Assessment of Fusion Gene Status in Sarcomas Using a Custom Made Fusion Gene Microarray

Abstract

Sarcomas are relatively rare malignancies and include a large number of histological subgroups. Based on morphology alone, the differential diagnoses of sarcoma subtypes can be challenging, but the identification of specific fusion genes aids correct diagnostication. The presence of individual fusion products are routinely investigated in Pathology labs. However, the methods used are time-consuming and based on prior knowledge about the expected fusion gene and often the most likely break-point. In this study, 16 sarcoma samples, representing seven different sarcoma subtypes with known fusion gene status from a diagnostic setting, were investigated using a fusion gene microarray. The microarray was designed to detect all possible exon-exon breakpoints between all known fusion genes in a single analysis. An automated scoring of the microarray data from the 38 known sarcoma-related fusion genes identified the correct fusion gene among the top-three hits in 11 of the samples. The analytical sensitivity may be further optimised, but we conclude that a sarcoma-fusion gene microarray is suitable as a time-saving screening tool to identify the majority of the correct fusion genes.

Identification of the TAF15–ZNF384 fusion gene in two new cases of acute lymphoblastic leukemia with a t(12;17)(p13;q12)

“…Today, fusion gene detection in the clinical diagnostic setting is based on FISH (mostly interphase FISH) or RT-PCR. Either as an array, or using targeted next generation sequencing, it will soon be feasible to detect all known gene fusions in cancer in a single experiment, also applicable in a diagnostic setting (Lovf et al, 2011, Lovf et al, 2013. As outlined in the discussion, all variants of disease specific rearrangements are important to investigate, as subtypes of them may impact…”

Hypothesis: Artifacts, Including Spurious Chimeric RNAs with a Short Homologous Sequence, Caused by Consecutive Reverse Transcriptions and Endogenous Random Primers

“…There have been about 800 different chromosomal rearrangements, including translocations 18 - 20 , in association with about 1,000 fusion genes 20 , documented in the literature. On the other hand, one reported microarray chip collects 548 chimeric RNAs that have been preliminarily verified 21 , 22 , but not all of them are associated with a known fusion gene as the genomic basis. The best example of such fusion genes is the product of Philadelphia chromosome that results from a reciprocal translocation involving the long arms of chromosomes 9 and 22, t(9;22) (q34;q11) 23 .…”