Figure 2 from Poor Prognosis among Radiation-Associated Bladder Cancer Is Defined by Clinicogenomic Features
Year: 2024
Type: other
Abstract: Mutational characterization of the CTRL and RT cohorts. BAM files corresponding to the FoundationOne sequencing assay were back converted to FASTQ format and aligned to GRCh38. A, The number of alterations per sample was calculated and plotted by variant type (insertions, SNVs, silent, intronic, missense, nonsense, and deletions). Pairwise comparisons between CTRL (gold), RT–short latency (dark blue), and RT–long latency (light blue) tumors were made using the Wilcoxon rank-sum test, with P values listed above their corresponding comparison. B, Histogram of VAF (alternate read count/total read depth) for CTRL (gold), RT–short latency (dark blue), and RT–long latency (light blue) tumors, variants are bin by a frequency of 0.01 (1%). Dashed line represents a VAF of 0.05 (5%). Inset boxplots represent alterations per sample either above or below the 5% VAF threshold and grouped by latency. Pairwise comparisons between CTRL (gold), RT–short latency (dark blue), and RT–long latency (light blue) tumors were made using the Wilcoxon rank-sum test, with P values listed above their corresponding comparison. Boxplots are represented by the IQR and midline at the median. Error bars equal the Q1/Q3 ± 1.5 × IQR. Oncoplots of recurrent mutations occurring above a frequency of 10% in the (C) CTRL and (D) RT cohorts. Only mutations with a VAF of ≥5% were included. E, Mutation enrichment was performed using the maftools package, and genes with an FDR >0.05 are indicated. Bars to the left of the dashed line represent CTRL vs. RT, with bars to the right of the dashed line indicating significant gene based on a 1 vs. other comparison. F, Comparison of KDM6A mutations between non-RT (TCGA and CTRL) and RT (RT and DFCI) cohorts. WT, wild type.
Authors: N. Ari Wijetunga, Kathryn H. Gessner, Krishna Kanchi, Jay A. Moore, Zoe Fleischmann, Dexter X. Jin, Garrett M. Frampton, Michael Sturdivant, Michael Repka, Shivani Sud, David L. Corcoran, Matthew D. Galsky, Matthew I. Milowsky, Sara E. Wobker, William Y. Kim, Tracy L. Rose, Jeffrey S. Damrauer
Language: English
Subfield: Surgery
Field: Medicine
Domain: Health Sciences
Open Access status: gold
OpenAlex ID: W4402243277