Improve Research Reproducibility A Bio-protocol resource
Concise Method
tooltip

2.4. HRD Score Calculation

YH Yi-Wen Hsiao
TL Tzu-Pin Lu
ask Ask a question
Favorite

The copy number segmentation file with annotations (TCGA_mastercalls.abs_segtabs.fixed.txt) and the purity/ploidy file (TCGA_mastercalls.abs_tables_JSedit.fixed.txt) that was generated by ABSOLUTE software were downloaded from the above-mentioned Pan-Cancer Atlas portal. These two files were then compiled to generate the input format supported by the scarHRD R package [36] for the calculation of the counts of each HRD component (HRD-loss of heterozygosity (HRD-LOH), HRD-large-scale state transitions (HRD-LST), and HRD-telomeric allelic imbalance (HRD-TAI)) and then summarized the total HRD score. Here, we evaluated the global and geneset-specific HRD scores based on previously reported genesets across cancers.

Copyright and License information:  ©2021 by the authors.
Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).

Do you have any questions about this protocol?

Post your question to gather feedback from the community. We will also invite the authors of this article to respond.

post Post a Question
0 Q&A