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Gene Mutation Panels

Mutanom chip technology

Gene Mutation Panels for Personalized Precision Tumor Therapy

Gene mutations are permanent changes in individual gene segments. Such changes can either occur only in the tumor (somatic mutations, not hereditary) or in all of the body’s cells (germline mutations, hereditary). Mutations play a key part in a tumor’s genesis and its further development. In precision medicine, they are of vital importance. They can either be the target of new drugs or, by analyzing the changes they yield in metabolic pathways and signal cascades, indicate a specific, indirect therapeutic procedure. When considering the significance of mutations for the tumor development and its treatment, it is necessary to differentiate between driver mutations and subordinate passenger mutations. The mutational pattern in tumor diseases varies greatly from person to person. Since more and more, mutations are the target of new cancer drugs, it is imperative to know the respective tumor disease’s individual mutational status. With next-generation sequencing (NGS), a quantum leap in the technology of mutational analysis has been made. This is the basis for analyzing a large number of mutations simultaneously. The degree of parallel analysis offered by NextGen Oncology ranges from 161 cancer and tumor suppressor genes (focused gene panels) to all of the human body’s more than 20.000 genes. Depending on the clinical issue, a 161-gene-assay might suffice. The content of the 161-gene Oncomine® Comprehensive Assay is given in the Table below.

Hotspot genes

AKT1, ERBB2, GNAS, MAGOH, PIK3CA, STAT3 MAP2K4, ALK, ERB83, HNF1A, MAP2K1, PPP2R1A, U2AF1, MDM4, AR, ERBB4, HRAS, MAP2K2, PTPN11, XPO1, MYC, ARAF, ESR1, IDH1, MAPK1, RAC1, AKT2, MYCN, BRAF, EZH2, IDH2, MAX, RAF1, AKT3, NTRK1, BTK, FGFR1, JAK1, MED12, RET, AXL, NTRK2, CBL, FGFR2, JAK2, MET, RHEB, CCND1, PDGFRB, CDK4, FGFR3, JAK3, MTOR, RHOA, CDK6, PIK3CB, CHEK2, FLT3, KDR, MYD88, SF3B1, ERCC2, ROS, CSF1R, FOXL2, KIT, NFE2L2, SMO, FGFR4, SMAD4, CTNNB1, GATA2, KNSTRN, NRAS, SPOP, H3F3A TERT, DDR2 GNA1, KRAS, PDGFRA, SRC, HIST1H3B, TOP1, EGF, GNAQ

Full-length genes

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

Copy number genes

AKT1, ERBB2 KIT, MYCN, ALK, CDKN2B, NTR3, AR, FGFR1, KRAS, PDGFRA, AXL, ESR1, PDGFRB, CCND1, FGFR2, MDM4, PIK3CA, BRAF, FGF19, PIK3CB,CCNE1, FGFR3, MET, TERT, CCND2, FGF3, RICTOR, CDK4, FGFR4, MYC, AKT2, CDK2, NTRK1, TSC1, CDK6, FLT3, MYCL, AKT3, CDKN2A, NTRK2, TSC2, EGFR, IGF1R

Gene fusions (inter- and intragenic)

ALK, ETV5, RAF1, CDKN2A, MDM4, NRG1, PTEN, AXL, FGFR1, RET, ERB84, MET, NTRK2, RAD51B, BRAF, FGFR2, ROS1, ESR1, MYB, NUTM1, RB1, EGFR, FGFR3, AKT2, FGR, MYBL1, PDGFRB, RELA, ERBB2, NTRK1, AR, FLT3, NF1, PIK3CA, RSPO2, ERG, NTRK3, BRCA1, JAK2, NOTCH1, PRKACA, RSPO3, ETV1, PDGFRA, BRCA2, KRAS, NOTCH4, PRKACB, TERT, ETV4, PPARG

However, depending on the tumor origin more complex issues need larger gene panels to be analyzed. NextGen Oncology can offer more comprehensive gene panels in extreme cases including all human genes (exome). We would be happy to consult you in determining which of the different gene panels is best suited to your individual case.

Most importantly, for all mutations detected a worldwide search in important reknown databases is performed to identify drugs, therapies and clinical studies relevant for the specified mutation and individual disease.

NextGen Oncology offers clinical reporting of the data based on Oncomine® Knowledge Base Reporter (Thermo Fisher Scientific) and/or NAVIFY® Mutation Profiler (Roche).

The Figure below shows an excerpt (Summary page) of a typical Oncomine Knowledgebase Report.

Figure. Excerpt from an Oncomine® Knowledge Base Report (summary page only).

Test Requirements

Cryopreserved tumor tissue is ideal for our high-resolution chip technology. However, formalin-fixed paraffin-embedded tissues have turned out to be usually sufficient, too. Minuscule tissue samples (for instance, a few of slices skin from a punch biopsy or tissue collected in fine-needle aspiration biopsies) suffice. Detailed information can be found in our Specimen Collection and Transport Kits.

Duration of Testing

Depending on the size of the selected gene mutation panel turnearound time is 2 to 6 weeks. We will contact the respective pathological institute to arrange for the FFPE tissue blocks. A single call will do, just ring us at 0211 4477 4388 (landline) or 0171 784 989 4 (cell). We will take care of the entire logistic process for you.

We are glad to consult you in finding the right treatment!