Solid Tumors GeneTrails Solid Tumor Panel with Reflex to Solid Tumor Fusion Gene Panel

Test Code:

5440
Department:

Solid Tumors
Test Synonyms:

Solid Tumor Panel Version 3 • ACVR1 • AKT1 • AKT2 • AKT3 • ALK • AMER1 • APC • APLNR • AR • ARAF • ARID1A • ARID2 • ASF1A • ATM • ATR • ATRX • AURKA • AXIN1 • B2M • BAP1 • BARD1 • BRAF • BRCA1 • BRCA2 • BRD4 • BRIP1 • BUB1B • EMSY • CASP8CCND1 • CCND2 • CCND3 • CCNE1 • CD274 (PD-L1) • CDH1 • CDK12 • CDK4 • CDK6 • CDKN1B • CDKN2A • CHD4 • CHEK1 • CHEK2 • CIC • COL2A1 • CTNNB1 • DDR2 • DDX11 • DDX3X • DICER1 • EGFR • EGLN1 • EGLN2 • EIF1AX • EPAS1 • ERBB2 • ERBB3 • ERBB4 • ERCC2 • ERCC3 • ERCC5 • ESR1 • FAM175A • FANCA • FANCC • FANCD2 • FANCE • FANCF • FANCG • FANCM • FBXW7 • FGF19 • FGF3 • FGF4 • FGFR1 • FGFR2 • FGFR3 • FGFR4 • FH • FUBP1 • GATA3 • GNA11 • GNAQ • GNAS • H3F3A • HIST1H3B • HIST1H3C • HLA-A • HLA-B • HLA-C • HOXB13 • HRAS • IDH1 • IDH2 • IDO1 • IDO2 • IFNGR1 • IFNGR2 • INPP4B • IRF1 • JAK1 • JAK2 • KDR • KEAP1 • KIF1B • KIT • KLF4 • KRAS • LZTR1 • MAP2K1 (MEK1) • MAP2K2 (MEK2) • MAP2K4 • MAP3K1 • MAPK1 • MAX • MC1R • MDC1 • MDH2 • MDM2 • MDM4 • MEN1 • MET • MLH1 • MLH3 • MRE11A • MSH2 • MSH3 • MSH6 • MTAP • MTOR • MUTYH • MYC • MYCN • MYOD1 • NBN • NDUFAB1 • NF1 • NF2 • NRAS • NTRK1 • NTRK2 • NTRK3 • PALB2 • PBRM1 • PDCD1LG2 • PDGFRA • PIK3CA • PIK3CB • PIK3R1 • PLAG1 • PLCG1 • PMS1 • PMS2 • POLE • PPM1D • PPP2R1A • PPP6C • PRKAR1A • PRKCA • PSMB5 • PTCH1 • PTEN • PTPN11 • PTPRB • RAC1 • RAD50 • RAD51 • RAD51B • RAD51C • RAD51D • RAD52 • RAD54L • RAF1 • RASA1 • RB1 • RECQL • RET • REV7 • RHEB • RICTOR • RINT1 • RIT1 • RNF139 • RNF43 • ROS1 • RPTOR • RRAS • SDHA • SDHAF1 • SDHAF2 • SDHAF3 • SDHAF4 • SDHB • SDHC • SDHD • SETD2 • SF3B1 • SMAD4 • SMARCA2 • SMARCA4 • SMARCB1 • SMARCE1 • SMO • SOCS1 • SPEN • SPOP • STAG2 • STAT3 • STK11 • SUFU • TAP1 • TAP2 • TAPBP • TCEB1 • TERT • TMEM127 • TP53 • TP53BP1 • TRAF7 • TSC1 • TSC2 • VHL • XRCC1 • YAP1 • YES1
CPT Code(s):

81445

Background:

Features included:

Tumor mutation burden estimate (TMB)
Identification of microsatellite instability (MSI)
Genes related to resistance to immune checkpoint inhibitor treatment (HLA genes, B2M, JAK1, JAK2, IFNGR1, IFGR2)

The GeneTrails® Solid Tumor Panel (STP) is a next-generation sequencing (NGS) test used to screen for clinically informative gene alterations that are important in making therapeutic decisions, including SNVs, in/dels, and copy number alterations. The test can detect microsatellite instability and can provide an estimate of tumor mutation burden (TMB). The STP is intended for the analysis of solid tumors from patients with clinically advanced disease (stage III or IV). It covers genes that are informative for the use of FDA-approved therapies in non-small cell lung cancer (EGFR, BRAF, ALK, ROS1), colorectal cancer (KRAS, NRAS, BRAF), breast cancer (PIK3CA), and bladder cancer (FGFR2/3).^1-6

This panel will be reflexed to the GeneTrails Gene Fusion Panel when appropriate to screen for actionable kinase gene fusions if the Solid Tumor Panel results are negative.

Gene List:

ACVR1	CCND1	ERCC2	HLA-A	MDC1	PDGFRA	RB1	SOCS1
AKT1	CCND2	ERCC3	HLA-B	MDH2	PIK3CA	RECQL	SPEN
AKT2	CCND3	ERCC5	HLA-C	MDM2	PIK3CB	RET	SPOP
AKT3	CCNE1	ESR1	HOXB13	MDM4	PIK3R1	REV7	STAG2
ALK	CD274 (PD-L1)	FAM175A	HRAS	MEN1	PLAG1	RHEB	STAT3
AMER1	CDH1	FANCA	IDH1	MET	PLCG1	RICTOR	STK11
APC	CDK12	FANCC	IDH2	MLH1	PMS1	RINT1	SUFU
APLNR	CDK4	FANCD2	IDO1	MLH3	PMS2	RIT1	TAP1
AR	CDK6	FANCE	IDO2	MRE11A	POLE	RNF139	TAP2
ARAF	CDKN1B	FANCF	IFNGR1	MSH2	PPM1D	RNF43	TAPBP
ARID1A	CDKN2A	FANCG	IFNGR2	MSH3	PPP2R1A	ROS1	TCEB1
ARID2	CHD4	FANCM	INPP4B	MSH6	PPP6C	RPTOR	TERT
ASF1A	CHEK1	FBXW7	IRF1	MTAP	PRKAR1A	RRAS	TMEM127
ATM	CHEK2	FGF19	JAK1	MTOR	PRKCA	SDHA	TP53
ATR	CIC	FGF3	JAK2	MUTYH	PSMB5	SDHAF1	TP53BP1
ATRX	COL2A1	FGF4	KDR	MYC	PTCH1	SDHAF2	TRAF7
AURKA	CTNNB1	FGFR1	KEAP1	MYCN	PTEN	SDHAF3	TSC1
AXIN1	DDR2	FGFR2	KIF1B	MYOD1	PTPN11	SDHAF4	TSC2
B2M	DDX11	FGFR3	KIT	NBN	PTPRB	SDHB	VHL
BAP1	DDX3X	FGFR4	KLF4	NDUFAB1	RAC1	SDHC	XRCC1
BARD1	DICER1	FH	KRAS	NF1	RAD50	SDHD	YAP1
BRAF	EGFR	FUBP1	LZTR1	NF2	RAD51	SETD2	YES1
BRCA1	EGLN1	GATA3	MAP2K1 (MEK1)	NRAS	RAD51B	SF3B1
BRCA2	EGLN2	GNA11	MAP2K2 (MEK2)	NTRK1	RAD51C	SMAD4
BRD4	EIF1AX	GNAQ	MAP2K4	NTRK2	RAD51D	SMARCA2
BRIP1	EPAS1	GNAS	MAP3K1	NTRK3	RAD52	SMARCA4
BUB1B	ERBB2	H3F3A	MAPK1	PALB2	RAD54L	SMARCB1
EMSY	ERBB3	HIST1H3B	MAX	PBRM1	RAF1	SMARCE1
CASP8	ERBB4	HIST1H3C	MC1R	PDCD1LG2	RASA1	SMO

Methodology:

The Solid Tumor Panel is performed on DNA extracted from formalin-fixed, paraffin-embedded (FFPE) tumor tissue using next-generation sequencing. The NGS library preparation is based on custom QiaSeq chemistry (Qiagen) that includes unique molecular indices for the assessment of library complexity. Sequencing is performed on Illumina NextSeq500/550 instruments and the data are analyzed through custom bioinformatics pipelines. The DNA library is generated by 9,229 custom-designed primer extension assays covering 613,343 base pairs across 225 cancer-related genes (whole exons of 199 genes, hotspot regions of 26 genes). This panel is routinely sequenced to an average read depth of ~2,000, providing high sensitivity for SNVs, in/dels and copy number alterations. Variants are identified using both FreeBayes and MuTect2 algorithms in a custom sequencing analysis pipeline. Included in the panel are 227 short repeats that are used to assess microsatellite instability. TMB is estimated by determining the number of likely somatic mutations and normalizing this to mutations per megabase of sequence.

Input DNA: 50 ng
Minimum read depth per amplicon: 250

Specimen Requirements:

A paraffin block or
10 unstained sections of tumor (4-5 microns)(15 sections for small biopsies)

A REQUISITION FORM MUST ACCOMPANY ALL SAMPLES. Please include detailed clinical information.

Test Performed (Days):

Twice Weekly

Turn Around Time:

10-17 days

Shipment Sensitivity Requirements:

Package and ship specimen to remain cold, but not frozen.
Ship via overnight express, using the FedEx priority overnight label provided.
Contact Client Services at (855) 535-1522 for shipping kits and instructions

References:

Shaw AT, et al. Ceritinib in ALK-rearranged non-small-cell lung cancer. N Engl J Med. 2014 Mar 27;370(13):1189-97.
Shaw AT, et al. Crizotinib versus chemotherapy in advanced ALK-positive lung cancer. N Engl J Med. 2013 Jun 20;368(25):2385-94.
Shaw AT, et al. Crizotinib in ROS1-rearranged non-small-cell lung cancer. N Engl J Med. 2014 Nov 20;371(21):1963-71.
Elisei R, et al. Cabozantinib in progressive medullary thyroid cancer J Clin Oncol. 2013 Oct 10;31(29):3639-46.
Dimitriadis E, et a. BRAF alterations in pediatric low grade gliomas and mixed neuronal-glial tumor. J Neurooncol. 2013 Jul;113(3):353-8.
Graham RP, et al. Fibroblast growth factor receptor 2 translocations in intrahepatic cholangiocarcinoma Hum Pathol. 2014 Aug;45(8):1630-8

Additional Info: