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Parallel DNA/RNA NGS Using an Identical Target Enrichment Panel in the Analysis of Hereditary Cancer Predisposition

dc.contributor.authorKleiblová, Petra
dc.contributor.authorČerná, Marta
dc.contributor.authorZemánková, Petra
dc.contributor.authorMatějková, Kateřina
dc.contributor.authorNehasil, Petr
dc.contributor.authorHojný, Jan
dc.contributor.authorHoráčková, Klára
dc.contributor.authorJanatová, Markéta
dc.contributor.authorSoukupová, Jana
dc.contributor.authorŠťastná, Barbora
dc.contributor.authorKleibl, Zdeněk
dc.date.accessioned2024-08-28T10:17:47Z
dc.date.available2024-08-28T10:17:47Z
dc.date.issued2024
dc.identifier.urihttps://hdl.handle.net/20.500.14178/2591
dc.description.abstractGermline 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.en
dc.language.isoen
dc.relation.urlhttps://doi.org/10.14712/fb2024070010062
dc.rightsCreative Commons Uveďte původ 4.0 Internationalcs
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.titleParallel DNA/RNA NGS Using an Identical Target Enrichment Panel in the Analysis of Hereditary Cancer Predispositionen
dcterms.accessRightsopenAccess
dcterms.licensehttps://creativecommons.org/licenses/by/4.0/legalcode
dc.date.updated2024-08-28T10:17:47Z
dc.subject.keywordRNAen
dc.subject.keywordDNAen
dc.subject.keywordparallelen
dc.subject.keywordsequence captureen
dc.subject.keywordNGSen
dc.subject.keywordCZECANCAen
dc.subject.keywordhereditary cancer predispositionen
dc.subject.keywordgermline genetic testingen
dc.subject.keywordaberrant splicingen
dc.subject.keywordgene expressionen
dc.subject.keywordreproducibilityen
dc.subject.keyworddeep intronic Varianten
dc.subject.keywordCHEK2en
dc.subject.keywordBRCA2en
dc.subject.keywordATMen
dc.subject.keywordBRCA1en
dc.subject.keywordTSC2en
dc.subject.keywordalternative splicingen
dc.identifier.eissn2533-7602
dc.relation.fundingReferenceinfo:eu-repo/grantAgreement/FN/I-FN/RVO-VFN64165
dc.relation.fundingReferenceinfo:eu-repo/grantAgreement/MZ0/NU/NU23-03-00150
dc.relation.fundingReferenceinfo:eu-repo/grantAgreement/MSM//SVV260516
dc.relation.fundingReferenceinfo:eu-repo/grantAgreement/MSM//LX22NPO5102
dc.relation.fundingReferenceinfo:eu-repo/grantAgreement/UK/COOP/COOP
dc.relation.fundingReferenceinfo:eu-repo/grantAgreement/MSM//SVV260691
dc.date.embargoStartDate2024-08-28
dc.type.obd73
dc.type.versioninfo:eu-repo/semantics/publishedVersion
dc.identifier.doi10.14712/fb2024070010062
dc.identifier.utWos001243028900004
dc.identifier.eidScopus2-s2.0-85189029261
dc.identifier.obd649441
dc.identifier.pubmed38830124
dc.subject.rivPrimary30000::30100
dc.subject.rivSecondary30000::30100::30101
dcterms.isPartOf.nameFolia Biologica
dcterms.isPartOf.issn0015-5500
dcterms.isPartOf.journalYear2024
dcterms.isPartOf.journalVolume70
dcterms.isPartOf.journalIssue1
uk.faculty.primaryId108
uk.faculty.primaryName1. lékařská fakultacs
uk.faculty.primaryNameFirst Faculty of Medicineen
uk.faculty.secondaryId53
uk.faculty.secondaryId115
uk.faculty.secondaryNameVšeobecná fakultní nemocnice v Prazecs
uk.faculty.secondaryNameVšeobecná fakultní nemocnice v Prazeen
uk.faculty.secondaryNamePřírodovědecká fakultacs
uk.faculty.secondaryNameFaculty of Scienceen
uk.department.primaryId1538
uk.department.primaryNameÚstav lékařské biochemie a laboratorní diagnostiky 1. LF UK a VFNcs
uk.department.primaryNameInstitute of Medical Biochemistry and Laboratory Diagnosticsen
uk.department.secondaryId5000002630
uk.department.secondaryId1522
uk.department.secondaryId1535
uk.department.secondaryId1496
uk.department.secondaryId1048
uk.department.secondaryId5000002628
uk.department.secondaryId1034
uk.department.secondaryId1541
uk.department.secondaryNameÚstav patologie 1.LF a VFNcs
uk.department.secondaryNameÚstav patologie 1.LF a VFNen
uk.department.secondaryNameKlinika pediatrie a dědičných poruch metabolismu 1. LF a VFNcs
uk.department.secondaryNameDepartment of Paediatrics and Inherited Metabolic Disorders 1. LF UK a VFNen
uk.department.secondaryNameÚstav biologie a lékařské genetiky 1. LF UK a VFNcs
uk.department.secondaryNameInstitute of Biology and Medical Geneticsen
uk.department.secondaryNameÚstav patologické fyziologie 1. LF UKcs
uk.department.secondaryNameInstitute of Pathological Physiologyen
uk.department.secondaryNameKatedra biochemiecs
uk.department.secondaryNameDepartment of Biochemistryen
uk.department.secondaryNameÚstav lékařské biochemie a laboratorní diagnostiky 1.LF a VFNcs
uk.department.secondaryNameÚstav lékařské biochemie a laboratorní diagnostiky 1.LF a VFNen
uk.department.secondaryNameKatedra genetiky a mikrobiologiecs
uk.department.secondaryNameDepartment of Genetics and Microbiologyen
uk.department.secondaryNameÚstav patologie 1. LF UK a VFNcs
uk.department.secondaryNameInstitute of Pathologyen
dc.description.pageRange62-73
dc.type.obdHierarchyCsČLÁNEK V ČASOPISU::článek v časopisu::původní článekcs
dc.type.obdHierarchyEnJOURNAL ARTICLE::journal article::original articleen
dc.type.obdHierarchyCode73::152::206en
uk.displayTitleParallel DNA/RNA NGS Using an Identical Target Enrichment Panel in the Analysis of Hereditary Cancer Predispositionen


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