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Results

CGP Precision oncology

NeoPainel Somático: comprehensive genomic profiling of the tumor.

Somatic alterations in 560 cancer-associated genes, plus TMB and MSI, from tumor tissue DNA. Alterations are classified by clinical significance to support the choice of targeted therapies, immunotherapy and clinical trials.

Talk to a specialist Learn about Neo360
See what the test analyzes
Accepted samples
Tumor tissue in paraffin (FFPE) (preferred), Extracted DNA
Turnaround time and when it starts
15 calendar days, after acceptance of the sample
Medical order
Required. View requirements and limitations.

Clinical scope

A single test for the molecular profile of the tumor.

Alteration classes that often require separate tests are assessed in the same assay, from DNA extracted from tumor tissue.

01 / Alterations

Three classes of DNA alteration

Sequence variants, copy number alterations and fusions or rearrangements detectable in DNA, within the regions captured by the panel.

02 / Biomarkers

TMB and MSI in the same report

Tumor mutational burden is calculated over the coding region with adequate coverage in the sample itself. Microsatellite instability is assessed at dedicated panel loci.

03 / Interpretation

Classification by clinical relevance

Alterations are classified according to AMP/ASCO/CAP guidelines to support decisions on targeted therapies, immunotherapy and clinical trials.

Clinical use

How the result supports clinical decisions.

The result should be interpreted by the treating physician together with clinical and histopathological data. Therapy selection depends on tumor type, current regulatory approvals and clinical judgment.

  1. 01

    Targeted therapies

    Identification of alterations that may guide the choice of targeted therapies, according to tumor type.

  2. 02

    Immunotherapy

    TMB and MSI are among the biomarkers considered when evaluating immunotherapy.

  3. 03

    Clinical trials

    Classified alterations that may support the search for clinical trials.

  4. 04

    Diagnosis and prognosis

    Alterations with diagnostic or prognostic significance, depending on the tumor context.

Scope and limits

Broad scope with explicit limitations.

The panel covers the coding regions of 560 cancer-associated genes, with additional content for fusions, copy number and microsatellites.

The analysis considers

Sequence, copy number, fusions and biomarkers.

  • SNVs, indels and multinucleotide variants in the coding regions of 560 genes.
  • Copy number alterations, with additional probes in 58 genes.
  • DNA fusions and rearrangements, from intronic regions of 14 genes: ALK, BCR, BRAF, EGFR, ETV6, EWSR1, FGFR2, FGFR3, NTRK1, NUTM1, PAX8, RET, ROS1 and TMPRSS2.
  • Tumor mutational burden (TMB) and microsatellite instability (MSI).

Important limitations

A tumor profile, not a hereditary analysis.

  • The analysis is performed without a matched normal sample: germline variants may not be reliably distinguished from somatic ones.
  • Sensitivity depends on the tumor cell fraction, DNA quantity and quality, and the coverage obtained.
Learn about Neo360, which includes germline analysis

How to interpret TMB and MSI: TMB is considered high at 10 or more mutations per megabase, the threshold used in the FDA approval of pembrolizumab for TMB-high solid tumors. MSI is classified as MSI-H (high instability) or MSS (stable).

Panel content

The 560 genes analyzed.

HGNC-approved gene symbols in alphabetical order, according to the current technical content of the panel.

See the full gene list
ABL1 ABL2 ABRAXAS1 ACVR1 ACVR2A ADGRA2 AFF3 AKT1 AKT2 AKT3 ALK ALOX12B AMER1 ANKRD11 ANKRD26 APC AR ARAF ARID1A ARID1B ARID2 ARID5B ASXL1 ASXL2 ATAD5 ATF1 ATM ATR ATRX AURKA AURKB AXIN1 AXIN2 AXL B2M BAP1 BARD1 BBC3 BCL10 BCL2 BCL2L1 BCL2L11 BCL6 BCOR BCORL1 BCR BIRC3 BLM BMPR1A BRAF BRCA1 BRCA2 BRD3 BRD4 BRIP1 BTG1 BTK CALR CAMTA1 CARD11 CASP8 CBFB CBL CCND1 CCND2 CCND3 CCNE1 CD274 CD276 CD74 CD79A CD79B CDC73 CDH1 CDK12 CDK4 CDK6 CDK8 CDKN1A CDKN1B CDKN2A CDKN2B CDKN2C CEBPA CENPA CHD2 CHD4 CHEK1 CHEK2 CIC CNBD1 CNTNAP2 COP1 CREBBP CRKL CRLF2 CSF1R CSF3R CSMD3 CSNK1A1 CTCF CTLA4 CTNNA1 CTNNA2 CTNNB1 CTNND2 CUL3 CUX1 CXCR4 CYLD DAXX DCC DDB2 DDR2 DDX41 DICER1 DIS3 DNAJB1 DNMT1 DNMT3A DNMT3B DOT1L DROSHA E2F3 EED EGFL7 EGFR EIF1AX EIF4A2 EIF4E ELOC EML4 EMSY EP300 EPAS1 EPCAM EPHA3 EPHA5 EPHA7 EPHB1 ERBB2 ERBB3 ERBB4 ERCC1 ERCC2 ERCC3 ERCC4 ERCC5 ERG ERRFI1 ESR1 ETV1 ETV4 ETV5 ETV6 EWSR1 EZH2 FANCA FANCB FANCC FANCD2 FANCE FANCF FANCG FANCI FANCL FANCM FAS FAT1 FAT3 FBXW7 FGF1 FGF10 FGF12 FGF14 FGF19 FGF2 FGF23 FGF3 FGF4 FGF5 FGF6 FGF7 FGF8 FGF9 FGFR1 FGFR2 FGFR3 FGFR4 FH FHIT FIP1L1 FLCN FLT1 FLT3 FLT4 FOXA1 FOXL2 FOXO1 FOXP1 FRS2 FUBP1 FYN GABRA6 GATA1 GATA2 GATA3 GATA4 GATA6 GEN1 GID4 GLI1 GNA11 GNA13 GNAQ GNAS GPC5 GPS2 GREM1 GRIN2A GRM3 GSK3B H1-2 H2BC5 H3-3A H3-3B H3-4 H3-5 H3C10 H3C11 H3C12 H3C13 H3C15 H3C2 H3C3 H3C4 H3C6 H3C7 H3C8 HGF HLA-A HLA-B HLA-C HNF1A HNRNPK HOXB13 HRAS HSD3B1 HSP90AA1 ICOSLG ID3 IDH1 IDH2 IFNGR1 IGF1 IGF1R IGF2 IKBKE IKZF1 IL10 IL7R INHA INHBA INPP4A INPP4B INSR IRF2 IRF4 IRS1 IRS2 JAK1 JAK2 JAK3 JUN KAT6A KDM5A KDM5C KDM6A KDR KEAP1 KEL KIF5B KIT KLF4 KLHL6 KMT2A KMT2B KMT2C KMT2D KRAS LAMP1 LATS1 LATS2 LMO1 LRP1B LYN LZTR1 MAD2L2 MAGI2 MALAT1 MALT1 MAP2K1 MAP2K2 MAP2K4 MAP3K1 MAP3K13 MAP3K14 MAPK1 MAPK3 MAX MCL1 MDC1 MDM2 MDM4 MED12 MEF2B MEN1 MET MGA MITF MLH1 MLH3 MLLT3 MPL MRE11 MSH2 MSH3 MSH4 MSH5 MSH6 MST1 MST1R MTAP MTOR MUC16 MUTYH MYB MYC MYCL MYCN MYD88 MYOD1 NAB2 NBEA NBN NCOA3 NCOR1 NEGR1 NF1 NF2 NFE2L2 NFKBIA NKX2-1 NKX3-1 NOTCH1 NOTCH2 NOTCH3 NOTCH4 NPM1 NRAS NRG1 NSD1 NSD2 NSD3 NTRK1 NTRK2 NTRK3 NUP93 NUTM1 PAK1 PAK3 PAK5 PALB2 PARP1 PARP2 PARP3 PAX3 PAX5 PAX7 PAX8 PBRM1 PDCD1 PDCD1LG2 PDGFB PDGFRA PDGFRB PDK1 PDPK1 PGR PHF6 PHOX2B PIK3C2A PIK3C2B PIK3C2G PIK3C3 PIK3CA PIK3CB PIK3CD PIK3CG PIK3R1 PIK3R2 PIK3R3 PIM1 PLCG2 PLK2 PMAIP1 PMS1 PMS2 PNRC1 POLD1 POLE PPARG PPM1D PPP2R1A PPP2R2A PPP6C PRDM1 PREX2 PRKAR1A PRKCI PRKDC PRKN PRSS8 PSIP1 PTCH1 PTEN PTPN11 PTPRD PTPRS PTPRT QKI RAB35 RAC1 RAD21 RAD50 RAD51 RAD51B RAD51C RAD51D RAD52 RAD54L RAF1 RANBP2 RARA RASA1 RB1 RBM10 RECQL RECQL4 REL RET RGS7 RHEB RHOA RICTOR RIT1 RNF43 ROBO1 ROBO2 ROS1 RPS6KA4 RPS6KB1 RPS6KB2 RPTOR RUNX1 RUNX1T1 RYBP SDHA SDHAF2 SDHB SDHC SDHD SETBP1 SETD2 SF3B1 SH2B3 SH2D1A SHQ1 SLIT2 SLX4 SMAD2 SMAD3 SMAD4 SMARCA4 SMARCB1 SMARCD1 SMC1A SMC3 SMO SNCAIP SOCS1 SOX10 SOX17 SOX2 SOX9 SPEN SPOP SPTA1 SRC SRSF2 STAG1 STAG2 STAT3 STAT4 STAT5A STAT5B STK11 STK40 SUFU SUZ12 SYK TAF1 TBX3 TCF3 TCF7L2 TEK TENT5C TERC TERT TET1 TET2 TFE3 TFRC TGFBR1 TGFBR2 TMEM127 TMPRSS2 TNFAIP3 TNFRSF14 TOP1 TOP2A TP53 TP63 TRAF2 TRAF7 TRRAP TSC1 TSC2 TSHR U2AF1 VAV1 VEGFA VHL VTCN1 WRN WT1 XIAP XPO1 XRCC1 XRCC2 XRCC3 XRCC5 YAP1 YES1 ZBTB2 ZBTB7A ZFHX3 ZNF217 ZNF703 ZRSR2

Choice of test

NeoPainel Somático or Neo360?

Both analyze the tumor with the same 560-gene panel. Neo360 adds hereditary cancer predisposition and pharmacogenomics in an integrated report.

Feature NeoPainel SomáticoNeo360
Samples Tumor: paraffin block (FFPE) or extracted DNATumor and germline sample: blood, buccal swab or DNA
Somatic tumor profile 560 genes, TMB and MSI560 genes, TMB and MSI
Hereditary cancer predisposition Not included106 genes, from whole-genome sequencing
Pharmacogenomics Not included6 genes and 12 drugs
Report Somatic tumor profileIntegrated report in three parts
Samples
NeoPainel SomáticoTumor: paraffin block (FFPE) or extracted DNA
Neo360Tumor and germline sample: blood, buccal swab or DNA
Somatic tumor profile
NeoPainel Somático560 genes, TMB and MSI
Neo360560 genes, TMB and MSI
Hereditary cancer predisposition
NeoPainel SomáticoNot included
Neo360106 genes, from whole-genome sequencing
Pharmacogenomics
NeoPainel SomáticoNot included
Neo3606 genes and 12 drugs
Report
NeoPainel SomáticoSomatic tumor profile
Neo360Integrated report in three parts

Why germline analysis matters: without a matched normal sample, a variant found in the tumor may be germline. Variants with an allele frequency near 50% or 100% in hereditary predisposition genes should be confirmed in a non-tumor sample, with genetic counseling. Neo360 includes this analysis for 106 hereditary cancer genes.

Testing process

From tumor block to report.

A single workflow for the molecular profile of the tumor, from order to interpretation.

  1. 01

    Medical order

    The order provides the tumor type and the clinical data that guide interpretation.

  2. 02

    Sample shipment

    Paraffin block with the tumor area selected by the pathologist, or DNA extracted from the tumor.

  3. 03

    Sequencing and bioinformatics

    Hybrid capture, sequencing and analysis of variants, copy number, fusions, TMB and MSI.

  4. 04

    Report and interpretation

    Alterations classified by clinical relevance, with biomarkers and technical limitations.

Frequently asked questions

Before requesting the test.

What sample is needed?

A paraffin block (FFPE) with tumor tissue, with the tumor area selected by the pathologist, or DNA extracted from tumor tissue. Our team provides guidance on shipping the sample.

Does the test identify hereditary cancer?

That is not its purpose. The test analyzes only the tumor sample, without a matched normal sample, and germline variants may not be reliably distinguished. Suggestive findings in predisposition genes should be confirmed in a non-tumor sample, with genetic counseling. Neo360 includes germline analysis.

What do TMB and MSI mean?

Tumor mutational burden (TMB) estimates the number of somatic mutations per megabase of tumor DNA and is considered high at 10 or more mutations per megabase. Microsatellite instability (MSI) classifies the tumor as MSI-H or MSS. Both are panel-based estimates.

Does the test detect any gene fusion?

No. Fusions and rearrangements are assessed in DNA, in the captured intronic regions of 14 genes. The test does not assess transcript expression and does not replace RNA, FISH or immunohistochemistry analysis when indicated.

When will the report be ready?

15 calendar days, after acceptance of the sample .

Does the test require a medical request?

Yes. The tumor type and the clinical and histopathological data guide the analysis and the interpretation of the alterations found.

Next step

Discuss the case with our team.

We provide guidance on the sample, documentation and limits of NeoPainel Somático before shipment.

Talk to a specialist 0800 080 0420

Test information

Technical details for NeoPainel Somático

Method, scope, requirements and limitations

Comprehensive genomic profiling of the tumor: somatic alterations in 560 cancer-associated genes, plus TMB and MSI, from tumor tissue DNA.

Applications
Precision oncology
Accepted samples
Tumor tissue in paraffin (FFPE) (preferred), Extracted DNA
Estimated turnaround time
15 calendar days, after acceptance of the sample
Methodology
Hybrid capture with the Twist Oncology DNA CGP panel, without unique molecular identifiers (UMI), and sequencing on the MGI DNBSEQ platform with paired-end reads. Reads are aligned to the GRCh38 reference genome. Sequence variants are called with SAGE, with Mutect2 as a complementary caller, and annotated with PAVE and Ensembl VEP. Tumor copy number, purity and ploidy are estimated with AMBER, COBALT and PURPLE, and rearrangements with ESVEE and LINX. TMB is calculated with pyTMB over the coding region with at least 100x coverage in the sample itself, after excluding variants that are common in the population (gnomAD). MSI is assessed with MSIsensor2. Alterations are classified according to AMP/ASCO/CAP guidelines (2017).
Analytical scope
Coding regions of 560 cancer-associated genes, selected intronic regions for rearrangement detection in 14 genes (ALK, BCR, BRAF, EGFR, ETV6, EWSR1, FGFR2, FGFR3, NTRK1, NUTM1, PAX8, RET, ROS1 and TMPRSS2), additional copy number probes in 58 genes and microsatellite loci. Assesses SNVs, indels and multinucleotide variants, copy number alterations, DNA fusions and rearrangements, TMB and MSI.
Genes analyzed
560 genes analyzed.
See full content

ABL1, ABL2, ABRAXAS1, ACVR1, ACVR2A, ADGRA2, AFF3, AKT1, AKT2, AKT3, ALK, ALOX12B, AMER1, ANKRD11, ANKRD26, APC, AR, ARAF, ARID1A, ARID1B, ARID2, ARID5B, ASXL1, ASXL2, ATAD5, ATF1, ATM, ATR, ATRX, AURKA, AURKB, AXIN1, AXIN2, AXL, B2M, BAP1, BARD1, BBC3, BCL10, BCL2, BCL2L1, BCL2L11, BCL6, BCOR, BCORL1, BCR, BIRC3, BLM, BMPR1A, BRAF, BRCA1, BRCA2, BRD3, BRD4, BRIP1, BTG1, BTK, CALR, CAMTA1, CARD11, CASP8, CBFB, CBL, CCND1, CCND2, CCND3, CCNE1, CD274, CD276, CD74, CD79A, CD79B, CDC73, CDH1, CDK12, CDK4, CDK6, CDK8, CDKN1A, CDKN1B, CDKN2A, CDKN2B, CDKN2C, CEBPA, CENPA, CHD2, CHD4, CHEK1, CHEK2, CIC, CNBD1, CNTNAP2, COP1, CREBBP, CRKL, CRLF2, CSF1R, CSF3R, CSMD3, CSNK1A1, CTCF, CTLA4, CTNNA1, CTNNA2, CTNNB1, CTNND2, CUL3, CUX1, CXCR4, CYLD, DAXX, DCC, DDB2, DDR2, DDX41, DICER1, DIS3, DNAJB1, DNMT1, DNMT3A, DNMT3B, DOT1L, DROSHA, E2F3, EED, EGFL7, EGFR, EIF1AX, EIF4A2, EIF4E, ELOC, EML4, EMSY, EP300, EPAS1, EPCAM, EPHA3, EPHA5, EPHA7, EPHB1, ERBB2, ERBB3, ERBB4, ERCC1, ERCC2, ERCC3, ERCC4, ERCC5, ERG, ERRFI1, ESR1, ETV1, ETV4, ETV5, ETV6, EWSR1, EZH2, FANCA, FANCB, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCI, FANCL, FANCM, FAS, FAT1, FAT3, FBXW7, FGF1, FGF10, FGF12, FGF14, FGF19, FGF2, FGF23, FGF3, FGF4, FGF5, FGF6, FGF7, FGF8, FGF9, FGFR1, FGFR2, FGFR3, FGFR4, FH, FHIT, FIP1L1, FLCN, FLT1, FLT3, FLT4, FOXA1, FOXL2, FOXO1, FOXP1, FRS2, FUBP1, FYN, GABRA6, GATA1, GATA2, GATA3, GATA4, GATA6, GEN1, GID4, GLI1, GNA11, GNA13, GNAQ, GNAS, GPC5, GPS2, GREM1, GRIN2A, GRM3, GSK3B, H1-2, H2BC5, H3-3A, H3-3B, H3-4, H3-5, H3C10, H3C11, H3C12, H3C13, H3C15, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, HGF, HLA-A, HLA-B, HLA-C, HNF1A, HNRNPK, HOXB13, HRAS, HSD3B1, HSP90AA1, ICOSLG, ID3, IDH1, IDH2, IFNGR1, IGF1, IGF1R, IGF2, IKBKE, IKZF1, IL10, IL7R, INHA, INHBA, INPP4A, INPP4B, INSR, IRF2, IRF4, IRS1, IRS2, JAK1, JAK2, JAK3, JUN, KAT6A, KDM5A, KDM5C, KDM6A, KDR, KEAP1, KEL, KIF5B, KIT, KLF4, KLHL6, KMT2A, KMT2B, KMT2C, KMT2D, KRAS, LAMP1, LATS1, LATS2, LMO1, LRP1B, LYN, LZTR1, MAD2L2, MAGI2, MALAT1, MALT1, MAP2K1, MAP2K2, MAP2K4, MAP3K1, MAP3K13, MAP3K14, MAPK1, MAPK3, MAX, MCL1, MDC1, MDM2, MDM4, MED12, MEF2B, MEN1, MET, MGA, MITF, MLH1, MLH3, MLLT3, MPL, MRE11, MSH2, MSH3, MSH4, MSH5, MSH6, MST1, MST1R, MTAP, MTOR, MUC16, MUTYH, MYB, MYC, MYCL, MYCN, MYD88, MYOD1, NAB2, NBEA, NBN, NCOA3, NCOR1, NEGR1, NF1, NF2, NFE2L2, NFKBIA, NKX2-1, NKX3-1, NOTCH1, NOTCH2, NOTCH3, NOTCH4, NPM1, NRAS, NRG1, NSD1, NSD2, NSD3, NTRK1, NTRK2, NTRK3, NUP93, NUTM1, PAK1, PAK3, PAK5, PALB2, PARP1, PARP2, PARP3, PAX3, PAX5, PAX7, PAX8, PBRM1, PDCD1, PDCD1LG2, PDGFB, PDGFRA, PDGFRB, PDK1, PDPK1, PGR, PHF6, PHOX2B, PIK3C2A, PIK3C2B, PIK3C2G, PIK3C3, PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3R1, PIK3R2, PIK3R3, PIM1, PLCG2, PLK2, PMAIP1, PMS1, PMS2, PNRC1, POLD1, POLE, PPARG, PPM1D, PPP2R1A, PPP2R2A, PPP6C, PRDM1, PREX2, PRKAR1A, PRKCI, PRKDC, PRKN, PRSS8, PSIP1, PTCH1, PTEN, PTPN11, PTPRD, PTPRS, PTPRT, QKI, RAB35, RAC1, RAD21, RAD50, RAD51, RAD51B, RAD51C, RAD51D, RAD52, RAD54L, RAF1, RANBP2, RARA, RASA1, RB1, RBM10, RECQL, RECQL4, REL, RET, RGS7, RHEB, RHOA, RICTOR, RIT1, RNF43, ROBO1, ROBO2, ROS1, RPS6KA4, RPS6KB1, RPS6KB2, RPTOR, RUNX1, RUNX1T1, RYBP, SDHA, SDHAF2, SDHB, SDHC, SDHD, SETBP1, SETD2, SF3B1, SH2B3, SH2D1A, SHQ1, SLIT2, SLX4, SMAD2, SMAD3, SMAD4, SMARCA4, SMARCB1, SMARCD1, SMC1A, SMC3, SMO, SNCAIP, SOCS1, SOX10, SOX17, SOX2, SOX9, SPEN, SPOP, SPTA1, SRC, SRSF2, STAG1, STAG2, STAT3, STAT4, STAT5A, STAT5B, STK11, STK40, SUFU, SUZ12, SYK, TAF1, TBX3, TCF3, TCF7L2, TEK, TENT5C, TERC, TERT, TET1, TET2, TFE3, TFRC, TGFBR1, TGFBR2, TMEM127, TMPRSS2, TNFAIP3, TNFRSF14, TOP1, TOP2A, TP53, TP63, TRAF2, TRAF7, TRRAP, TSC1, TSC2, TSHR, U2AF1, VAV1, VEGFA, VHL, VTCN1, WRN, WT1, XIAP, XPO1, XRCC1, XRCC2, XRCC3, XRCC5, YAP1, YES1, ZBTB2, ZBTB7A, ZFHX3, ZNF217, ZNF703, ZRSR2

Medical order
Required

Requirements

Medical order with the tumor type and the clinical and histopathological information. A paraffin block (FFPE) with tumor tissue, with the tumor area selected by the pathologist, or DNA extracted from tumor tissue.

Limitations

Analysis of the tumor sample only, without a matched normal sample: germline variants may not be reliably distinguished from somatic ones. Variants with an allele frequency near 50% or 100% in hereditary cancer predisposition genes should be confirmed in a non-tumor sample, with genetic counseling. Sensitivity depends on the tumor cell fraction, DNA quantity and quality, and the coverage obtained. Samples with low tumor fraction or degraded DNA may yield false-negative results, especially for low-allele-frequency subclonal variants and for copy number alterations. Formalin fixation may cause sequencing artifacts; low-allele-frequency variants are interpreted with caution. Fusions and rearrangements are assessed only in DNA and in the captured intronic regions: the test does not detect every possible fusion, does not assess transcript expression and does not replace RNA, FISH or immunohistochemistry analysis when indicated. Copy number alterations are assessed at higher resolution in genes with probe enrichment; small deletions, low-coverage regions and low-level gains may not be detected. TMB and MSI are estimates obtained from a gene panel; their values are not directly interchangeable with those of other methods or panels. The test does not assess epigenetic alterations, variants outside the captured regions, repeat expansions or balanced rearrangements outside the target regions.

Additional information

Clinical classification reflects the scientific knowledge available on the report release date and may be revised. The result should be interpreted by the treating physician together with clinical and histopathological data; therapy selection depends on tumor type, current regulatory approvals and clinical judgment.