The Archer® FusionPlex® Sarcoma kit is a targeted sequencing assay to simultaneously detect and identify fusions of 26 genes associated with soft tissue cancers. Using Archer’s proprietary Anchored Multiplex PCR (AMP™)-based enrichment, fusions of all genes in this kit can be identified in a single sequencing assay, even without prior knowledge of fusion partners or breakpoints.
For Research Use Only. Not for use in diagnostic procedures.
# of GSP2s
Input nucleic acid required*
Recommended # of reads
Unique molecular on-target %
Fresh frozen or FFPE
*Input recommendations for FFPE samples vary depending on Archer Preseq® RNA QC score; 50ng input recommended in absence of PreSeq screening
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Sarcoma is broadly defined as a cancer arising from cells of mesenchymal origin. Mesenchymal cells develop into and comprise connective tissues such as bone and cartilage as well as tissues of the lymphatic and circulatory systems. Sarcomas are relatively rare—only about 15,000 new cases are reported each year in the United States (1). Nevertheless, sarcomas account for more than 20% of all childhood malignancies. The majority of sarcoma cases are soft tissue sarcomas originating in fat, muscle and tissue of the trunk, arms or legs; however, malignant bone tumors also comprise over 10% of sarcoma instances. Because early-stage sarcomas frequently elude identification until substantial metastasis has occurred, sarcomas bear a particularly high mortality rate and represent an important challenge for cancer research (1).
Chromosomal translocations are genomic rearrangements that result in gene fusions that drive the pathogenesis of many types of cancer. Current estimates attribute 20-30% of sarcomas to these translocations (3,4). Several translocations were found to be 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 (4). Similarly, in the case of synovial sarcoma, which can be difficult to identify histologically, the prevalence of SS18-SSX1 translocations is so dramatic that molecular detection of this fusion might be necessary to make a conclusive determination (5).
|Aneurysmal bone cyst||t(16;17)(q22;p13)
|Angiomatoid fibrous histiocytoma||t(12;22)(q13;q12)
|Alveolar soft-part sarcoma||der(17)t(X;17)(p11;q25)||ASPSCR1-TFE3|
giant cell fibroblastoma
|Desmoplastic small round-cell tumor||t(11;22)(p13;q12)||EWSR1-WT1|
|Endometrial stromal sarcoma||t(7;17)(p15;q11)
Primitive neuroectodemal tumor (PNET)
|Ewing-like bone sarcoma||inv(X)(p11.4p11.22)
|Giant cell fibroblastoma||t(17;22)(q21;q13)||COLIA1-PDGFB|
|Inflammatory myofibroblastic tumor||t(1;2)(q22;p23)
|Low-grade fibromyxoid sarcoma||t(7;16)(q33;p11)
|Myoepithelial tumor of
soft tissue and bone
t with 16p11
|Pulmonary myxoid sarcoma||t(2;22)(q34;q12)||EWSR1-CREB1|
|Solitary fibrous tumor||inv(12)(q13q13)||NAB2-STAT6|
|Spindle cell rhabdomyosarcoma||t(6;8)(p21;q13)
|Undifferentiated small round
blue cell tumor
Chromosomal translocations have been traditionally detected using methods that vary in sensitivity, scalability and the ability to multiplex. These methods include:
IHC is a relatively straightforward method to detect proteins in fixed tissue sections using antibodies specific to the target protein. IHC can indirectly detect translocations if the gene fusion leads to overexpression of a fusion protein above background levels, with the intensity of the staining indicative of fusion protein expression level. Although not technically challenging, a key limitation to IHC as an effective translocation detection strategy is the need for antibodies that target one of the fusion partners. Also, IHC only provides a qualitative analysis because of the nonlinear chromogenic signal, and the limited number of chromogenic signals available prevents the use of IHC for multiplexing.
FISH relies on a fluorescent DNA probe that hybridizes to the target gene in chromosomal DNA, and translocations are often detected by visually determining the colocalization of two fluorescent probes that hybridize to flanking sequences in the target fusion event. FISH is more objective than IHC, because colocalization of the two fluorescent probes is positive for the fusion event. But there is some subjectivity because of the level of colocalization, especially when the two genes are normally in close proximity. FISH is also technically challenging, laborious by both the preparation and preview, poorly scalable and limited in multiplexing.
RT-PCR is an inexpensive and robust method to detect gene fusions using very low input amounts by reverse transcribing messenger RNA into complementary DNA (cDNA) and then amplifying and detecting the target genes. The method yields a relatively straightforward yes-or-no readout, but the sequences of both fusion partners must be known to craft forward and reverse primers to amplify the fusion sequence. RT-PCR also is limited in scalability and clinical sensitivity.
Gene fusions can be detected by histological and molecular methods, including IHC, FISH and RT-PCR (from left to right)
Because of limitations associated with these traditional methods, cutting-edge technologies are increasingly defining novel sarcoma subtypes through the identification of new chromosomal translocations (6-8).
ArcherDX has developed a kit for the rapid detection of sarcoma-associated translocations from total nucleic acid isolated from tumor samples—including FFPE preserved specimens. Anchored Multiplex PCR (AMP) enables rapid preparation of highly multiplexed next generation sequencing (NGS) libraries for targeted capture of mRNAs produced from fusion genes. The Archer technology permits the simultaneous detection of both known recurrent fusions as well as previously unidentified fusions at key breakpoints in target genes. Archer’s sarcoma kit offers a complete fusion detection solution, from library preparation through data analysis, for both the Illumina® and Ion Torrent™ platforms.
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