Nanopore sequencing of full-length BRCA1 mRNA transcripts reveals co-occurrence of known exon skipping events.
Background: Laboratory assays evaluating the effect of DNA sequence variants on BRCA1 mRNA splicing may contribute to classification by providing molecular evidence. However, our knowledge of normal and aberrant BRCA1 splicing events to date has been limited to data derived from assays targeting par...
| Publicado en: | Breast Cancer Research Vol. 19; pp. 1 - 10 |
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| Autores principales: | , , , , , , , |
| Formato: | Journal Article |
| Publicado: |
BioMed Central
11/28/2017
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| Acceso en línea: | Ver este registro en EBSCOhost |
| fields | @attributes: recordID: 1 pdfLink: plink: https://search.ebscohost.com/login.aspx?direct=true&db=ccm&AN=126454412&site=ehost-live header: @attributes: shortDbName: ccm uiTerm: 126454412 longDbName: CINAHL Complete uiTag: AN controlInfo: bkinfo: dissinfo: jinfo: jid: 14655411 8UYJ jtl: Breast Cancer Research issn: 14655411 maglogo: N pubinfo: dt: 11/28/2017 vid: 19 pid: 24147 pub: BioMed Central artinfo: ui: 126454412 126454412 NLM29183387 10.1186/s13058-017-0919-1 NLM29183387 126454412 ppf: 1 ppct: 9 formats: fmt: @attributes: type: P tig: atl: Nanopore sequencing of full-length BRCA1 mRNA transcripts reveals co-occurrence of known exon skipping events. aug: au: de Jong, Lucy C. Cree, Simone Lattimore, Vanessa Wiggins, George A. R. Spurdle, Amanda B. Miller, Allison Kennedy, Martin A. Walker, Logan C. affil: Department of Pathology, University of Otago, Christchurch, New Zealand sug: subj: Genes, BRCA RNA Sequence Analysis Methods Genes Female Cell Line, Tumor DNA Nucleotides Scales Female ab: Background: Laboratory assays evaluating the effect of DNA sequence variants on BRCA1 mRNA splicing may contribute to classification by providing molecular evidence. However, our knowledge of normal and aberrant BRCA1 splicing events to date has been limited to data derived from assays targeting partial transcript sequences. This study explored the utility of nanopore sequencing to examine whole BRCA1 mRNA transcripts and to provide accurate categorisation of in-frame and out-of-frame splicing events.Methods: The exon structure of BRCA1 transcripts from a previously studied control lymphoblastoid cell line were assessed using MinION nanopore sequencing of long-range reverse transcriptase-PCR amplicons.Results: Our study identified and characterised 32 complete BRCA1 isoforms, including 18 novel isoforms which showed skipping of multiple contiguous and/or non-contiguous exons. Furthermore, we show that known BRCA1 exon skipping events, such as Δ(9,10) and Δ21, can co-occur in a single transcript, with some isoforms containing four or more alternative splice junctions. Fourteen novel isoforms were formed entirely from a combination of previously identified alternative splice junctions, suggesting that the total number of BRCA1 isoforms might be lower than the number of splicing events reported previously.Conclusions: Our results highlight complexity in BRCA1 transcript structure that has not been described previously. This finding has key implications for predicting the translation frame of splicing transcripts, important for interpreting the clinical significance of spliceogenic variants. Future research is warranted to quantitatively assess full-length BRCA1 transcript levels, and to assess the application of nanopore sequencing for routine evaluation of potential spliceogenic variants. pubtype: Academic Journal doctype: Journal Article ougenre: Article language: English refInfo: holdings: @attributes: islocal: N |
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