Development of detection method for novel fusion gene using GeneChip exon array

Yusaku Wada,Tetsuo Noda,Masaaki Matsuura,Koichi Nagasaki,Masaru Ushijima,Minoru Sugawara,Satoshi Miyata,Yoshio Miki

doi:10.1186/2043-9113-4-3

Yusaku Wada, Tetsuo Noda + Show 6 more

Open Access

https://doi.org/10.1186/2043-9113-4-3

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Abstract

BackgroundFusion genes have been recognized to play key roles in oncogenesis. Though, many techniques have been developed for genome-wide analysis of fusion genes, a more efficient method is desired.ResultsWe introduced a new method of detecting the novel fusion gene by using GeneChip Exon Array that enables exon expression analysis on a whole-genome scale and TAIL-PCR. To screen genes with abnormal exon expression profiles, we developed computational program, and confirmed that the program was able to search the fusion partner gene using Exon Array data of T-cell acute lymphocytic leukemia (T-ALL) cell lines. It was reported that the T-ALL cell lines, ALL-SIL, BE13 and LOUCY, harbored the fusion gene NUP214-ABL1, NUP214-ABL1 and SET-NUP214, respectively. The program extracted the candidate genes with abnormal exon expression profiles: 1 gene in ALL-SIL, 1 gene in BE13, and 2 genes in LOUCY. The known fusion partner gene NUP214 was included in the genes in ALL-SIL and LOUCY. Thus, we applied the proposed program to the detection of fusion partner genes in other tumors. To discover novel fusion genes, we examined 24 breast cancer cell lines and 20 pancreatic cancer cell lines by using the program. As a result, 20 and 23 candidate genes were obtained for the breast and pancreatic cancer cell lines respectively, and seven genes were selected as the final candidate gene based on information of the EST data base, comparison with normal cell samples and visual inspection of Exon expression profile. Finding of fusion partners for the final candidate genes was tried by TAIL-PCR, and three novel fusion genes were identified.ConclusionsThe usefulness of our detection method was confirmed. Using this method for more samples, it is thought that fusion genes can be identified.

Highlights

Fusion genes have been recognized to play key roles in oncogenesis
Samples Twenty-four breast cancer cell lines (AU565, BT474, DU4475, HCC38, HCC70, HCC202, HCC1143, HCC1187, HCC1419, HCC1428, HCC1569, HCC1806, HCC1954, MCF7, MDA-MB-157, MDA-MB-231, MDA-MB-330, MDA-MB-361, MDA-MB-435S, MDAMB-468, SK-BR-3, UACC812, UACC893, ZR-75-1) were obtained from American Type Culture Collection (ATCC), and maintained in under the conditions recommended by the supplier
Exon expression profiles of EWSR1 and ATF1 were characterized (Figure 2), and the following features were observed. 1: Probe sets in the exon region had high signal intensity, and probe sets in the intron region had low signal intensity. 2: In some probe sets, all samples had equivalent signal intensity

Summary

Introduction

Fusion genes have been recognized to play key roles in oncogenesis. The discovery of a characteristic small chromosome, called Philadelphia chromosome, in chronic myeloid leukemia, is the first recurrent chromosome rearrangement to be seen in a human cancer [1]. This rearrangement was eventually identified as a translocation between chromosome 9 and 22 [2], resulting in the fusion of the BCR gene on chromosome 22 with the ABL1 gene. It is known that fusion genes have a key role in oncogenesis in hematological tumors and sarcomas. Fusion genes are regarded as attractive targets of molecular targeted treatments because of their high specificity to tumors

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