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Assay Information

Assay Information

Somatic Mutation Analysis Clonality Studies
Multigene NGS
(Life Technologies Ion Torrent)		 Single Gene
(Rotor-Gene Q-PCR)
(Invivoscribe)
MGP-1

22 Gene Panel

AKT1, ALK, BRAF, CTNNB1, DDR2, EGFR, ERBB2, ERBB4, FBXW7, FGFR1, FGFR2, FGFR3, KRAS, MAP2K1, MET, NOTCH1, NRAS, PIK3CA, PTEN, SMAD4, STK11, TP53

 MGP-2

50 Gene Panel

ABL1, AKT1, ALK, APC, ATM, BRAF, CDH1, CDKN2A, CSF1R, CTNNB1, EGFR, ERBB2, ERBB4, EZH3, FBXW7, FGFR1, FGFR2, FGFR3, FLT3, GNA11, GNAQ, GNAS, HNF1A, HRAS, IDH1, IDH2, JAK2, JAK3, KDR, KIT, KRAS, MET, MLH1, MPL, NOTCH1, NPM1, NRAS, PDGFRA, PIK3CA, PTEN, PTPN11, RB1, RET, SMAD4, SMARCB1, SMO, SRC, STK11, TP53, VHL

Please call for additional information if considering a referral.

 BRAF

Therascreen CE-IVD Assay

Detection of selected variants at Codon 600 of BRAF.

 B-Cell Clonality

Invivoscribe CE-IVD Assay

  • IgK-A
  • IgK-B
  • IgH-FR2
  • IgH-FR3
  • IgH-FR1 (Optional)

 

 T-Cell Clonality

Invivoscribe CE-IVD Assay

  • TCR-β A
  • TCR-β B
  • TCR-β C
  • TCR-γ A
  • TCR-γ B
  • TCR-δ (Optional)

 

Full List of Mutations Assessed in MGP-1
Full List of Mutations Assessed in MGP-2

Sample Somatic Mutation Analysis Report (v3.2)

Turnaround Times: (June 2016)

  Somatic Mutation Analysis Clonality Studies
MGP-1 MGP-2 BRAF B-Cell T-Cell B&T-Cell
Target TAT (days) 8-10 8-10 6 8-10 8-10 8-10
Mean TAT (days) 7.66 6.82 4.77 6.17 6.50 8.67
(Ex. Repeats) 7.04 - - - - -
% Within TAT 89.52 100 100 100 100 100
(Ex. Repeats) 100 - - - - -

 

Repeats: Please note that given the length/complexity of the NGS pipeline, there is unfortunately no realistic possibility of repeating any samples upon which analysis fails within target TAT. You will be informed of analysis failures straight away and potential options discussed.

Specimen Requirements:

Specimen requirements for NGS and BRAF analysis are as follows:

  • Fixed tissue (including FNA, resection specimen, core biopsy etc.): One (1) formalin-fixed paraffin-embedded (FFPE) block from a biopsy or surgical resection should be provided. The combined area of tumour tissue (not total tissue) must be a minimum area of 4mm2.
  • Curls and unstained slides: For large tissue samples (>1.5cm2) 1x10µM section, medium tissue samples (1-1.5cm2) 2x10µM sections, small tissue samples (0.5-1cm2) 3x10µM sections and for multiple small tissue fragments 6-8x10µM sections.

Please provide a stained H&E with the tumour area marked on the slide. Cases which require re-extraction and re-testing due to inadequate indication of tumour load will be charged twice. If on the rare occasion that the H&E slide is not provided, it is essential that all requests include an indication of percentage of tumour DNA content within the sample. Tumour percentage can be estimated as >5%, >25%, >50%, >75%, 100% as often full numeration is not possible. Samples with < 5% tumour content will be returned untested.

Specimen requirements for Clonality analysis are as follows:

  • Extracted DNA
  • Cytology specimens: Preferably fresh (unfixed) in 1.5 mL Eppendorf tubes. If the material has been fixed, please let us know what fixative was used and for how long.
  • Formalin fixed paraffin embedded (FFPE) blocks
  • FFPE Curls and unstained slides (specifications as for NGS/BRAF detailed above)

Please send a histology report and a H&E slide along with your request form, if possible.