Breast Cancer Research in New Zealand partnership

Dr Logan Walker
University of Otago, Christchurch
Funder(s): Breast Cancer Cure (fully funded)
Analysis of full-length transcripts for variant classification in breast cancer
24 months

Lay summary

Analysis of ‘naturally occurring’ mRNA splice isoforms for breast cancer susceptibility genes aids in the interpretation of in vitro splicing assays for sequence variant classification. However, current Polymerase Chain Reaction (PCR)-based or short-read sequencing platforms are unable to establish whether these individual splicing events co-occur in the same transcript. Such uncertainty may lead to a misinterpretation of in-frame and out-of-frame splicing events and confound variant classification efforts. New nanopore sequencing technology generates read lengths that greatly exceed those of more commonly used sequencing platforms, enabling complex exon structure of mRNA transcripts to be characterised. We were the first group to use this technology to resolve the exon structure of whole BRCA1 mRNA transcripts and now propose to develop a comprehensive map of isoforms from non-BRCA breast cancer susceptibility genes. These data will play a critical role in the development of international variant classification guidelines for these genes.

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