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

TY - JOUR

T1 - Migrating the SNP array-based homologous recombination deficiency measures to next generation sequencing data of breast cancer

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.

U2 - 10.1038/s41523-018-0066-6

DO - 10.1038/s41523-018-0066-6

M3 - Journal article

C2 - 29978035

AN - SCOPUS:85055673506

SN - 2374-4677

VL - 4

SP - 1

EP - 4

JO - npj Breast Cancer

JF - npj Breast Cancer

IS - 1

M1 - 16

ER -