Specimen Collection Manual and Test Catalog

Fresh, undiluted FNA of cyst fluid (preferred), RPMI aliquot, RPMI supernatant or sample in PreservCyt container. Minimum 600 uL.
For non-Geisinger sites, send fresh, undiluted FNA of cyst fluid or bile duct brushing. Alternately, send fluid/brushing in RPMI media or a PreserveCyt container.
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.

Deliver to cytology for processing and aliquoting. Do not centrifuge the sample.

Refrigerated (2-8°C) 

Refrigerated (2-8°C), 3 days.  Specimen must be extracted within 3 days.
For RPMI media samples, extract within 3 days (preferred) or up to 30 days.
For PreservCyt samples, extract within 3 days (preferred) or up to 90 days.

Insufficient DNA and/or RNA. Wrong collection tube. Improper storage or transport temperature. Stability limits exceeded.
Special Note: FFPE sample (if testing can only be performed from a cell block, please order CUSTG50GP).

Negative (no mutations detected).

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 pancreatic cyst and bile duct fluid gene panel:

DNA based mutation analysis includes the following genes: ACVR1B, AKT1, AKT2, APC, ARAF, ARID1A, ARID1B, ARID2, ATM, ATR, ATRX, AXIN1, AXIN2, BAP1, BARD1, BRAF, BRCA1, BRCA2, BRIP1, CASP8, CDK12, CDKN2A, CDKN2B, CHEK1, CHEK2, CTNNB1, DAXX, EGFR, ELF3, EP300, EPCAM, EPHA2, ERBB2, ERBB3, ERBB4, FANCA, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCL, FAT1, FGFR1, FGFR2, FGFR3, FGFR4, GNAS, HDAC2, HIF1A, HNF1A, HRAS, IDH1, IDH2, KIT, KRAS, MAP2K4, MEN1, MET, MLH1, MRE11, MSH2, MSH6, MTOR, NBN, NF1, NF2, NOTCH1, NRAS, NTRK1, NTRK2, NTRK3, PALB2, PBRM1, PIK3CA, PMS1, PMS2, PTEN, RAD50, RAD51, RAD51B, RAD51C, RAD51D, RAD54L, RET, RNF43, ROS1, SMAD2, SMAD4, SMO, SRC, STK11, TERT, TGFBR2, TP53, TSC1, TSC2, VHL. 

Copy number variant analysis includes the following genes: ACVR1B, AKT1, AKT2, APC, ARAF, ARID1A, ARID1B, ARID2, ATM, ATR, ATRX, , AXIN1, AXIN2, BAP1, BARD1, BRAF, BRCA1, BRCA2, BRIP1, CASP8, CDK12, CDKN2A, CDKN2B, CHEK1, CHEK2, DAXX, EGFR, ELF3, EP300, EPCAM, EPHA2, ERBB2, ERBB3, ERBB4, FANCA, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCL, FAT1, FGFR1, FGFR2, FGFR3, FGFR4, GNAS, HDAC2, HNF1A, IDH2, KIT, KRAS, MAP2K4, MEN1, MET, MLH1, MRE11, MSH2, MSH6, MTOR, NBN, NF1, NF2, NOTCH1, NRAS, NTRK1, NTRK3, PALB2, PBRM1, PIK3CA, PMS1, PMS2, PTEN, RAD50, RAD51, RAD51B, RAD51C, RAD51D, RAD54L, RET, RNF43, ROS1, SMAD2, SMAD4, SMO, SRC,  STK11, TERT, TGFBR2, TP53, TSC1, TSC2, VHL. 

RNA based fusion analysis includes the following driver genes: AKT1, AKT2, ALK, BRAF, BRCA1, CDKN2A, ERBB2, ERBB4, EGFR, FGFR1, FGFR2, FGFR3, MET, NOTCH1, NTRK1, NTRK2, NTRK3, NUTM1, PIK3CA, PRKACA, PRKACB, RAF1, RET, ROS1, TERT. 

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

Next Generation Sequencing
RNA extraction

Oncomine Comprehensive Assay Plus, Solid Tumor Gene Panel, Solid Tumor DNA/RNA Gene Panel, NGS, Next-Generation Sequencing, Pancreatic Cyst and Bile Duct Fluid Gene Panel, Pancreatic cyst fluid, FNA, bile duct brushing

The MyGenVarCyto Pancreatic Cyst and Bile Duct Fluid 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.

Yi Ding MD, PhD