dc.contributor.author |
Sztupinszki Zsofia |
|
dc.contributor.author |
Diossy Miklos |
|
dc.contributor.author |
Krzystanek Marcin |
|
dc.contributor.author |
Reiniger, Lilla |
|
dc.contributor.author |
Csabai, István |
|
dc.contributor.author |
Favero Francesco |
|
dc.contributor.author |
Birkbak Nicolai J |
|
dc.contributor.author |
Eklund Aron C |
|
dc.contributor.author |
Syed Ali |
|
dc.contributor.author |
Szállási, Zoltán |
|
dc.date.accessioned |
2018-10-02T09:33:54Z |
|
dc.date.available |
2018-10-02T09:33:54Z |
|
dc.date.issued |
2018 |
|
dc.identifier.citation |
pagination=16, pages: 4;
journalVolume=4;
journalIssueNumber=1;
journalTitle=NPJ BREAST CANCER; |
|
dc.identifier.uri |
http://repo.lib.semmelweis.hu//handle/123456789/6418 |
|
dc.identifier.uri |
doi:10.1038/s41523-018-0066-6 |
|
dc.description.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. |
|
dc.relation.ispartof |
urn:issn:2374-4677 |
|
dc.title |
Migrating the SNP array-based homologous recombination deficiency measures to next generation sequencing data of breast cancer |
|
dc.type |
Journal Article |
|
dc.date.updated |
2018-09-05T12:36:27Z |
|
dc.language.rfc3066 |
en |
|
dc.identifier.mtmt |
3408137 |
|
dc.contributor.department |
ELTE/Természettudományi Kar |
|
dc.contributor.department |
SE/AOK/I/I. Sz. Patológiai és Kísérleti Rákkutató Intézet |
|
dc.contributor.department |
SE/AOK/I/II. Sz. Patológiai és Kísérleti Rákkutató Intézet |
|
dc.contributor.institution |
Eötvös Loránd Tudományegyetem |
|
dc.contributor.institution |
Semmelweis Egyetem |
|