Parallel DNA/RNA NGS Using an Identical Target Enrichment Panel in the Analysis of Hereditary Cancer Predisposition
Jazyk angličtina Země Česko Médium print
Typ dokumentu časopisecké články
Grantová podpora
NU23-03-00150
Ministerstvo Zdravotnictví Ceské Republiky
RVO-VFN 64165
Ministerstvo Zdravotnictví Ceské Republiky
SVV 260516
Univerzita Karlova v Praze
LX22NPO5102
Ministerstvo Školství, Mládeže a Tělovýchovy
PubMed
38830124
DOI
10.14712/fb2024070010062
PII: fb_2024070010062
Knihovny.cz E-zdroje
- Klíčová slova
- ATM, BRCA1, BRCA2, CHEK2, CZECANCA, DNA, NGS, RNA, TSC2, aberrant splicing, alternative splicing, deep intronic variant, gene expression, germline genetic testing, hereditary cancer predisposition, parallel, reproducibility, sequence capture,
- MeSH
- DNA genetika MeSH
- genetická predispozice k nemoci * MeSH
- lidé MeSH
- nádory genetika diagnóza MeSH
- reprodukovatelnost výsledků MeSH
- RNA genetika MeSH
- sekvenční analýza DNA metody MeSH
- sekvenční analýza RNA metody MeSH
- vysoce účinné nukleotidové sekvenování * metody MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- DNA MeSH
- RNA MeSH
Germline DNA testing using the next-gene-ration sequencing (NGS) technology has become the analytical standard for the diagnostics of hereditary diseases, including cancer. Its increasing use places high demands on correct sample identification, independent confirmation of prioritized variants, and their functional and clinical interpretation. To streamline these processes, we introduced parallel DNA and RNA capture-based NGS using identical capture panel CZECANCA, which is routinely used for DNA analysis of hereditary cancer predisposition. Here, we present the analytical workflow for RNA sample processing and its analytical and diagnostic performance. Parallel DNA/RNA analysis allowed credible sample identification by calculating the kinship coefficient. The RNA capture-based approach enriched transcriptional targets for the majority of clinically relevant cancer predisposition genes to a degree that allowed analysis of the effect of identified DNA variants on mRNA processing. By comparing the panel and whole-exome RNA enrichment, we demonstrated that the tissue-specific gene expression pattern is independent of the capture panel. Moreover, technical replicates confirmed high reproducibility of the tested RNA analysis. We concluded that parallel DNA/RNA NGS using the identical gene panel is a robust and cost-effective diagnostic strategy. In our setting, it allows routine analysis of 48 DNA/RNA pairs using NextSeq 500/550 Mid Output Kit v2.5 (150 cycles) in a single run with sufficient coverage to analyse 226 cancer predisposition and candidate ge-nes. This approach can replace laborious Sanger confirmatory sequencing, increase testing turnaround, reduce analysis costs, and improve interpretation of the impact of variants by analysing their effect on mRNA processing.
Department of Biochemistry Faculty of Science Charles University Prague Czech Republic
Department of Genetics and Microbiology Faculty of Science Charles University Prague Czech Republic
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