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Targeted RNA-seq successfully identifies normal and pathogenic splicing events in breast/ovarian cancer susceptibility and Lynch syndrome genes

Brandão, Rita D.; Mensaert, Klaas; López-Perolio, Irene; Tserpelis, Demis; Xenakis, Markos; Lattimore, Vanessa; Walker, Logan C.; Kvist, Anders LU ; Vega, Ana and Gutiérrez-Enríquez, Sara, et al. (2019) In International Journal of Cancer 145(2). p.401-414
Abstract

A subset of genetic variants found through screening of patients with hereditary breast and ovarian cancer syndrome (HBOC) and Lynch syndrome impact RNA splicing. Through target enrichment of the transcriptome, it is possible to perform deep-sequencing and to identify the different and even rare mRNA isoforms. A targeted RNA-seq approach was used to analyse the naturally-occurring splicing events for a panel of 8 breast and/or ovarian cancer susceptibility genes (BRCA1, BRCA2, RAD51C, RAD51D, PTEN, STK11, CDH1, TP53), 3 Lynch syndrome genes (MLH1, MSH2, MSH6) and the fanconi anaemia SLX4 gene, in which monoallelic mutations were found in non-BRCA families. For BRCA1, BRCA2, RAD51C and RAD51D the results were validated by capillary... (More)

A subset of genetic variants found through screening of patients with hereditary breast and ovarian cancer syndrome (HBOC) and Lynch syndrome impact RNA splicing. Through target enrichment of the transcriptome, it is possible to perform deep-sequencing and to identify the different and even rare mRNA isoforms. A targeted RNA-seq approach was used to analyse the naturally-occurring splicing events for a panel of 8 breast and/or ovarian cancer susceptibility genes (BRCA1, BRCA2, RAD51C, RAD51D, PTEN, STK11, CDH1, TP53), 3 Lynch syndrome genes (MLH1, MSH2, MSH6) and the fanconi anaemia SLX4 gene, in which monoallelic mutations were found in non-BRCA families. For BRCA1, BRCA2, RAD51C and RAD51D the results were validated by capillary electrophoresis and were compared to a non-targeted RNA-seq approach. We also compared splicing events from lymphoblastoid cell-lines with those from breast and ovarian fimbriae tissues. The potential of targeted RNA-seq to detect pathogenic changes in RNA-splicing was validated by the inclusion of samples with previously well characterized BRCA1/2 genetic variants. In our study, we update the catalogue of normal splicing events for BRCA1/2, provide an extensive catalogue of normal RAD51C and RAD51D alternative splicing, and list splicing events found for eight other genes. Additionally, we show that our approach allowed the identification of aberrant splicing events due to the presence of BRCA1/2 genetic variants and distinguished between complete and partial splicing events. In conclusion, targeted-RNA-seq can be very useful to classify variants based on their putative pathogenic impact on splicing.

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publication status
published
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keywords
alternative splicing, BRCA1/2, inherited breast/ovarian cancer syndrome, lynch syndrome, targeted RNA-seq
in
International Journal of Cancer
volume
145
issue
2
pages
401 - 414
publisher
John Wiley & Sons
external identifiers
  • scopus:85061251934
ISSN
0020-7136
DOI
10.1002/ijc.32114
language
English
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yes
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be286bbe-1117-48ec-bc3f-7f02d16f1442
date added to LUP
2019-02-22 12:54:45
date last changed
2019-06-28 09:57:32
@article{be286bbe-1117-48ec-bc3f-7f02d16f1442,
  abstract     = {<p>A subset of genetic variants found through screening of patients with hereditary breast and ovarian cancer syndrome (HBOC) and Lynch syndrome impact RNA splicing. Through target enrichment of the transcriptome, it is possible to perform deep-sequencing and to identify the different and even rare mRNA isoforms. A targeted RNA-seq approach was used to analyse the naturally-occurring splicing events for a panel of 8 breast and/or ovarian cancer susceptibility genes (BRCA1, BRCA2, RAD51C, RAD51D, PTEN, STK11, CDH1, TP53), 3 Lynch syndrome genes (MLH1, MSH2, MSH6) and the fanconi anaemia SLX4 gene, in which monoallelic mutations were found in non-BRCA families. For BRCA1, BRCA2, RAD51C and RAD51D the results were validated by capillary electrophoresis and were compared to a non-targeted RNA-seq approach. We also compared splicing events from lymphoblastoid cell-lines with those from breast and ovarian fimbriae tissues. The potential of targeted RNA-seq to detect pathogenic changes in RNA-splicing was validated by the inclusion of samples with previously well characterized BRCA1/2 genetic variants. In our study, we update the catalogue of normal splicing events for BRCA1/2, provide an extensive catalogue of normal RAD51C and RAD51D alternative splicing, and list splicing events found for eight other genes. Additionally, we show that our approach allowed the identification of aberrant splicing events due to the presence of BRCA1/2 genetic variants and distinguished between complete and partial splicing events. In conclusion, targeted-RNA-seq can be very useful to classify variants based on their putative pathogenic impact on splicing.</p>},
  author       = {Brandão, Rita D. and Mensaert, Klaas and López-Perolio, Irene and Tserpelis, Demis and Xenakis, Markos and Lattimore, Vanessa and Walker, Logan C. and Kvist, Anders and Vega, Ana and Gutiérrez-Enríquez, Sara and Díez, Orland and de la Hoya, Miguel and Spurdle, Amanda B. and De Meyer, Tim and Blok, Marinus J.},
  issn         = {0020-7136},
  keyword      = {alternative splicing,BRCA1/2,inherited breast/ovarian cancer syndrome,lynch syndrome,targeted RNA-seq},
  language     = {eng},
  month        = {01},
  number       = {2},
  pages        = {401--414},
  publisher    = {John Wiley & Sons},
  series       = {International Journal of Cancer},
  title        = {Targeted RNA-seq successfully identifies normal and pathogenic splicing events in breast/ovarian cancer susceptibility and Lynch syndrome genes},
  url          = {http://dx.doi.org/10.1002/ijc.32114},
  volume       = {145},
  year         = {2019},
}