Archer FusionPlex
Oncology Research Kit


Introduction

The Archer® FusionPlex® Oncology Research Kit is a targeted next generation sequencing (NGS) assay to simultaneously detect and identify fusions and other mutations associated with 74 genes found in RNA transcripts that are linked to various cancers. This kit is extensive and purpose-built to advance fusion discovery, including research efforts in the area of Ph-like ALL fusions.

Highlights

  • Novel fusion detection - AMP chemistry allows for identification of novel fusion partners
  • Expert design - designed for all breakpoints from a vast, internally curated knowledge base
  • Extensive - the most comprehensive FusionPlex kit available, including critical pediatric markers such as Ph-ALL fusions

For Research Use Only. Not for use in diagnostic procedures. For Research Use Only. Not for use in diagnostic procedures.



Product information

Illumina®

AB0009 - 8-reactions
AB0031 - 16-reactions - starter kit
AB0061 - 48-reactions

Ion Torrent™

AB0010 - 8-reactions
AB0032 - 16-reactions - starter kit
AB0062 - 48-reactions

Archer Analysis

Local installation
Analysis Unlimited

Demo Data Get a quote

Documents

Product InsertProtocol for IlluminaProtocol for Ion Torrent
Publications Posters

Specifications and performance

74

Gene targets

393

# of GSP2s

≥10ng

Input nucleic acid required*

3 million

Recommended # of reads


>96%

Unique molecular on-target %


2.5 hours

Hands-on time


9 hours

Total time

Illumina or
Ion Torrent

Platform

Fresh frozen or FFPE

Sample types

*Input recommendations for FFPE samples vary depending on Archer Preseq® RNA QC score; 50ng input recommended in absence of PreSeq screening

Gene targets


ABL1
ABL2
AKT1
AKT2
AKT3
ALK
ARHGAP26
AXL
BRAF
BRD3
BRD4
CRLF2
CSF1R
EGFR
EPOR
ERBB2
ERBB4
ERG
ESR1
ESRRA
ETV1
ETV4
ETV5
ETV6
EWSR1
FGFR1
FGFR2
FGFR3
FGR
IL2RB
INSR
JAK1
JAK2
JAK3
KIT
MAML2
MAST1
MAST2
MET
MSMB
MUSK
MYB
MYC
NOTCH1
NOTCH2
NRG1
NTRK1
NTRK2
NTRK3
NUMBL
NUT
PDGFRA
PDGFRB
PIK3CA
PKN1
PPARG
PRKCA
PRKCB
PTK2B
RAF1
RARA
RELA
RET
ROS1
RSPO2
RSPO3
SYK
TERT
TFE3
TFEB
THADA
TMPRSS2
TSLP
TYK2

Need to modify this panel?

Add any of our wet lab-validated designs to this panel with Archer Assay Designer to build an assay that fits your exact requirements.

Additional product information

Talk: Gene fusion detection in FFPE tumors by NGS

 

Detecting fusions using the Archer FusionPlex Oncology Research Kit

ArcherDX has developed a comprehensive kit to rapidly detect translocations from total nucleic acid isolated from tumor samples, including FFPE preserved specimens. Anchored Multiplex PCR (AMP™) enrichment chemistry enables targeted amplification of fusion mRNAs, creating libraries that are optimal for multiplex NGS-based fusion detection. Archer technology permits the simultaneous detection of both known recurrent fusions as well as previously unidentified fusions at key breakpoints in target genes. The Archer FusionPlex Oncology Research Kit offers comprehensive NGS-based fusion detection, from library preparation through data analysis.

Ph-like acute lymphoblastic leukemia

The FusionPlex Oncology Research Kit includes targets found in Philadelphia chromosome-like acute lymphoblastic leukemia (Ph-like ALL), which is characterized by modifications in lymphoid transcription factor genes, poor outcomes, and a gene-expression profile similar to that of BCR-ABL1 ALL. Recent clinical and xenograft studies have revealed that the Ph-like ALL gene expression profile includes multiple genomic alterations, which are listed in the table below (table derived from [8]).

Kinase fusions identified in Ph-like acute lymphoblastic leukemia

Kinase Gene Fusion Partners 5' Genes
ABL1 6 ETV6, NUP214, RCSD1, RANBP2, SNX2, ZMIZ1
ABL2 3 PAG1, RCSD1
CSF1R 1 SSBP2
PDGFRB 4 EBF1, SSBP2, TNIP1, ZEB2
CRLF2 2 P2RY8
JAK2 10 ATF7IP, BCR, ETV6, PAX5, PPFIBP1, SSBP2, STRN3, TERF2, TPR
EPOR* 2 IGH, IGK
IL2RB 1 MYH9
NTRK3 1 ETV6
PTK2B 2 KDM6A, STAG2
TSLP 1 IQGAP2
TYK2 1 MYB

*FusionPlex Oncology Research Kit will only detect an EPOR truncation

Precision genomics and gene fusions

The landmark discovery that gene fusions drive the development of specific cancer subtypes empowered the development of a host of targeted therapies. The exclusivity of oncogenic fusion genes to cancer cells makes them attractive targets for such therapy. Furthermore, gene fusions are also used as diagnostic and prognostic biomarkers to confirm diagnosis and monitor clinical outcome in response to therapy, respectively. The advent of next-generation sequencing greatly expedited the discovery and characterization of gene fusions in a wide variety of cancer types.

Two of the most successful cancer drugs developed to date are crizotinib and imatinib. These drugs target specific tyrosine kinases that form chimeric fusions. Crizotinib is FDA approved for ALK positive fusions in NSCLC and Imatinib induces remission in leukemia patients that are positive for BCR-ABL fusions (6).

Discovery of fusions coincides with improved DNA sequencing technology

Figure 1. Gene fusion discovery coincides with the improvement of DNA sequencing technologies. Above the timeline, the colored boxes represent the year in which the denoted gene fusion was discovered, while arrows below the timeline represent the year in which certain DNA sequencing technologies became available (graphic derived from [7]). The acronyms below the gene fusions represent the type of cancer with which it is associated:

  • ACC - adenoid cystic carcinoma
  • ALCL - anaplastic large cell lymphoma
  • ALL - acute lymphocytic leukemia
  • AML - acute myeloid leukemia
  • APL - acute promyelocytic leukemia
  • BC - bladder cancer
  • BL - Burkitt lymphoma
  • CF - congenital fibrosarcoma
  • CML - chronic myelogenous leukemia
  • CRC - colorectal cancer
  • ES - Ewing sarcoma
  • FTC - follicular thyroid carcinoma
  • GBM - glioblastoma multiforma
  • IMT - inflammatory myofibroblastic tumor
  • MC - mucoepidermoid carcinoma
  • ML - myxoid liposarcoma
  • NMC - nut midline carcinoma
  • NSCLC - non-small cell lung cancer
  • PA - pilocytic astrocytoma
  • PC - prostate cancer
  • PRCC - pediatric renal cell carcinoma
  • SBC - secretory breast carcinoma
  • SOC - serious ovarian cancer
  • SS - synovial sarcoma

Resources

  1. Cantwell-Dorris et al. BRAFV600E: Implications for Carcinogenesis and Molecular Therapy. MOL Cancer Ther. 10(3):385-94(2011)
  2. Ma et al. c-MET mutational analysis in small cell lung cancer: novel juxtamembrane domain mutations regulating cytoskeletal functions. Cancer Res. 63(19):6272-81 (2003).
  3. Ashworth et al. Deletion-based mechanisms of NOTCH1 activation in T-ALL: key roles for RAG recombinase and a conserved internal translational start site in NOTCH1. Blood. 116(25):5455-5464 (2010).
  4. Ozawa et al. PDGFRA gene rearrangements are frequent genetic events in PDGFRA-amplified glioblastomas. Genes & Dev. 24: 2205-2218 (2010).
  5. E. Lierman et al., FIP1L1-PDGFRalpha D842V, a novel panresistant mutant, emerging after treatment of FIP1L1-PDGFRalpha T674I eosinophilic leukemia with single agent sorafenib. Leukemia. 23:845-851 (2009).
  6. 1. S. E. Jackson, J. D. Chester, Personalised cancer medicine. Int. J. Cancer. 137, 262–266 (2015).
  7. M. J. Annala, B. C. Parker, W. Zhang, M. Nykter, Fusion genes and their discovery using high throughput sequencing. Cancer Lett. 340, 192–200 (2013).
  8. K. G. Roberts et al., Targetable kinase-activating lesions in Ph-like acute lymphoblastic leukemia. N. Engl. J. Med. 371, 1005–1015 (2014).

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How to contact us

Address

2477 55th Street, Suite 202

Boulder, CO 80301

Phone

Phone: (877) 771 1093

Phone: (303) 357 9001

All content © 2018 ArcherDX, Inc.

For Research Use Only. Not for use in diagnostic procedures. For Research Use Only. Not for use in diagnostic procedures.