gbm pyrosequencing samples Search Results


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MGMT promoter methylation trends in DNA methylation array samples . ( A ) Frequency of positive results for all glioma array samples above and below the cutoff of VAF = 0.245. ( B ) Cumulative mean frequency of positive results for all glioma array samples as a function of VAF. ( C ) Frequency of positive results for <t>GBM</t> array samples above and below the cutoff of TERT VAF = 0.325. ( D ) Cumulative mean frequency of positive results in GBM array samples as a function of TERT VAF. ( E ) Frequency of positive results in <t>GBM</t> <t>pyrosequencing</t> samples using MGMT cutoff of 10.0% versus GBM array samples. ( F ) Frequency of positive results in GBM pyrosequencing samples using MGMT cutoff of 7.28% versus GBM array samples. ( G ) Frequency of positive results in GBM pyrosequencing samples with TERT VAF < 0.115, using MGMT cutoff of 7.28%, versus GBM array samples with TERT VAF < 0.325. ( H ) Frequency of positive results in GBM pyrosequencing samples with TERT VAF ≥ 0.115, using MGMT cutoff of 7.28%, versus GBM array samples with TERT VAF ≥ 0.325. ( I ) Frequency of positive results for IDHmut astrocytoma above and below the cutoff of IDH VAF = 0.325 (left), by methylation class match (center), and above and below the cutoff of classifier score = 0.955 (right). ( J ) Cumulative mean frequency of positive results in IDHmut astrocytoma array samples as a function of IDH VAF (Fisher’s exact test for panels A, C, E, F, G, H, I; GBM: IDH-wildtype glioblastoma, IDHmut astrocytoma: IDH-mutant astrocytoma)
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MGMT promoter methylation trends in DNA methylation array samples . ( A ) Frequency of positive results for all glioma array samples above and below the cutoff of VAF = 0.245. ( B ) Cumulative mean frequency of positive results for all glioma array samples as a function of VAF. ( C ) Frequency of positive results for GBM array samples above and below the cutoff of TERT VAF = 0.325. ( D ) Cumulative mean frequency of positive results in GBM array samples as a function of TERT VAF. ( E ) Frequency of positive results in GBM pyrosequencing samples using MGMT cutoff of 10.0% versus GBM array samples. ( F ) Frequency of positive results in GBM pyrosequencing samples using MGMT cutoff of 7.28% versus GBM array samples. ( G ) Frequency of positive results in GBM pyrosequencing samples with TERT VAF < 0.115, using MGMT cutoff of 7.28%, versus GBM array samples with TERT VAF < 0.325. ( H ) Frequency of positive results in GBM pyrosequencing samples with TERT VAF ≥ 0.115, using MGMT cutoff of 7.28%, versus GBM array samples with TERT VAF ≥ 0.325. ( I ) Frequency of positive results for IDHmut astrocytoma above and below the cutoff of IDH VAF = 0.325 (left), by methylation class match (center), and above and below the cutoff of classifier score = 0.955 (right). ( J ) Cumulative mean frequency of positive results in IDHmut astrocytoma array samples as a function of IDH VAF (Fisher’s exact test for panels A, C, E, F, G, H, I; GBM: IDH-wildtype glioblastoma, IDHmut astrocytoma: IDH-mutant astrocytoma)

Journal: Acta Neuropathologica Communications

Article Title: Variant allelic frequencies of driver mutations can identify gliomas with potentially false-negative MGMT promoter methylation results

doi: 10.1186/s40478-023-01680-0

Figure Lengend Snippet: MGMT promoter methylation trends in DNA methylation array samples . ( A ) Frequency of positive results for all glioma array samples above and below the cutoff of VAF = 0.245. ( B ) Cumulative mean frequency of positive results for all glioma array samples as a function of VAF. ( C ) Frequency of positive results for GBM array samples above and below the cutoff of TERT VAF = 0.325. ( D ) Cumulative mean frequency of positive results in GBM array samples as a function of TERT VAF. ( E ) Frequency of positive results in GBM pyrosequencing samples using MGMT cutoff of 10.0% versus GBM array samples. ( F ) Frequency of positive results in GBM pyrosequencing samples using MGMT cutoff of 7.28% versus GBM array samples. ( G ) Frequency of positive results in GBM pyrosequencing samples with TERT VAF < 0.115, using MGMT cutoff of 7.28%, versus GBM array samples with TERT VAF < 0.325. ( H ) Frequency of positive results in GBM pyrosequencing samples with TERT VAF ≥ 0.115, using MGMT cutoff of 7.28%, versus GBM array samples with TERT VAF ≥ 0.325. ( I ) Frequency of positive results for IDHmut astrocytoma above and below the cutoff of IDH VAF = 0.325 (left), by methylation class match (center), and above and below the cutoff of classifier score = 0.955 (right). ( J ) Cumulative mean frequency of positive results in IDHmut astrocytoma array samples as a function of IDH VAF (Fisher’s exact test for panels A, C, E, F, G, H, I; GBM: IDH-wildtype glioblastoma, IDHmut astrocytoma: IDH-mutant astrocytoma)

Article Snippet: Only 3 of 14 GBM pyrosequencing samples (21%) below the pyrosequencing-specific VAF cutoff of 0.115 tested positive, versus 35 of 65 array samples (54%) below the array-specific VAF cutoff of 0.325 ( p = 0.039, Fig. G).

Techniques: Methylation, DNA Methylation Assay, Mutagenesis

Driver mutation VAF , MGMT promoter methylation scores, and tumor cellularity . ( A ) Linear regression of MGMT promoter pyrosequencing score versus driver mutation VAF for all glioma samples. ( B ) Linear regression of MGMT promoter pyrosequencing score versus TERT promoter mutation VAF for GBM. ( C ) Linear regression of MGMT promoter pyrosequencing score versus IDH mutation VAF for IDHmut astrocytoma. ( D ) Linear regression of MGMT promoter pyrosequencing score versus IDH mutation VAF for IDHmut oligodendroglioma. ( E ) Linear regression of microscopically estimated cellularity versus cellularity calculated from driver mutation VAF (2×VAF×100%) for all glioma samples. ( F ) Differences between microscopically estimated cellularity and cellularity calculated from VAF (Y-axis) plotted as a function of VAF (X-axis), for all glioma samples. ( G ) TERT promoter mutation VAF by ddPCR in high versus low cellularity areas of GBM tissue samples. ( H ) MGMT promoter methylation score by ddPCR in high versus low cellularity areas of GBM tissue samples (GBM: IDH-wildtype glioblastoma, IDHmut astrocytoma: IDH-mutant astrocytoma, IDHmut oligodendroglioma: IDH-mutant and 1p/19q co-deleted oligodendroglioma, pyroseq: pyrosequencing, ddPCR: droplet digital PCR)

Journal: Acta Neuropathologica Communications

Article Title: Variant allelic frequencies of driver mutations can identify gliomas with potentially false-negative MGMT promoter methylation results

doi: 10.1186/s40478-023-01680-0

Figure Lengend Snippet: Driver mutation VAF , MGMT promoter methylation scores, and tumor cellularity . ( A ) Linear regression of MGMT promoter pyrosequencing score versus driver mutation VAF for all glioma samples. ( B ) Linear regression of MGMT promoter pyrosequencing score versus TERT promoter mutation VAF for GBM. ( C ) Linear regression of MGMT promoter pyrosequencing score versus IDH mutation VAF for IDHmut astrocytoma. ( D ) Linear regression of MGMT promoter pyrosequencing score versus IDH mutation VAF for IDHmut oligodendroglioma. ( E ) Linear regression of microscopically estimated cellularity versus cellularity calculated from driver mutation VAF (2×VAF×100%) for all glioma samples. ( F ) Differences between microscopically estimated cellularity and cellularity calculated from VAF (Y-axis) plotted as a function of VAF (X-axis), for all glioma samples. ( G ) TERT promoter mutation VAF by ddPCR in high versus low cellularity areas of GBM tissue samples. ( H ) MGMT promoter methylation score by ddPCR in high versus low cellularity areas of GBM tissue samples (GBM: IDH-wildtype glioblastoma, IDHmut astrocytoma: IDH-mutant astrocytoma, IDHmut oligodendroglioma: IDH-mutant and 1p/19q co-deleted oligodendroglioma, pyroseq: pyrosequencing, ddPCR: droplet digital PCR)

Article Snippet: Only 3 of 14 GBM pyrosequencing samples (21%) below the pyrosequencing-specific VAF cutoff of 0.115 tested positive, versus 35 of 65 array samples (54%) below the array-specific VAF cutoff of 0.325 ( p = 0.039, Fig. G).

Techniques: Mutagenesis, Methylation, Digital PCR

False negative results in IDH-wildtype glioblastoma with low TERT VAF . ( A ) MGMT promoter methylation results for 12 GBM samples (6 with TERT VAF ≤ 0.10, 6 with TERT VAF ≥ 0.25) comparing initial pyrosequencing methylation scores (left Y-axis, cutoff for positive = 10.0%, horizontal solid red line) to results on re-testing with DNA methylation array (right Y-axis). ( B ) MGMT promoter methylation results for the same 12 GBM samples comparing initial pyrosequencing methylation levels to results on re-testing with ddPCR. (GBM: IDH-wildtype glioblastoma, pos: positive, equiv: equivocal, neg: negative, QNS: quality/quantity of DNA not sufficient for reliable test result, ddPCR: droplet digital PCR)

Journal: Acta Neuropathologica Communications

Article Title: Variant allelic frequencies of driver mutations can identify gliomas with potentially false-negative MGMT promoter methylation results

doi: 10.1186/s40478-023-01680-0

Figure Lengend Snippet: False negative results in IDH-wildtype glioblastoma with low TERT VAF . ( A ) MGMT promoter methylation results for 12 GBM samples (6 with TERT VAF ≤ 0.10, 6 with TERT VAF ≥ 0.25) comparing initial pyrosequencing methylation scores (left Y-axis, cutoff for positive = 10.0%, horizontal solid red line) to results on re-testing with DNA methylation array (right Y-axis). ( B ) MGMT promoter methylation results for the same 12 GBM samples comparing initial pyrosequencing methylation levels to results on re-testing with ddPCR. (GBM: IDH-wildtype glioblastoma, pos: positive, equiv: equivocal, neg: negative, QNS: quality/quantity of DNA not sufficient for reliable test result, ddPCR: droplet digital PCR)

Article Snippet: Only 3 of 14 GBM pyrosequencing samples (21%) below the pyrosequencing-specific VAF cutoff of 0.115 tested positive, versus 35 of 65 array samples (54%) below the array-specific VAF cutoff of 0.325 ( p = 0.039, Fig. G).

Techniques: Methylation, DNA Methylation Assay, Digital PCR

Patient cohort characteristics

Journal: Acta Neuropathologica Communications

Article Title: Variant allelic frequencies of driver mutations can identify gliomas with potentially false-negative MGMT promoter methylation results

doi: 10.1186/s40478-023-01680-0

Figure Lengend Snippet: Patient cohort characteristics

Article Snippet: Only 3 of 14 GBM pyrosequencing samples (21%) below the pyrosequencing-specific VAF cutoff of 0.115 tested positive, versus 35 of 65 array samples (54%) below the array-specific VAF cutoff of 0.325 ( p = 0.039, Fig. G).

Techniques: Pyrosequencing Assay, Methylation, Mutagenesis