Migrating the SNP array-based homologous recombination deficiency measures to next generation sequencing data of breast cancer

Zsófia Sztupinszki, Miklos Diossy, Marcin Krzystanek, Lilla Reiniger, Istvan Csabai, Francesco Favero, Nicolai J. Birkbak, Aron C. Eklund, Ali Syed, Zoltan Szallasi*

*Corresponding author for this work

    Research output: Contribution to journalJournal articleResearchpeer-review

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    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.
    Original languageEnglish
    Article number16
    Journaln p j Breast Cancer
    Volume4
    Number of pages4
    ISSN2374-4677
    DOIs
    Publication statusPublished - 2018

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