Examples of WGS in a sentence
Based on the TCGA WGS data, we estimated the respective sensitivity and specificity for SAVnet as roughly 46% and 42% and MiSplice as 87% and 81%.
Although this represents a more comprehensive analysis due to the joint analysis of WGS and WES, it is unclear how many of the non-codingsplice-site-creating mutations (nc-SCMs) are unique to this analysis when compared to their own publication (Jayasinghe et al.
If your laboratory does not have WGS capabilities and needs assistance sequencing isolates resulting from LFFM testing, contact the ORA Technical Leads for assistance; a LFFM WGS Track lab may be able to assist.
If there is a need to reduce the number of figures, I would suggest this be moved to supplement.Reviewer #2 (Remarks to the Author): Expertise in bioinformatics, transcriptomics and splicing Review comments:The authors use available WGS, WXS and RNAseq data to identify somatic mutations which potentially cause splicing alterations in cis.
In summary, we found 150 novel nc-SCMs from WGS and 178 novel nc-SCMs from WES, which are more than half of the ~600 events described in the paper.
Reviewer #2 (Remarks to the Author) Review comments: The authors use available WGS, WXS and RNAseq data to identify somatic mutations which potentially cause splicing alterations in cis.
If a laboratory is also participating in the LFFM WGS Track, it is expected that the sequencing will be prioritized and supported by the WGS Track.Other laboratories may utilize existing partnerships to accomplish sequencing.
The motivation to filter sites with less than 10 control samples is because one cancer type, DLBC, has only 7 samples with both WGS mutation calls and RNA-Seq data (see figure below).
In the revision, we have removed DLBC, and reduced the sample size from 790 to 783 for TCGA WGS data included in the study.
Overall, this manuscript shows the utility of integrating WGS and RNAseq data to stratify somatic mutations in non-coding regions and gives some insight how even non-coding mutations can be functionally relevant in disease by altering splicing patterns.