The application of nonsense-mediated mRNA decay inhibition to the identification of breast cancer susceptibility genes

Johnson, Julie K., Waddell, Nic, kConFab Investigators and Chenevix-Trench, Georgia (2012) The application of nonsense-mediated mRNA decay inhibition to the identification of breast cancer susceptibility genes. BMC Cancer, 12 246: 246.1-246.12. doi:10.1186/1471-2407-12-246

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Author Johnson, Julie K.
Waddell, Nic
kConFab Investigators
Chenevix-Trench, Georgia
Total Author Count Override 158
Title The application of nonsense-mediated mRNA decay inhibition to the identification of breast cancer susceptibility genes
Journal name BMC Cancer   Check publisher's open access policy
ISSN 1471-2407
Publication date 2012-06-15
Sub-type Article (original research)
DOI 10.1186/1471-2407-12-246
Open Access Status DOI
Volume 12
Issue 246
Start page 246.1
End page 246.12
Total pages 12
Place of publication London, United Kingdom
Publisher BioMed Central
Collection year 2013
Language eng
Formatted abstract
Identification of novel, highly penetrant, breast cancer susceptibility genes will require the application of additional strategies beyond that of traditional linkage and candidate gene approaches. Approximately one-third of inherited genetic diseases, including breast cancer susceptibility, are caused by frameshift or nonsense mutations that truncate the protein product [1]. Transcripts harbouring premature termination codons are selectively and rapidly degraded by the nonsense-mediated mRNA decay (NMD) pathway. Blocking the NMD pathway in any given cell will stabilise these mutant transcripts, which can then be detected using gene expression microarrays. This technique, known as gene identification by nonsense-mediated mRNA decay inhibition (GINI), has proved successful in identifying sporadic nonsense mutations involved in many different cancer types. However, the approach has not yet been applied to identify germline mutations involved in breast cancer. We therefore attempted to use GINI on lymphoblastoid cell lines (LCLs) from multiple-case, non- BRCA1/2 breast cancer families in order to identify additional high-risk breast cancer susceptibility genes.


We applied GINI to a total of 24 LCLs, established from breast-cancer affected and unaffected women from three multiple-case non-BRCA1/2 breast cancer families. We then used Illumina gene expression microarrays to identify transcripts stabilised by the NMD inhibition.


The expression profiling identified a total of eight candidate genes from these three families. One gene, PPARGC1A, was a candidate in two separate families. We performed semi-quantitative real-time reverse transcriptase PCR of all candidate genes but only PPARGC1A showed successful validation by being stabilised in individuals with breast cancer but not in many unaffected members of the same family. Sanger sequencing of all coding and splice site regions of PPARGC1A did not reveal any protein truncating mutations. Haplotype analysis using short tandem repeat microsatellite markers did not indicate the presence of a haplotype around PPARGC1A which segregated with disease in the family.

The application of the GINI method to LCLs to identify transcripts harbouring germline truncating mutations is challenging due to a number of factors related to cell type, microarray sensitivity and variations in NMD efficiency.
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2013 Collection
School of Medicine Publications
Institute for Molecular Bioscience - Publications
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Created: Wed, 05 Sep 2012, 12:18:13 EST by Susan Allen on behalf of Institute for Molecular Bioscience