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

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

Research output: Contribution to journalArticle

6 Citations (Scopus)

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
Journalnpj Breast Cancer
Volume4
Issue number1
DOIs
Publication statusPublished - Dec 1 2018

ASJC Scopus subject areas

  • Oncology
  • Radiology Nuclear Medicine and imaging
  • Pharmacology (medical)

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    Sztupinszki, Z., Diossy, M., Krzystanek, M., Reiniger, L., Csabai, I., Favero, F., Birkbak, N. J., Eklund, A. C., Syed, A., & Szallasi, Z. (2018). Migrating the SNP array-based homologous recombination deficiency measures to next generation sequencing data of breast cancer. npj Breast Cancer, 4(1), [16]. https://doi.org/10.1038/s41523-018-0066-6