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

doi:10.1038/s41523-018-0066-6

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^*

^*Corresponding author for this work

18 Citations (Scopus)

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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 language	English
Article number	16
Journal	npj Breast Cancer
Volume	4
Issue number	1
Pages (from-to)	1-4
Number of pages	4
DOIs	https://doi.org/10.1038/s41523-018-0066-6
Publication status	Published - 2018

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Migrating the SNP array-based homologous recombination deficiency measures to next generation sequencing data of breast cancerFinal published version, 650 KBLicence: CC BY

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

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.",

author = "Zsofia Sztupinszki and Miklos Diossy and Marcin Krzystanek and Lilla Reiniger and Istv{\'a}n Csabai and Francesco Favero and Birkbak, {Nicolai J.} and Eklund, {Aron C.} and Ali Syed and Zoltan Szallasi",

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AU - Sztupinszki, Zsofia

AU - Diossy, Miklos

AU - Krzystanek, Marcin

AU - Reiniger, Lilla

AU - Csabai, István

AU - Favero, Francesco

AU - Birkbak, Nicolai J.

AU - Eklund, Aron C.

AU - Syed, Ali

AU - Szallasi, Zoltan

PY - 2018

Y1 - 2018

N2 - 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.

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

Abstract

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