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Specimen Collection Manual and Test Catalog

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MYGENVAR GASTROESOPHAGEAL NEOPLASM GENE PANEL, NEXT GENERATION SEQUENCING

Geisinger Epic Procedure Code:  LAB4074    Geisinger Epic ID:  168371
Test Restriction:  LAB ORDER ONLY

SPECIMEN COLLECTION
Specimen type:  Formalin-fixed, paraffin-embedded tissue (FFPE) OR Fresh tissue (including bone marrow aspirate)
Preferred collection container: 
Specimen required: 
PREFERRED:
FFPE tissue:  Six (6) unstained slides (USS), 10 µm thickness each, in slide folder (protected from light)
Bone marrow: 3 mL lavender-top K2 EDTA tube (part of Bone Marrow Panel Collection – Bone Marrow Aspirate – Two [2] K2 EDTA Tube[s])
Fresh tissue:  Place in liquid medium (e.g., RPMI)
Special notes: 
FFPE tissue: For non-Geisinger sites, send six (6) USS/10 µm thickness, H&E slide, source of specimen and tumor assessment.  Alternatively, send the FFPE block and additional information. 
Bone marrow: For non-Geisinger sites, collection tube is included in the bone marrow (BM) collection kit.

NOTE: Isolated/extracted nucleic acids are acceptable only from CLIA-certified laboratories or a laboratory meeting equivalent requirements as determined by CAP and/or CMS.



SPECIMEN PROCESSING
Processing instructions: 
Mix well immediately. Do not centrifuge or separate plasma from cells.
Transport temperature: 
FFPE tissue:  Room temperature (18-25°C)
Bone marrow/fresh tissue:: Refrigerated (2-8°C) 
Specimen stability: 
FFPE Tissue: Room temperature (18-25°C), indefinitely
Bone marrow/fresh tissue: Refrigerated (2-8°C), 3 days.  Specimen must be extracted within 3 days.
Rejection criteria: 
FFPE blocks containing no tumor (evaluated by pathologist). FFPE tissues that have been decalcified. Insufficient DNA and/or RNA. Wrong collection tube. Improper storage or transport temperature. Stability limits exceeded. Shared or comingled specimens.

TEST DETAILS
Reference interval: 
Negative (no mutations detected).
Additional information: 
For molecular testing, original tube is required.
CPT code(s):  81459
Note: The billing party has sole responsibility for CPT coding.  Any questions regarding coding should be directed to the payer being billed.
The CPT codes provided by GML are based on AMA guidelines and are for informational purposes only.

Test includes: 
This custom testing gene panel uses targeted next-generation sequencing (NGS) to detect genomic alterations including: tumor mutation burden (TMB), microsatellite instability (MSI), single base-pair mutations and small insertions/deletions in the coding regions or adjacent intron/exon boundaries, copy number variants (CNV), gene rearrangements (RNA fusion) and exon skipping.            

The following mutations will be reported on the gastroesophageal neoplasm gene panel:

DNA based mutation analysis includes the following genes: AKT1, AKT2, AKT3, ALK, APC, ARID1A, ATM, ATR, BARD1, BLM, BRAF, BRCA1, BRCA2, BRIP1, CDH1, CDK12, CDKN2A, CHEK1, CHEK2, CTNNB1, EGFR, EPCAM, ERBB2, ERBB3, ERBB4, FANCA, FANCC,FANCD2, FANCE,FANCF, FANCL, FGFR1, FGFR2, FGFR3, GNAS, HDAC2, HRAS, KIT, KRAS, MAP2K1, MET, MLH1, MRE11, MSH2, MSH3, MSH6, NBN, NF1, NFE2L2, NOTCH1, NRAS, NTRK1, NTRK2, NTRK3, PALB2, PDGFRA, PIK3CA, PMS1, PMS2, POLE, PTEN, PTPN11, RAD50, RAD51, RAD51B, RAD51C, RAD51D, RAD54L, RB1, RNF43, SDHA, SDHB, SDHC, SDHD, SMAD4, SMARCA4, SMO, SRC, STK11, TERT, TGFBR2, TP53.                

Copy number variant analysis includes the following genes: AKT1, AKT2, AKT3, ALK, APC, ARID1A, ATM, ATR, BARD1,BLM, BRAF, BRCA1, BRCA2, BRIP1,CDH1, CDK12, CDKN2A, CHEK1, CHEK2, EGFR, EPCAM, ERBB2, ERBB3, ERBB4, FANCA, FANCC, FANCD2, FANCE ,FANCF, FANCL, FGFR1, FGFR2, FGFR3, GNAS,HDAC2, KIT, KRAS, MAP2K1, MET, MLH1, MRE11, MSH2, MSH3, MSH6, NBN, NF1, NFE2L2, NOTCH1, NRAS, NTRK1, NTRK3, PALB2,PDGFRA, PIK3CA, PMS1, PMS2, POLE, PTEN, PTPN11, , RAD50, RAD51, RAD51B, RAD51C, RAD51D, RAD54L, RB1, RNF43, SDHA, SDHB, SDHD, SMAD4, SMARCA4, SMO, SRC, STK11, TERT, TGFBR2, TP53.

RNA based fusion analysis includes the following driver genes: AKT1, AKT2, AKT3, ALK, BRAF, BRCA1, CDKN2A, ERBB2, ERBB4, EGFR, FGFR1, FGFR2, FGFR3, MET, NOTCH1, NTRK1, NTRK2, NTRK3, PIK3CA, TERT.

RNA based exon analysis includes the following genes: BRAF, BRCA1, EGFR, MET, NTRK1.


Methodology: 
DNA/RNA Extraction
Next Generation Sequencing
Synonyms: 
Oncomine Comprehensive Assay Plus, Solid Tumor Gene Panel, Solid Tumor DNA/RNA Gene Panel, NGS, Next-Generation Sequencing, UPGIGP
Clinical significance: 
The MyGenVar Gastroesophageal Neoplasm Gene Panel targets DNA and RNA variants by high-throughput sequencing. It helps determine diagnostic classification and provide prognostic or therapeutic information for clinical management.
Doctoral Director(s): 
Yi Ding MD, PhD
Review Date:  09/24/2024

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