Platform Molecular Diagnostics UZ Ghent (MDG)

The MDG platform's core activity is the detection of specific somatic defects in the DNA, cfDNA and RNA of the malignant tissues, blood or bone marrow of patients with cancer.

Please refer to the Guidelines for test requests and Sample Instructions.

Accredited MDG tests in routine

SOLID TUMORS:

• DNA NGS SOLID TUMOR panel: detection of SNVs and indels in 112 genes: AKT1, ALK, APC, AR, ARID1A, ATM, BAP1, BARD1, BCOR, BRAF, BRCA1, BRCA2, BRIP1, CCND1, CCNE1, CDH1, CDK4, CDK6, CDK12, CDKN2A, CDKN2B, CHEK1, CHEK2, CTNNB1, DDX3X, DGCR8, DICER1, DPYD, DROSHA, EGFR, EIF1AX, ELP1, ERBB2, ERBB3, ESR1, FBXW7, FGFR1, FGFR2, FGFR3, FGFR4, FOXL2, FRK, GATA3, GNA11, GNAQ, GNAS, GPR161, H3-3A, H3-3B, H3C2, H3C3, HNF1A, HRAS, IDH1, IDH2, IL6ST, JAK1, JAK2, KBTBD4, KEAP1, KIT, SCRATCH, MAP2K1, MDM2, MET, MRE11, MTAP, MYC, MYCN, MYOD1, NBN, NF1, NF2, NOTCH1, NRAS, NTRK1, NTRK2, NTRK3, PALB2, PDGFRA, PDGFRB, PIK3CA, PIK3R1, POLE, PRKCA, PTCH1, PTEN, PTPN11, RAD50, RAD51B, RAD51C, RAD51D, RB1, RET, RNF43, ROS1, SDHA, SDHB, SDHC, SDHD, SF3B1, SMAD4, SMARCA4, SMARCB1, SMO, SPOP, STAT3, STK11, SUFU, TERT, TP53, VHL using the KAPA HyperCap technology (Roche).

The specifications of the regions examined and the reference sequences of the genes can be accessed here. The quality of the DNA sample extracted from tumor material is checked using a DNA quality test. A capture-based NGS technology is used for enrichment of the regions of interest of the 112 genes followed by sequencing with the Illumina technology. Data analysis is performed using an in-house bcbio workflow. The sequencing reads are aligned with a reference sequence (hg38). For release of NGS results there is aimed for a minimum coverage of 300x. All 112 genes are looked at in the tumor samples. Only pathogenic variants, presumably pathogenic variants and variants of unknown significance (VUS) are reported (Richards et al. Genet Med 2015).The limit for detecting a variant is 5%. As an exception, known hotspot variants are also reported when the variant's allele frequency (VAF) is between 2 - 5% and the coverage is > 300x and the variant is present in > 10 reads. With this test, somatic and a germline variants cannot be distinguished.

Additionally, this panel allows MSI analysis based on 17 microsatellite regions: BAT25, BCL2L11, BTBD7, D18S55, EML4, GRIN2A, GTF2IP1, KDM6A, KIF5B, MRE11A, NR21, NR24, NR27, PIP5K1A, RYR3, SMARCB1, TGFBR2 using the mSINGS script (Salipante et al. Clinical Chemistry 2014). This analysis has a sensitivity of 74% and specificity of 100%. The limit for detecting microsatellite instability is 30% tumor cells.

• cfDNA NGS SOLID TUMOR panel: detection of SNVs and indels in 112 genes: AKT1, ALK, APC, AR, ARID1A, ATM, BAP1, BARD1, BCOR, BRAF, BRCA1, BRCA2, BRIP1, CCND1, CCNE1, CDH1, CDK4, CDK6, CDK12, CDKN2A, CDKN2B, CHEK1, CHEK2, CTNNB1, DDX3X, DGCR8, DICER1, DPYD, DROSHA, EGFR, EIF1AX, ELP1, ERBB2, ERBB3, ESR1, FBXW7, FGFR1, FGFR2, FGFR3, FGFR4, FOXL2, FRK, GATA3, GNA11, GNAQ, GNAS, GPR161, H3-3A, H3-3B, H3C2, H3C3, HNF1A, HRAS, IDH1, IDH2, IL6ST, JAK1, JAK2, KBTBD4, KEAP1, KIT, KRAS, MAP2K1, MDM2, MET, MRE11, MTAP, MYC, MYCN, MYOD1, NBN, NF1, NF2, NOTCH1, NRAS, NTRK1, NTRK2, NTRK3, PALB2, PDGFRA, PDGFRB, PIK3CA, PIK3R1, POLE, PRKCA, PTCH1, PTEN, PTPN11, RAD50, RAD51B, RAD51C, RAD51D, RB1, RET, RNF43, ROS1, SDHA, SDHB, SDHC, SDHD, SF3B1, SMAD4, SMARCA4, SMARCB1, SMO, SPOP, STAT3, STK11, SUFU, TERT, TP53, VHL using KAPA EvoPrep technology (Roche).

The specifications of the analyzed regions and the reference sequences of the genes can be consulted here. The quality of the cfDNA sample extracted from the liquid biopsy of solid tumor patients is checked using a cfDNA quality test. A capture-based NGS technology is used for enrichment of the regions of interest of the 112 genes, followed by sequencing with Illumina technology. Data analysis is performed using an in-house bcbio workflow. The sequencing reads are aligned to a reference sequence (hg38). For release of the NGS results, a minimum coverage of 1000x UMI-based reads for the regions of interest is targeted. All 112 genes are examined in these liquid biopsy samples from solid tumor patients. Only pathogenic variants, likely pathogenic variants, and variants of unknown significance (VUS) are reported (Richards et al., Genet Med 2015). The detection limit for a variant is 0.4% VAF in at least 8 UMI-based reads. Based on this test, it is not possible to distinguish between an acquired and a germline variant.

• RNA NGS PANCANCER panel: detection of fusions and splice variants in 175 genes: ABL1, ABL2, AFF2, ALK, BCL11B, BCOR, BCR, BRAF, CAMTA1, CBFA2T3, CBFB, CD28, CHMP2A, CIC, COL6A3, CREBBP, CRLF2, CSF1, CSF1R, CTNNB1, DEK, DUX4, EBF1, EGFR, EPC1, EPOR, ERBB2, ERG, ESR1, ETV5, ETV6, EWSR1, FGFR1, FGFR2, FGFR3, FIPL1, FLT3, FN1, FOS, FOSB, FOXO1, FOXR2, FRK, FUS, GLI1, GLIS2, GPI, GREB1, GRM1, HLF, HMGA2, HOXA10, HOXA11, HOXA9, IKZF1, IL2RB, JAK2, JAZF1, KDM2B, KMT2A, KRAS, LYL1, LYN, MAML2, MAML3, MAP3K3, MAP3K8, MDM2, MEAF6, MECOM, MEF2D, MET, MITF, MLLT10, MLLT4, MN1, MRTF, MRTFA, MSANTD3, MYB, MYBL1, MYC, MYH11, MYOD1, NCOA1, NCOA2, NOTCH1, NOTCH2, NOTCH3, NPM1, NR1D1, NR4A2, NR4A3, NRG1, NTRK1, NTRK2, NTRK3, NUP214, NUP98, NUTM1, OGA, P2RY8, PATZ1, PAX3, PAX5, PAX7, PBX1, PCM1, PDGFB, PDGFRA, PDGFRB, PHF1, PICALM, PLAG1, PML, PPARG, PRDM10, PRDM16, PRKACA, PRKCA, PRKCB, PRKCD, PRKD1, PRKD2, PRKD3, PTEN, PTK2B, RAB7A, RAD51B, RAF1, RARA, RARB, RARG, RASGRF1, RMB15, RELA, RET, ROS1, RSPO2, RSPO3, RUNX1, RUNX1T1, SET, SRF, SS18, STAT6, STIL, SUZ12, TAF15, TAL1, TCF3, TCF12, TCFP2, TFE3, TFEB, TFG, THADA, TLX1, TLX3, TMPRSS2, TRIM11, TSLP, TYK2, UBTF, USP6, VCP, VGLL2, VGLL3, WT1, YAP1, YWHAE, ZCCHC7, ZFTA, ZNF362, ZNF384 with the TWIST RNA NGS technology.

The specifications of the analyzed regions and the reference sequences of the genes can be consulted here. The quality of the extracted RNA from paraffin embedded tumor tissue is analysed with a RNA quality test. A capture-based NGS technology is used for the enrichment of the regions of interest of the 175 genes followed by the sequencing with the Illumina technology. Data-analysis is performed with the nextflow nf-core/rna fusion pipeline. The sequencing reads are aligned with a reference sequence (hg38). For release of results, a minimum of 5 unique reads is required for fusion detection.

• MDG-MGMT assay: detection of MGMT promoter methylation in glioblastoma.

HEMATOLOGIC DISORDERS:

• DNA NGS HEMATO panel: detection of SNVs and indels in 219 genes: ABL1, AKT1, ANKRD26, ARAF, ARID1A, ARID1B, ARID2, ASXL1, ASXL2, ATM, B2M, BAX, BCL10, BCL2, BCL6, BCL7A, BCOR, BCORL1, BIRC3, BRAF, BTG1, BTG2, BTK, CALR, CARD11, CARMIL2, CBFB, CBL, CBLB, CCL22, CCND1, CCND2, CCND3, CCR4, CCR6, CCR7, CD19, CD28, CD33, CD58, CD70, CD79A, CD79B, CD83, CDKN2A, CDKN2B, CEBPA, CHEK2, CREBBP, CRLF2, CSF1R, CSF3R, CTCF, CUX1, CXCR4, CYBB, DDX3X, DDX41, DHX15, DIS3, DKC1, DNMT3A, DTX1, EBF1, EGR2, ELANE, EP300, ERBB3, ERCC6L2, ERG, ETNK1, ETV6, EZH2, FADD, FAS, FBXW7, FGFR2, FGFR3, FGFR4, FLT3, FOXO1, FYN, GATA1, GATA2, GFI1, GNA13, GNAI2, GNAS, GNB1, H1-4, H3-3A, HAVCR2, HAX1, HRAS, ID3, IDH1, IDH2, IKZF1, IL2RA, IL6ST, IL7R, INO80, IRF4, IRF8, JAK1, JAK2, JAK3, JUNB, KDM6A, KIT, KLF2, KMT2A, KMT2D, KRAS, LUC7L2, MAP2K1, MAP3K1, MBD4, MEF2B, MEFV, MEN1, MPL, MSC, MYC, MYD88, NF1, NFE2, NFKBIE, NLRC4, NLRP3, NOD2, NOTCH1, NOTCH2, NPM1, NR3C1, NT5C2, NTRK1, NTRK2, NTRK3, NRAS, NSD2, NUDT15, PAX5, PDGFRA, PHF6, PHIP, PIGA, PIK3AP1, PIK3CA, PIK3CD, PIK3R1, PIM1, PIM2, PLCG1, PLCG2, POT1, POU2AF1, PPM1D, PRDM1, PRF1, PRKCB, PRPF8, PRPS1, PTEN, PTPN1, PTPN11, PTPRD, RAD21, RAP1B, RB1, RHOA, RIT1, RTEL1, RUNX1, SAMD9, SAMD9L, SBDS, SETBP1, SETD2, SF3B1, SGK1, SH2B3, SH2D1A, SMARCA2, SMARCA4, SMC1A, SMC3, SOCS1, SRSF2, STAG1, STAG2, STAT1, STAT3, STAT5B, STAT6, STING1, TCF3, TERC, TERT, TET1, TET2, TET3, TINF2, TLR8, TNFAIP3, TNFRSF1A, TNFRSF14, TP53, TPMT, TRAF2, U2AF1, UBA1, UBTF, VAV1, WT1, XPO1, ZBTB7A, ZRSR2 using the KAPA HyperCap technology (Roche).

The specifications of the regions examined and the reference sequences of the genes can be consulted in the Laboratory of clinical biology guide https://labgids.uzgent.be/. A capture-based NGS technology is used for enrichment of the regions of interest from the 219 genes followed by sequencing with the Illumina technology. Data analysis is performed using an in-house bcbio workflow. The sequencing reads are aligned with a reference sequence (hg38). A minimum coverage of 300x for regions of interest is targeted for release of NGS results. All 219 genes are looked at in the hemato-onco samples. Only pathogenic variants, suspected pathogenic variants and variants of unknown significance (VUS) are reported (Richards et al. Genet Med 2015). The limit for detecting a variant is 5% VAF. With this test, somatic and a germline variants cannot be distinguished.

• MDG-MPN1-mini assay: detection of SNVs and indels in CALR, JAK2 and MPL in MPN. An in-house PCR-based NGS enrichment is used followed by sequencing with Illumina technology. Data analysis is performed using an in-house bcbio workflow. The sequencing reads are aligned with a reference sequence (hg38). A minimum coverage of 300x for the regions of interest is targeted for release of the NGS results. Only pathogenic variants, presumably pathogenic variants and variants of unknown significance (VUS) are reported (Richards et al. Genet Med 2015). The limit for detecting a variant is 5%. As an exception, known hotspot variants that are also reported when the variant's allele frequency (VAF) is between 2 - 5% and the coverage is > 300x and the variant is present in > 10 reads. With this test, somatic and a germline variants cannot be distinguished.

The specifications of the analyzed regions and the reference sequences of the genes can be consulted here. A capture-based NGS technology is used for the enrichment of the regions of interest of the 175 genes followed by the sequencing with the Illumina technology. Data-analysis is performed with the nextflow nf-core/rna fusion pipeline. The sequencing reads are aligned with a reference sequence (hg38). For release of results, a minimum of 50 unique reads is required for fusion detection.

MDG tests under development:

- methylation profiling for solid tumor samples

- comprehensive genomic profiling (CGP) of solid tumor samples on liquid biopsies and on FFPE samples

- homologous recombination deficiency (HRD) testing of ovarian cancer samples

Last updated: 07 April 2026 - 11:22
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