paper evaluates the CARE pipeline for identifying druggable targets in pediatric cancers using RNA-Seq data from 33 patients, showing 94% of cases had clinically significant findings.

npj Precision Oncology · Mar 21, 2025Peer-reviewedGenetic & Genomic Medicine

A new SARS-CoV-2 lineage that shares mutations with known Variants of Concern is rejected by automated sequence repository quality control

Bryan P. Thornlow, Angie S. Hinrichs, Miten Jain, Namrita Dhillon, Scott La, Joshua D. Kapp, Ikenna Anigbogu, Molly Cassatt‐Johnstone, Jakob McBroome, Maximilian Haeussler, Yatish Turakhia, Terren R. Chang, Hugh E. Olsen, Jeremy R. Sanford, Michael D. Stone, , Russell B Corbett-Detig

The paper reports a SARS-CoV-2 lineage with mutations from known variants of concern that is rejected by sequence repositories due to a deletion, suggesting underestimation of its frequency.

bioRxiv · Apr 5, 2021 · PreprintGenomics

The case for using Mapped Exonic Non-Duplicate (MEND) read counts in RNA-Seq experiments: examples from pediatric cancer datasets

Holly C. Beale, Jacquelyn M. Roger, Matthew A. Cattle, Liam T. McKay, Drew Thompson, Katrina Learned, A. Geoffrey Lyle, Ellen Towle Kephart, Rob Currie, Du Linh Lam, Lauren Sanders, Jacob Pfeil, John Vivian, Isabel Bjork, Sofie R. Salama, , Olena M. Vaske

The paper evaluates the informativeness of reads in bulk RNA-Seq datasets and recommends using MEND reads for accurate gene expression quantification in pediatric cancer studies.

GigaScience · Mar 1, 2021Peer-reviewedGenomics

A Bayesian Framework for Detecting Gene Expression Outliers in Individual Samples

John Vivian, Jordan M. Eizenga, Holly C. Beale, Olena M. Vaske, Benedict Paten

This paper introduces a Bayesian framework to detect gene expression outliers in single samples by creating a consensus background distribution without requiring a manual comparison set.

JCO Clinical Cancer Informatics · Feb 25, 2020Peer-reviewedBioinformatics

Genomic profiling of childhood tumor patient-derived xenograft models to enable rational clinical trial design

Jo Lynne Rokita, Komal S. Rathi, Maria Cardenas, Kristen A. Upton, Joy C. Jayaseelan, Katherine L. Cross, Jacob Pfeil, Laura E. Egolf, Gregory P. Way, Alvin Farrel, Nathan M. Kendsersky, Khushbu Patel, Krutika Satish Gaonkar, Apexa Modi, Esther R. Berko, , John M. Maris

This paper genomically characterizes 261 pediatric cancer patient-derived xenograft models to guide rational clinical trial design and drug development.

Cell Reports · Nov 1, 2019Peer-reviewedGenomics