Open Access Highly Accessed Research article

Identification of gene fusion transcripts by transcriptome sequencing in BRCA1-mutated breast cancers and cell lines

Kevin CH Ha12, Emilie Lalonde12, Lili Li134, Luca Cavallone34, Rachael Natrajan5, Maryou B Lambros5, Costas Mitsopoulos5, Jarle Hakas5, Iwanka Kozarewa5, Kerry Fenwick5, Chris J Lord5, Alan Ashworth5, Anne Vincent-Salomon6, Mark Basik478, Jorge S Reis-Filho5, Jacek Majewski12 and William D Foulkes1347*

Author Affiliations

1 Department of Human Genetics, McGill University, Room N5-13, Stewart Biology Building, 1205 Dr. Penfield Ave, Montreal, Quebec, H3A 1B1, Canada

2 McGill University and Genome Quebec Innovation Centre, 740 Dr. Penfield Ave, Montreal, Quebec, H3A 1A4, Canada

3 Program in Cancer Genetics, McGill University, 546 Pine Ave, Montreal, Quebec, H2W 1S6, Canada

4 Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, 3755 Côte-Ste-Catherine Road, Montreal, Quebec, H3T 1E2, Canada

5 The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK

6 Institut Curie, 26 Rue d'Ulm, 75248, Paris, France

7 Department of Oncology, Lady Davis Institute, Jewish General Hospital, McGill University, 3755 Côte-Ste-Catherine Road, Montreal, H3T 1E2, Canada

8 Department of Surgery, Lady Davis Institute, Jewish General Hospital, McGill University, 3755 Côte-Ste-Catherine Road, Montreal, Quebec, H3T 1E2, Canada

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BMC Medical Genomics 2011, 4:75  doi:10.1186/1755-8794-4-75

Published: 27 October 2011

Additional files

Additional file 1:

Read statistics of RNA-Seq samples. A summary of read statistics of the RNA-Seq samples used in this study.

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Additional file 2:

Primer sequences for experimental validation. This document contains the primer sequences used for experimental validation of candidate gene fusions (Sanger sequencing and RT-PCR).

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Additional file 3:

Schematic and expression profile of MTAP-PCDH7 gene fusion. (A) Schematic illustrating paired-end reads that flank the fusion junction between exon 6 of MTAP and exon 3 of PCDH7. Reads are indicated by black solid lines. Paired reads are indicated by the dotted line joining two reads. Reads the span across the junction are highlighted by red solid lines; and (B) Expression plots of MTAP and PCDH7 as measured by the log2 FC between the RPKM values of each exon in SUM149PT versus the average of all other MTAP-PCDH7-negative samples.

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Additional file 4:

Expression profile of ADNP-C20orf132 gene fusion. We extracted cDNA from primary tumor T50 and confirmed the presence of both isoforms of ADNP-C20orf132 by (A) RT-PCR. In both cases, we confirmed the presence of both isoforms (lanes 1 and 2) of this gene fusion. Lane 3 is a 50 bp ladder control. (B) Expression plots of ADNP and C20orf132 as measured by the log2 FC between the RPKM values of each exon in the T50 versus the average of all other ADNP-C20orf132-negative samples.

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Additional file 5:

Genomic features overlapping or near candidate fusion genes. (A) We queried existing data to summarize known structural variation that overlaps or is within proximity of our candidate fusion genes; and (B) a list of overlapping CNVs reported in the Database of Genomic Variants.

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