Sarcoma Gene Fusion Panel By Nanofluidics
Sarcomas are relatively rare with around 15,000 new cases reported each year in the United States. Nevertheless, sarcomas account for more than 20% of all childhood malignancies. Current estimates associate 20-30% of sarcomas to with chromosomal translocations, which are genomic rearrangements that result in gene fusions that drive the pathogenesis of many types of cancer. Several translocations are recurrently associated with specific sarcoma subtypes. For example, translocations between the EWSR1 and FLI1 genes are thought to underlie 85% of Ewing sarcomas, a rare bone cancer that occurs most frequently in adolescents. Similarly, in the case of synovial sarcoma, there is high prevalence of SS18-SSX1 translocations. Detection of gene fusions in sarcoma is can be of diagnostic, therapeutic and prognostic significance.
This assay uses Real-Time PCR, a robust and inexpensive method, to detect gene fusions using very low input amounts by reverse transcribing messenger RNA (mRNA) into complementary DNA (cDNA) and then amplifying and detecting the target genes. Using the Fluidigm BioMark HD System, the samples are loaded into individual inlets and then distributed across multiple reaction chambers in small volumes, allowing for the detection of specific targets in the sample mix. For genes with low expression levels, preamplification of these cDNA samples increases the number of copies present to a detectable level for a greater number of genes. This is a qualitative test and will not estimate the copies of the fusion transcripts. The lower limit of fusion detection is 1 tumor cell carrying the fusion in a background of 1,000 to 10,000 cells. The test is designed to detect the most common fusion transcripts reported for the genes in sarcoma tumor sub-types. Rare fusion transcripts may not be detected. Fusions involving different breakpoint other than the ones targeted in current assay will not be detected. An alternative method such as FISH should be considered for additional confirmation when the findings of PCR-based fusion detection are not compatible with clinical and morphologic features.
The Sarcoma Gene Fusions (SGF) Assay is based on a qualitative Real-Time PCR screening method to detect 12 genes with 36 fusions in exonic regions of genes with therapeutic and/or prognostic importance associated with soft tissue cancers. This is a qualitative test and will not estimate the copies of the fusion transcripts. The lower limit of fusion detection according to the tumor RNA serial dilutions is 0.1-0.01%.
The current panel of fusion genes interrogated includes:
ASPSCR1-Ex7_TFE3-Ex6 (TYPE 1), EWSR1-Ex7_FLI1-Ex6 (TYPE 1), NAB2-Ex4_STAT6-Ex2, ASPSCR1-Ex7_TFE3-Ex5 (TYPE 2), EWSR1-Ex7_FLI1-Ex5 (TYPE 2), NAB2-Ex6_STAT6-Ex16, BCOR-Ex15_CCNB3-Ex5, EWSR1-Ex10_FLI1-Ex6 (TYPE 3), NAB2-Ex6_STAT6-Ex17, ETV6-Ex4_NTRK3-Ex14, EWSR1-Ex10_FLI1-Ex5 (TYPE 4), PAX3-Ex7_FOXO1-Ex2, ETV6-Ex5_NTRK3-Ex15, EWSR1-Ex7_WT1-Ex8, PAX3-Ex7_MAML3-Ex2, EWSR1-Ex8_ATF1-Ex4 (TYPE 1), EWSR1-Ex9_WT1-Ex8, PAX3-Ex6_NCOA1-Ex15 (TYPE1), EWSR1-Ex7_ATF1-Ex4 (TYPE 2), FUS-Ex5_ATF1-Ex5, PAX3-Ex7_NCOA1-Ex14 (TYPE 2), EWSR1-Ex10_ATF1-Ex5 (TYPE 3), HEY1-Ex4_NCOA2-Ex13, PAX3-Ex7_NCOA2-Ex12, EWSR1-Ex7_ATF1-Ex7 (TYPE 4), LMNA-Ex2_NTRK1-Ex11, PAX7-Ex7_FOXO1-Ex2, EWSR1-Ex7_CREB1-Ex7, LMNA-Ex10_NTRK1-Ex11, SS18-Ex10_SSX1-Ex6, EWSR1-Ex7_ERG-Ex8, MYH9-Ex1_USP6-Ex1 (TYPE 1), SS18-Ex10_SSX2-Ex6, EWSR1-Ex7_ERG-Ex11, MYH9-EX1_USP6-Ex2 (TYPE 2), SS18-Ex10_SSX4-Ex6.
7 to 10 working days
A minimum of 10 unstained slides containing formalin-fixed paraffin embedded (FFPE) tissue from soft tissues and malignant bone tumors, with areas to be tested indicated on 1 H&E stained slide and covered.
81401, 81479, 81191
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