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| Organization: | Alberta Precision Laboratories | ||||||||
| Message Alert: | PLEASE NOTE: This Test Directory is in an interim state and due to changes pertaining to the DynaLIFE transition, performing site for routing has not been updated. Please refer to Laboratory Information System for appropriate routing. | ||||||||
| Test Name/Synonym: | Combined Cancer Biomarker Comprehensive DNA Panel and Pan-Solid Tumor Fusion RNA Panel, Tumor (Synonyms: GIST, tumor BRCA1/2, glioma, meningioma, GBM, MDM2, KIT, 1p, 1p19q, 19q, high-grade serous carcinomas, renal, pan-solid tumor DNA panel, solid tumor diagnosis, melanoma, microsatellite instability, prostate cancer, brain cancer, breast cancer, endometrial cancer, ovarian cancer, colon cancer, thyroid cancer, sarcoma, pan-cancer, renal cancer, kidney cancer) | ||||||||
| Clinical Indications: | For the investigation of DNA single nucleotide variants, small insertion/deletion, copy number alterations and genomic signatures across a wide variety of disease states as well as diagnostic gene fusion detection in solid tumors (see above synonyms section). | ||||||||
| Test Includes: | For Cancer Biomarker Comprehensive DNA Panel: The Cancer Biomarker Comprehensive DNA panel is a pan-solid tumor assay validated to detect single nucleotide variants (SNVs), small insertions or deletions (indels), amplifications, and homozygous-type deletions in the following 130 genes: ACVR1, AKT1, AKT3, ALK, APC, AR, ARAF, ARHGAP35, ARID1A, ATM, ATRX, BAP1, BARD1, BCOR, BRAF, BRCA1, BRCA2, BRIP1, CCND1, CCNE1, CDC42, CDH1, CDK12, CDK4, CDK6, CDKN2A, CDKN2B, CHEK2, CIC, CTNNB1, DICER1, EGFR, EIF1AX, ELOC, EPCAM, ERBB2, ERBB3, ERBB4, ESR1, EZH1, EZH2, FBXW7, FGFR1, FGFR2, FGFR3, FGFR4, FH, FLCN, FOXL2, FUBP1, GNA11, GNAQ, GNAS, H3F3A, H3F3B, HIST1H3B, HIST1H3C, HNF1A, HOXB13, HRAS, IDH1, IDH2, KEAP1, KLF4, KIT, KRAS, MAP2K1, MAP2K2, MAP2K4, MAPK1, MDM2, MDM4, MEN1, MET, MLH1, MSH2, MSH6, MTOR, MYC, MYCN, MYD88, MYOD1, NBN, NF1, NF2, NRAS, NTRK1, NTRK2, NTRK3, PALB2, PBRM1, PDGFRA, PDGFRB, PIK3CA, PIK3CB, PIK3R1, PLEKHS1, PMS2, POLE, POLR2A, PPP2R1A, PRKCA, PRKD1, PTEN, RAD51C, RAD51D, RAC1, RAF1, RB1, RET, ROS1, SDHA, SDHB, SDHC, SDHD, SETD2, SMAD4, SMARCA4, SMARCB1, SMO, SPOP, STK11, TERT, TFEB, TP53, TRAF7, TSC1, TSC2, TSHR, and VHL. Loss-of-heterozygosity (LOH) with corresponding copy number status (gain, loss, or copy-neutral) is assessed in all chromosome arms and reported when clinically valuable. The acceptable minimum depth of coverage is 100X and the mean depth is 1000X. Certain regions of some genes are not reported due to low coverage (a list of these regions is available upon request). For Pan-Solid Tumor Fusion RNA Panel: The Pan-Solid Tumor Fusion RNA Panel is used for the detection of fusions, oncogenic isoforms and/or selected single nucleotide variants (SNVs) and small insertions/deletions (indels) in the following 103 genes: AKT1, AKT3, ALK, AR, ARHGAP26, BCOR (including BCOR ITD), BRAF, BRD3, BRD4, CAMTA1, CCNB3, CIC, CSF1, CSF1R, CTNNB1, DNAJB1, EGF, EGFR, EPC1, ERBB2, ERBB4, ERG, ESR1, ETV1, ETV4, ETV5, ETV6, EWSR1, FGFR1, FGFR2, FGFR3, FOS, FOSB, FOXO1, FOXO4, FUS, GLI1, GLI2, GNAS, HMGA2, HRAS, IDH1, IDH2, JAZF1, KRAS, MAML2, MAP2K1, MEAF6, MET, MKL2, MN1, MSANTD3, MYB, MYBL1, MYOD1, NCOA1, NCOA2, NOTCH1, NOTCH2, NOTCH3, NR4A3, NRAS, NRG1, NTRK1, NTRK2, NTRK3, NUTM1, PAX3, PDGFB, PDGFRA, PDGFRB, PHF1, PLAG1, PPARG, PRDM10, PRKACA, PRKCA, PRKCB, PRKCD, PRKD1, PRKD2, PRKD3, RAF1, RELA, RET, ROS1, SRF, SS18, SS18L1, STAT6, TAF15, TCF12, TERT, TFCP2, TFE3, TFEB, THADA, THBS1, TMPRSS2, USP6, VGLL2, YAP1, YWHAE. Note that while selected SNVs/indels can be detected on this panel, RNA is not an ideal analyte for detecting these mutations, and this test cannot exclude SNVs/indels when not detected. The panel is primarily indicated for detection of fusions and oncogenic isoforms. | ||||||||
| Ordering Alert: | Test ordering restricted to oncologists, anatomical pathologists, molecular pathologists and medical geneticists. | ||||||||
| LABID (Connect Care): | LAB8032 | ||||||||
| Specimen Type: | For Cancer Biomarker Comprehensive DNA Panel: Formalin-fixed, paraffin-embedded (FFPE) tissue block, cytology direct smears, cell blocks, cytology fluid, nucleic acid preservative. For Pan-Solid Tumor Fusion RNA Panel: Formalin-fixed, paraffin-embedded (FFPE) tissue only. | ||||||||
| Primary Container: | See Specimen Collection Requirements | ||||||||
| Specimen Collection Requirements: | Five 10-micron unstained sections followed by a H&E slide then another five 10-micron unstained sections followed by a H&E slide. Cancer Biomarker Comprehensive DNA Panel requirements: For formalin-fixed paraffin-embedded tissue sections:
A formalin-fixed, paraffin-embedded tissue block (resection specimen, biopsy specimen, cell block) accompanied by a representative H&E (ideally the deepest level) is preferred. The assay requires a minimum of 20% tumor in the selected area (20 tumor nuclei per 100 total nuclei). When possible, non-Cytolyt®-exposed FFPE tissue is preferred over Cytolyt®-exposed FFPE tissue (cytology cell blocks). Alternatively, five 10-micron non-baked unstained slides accompanied by a representative H&E (ideally the deepest level) can be submitted. If the sample is relatively small (less than 10mm squared, for example a core biopsy 1mm in diameter and less than 1cm in length), particularly if the tissue has a low cell density, more than 5 (up to 10) 10-micron non-baked unstained slides may be sent to increase RNA yield for testing. Alternatively, precut scrolls can be submitted, accompanied by a representative H&E (ideally cut after the scrolls). Note: The tissue should not be exposed to decalcification solution. | ||||||||
| Test Resources: | Submit request using the applicable requisition or Connect Care online order entry:
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| Stability and Storage: | Room temperature | ||||||||
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| Method and Interpretation of Results: | For Cancer Biomarker Comprehensive DNA Panel: DNA extraction from formalin-fixed paraffin-embedded (FFPE) tissue was performed using the Thermo Fisher MagMAX FFPE DNA/RNA Ultra Kit on the KingFisher Apex purification system. The assay utilizes pools of primers to target the full coding sequence or hot-spot regions of 130 genes, 76 microsatellite loci, and several single nucleotide polymorphism (SNP) loci distributed across all the chromosomes. The template preparation of the Ion AmpliSeq-based libraries is performed in the Ion Chef System and massively parallel sequencing is performed in the Ion GeneStudio S5 Systems. Base calling is generated by the Torrent Suite Software (version 5.18.1). Variant calling, Oncomine variant annotations, and tumor mutational burden (TMB) status are generated by Ion Reporter software (version 5.20) with alignment to the reference human genome GRCh37/hg19. Copy number alterations (CNA) are evaluated using OncoCNV software (version 6.9). Loss-of-heterozygosity (LOH) is evaluated using SNPitty software. Microsatellite instability (MSI) analysis is performed using MSICall plugin (version 4.2). INTERPRETATION: Tier I, II, and III variants (per AMP/ASCO/CAP guidelines [1]) present at 5%-100% variant allele fraction (VAF) are reportable. Tier I variants have strong clinical significance with level A and B evidence. Tier II variants have potential clinical significance (level C and D evidence). Tier III variants are variants of unknown clinical significance. Functional assessment of the variants (oncogenicity) follows the ClinGen/CGC/VICC criteria [2]. MSI-High status is defined by an established MSICall score and/or the presence of mutations in the mismatch repair genes. This assay may be used as a screening test for tumors with TMB-High status where the TMB score is expected to be equal or superior to 10 mutations per megabase (mut/Mb); however, confirmation of the TMB-High status by an orthogonal method is encouraged if clinically indicated. All genomic coordinates are given with respect to GRCh37 (hg19). For cDNA and protein coordinates, reference transcripts are listed in the report. TEST LIMITATIONS: Small insertions or deletions occurring in a homopolymer sequence of 8 or more mononucleotide repeats are not detected. This assay requires a minimum of 10% tumor cellularity for the accurate detection of SNVs and small indels; 20% tumor cellularity for chromosomal LOH, MSI-High status, and TMB-High status, and 30%-50% tumor cellularity for homozygous-type deletions. For an accurate detection of gene amplification, the tumor cellularity requirement is variable and ranges from 10% tumor cellularity (if the number of copies per tumor cell is equal to or exceeds 32) to 100% tumor cellularity (if the number of copies per tumor cell is equal to or exceeds 5). A reliable distinction between variants located in the PMS2 gene and/or pseudogene(s) cannot be made due to the existence of homologous sequences and the confirmatory testing to determine the variant location cannot be performed on tissue specimens. PERFORMANCE METRICS: When the minimum specimen requirements are met, the positive percentage agreement is 99% for SNV, 96% for small indels (verified for indels of less than 40 bp in size), 100% for copy number alterations, 100% for LOH in chromosomal arms, and 100% for MSI-High detection, and the negative percentage agreement is 100%. The evaluation of TMB-High analysis in a small validation cohort yielded 100% positive percent agreement and 98% negative percentage agreement. Specimens with increased deamination artifacts or expected TMB values close to the 10 mut/Mb cut-off may be reported as indeterminate for TMB-High status. Rare polymorphisms may be present and could lead to false negative or false positive results. A negative (wild-type) result does not rule out the presence of a molecular alteration below the limits of detection of the assay. References: [1] Li M, et al. Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists. J Mol Diagn. 2017 Jan;19(1):4-23. [2] Horak P, et al. Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity): Joint recommendations of Clinical Genome Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant Interpretation for Cancer Consortium (VICC). Genet Med. 2022 May;24(5):986-998. Disclaimer: This assay does not distinguish between somatic (tumor-acquired) and germline (inherited) mutations. If the personal or familial history is suspicious for an inherited syndrome, referral to genetic counseling or germline testing (blood or buccal swab specimen) is encouraged. For Pan-Solid Tumor Fusion RNA Panel: RNA is analyzed using next generation sequencing (NGS) to detect gene fusions, oncogenic isoforms, and selected single nucleotide variants (SNVs) and insertions / deletions (indels). The assay utilizes a custom 103 gene Archer FusionPlex® panel, which uses anchored multiplex PCR (AMP) to enable partner-agnostic fusion detection. NGS libraries are sequenced on the Ion Torrent Genexus™ System and analyzed on Archer® Analysis with alignment to reference human genome GRCh37/hg19. The analysis is limited to tumor tissue and, therefore, this test is unable to distinguish between somatic (acquired) and germline (inherited) variants. | ||||||||
| Routine Turn Around Time: | 3 weeks | ||||||||
| Testing Schedule: | Weekly | ||||||||
| Performing Site: | University of Alberta Hospital or Foothills Medical Centre | ||||||||
| Contact Comments: |
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| Last Updated On: | Wednesday, February 28, 2024 | ||||||||
| Date of Last Review: | Feb 7 2024 12:00AM | ||||||||
| Registered Trademark Comments: | CYTOLYT® is a trademark of Hologic, Inc. FusionPlex® and Archer ® Analysis are registered trademarks of ARCHERDX, LLC Genexus™ is a trademark of Life Technologies Corporation | ||||||||
