2017 Publications Spotlight

Published Tue Dec 19, 2017


2017: A year in reveiw for ArcherDX

2017 was a big year for Archer...

Thanks to our customers (eh hem, YOU), 14 papers demonstrating the utility of Archer assays were published in peer-reviewed journals. Not only that, but 90 posters were presented at both national and international conferences. Congratulations to all of the authors who contributed – we really appreciate your hard work! And here’s an extra-special thanks to the many speakers who shared their experiences with our products at conferences. Working with people like you makes our job easy.

Here’s a recap of this year’s publications, with a list of all publications from 2017 below. But first, we’d like to bring special attention to Julie Vendrell’s paper on novel ALK fusion identification.

FusionPlex ARR v2 was shown to detect 37 ALK fusions in NSCLC with 100% accuracy, and identified novel fusions

Julie Vendrell et al. from CHU de Montpellier analyzed 37 NSCLC FFPE samples for ALK fusions using the Archer® FusionPlex® ARR v2 Panel and the Ion AmpliSeq™ RNA Lung Cancer Research Fusion Panel in parallel. These samples had previously been characterized by FISH and IHC, and included fusion-positive and fusion-negative samples. The results below show that the FusionPlex assay accurately identified ALK fusions in 100% (37/37) of samples, whereas the AmpliSeq assay accurately identified ALK fusions in 67.6% (25/37) of samples. Furthermore, the FusionPlex assay identified 1 rare and 2 novel ALK fusions, none of which were detected with the AmpliSeq assay. These fusions were confirmed with RT-PCR and Sanger sequencing. Importantly, 2 of the 3 ALK fusions that were only detected with the FusionPlex assay were sensitive to the ALK inhibitor, crizotinib.

“In contrast to the AmpliSeq amplicon-based approach that was unable to detect several variants, the Archer® AMP-based technique successfully identified all ALK fusion-positive samples, rendering this method highly applicable for routine ALK fusion detection and variant identification.” – Vendrell et al. 2017
Table 1. Detection of ALK rearrangements in clinical specimens using IHC, FISH, Ion AmpliSeq RNA Fusion kit, and Archer FusionPlex Kit.
Sample ID IHC results FISH results NGS results - Ion AmpliSeq RNA Fusion NGS results - Archer FusionPlex Results summary
S01 Negative Negative Negative Negative Concordance
S02 Negative Negative Negative Negative Concordance
S03 Negative Negative Negative Negative Concordance
S04 Negative Negative Negative Negative Concordance
S05 Negative Negative Negative Negative Concordance
S06 Negative Negative Negative Negative Concordance
S07 Negative Negative Negative Negative Concordance
S08 Negative Negative Negative Negative Concordance
S09 Negative Negative Negative Negative Concordance
S10 Negative Negative Negative Negative Concordance
S11 Negative Negative Negative Negative Concordance
S12 Negative Negative Negative Negative Concordance
S13 Negative Negative Negative Negative Concordance
S14 Positive Positive EML4-ALK (E6:A20) EML4-ALK (E6:A20) Concordance
S15 Positive Positive EML4-ALK (E6:A20) EML4-ALK (E6:A20) Concordance
S16 Positive Positive EML4-ALK (E6:A20) EML4-ALK (E6:A20) Concordance
S17 Positive Positive EML4-ALK (E6:A20) EML4-ALK (E6:A20) Concordance
S18 Positive Positive EML4-ALK (E6:A20) EML4-ALK (E6:A20) Concordance
S19 Positive Positive EML4-ALK (E13:A20) EML4-ALK (E13:A20) Concordance
S20 Positive Positive EML4-ALK (E13:A20) EML4-ALK (E13:A20) Concordance
S21 Positive Positive EML4-ALK (E13:A20) EML4-ALK (E13:A20) Concordance
S22 Positive Positive EML4-ALK (E13:A20) EML4-ALK (E13:A20) Concordance
S23 Positive Positive EML4-ALK (E13:A20) EML4-ALK (E13:A20) Concordance
S24 Positive Positive EML4-ALK (E13:A19) EML4-ALK (E13:A20) Discordance in the variant detected by NGS approaches
S25 Positive Positive EML4-ALK (E13:A20) EML4-ALK (E13:A20) Concordance
S26 Negative Negative Uncertain ALK Negative Discordance between NGS results
S27 Negative Negative Uncertain ALK Negative Discordance between NGS results
S28 Negative Negative Uncertain ALK Negative Discordance between NGS results
S29 Negative Negative Uncertain ALK Negative Discordance between NGS results
S30 Negative Negative Uncertain ALK Negative Discordance between NGS results
S31 Negative Negative Uncertain ALK Negative Discordance between NGS results
S32 Negative Negative Uncertain ALK Negative Discordance between NGS results
S33 Negative Negative Uncertain ALK Negative Discordance between NGS results
S34 Negative Negative Uncertain RET Negative Discordance between NGS results
S35 Positive Positive Uncertain ALK GCC2-ALK (G19:A20) Discordance between NGS results
S36 Positive Positive Uncertain ALK DCTN1-ALK (D26:A20) Discordance between NGS results
S37 Positive Positive Negative CLIP1-ALK (C22:A20) Discordance between NGS results

And many more publications and posters demonstrated the utility of Archer assays in:

  • molecular profiling of cancers
  • detection of mutations from liquid biopsies
  • characterization of immune repertoires

Explore more publications from 2017 below, or browse through our publications and posters webpages found at archerdx.com/support/documents

2017 Publications using AMP technology

  1. Loke, B. N. et al. Novel exon-exon breakpoint in CIC-DUX4 fusion sarcoma identified by anchored multiplex PCR (Archer FusionPlex Sarcoma Panel). J. Clin. Pathol. 0, 1-5 (2017).
  2. Vendrell, J. A. et al. Detection of known and novel ALK fusion transcripts in lung cancer patients using next-generation sequencing approaches. Scientific Reports 7, 1-11 (2017).
  3. Church, A. J. et al. Recurrent EML4-NTRK3 fusions in infantile fibrosarcoma and congenital mesoblastic nephroma suggest a revised testing strategy. Mod Pathol 228, 119 (2017).
  4. Davies, K. D. et al. Dramatic Response to Crizotinib in a Patient With Lung Cancer Positive for an HLA-DRB1-MET Gene Fusion. JCO Precision Oncology 1, 1-6 (2017).
  5. Haimes, J. D. et al. Uterine Inflammatory Myofibroblastic Tumors Frequently Harbor ALK Fusions With IGFBP5 and THBS1. Am. J. Surg. Pathol. 41, 773-780 (2017).
  6. Zehir, A. et al. Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. Nat. Med. 159, 676 (2017).
  7. Wang, L. et al. Identification of NTRK3 Fusions in Childhood Melanocytic Neoplasms. The Journal of Molecular Diagnostics 19, 387-396 (2017).
  8. Hue, S. S.-S. et al. Primary Bone Anaplastic Large Cell Lymphoma Masquerading as Ewing Sarcoma: Diagnosis by Anchored Multiplex PCR. J. Pediatr. Hematol. Oncol. (2017). [Epub ahead of print]
  9. Farhat, N. A. et al. Primary Benign and Malignant Thyroid Neoplasms With Signet Ring Cells: Cytologic, Histologic, and Molecular Features. Am. J. Clin. Pathol. 148, 251-258 (2017).
  10. Badar, T. et al. Detection of Novel t(12;17)(p12;p13) in Relapsed Refractory Acute Myeloid Leukemia by Anchored Multiplex PCR(AMP)-based Next-Generation Sequencing. Appl. Immunohistochem. Mol. Morphol. (2017). [Epub ahead of print]
  11. Zhao, L., Dias-Santagata, D., Sadow, P. M. & Faquin, W. C. Cytological, molecular, and clinical features of noninvasive follicular thyroid neoplasm with papillary-like nuclear features versus invasive forms of follicular variant of papillary thyroid carcinoma. Cancer 125, 323-331 (2017).
  12. Szurian, K., Kashofer, K. & Liegl-Atzwanger, B. Role of Next-Generation Sequencing as a Diagnostic Tool for the Evaluation of Bone and Soft-Tissue Tumors. Pathobiology (2017). [Epub ahead of print]
  13. Patel, N. R. et al. USP6 activation in nodular fasciitis by promoter-swapping gene fusions. Mod Pathol 30, 1577-1588 (2017).
  14. Afrin, S. et al. Targeted Next-Gen Sequencing for Detecting MLL Gene Fusions in Leukemia. Mol Cancer Res (2017). [Epub ahead of print]

Looking for more? Browse through our publications and posters webpages found at archerdx.com/support/documents.

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