A next generation sequencing (NGS) based assay designed to test for mutations, copy number variations and fusions in genes with diagnostic, prognostic, and therapeutic implications, plus microsatelite insatiability (MSI) and tumor mutation burden analysis, to inform options for check point inhibitory therapy.

HopeSeq Solid Tumor Gene List

Hotspot Mutation Analysis of 87 Genes
AKT1, AKT2, AKT3, ALK, AR, ARAF, AXL, BRAF, BTK, CBL, CCND1, CDK4, CDK6, CHEK2, CSF1R, CTNNB1, DDR2, EGFR, ERBB2, ERBB3, ERBB4, ERCC2, ESR1, EZH2, FGFR1, FGFR2,  FGFR3, FGFR4, FLT3, FOXL2, GATA2, GNA11, GNAQ, GNAS, H3F3A, HIST1H3B, HNF1A, HRAS, IDH1, IDH2, JAK1, JAK2, JAK3, KDR, KIT, KNSTRN, KRAS, MAGOH, MAP2K1, MAP2K2, MAP2K4, MAPK1, MAX, MDM4, MED12, MET, MTOR, MYC, MYCN, MYD88, NFE2L2, NRAS, NTRK1, NTRK2, NTRK3, PDGFRA, PDGFRB, PIK3CA, PIK3CB, PPP2R1A, PTPN11, RAC1, RAF1, RET, RHEB, RHOA, ROS1, SF3B1, SMAD4, SMO, SPOP, SRC, STAT3, TERT, TOP1, U2AF1, XPO1

Full-length Mutation Analysis of 48 Genes
ARID1A, ATM, ATR, ATRX, BAP1, BRCA1, BRCA2, CDK12, CDKN1B, CDKN2A, CDKN2B, CHEK1, CREBBP, FANCA, FANCD2, FANCI, FBXW7, MLH1, MRE11A, MSH2, MSH6, NBN, NF1, NF2, NOTCH1, NOTCH2, NOTCH3, PALB2, PIK3R1, PMS2, POLE, PTCH1, PTEN, RAD50, RAD51, RAD51B, RAD51C, RAD51D, RB1, RNF43, SETD2, SLX4, SMARCA4, SMARCB1, STK11, TP53, TSC1, TSC2

Fusion Analysis of 51 Genes
AKT2, ALK, AR, AXL, BRAF, BRCA1, BRCA2, CDKN2A, EGFR, ERBB2, ERBB4, ERG, ESR1, ETV1, ETV4, ETV5, FGFR1, FGFR2, FGFR3, FGR, FLT3, JAK2, KRAS, MDM4, MET, MYB,  MYBL1, NF1, NOTCH1, NOTCH4, NRG1, NTRK1, NTRK2, NTRK3, NUTM1, PDGFRA, PDGFRB, PIK3CA, PPARG, PRKACA, PRKACB, PTEN, RAD51B, RAF1, RB1, RELA, RET, ROS1, RSPO2, RSPO3, TERT

Copy Number Analysis of 47 Genes
AKT1, AKT2, AKT3, ALK, AR, AXL, BRAF, CCND1, CCND2, CCND3, CCNE1, CDK2, CDK4, CDK6, CDKN2A, CDKN2B, EGFR, ERBB2, ESR1, FGF3, FGF19, FGFR1, FGFR2, FGFR3, FGFR4,  FLT3, IGF1R, KIT, KRAS, MDM2, MDM4, MET, MYC, MYCL, MYCN, NTRK1, NTRK2, NTRK3, PDGFRA, PDGFRB, PIK3CA, PIK3CB, PPARG, RICTOR, TERT, TSC1, TSC2
 

References
  1. Rothberg JM, et al; An integrated semiconducted device enabling non-optical genome sequencing. Nature, 2011 Jul20; 475(7356):348-52
  2. Dancey JE, et al; The genetic basis for cancer treatment decisions. Cell, 2012 Feb 3; 148(3): 409-20. Review
  3. www.mycancergenome.org
  4. www.sanger.ac.uk/genetics/CGP/cosmic
  5. www.pharmgkb.org
 
Mnemonic
Solid Tumor NGS
 
Methodology
Insert method here
 
Performed
Mon-Fri
 
Reported
10-14 working days
 

Specimen Required

  • Patient Preparation:
  • Collect:
    • FFPE (formalin-fixed, paraffin-embedded) Block or
    • 1 H&E and 19 USS (unstained slides) at 10 microns
  • Specimen Preparation: FFPE or H&E and USS
  • Storage/Transport Temperature: Include ice pack during transport
  • Unacceptable Conditions: 
  • Remarks: 
  • Stability: Ambient:  ; Refrigerated:  ; Frozen:
 
CPT Code(s)
81455, 88301, 88381, G0452 (x2)
 
Aliases
Solid Tumor Next Generation Sequencing