Migrating the SNP array-based homologous recombination deficiency measures to next generation sequencing data of breast cancer
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Migrating the SNP array-based homologous recombination deficiency measures to next generation sequencing data of breast cancer. / Sztupinszki, Zsofia; Diossy, Miklos; Krzystanek, Marcin; Reiniger, Lilla; Csabai, István; Favero, Francesco; Birkbak, Nicolai J.; Eklund, Aron C.; Syed, Ali; Szallasi, Zoltan.
In: npj Breast Cancer, Vol. 4, No. 1, 16, 2018, p. 1-4.Research output: Contribution to journal › Journal article › Research › peer-review
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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
VL - 4
SP - 1
EP - 4
JO - npj Breast Cancer
JF - npj Breast Cancer
SN - 2374-4677
IS - 1
M1 - 16
ER -
ID: 211815841