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Migrating the SNP Array-based Homologous Recombination Deficiency Measures to Next Generation Sequencing Data of Breast Cancer

Overview
Journal NPJ Breast Cancer
Date 2018 Jul 7
PMID 29978035
Citations 146
Authors
Zsofia Sztupinszki
Miklos Diossy
Marcin Krzystanek
Lilla Reiniger
Istvan Csabai
Francesco Favero
Nicolai J Birkbak
Aron C Eklund
Ali Syed
Zoltan Szallasi
Affiliations
Soon will be listed here.
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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