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Test Code NGSPS / PancreaSEQ GC PancreaSeq® Genomic Classifier (GC), Pancreatic Cyst Fluid NGS Analysis

Important Note

** Requirements for Testing **

  1. Copy of Endoscopy Report or Cytology report Required
  2. UPMC Test Requisition Required (Link Below)

                     Solid_Tumor_Req.pdf (upmc.com)

Additional Codes

Software Test Code
Label Text NGSPS
EPIC LAB20554
UPMC PANCREASEQ GC

 

Performing Laboratory

University of Pittsburgh Medical Center (UPMC)

Useful For

 

PancreaSeq® Genomic Classifier (GC) is a diagnostic test for pancreatic cysts detected by imaging, including benign cysts (e.g., serous cystadenomas), mucinous cysts (IPMN/MCN), cystic pancreatic neuroendocrine tumors (PanNETs), and early detection of pancreatic ductal adenocarcinomas.

Method Name

Next Generation Sequencing, qRT-PCR

Report Available

7-14 Days

Analytic time for send out tests is the time it will take to perform testing once it has arrived at the performing reference lab. Please add 1 to 2 days from time of collection to allow for receipt at NorDx central lab and shipment of specimen, add another day if specimen is collected on the day before a weekend or holiday.

Specimen Type

FNA - Fine Needle Aspirate

Preferred Container

Vial containing 600µl of stabilization fluid (provided by NorDx Cytology Department)

PLEASE NOTE:

  • Preservative solution is light sensitive, always store vials in a dark place and at room temperature (+15 to +25°C) until expiration date.
  • If any crystallization forms inside the collection vial or if the preservative solution turns yellow, appropriately discard the tube and collect the specimen using another collection tube.

Specimen Collection and Handling

Collection Instructions:

  1. Take one vial containing 600µl of stabilization fluid and clearly mark the vial with a typed label containing at least two patientidentifiers.
  2. Place the pancreatic cyst fluid sample (200-600µl) into the vial.
  3. After collection, secure the tube cap and invert several times to mix the collected sample.
  4. Store the collected sample as follows:

• No longer than 3 hours at room temperature (+15 to +25°C)

• No longer than 24 hours at +2 to +8°C, i.e. in a refrigerator

• Up to 12 months at -15 to -25°C , i.e. in a freezer

Instructions for shipping a collected pancreatic cyst sample for PancreaSeq® testing:

  1. Ensure that all collection vials are labeled with at least two unique patient identifiers.
  2. Ship with ice packs by overnight delivery. Shipping with dry ice is recommended for multiple tubes and when a delay in shipment is possible.
  3. Include the completed test requisition form and either the cytology or endoscopy report.

Specimen Stability Information

Specimen Type Temperature Time
FNA (Fine Needle Aspirate) Refrigerated 24 hours
  Ambient 3 hours
  Frozen (-15 to 25°C) 12 months

 

Add On Capable

No.

CPT Code Information

CPT Code CPT Description CPT Disclaimer

81275

Kras gene variants exon 2

N/A
81479 x2 Tier 2 Molecular Pathology Procedures N/A
81403 Molecular Pathology Procedure level 4 N/A
81404 Molecular Pathology Procedure level 5 N/A
81276 Kras gene addl variants N/A

 

Clinical Significance

PancreaSeq Genomic Classifier (GC) is a 74-gene, DNA and RNA-based, targeted next-generation sequencing assay that tests for five classes of genetic alterations: (i) point mutations, (ii) indels, (iii) gene fusions (GF), (iv) copy number alterations (CNA) including loss of heterozygosity of tumor suppressor genes, and (v) gene expression alterations (GEA). In addition, it measures the expression of the CEACAM5 gene by qRT-PCR.

 

Genes detected:

SNVs and indels in AKT1, APC, BRAF, CTNNB1, GNAS, HRAS, IDH1, IDH2, KRAS, MEN1, MET, NF2, NRAS, PIK3CA, PTEN, STK11, TERT, TP53, TSC2, and VHL genes

Loss of heterozygosity (LOH) in the RNF43 (17q), SMAD4 (18q), TP53 (17p), VHL (3p), NF2 (22q), PTEN (10q) tumor suppressor genes and copy number alterations (CNAs) at 13 genomic regions

Gene fusions (GF) in the ALK (GFPT1, GTF2IRD1, EML4, TFG, CCDC149, STRN), BRAF (AGK, BCL2L11, TRIM24, POR, SND1, AKAP9, ZC3HAV1, MKRN1, PICALM, CCNY, GORASP2, AGK, FAM114A2, MACF1, ZBTB8A), ERBB4 (EZR), NTRK1 (TPM3, TFG, TPR, SSBP2, SQSTM1, IRF2BP2, BANP, ETV6), NTRK3 (SQSTM1, EML4, ETV6, RBPMS), ROS1 (CCDC30), RAF1 (AGGF1), PRKACB (ATP1B1, DNAJB1), and PRKACA (ATP1B1)

Gene expression (GE) of the KRT7, KRT20, CHRGR, and PGK1 genes

CEACAM5 gene mRNA expression as a marker of CEA elevation

The findings are subjected to algorithmic analysis to categorize as Negative or Positive for specific alterations associated with different cyst types and risk of progression.