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Updated: Feb 8, 2026

Recombineering Homologous Recombination Constructs in Drosophila
Published on: July 13, 2013
Migrating the SNP array-based homologous recombination deficiency measures to next generation sequencing data of
Zsofia Sztupinszki1, Miklos Diossy1, Marcin Krzystanek1
11Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet 208, Lyngby, 2800 Denmark.
Abstract:
The first genomic scar-based homologous recombination deficiency (HRD) measures were produced using SNP arrays. As array-based technology has been largely replaced by next generation sequencing approaches, it has become important to develop algorithms that derive the same type of genomic scar scores from next generation sequencing (whole exome "WXS", whole genome "WGS") data. In order to perform this analysis, we introduce here the scarHRD R package and show that using this method the SNP array-based and next generation sequencing-based derivation of HRD scores show good correlation (Pearson correlation between 0.73 and 0.87 depending on the actual HRD measure) and that the NGS-based HRD scores distinguish similarly well between BRCA mutant and BRCA wild-type cases in a cohort of triple-negative breast cancer patients of the TCGA data set.
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