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Genes Chromosomes Cancer. 2015 Nov;54(11):681-91. doi: 10.1002/gcc.22279. Epub 2015 Jul 30.

Recurrent fusion transcripts detected by whole-transcriptome sequencing of 120 primary breast cancer samples.

Kim J1, Kim S2, Ko S3, In YH4, Moon HG5,6, Ahn SK5, Kim MK5, Lee M6, Hwang JH7, Ju YS2,8, Kim JI7,8,9, Noh DY5,6, Kim S3, Park JH2, Rhee H2, Kim S4,10, Han W5,6.

Author information

1
Department of Surgery, Asan Medical Center, Seoul, Korea.
2
Macrogen Inc., Seoul, Korea.
3
Department of Statistics, Seoul National University, Seoul, Korea.
4
Medicinal Bioconvergence Research Center, Seoul, Korea.
5
Department of Surgery, Seoul National University Hospital, Seoul, Korea.
6
Cancer Research Institute, College of Medicine, Seoul National University, Seoul, Korea.
7
Department of Biomedical Science, Seoul National University Graduate School, Seoul, Korea.
8
Genomic Medicine Institute(GMI), Medical Research Center, Seoul National University, Seoul, Korea.
9
Department of Biochemistry, Seoul National University College of Medicine, Seoul, Korea.
10
Medicinal Bioconvergence Research Center, Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, College of Pharmacy, Seoul National University, Seoul, Korea.

Abstract

Relatively few recurrent gene fusion events have been associated with breast cancer to date. In an effort to uncover novel fusion transcripts, we performed whole-transcriptome sequencing of 120 fresh-frozen primary breast cancer samples and five adjacent normal breast tissues using the Illumina HiSeq2000 platform. Three different fusion-detecting tools (deFuse, Chimerascan, and TopHatFusion) were used, and the results were compared. These tools detected 3,831, 6,630 and 516 fusion transcripts (FTs) overall. We primarily focused on the results obtained using the deFuse software. More FTs were identified from HER2 subtype breast cancer samples than from the luminal or triple-negative subtypes (P < 0.05). Seventy fusion candidates were selected for validation, and 32 (45.7%) were confirmed by RT-PCR and Sanger sequencing. Of the validated fusions, six were recurrent (found in 2 or more samples), three were in-frame (PRDX1-AKR1A1, TACSTD2-OMA1, and C2CD2-TFF1) and three were off-frame (CEACAM7-CEACAM6, CYP4X1-CYP4Z2P, and EEF1DP3-FRY). Notably, the novel read-through fusion, EEF1DP3-FRY, was identified and validated in 6.7% (8/120) of the breast cancer samples. This off-frame fusion results in early truncation of the FRY gene, which plays a key role in the structural integrity during mitosis. Three previously reported fusions, PPP1R1B-STARD3, MFGE8-HAPL, and ETV6-NTRK3, were detected in 8.3, 3.3, and 0.8% of the 120 samples, respectively, by both deFuse and Chimerascan. The recently reported MAGI3-AKT3 fusion was not detected in our analysis. Although future work will be needed to examine the biological significance of our new findings, we identified a number of novel fusions and confirmed some previously reported fusions.

PMID:
26227178
DOI:
10.1002/gcc.22279
[Indexed for MEDLINE]

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