Eleven (55%) of the 20 patients had detectable nonsynonymous somatic mutations and in total, 48 mutations were detected in the aneurysm samples. The mutations were highly enriched in cancer-related genes and 77% were predictably deleterious. A p.Tyr562Asp somatic mutation was detected in the ...
a-b, Total number of nonsynonymous mutations and neoantigen load were not significantly different between risk groups (two-sided Wilcoxon rank-sum test). c-d, Poor risk tumors were associated with a lower number of frameshift indels (compared to intermediate risk), and a higher copy number burd...
Bar chart of rate of deleterious mutations across gene sequenced. Genes sequenced are shown on the x-axis. The number of deleterious somatic nonsynonymous mutations observed in each gene/number of amino acids in each CDS in plotted. Full size image Sequencing data is confirmed by Sanger sequencing...
Evidence of selection was assessed using the ratio of nonsynonymous to synonymous substitution rates (dN/dS) in the somatic mutations called in each species. The dNdScv (v.0.0.1.0) R package38was used to estimate dN/dS ratios for missense and truncating substitutions in each species separately. ...
The TMB was defined as the sum of the total number of nonsynonymous single-nucleotide variants (SNVs) and fs mutations. Peptide sequence information was obtained from UniProt (https://www.uniprot.org/) [41]. HLA typing data for each patient was available at TCIA (https://tcia.at/ home)...
Table 3. Numbers of somatic mutations and neoantigens predicted or observed using different approaches and validated using T-cell assays: Direct proteomic analysis of cancer MHC ligands (DPMHC), Computational prediction based on expressed nonsynonymous coding SNVs (CPENCS), Computational prediction based...
Several recurrent mutations in BRAF, VCAN, ALDH1L1, and MUC5B were identified, and many novel but infrequent mutations in other genes were also found. The aggressive cohort had more mutational burdens than the non-aggressive group (P = 0.004). Nonsynonymous mutations of 13 genes (MUC5B,...
one can check if the ratio of nonsynonymous (Ka) to synonymous (Ks) mutations per site is greater than 1 [7]. Relatedly, Yeet al.[8] and Rysliket al.[9] showed that mutational clusters can be indicative of activating mutations and that finding such clusters is a way to reduce the dr...
Using deep, error-corrected, targeted DNA sequencing we assayed for somatic mutations in CH-driver genes in peripheral blood mononuclear cells isolated from de-identified blood samples collected from 14 astronauts who flew Shuttle missions between 1998–2001. We identified 34 nonsynonymous mutations of ...
The TMB was defined as the sum of the total number of nonsynonymous single-nucleotide variants (SNVs) and fs mutations. Peptide sequence information was obtained from UniProt (https://www.uniprot.org/) [41]. HLA typing data for each patient was available at TCIA (https://tcia.at/ home)...