Journal: PLoS ONE

Article Title: Developing a clinically relevant radiosensitizer for temozolomide-resistant gliomas

doi: 10.1371/journal.pone.0238238

Figure Lengend Snippet: MGMT-expressing variants (i.e., LN229M, U251M, and GL261M) of three well-established GB cell lines were checked along with their parental cells as well as the T98G (an endogenous high MGMT expressor) and LN229TR2 (an MMR-deficient variant of LN229) GB cells for MGMT expression by Western blotting (panel A). Colony survival data are also shown for all three isogenic GB cell lines (panel B). The O6BG MGMT inhibitor (40 μΜ) was used to demonstrate that the artificially expressed MGMT proteins in LN229M, U251M, and GL261M cells were functional and respond to specific inhibition (i.e., the MGMT-positive cells are sensitized to both alkylating agents after the addition of the O6BG inhibitor).

Article Snippet: A rabbit polyclonal antibody that crossreacts with both human MGMT and mouse Mgmt proteins was purchased from Boster Biological Technology (Pleasanton, CA) and used in this Western-blot analysis.

Techniques: Expressing, Variant Assay, Western Blot, Functional Assay, Inhibition

Journal: PLoS ONE

Article Title: A new sensitive and fast assay for the detection of EGFR mutations in liquid biopsies

doi: 10.1371/journal.pone.0253687

Figure Lengend Snippet: Median age was 65.5 years for cohort I and 69.5 years for cohort II at the time of routine ctDNA EGFR analyses.

Article Snippet: In cohort II, the SensiScreen ® EGFR Liquid assay platform (PentaBase) showed equal performance to the ctEGFR Mutation Detection Kit (EntroGen) in single replicate as compared to 2≤3 replicates for EntroGen (used in the routine laboratory at Herlev University Hospital).

Techniques:

Journal: PLoS ONE

Article Title: A new sensitive and fast assay for the detection of EGFR mutations in liquid biopsies

doi: 10.1371/journal.pone.0253687

Figure Lengend Snippet: PCR curves obtained when challenging assays with cell lines or plasmids containing the indicated EGFR mutations. Plasmids were diluted 1:1 in WT gDNA to ensure a total template amount of 1600 copies. Reference assay PCR curves are represented by heavy coloured lines and mutation specific assay PCR curves by light coloured lines as indicated in figure legends. Abbreviations: Ct, Cycle threshold; EGFR, Epidermal growth factor receptor.

Article Snippet: In cohort II, the SensiScreen ® EGFR Liquid assay platform (PentaBase) showed equal performance to the ctEGFR Mutation Detection Kit (EntroGen) in single replicate as compared to 2≤3 replicates for EntroGen (used in the routine laboratory at Herlev University Hospital).

Techniques: Mutagenesis

Journal: PLoS ONE

Article Title: A new sensitive and fast assay for the detection of EGFR mutations in liquid biopsies

doi: 10.1371/journal.pone.0253687

Figure Lengend Snippet: A. Histograms showing the frequency and distribution of mutant copies detected in 102 replicates for assays. B. Boxplot showing the collectively recovered number of copies by the three assays and thereby the overall detected copy number by assays. Abbreviations: EGFR, Epidermal growth factor receptor.

Article Snippet: In cohort II, the SensiScreen ® EGFR Liquid assay platform (PentaBase) showed equal performance to the ctEGFR Mutation Detection Kit (EntroGen) in single replicate as compared to 2≤3 replicates for EntroGen (used in the routine laboratory at Herlev University Hospital).

Techniques: Mutagenesis

Journal: PLoS ONE

Article Title: A new sensitive and fast assay for the detection of EGFR mutations in liquid biopsies

doi: 10.1371/journal.pone.0253687

Figure Lengend Snippet: Repeatability and accuracy evaluation of SensiScreen ® EGFR Liquid assays: Number of copies mutated for Exon 19 deletion, T790M or L858R.

Article Snippet: In cohort II, the SensiScreen ® EGFR Liquid assay platform (PentaBase) showed equal performance to the ctEGFR Mutation Detection Kit (EntroGen) in single replicate as compared to 2≤3 replicates for EntroGen (used in the routine laboratory at Herlev University Hospital).

Techniques:

Journal: PLoS ONE

Article Title: A new sensitive and fast assay for the detection of EGFR mutations in liquid biopsies

doi: 10.1371/journal.pone.0253687

Figure Lengend Snippet: Graphs describing the LoB evaluation based on the characterization of repeated testing of cfDNA pooled from 58 healthy donors A. Curves representing the T790M LoB results. B. Curves representing the L858R LoB results. C. Curves representing the EGFR exon 19 deletion LoB results.

Article Snippet: In cohort II, the SensiScreen ® EGFR Liquid assay platform (PentaBase) showed equal performance to the ctEGFR Mutation Detection Kit (EntroGen) in single replicate as compared to 2≤3 replicates for EntroGen (used in the routine laboratory at Herlev University Hospital).

Techniques:

Journal: PLoS ONE

Article Title: A new sensitive and fast assay for the detection of EGFR mutations in liquid biopsies

doi: 10.1371/journal.pone.0253687

Figure Lengend Snippet: Overview of the EGFR phenotypes detected by the Therascreen ® (QIAGEN) versus SensiScreen ® EGFR Liquid assay (Pentabase) and IOT ® Oncomine cell-free nucleic acids assay (Thermo Fisher Scientific) using cohort I and agreement or disagreement between platforms (N = 34).

Article Snippet: In cohort II, the SensiScreen ® EGFR Liquid assay platform (PentaBase) showed equal performance to the ctEGFR Mutation Detection Kit (EntroGen) in single replicate as compared to 2≤3 replicates for EntroGen (used in the routine laboratory at Herlev University Hospital).

Techniques:

Journal: PLoS ONE

Article Title: A new sensitive and fast assay for the detection of EGFR mutations in liquid biopsies

doi: 10.1371/journal.pone.0253687

Figure Lengend Snippet: Overview of the EGFR phenotypes detected by the SensiScreen ® EGFR Liquid assay (PentaBase ApS) versus the ctEGFR Mutation Detection Kit (EntroGen) using cohort II and agreement or disagreement between platforms (N = 34).

Article Snippet: In cohort II, the SensiScreen ® EGFR Liquid assay platform (PentaBase) showed equal performance to the ctEGFR Mutation Detection Kit (EntroGen) in single replicate as compared to 2≤3 replicates for EntroGen (used in the routine laboratory at Herlev University Hospital).

Techniques: Mutagenesis

Journal: JAMA Oncology

Article Title: Association of Autologous Tumor Lysate-Loaded Dendritic Cell Vaccination With Extension of Survival Among Patients With Newly Diagnosed and Recurrent Glioblastoma

doi: 10.1001/jamaoncol.2022.5370

Figure Lengend Snippet: A, Kaplan-Meier plot comparing overall survival for patients with newly diagnosed glioblastoma treated with autologous tumor lysate-loaded dendritic cell vaccination (DCVax-L) and 1366 contemporaneous matched external control participants (ECPs) treated with standard of care, derived from 5 other contemporaneous matched randomized clinical trials. B, Cox hazard ratios of overall survival in prespecified subgroups of participants receiving DCVax-L or treated with standard of care in external trials. In the age subgroup, there were 50 participants in the DCVax-L group and 45 in the ECP group aged 65 years or greater and 182 and 184, respectively in the younger than 65 years group; in the residual disease subgroup, there were 86 patients in the DCVax-L group and 163 in the ECP group with significant residual disease and 146 and 210, respectively, with minimal residual disease; in the MGMT (O 6 -methylguanine-DNA methyltransferase) subgroup, there were 90 patients in the DCVax-L group and 199 in the ECP group with methylated MGMT and 131 and 349, respectively, with unmethylated MGMT. Subgroup analyses of survival, using the same parameters as the comparator publications, are presented with 95% confidence intervals to facilitate comparisons with the ECP.

Article Snippet: The MGMT (O 6 -methylguanine-DNA methyltransferase) gene promoter methylation status, IDH (isocitrate dehydrogenase) R132 mutation status, and postsurgery minimal (<2 cm 2 ) vs significant (≥2 cm 2 ) residual tumor were determined centrally (LabCorp; Mayo; ICON).

Techniques: Control, Derivative Assay, Clinical Proteomics, Methylation

Journal: Clinical cancer research : an official journal of the American Association for Cancer Research

Article Title: Genomic and phenotypic characterization of a broad panel of patient derived xenografts reflects the diversity of glioblastoma

doi: 10.1158/1078-0432.CCR-19-0909

Figure Lengend Snippet: Mutations and copy number variants (CNVs) from WES are shown for core glioma genetic drivers. When available (n=55), patient germline variants were subtracted. Molecular gene expression subtype was determined from RNAseq (14). DNA methylation group was determined from genome wide methylation profiling according to TCGA pan-glioma classification (15). MGMT promoter methylation was assessed by quantitative methylation-specific PCR performed at Mayo Clinic. TERT promoter mutations (C228T and C250T) were detected by Sanger sequencing.

Article Snippet: For 22 patients, MGMT methylation was assessed during clinical care; the majority of testing was performed at LabCorp (Burlington, NC).

Techniques: Gene Expression, DNA Methylation Assay, Genome Wide, Methylation, Sequencing

Journal: Clinical cancer research : an official journal of the American Association for Cancer Research

Article Title: Genomic and phenotypic characterization of a broad panel of patient derived xenografts reflects the diversity of glioblastoma

doi: 10.1158/1078-0432.CCR-19-0909

Figure Lengend Snippet: (A) Survival benefit across PDX models treated with RT, TMZ and RT/TMZ. Mice with established orthotopic tumors from 37 PDX lines were randomized to treatment with RT, TMZ, or RT/TMZ. Survival benefit was calculated as a ratio of survival of the treated mice to placebo treated mice. PDXs are grouped by MGMT status: M=MGMT methylated (N=14), U=MGMT unmethylated (N=14) and R=recurrent (N=9). (B) Comparison of patient and PDX survival following standard therapies for 20 matched pairs with xenografts established at initial diagnosis. Patient survival is shown in months and PDX survival in days.

Article Snippet: For 22 patients, MGMT methylation was assessed during clinical care; the majority of testing was performed at LabCorp (Burlington, NC).

Techniques: Methylation, Comparison, Biomarker Discovery

Journal: Cancer Imaging

Article Title: Assessment of MGMT promoter methylation status in glioblastoma using deep learning features from multi-sequence MRI of intratumoral and peritumoral regions

doi: 10.1186/s40644-024-00817-1

Figure Lengend Snippet: Segmentation illustration of tumor T1WI and CE-T1WI sequence imaging. Patient a is a 66-year-old male with unmethylated MGMT status, and patient b is a 68-year-old female with methylated MGMT status. The red region represents the NCR, the yellow region represents the ET, and the green region represents the PED

Article Snippet: The inclusion criteria included: (1) comprehensive imaging, pathological, and clinical data; (2) pathological confirmation of glioblastoma (WHO CNS 2021) with a definitive diagnosis of MGMT promoter methylation status (in house method developed by UCSF clinical labs, https://genomics.ucsf.edu/content/mgmt-promoter-methylation-assay ); (3) surgical intervention within one week following MRI examination; and (4) absence of any prior surgical, radiotherapy, or chemotherapy treatments before the MRI examination.

Techniques: Sequencing, Imaging, Methylation

Journal: Cancer Imaging

Article Title: Assessment of MGMT promoter methylation status in glioblastoma using deep learning features from multi-sequence MRI of intratumoral and peritumoral regions

doi: 10.1186/s40644-024-00817-1

Figure Lengend Snippet: Prediction results of MGMT promoter methylation status using different models

Article Snippet: The inclusion criteria included: (1) comprehensive imaging, pathological, and clinical data; (2) pathological confirmation of glioblastoma (WHO CNS 2021) with a definitive diagnosis of MGMT promoter methylation status (in house method developed by UCSF clinical labs, https://genomics.ucsf.edu/content/mgmt-promoter-methylation-assay ); (3) surgical intervention within one week following MRI examination; and (4) absence of any prior surgical, radiotherapy, or chemotherapy treatments before the MRI examination.

Techniques: Methylation

Journal: Neuro-Oncology Practice

Article Title: Correlation of commercially available quantitative MGMT (O-6-methylguanine-DNA methyltransferase) promoter methylation scores and GBM patient survival

doi: 10.1093/nop/npy028

Figure Lengend Snippet: Cox Regression Analysis of Overall Survival and Progression-Free Survival of 102 Primary Glioblastoma MGMT Unmethylated Patients With Substratification by MGMT Values

Article Snippet: Next, we evaluated whether the established LabCorp MGMT methylation threshold of 2 can stratify survival in our cohort.

Techniques: Biomarker Discovery

Journal: Neuro-Oncology Practice

Article Title: Correlation of commercially available quantitative MGMT (O-6-methylguanine-DNA methyltransferase) promoter methylation scores and GBM patient survival

doi: 10.1093/nop/npy028

Figure Lengend Snippet: Kaplan-Meier analysis is used to A, compare the MGMT (1-1.99) vs MGMT (<1) and MGMT (≥2) patients. The MGMT (1-1.99) group’s median OS (25.4 months) falls in between the MGMT (≥2) (38.8 months) and MGMT (<1) (17.3 months) median OS values (Log-rank P = .001). B, PFS showed the same trend, namely the MGMT (1-1.99) group generated a higher median OS of 11.8 months compared to the MGMT (<1) group but lower than the MGMT (≥ 2) group, yielding 11.8 months vs 7.92 months and 18.0 months (Log-rank P < .0001), respectively. MGMT indicates O-6-methylguanine-DNA methyltransferase; mo, months; OS, overall survival; PFS, progression-free survival.

Article Snippet: Next, we evaluated whether the established LabCorp MGMT methylation threshold of 2 can stratify survival in our cohort.

Techniques: Generated

Journal: Neuro-Oncology Practice

Article Title: Correlation of commercially available quantitative MGMT (O-6-methylguanine-DNA methyltransferase) promoter methylation scores and GBM patient survival

doi: 10.1093/nop/npy028

Figure Lengend Snippet: Cox Regression Analysis of Overall Survival and Progression-Free Survival of 165 Primary Glioblastoma Patients With Substratification by MGMT Values

Article Snippet: Next, we evaluated whether the established LabCorp MGMT methylation threshold of 2 can stratify survival in our cohort.

Techniques: Biomarker Discovery

Journal: Neuro-oncology Advances

Article Title: Prognostic value of O 6 -methylguanine-DNA methyltransferase methylation in isocitrate dehydrogenase mutant gliomas

doi: 10.1093/noajnl/vdac030

Figure Lengend Snippet: Summary of Cohort Characteristics and Treatments

Article Snippet: The majority of MGMT gene promoter methylation assays was performed by LabCorp or NeoGenomics Laboratories using bisulfite modification of tumor deoxyribonucleic acid (DNA) and polymerase chain reaction (PCR) to detect CpG methylation.

Techniques: Methylation, Biomarker Discovery

Journal: Neuro-oncology Advances

Article Title: Prognostic value of O 6 -methylguanine-DNA methyltransferase methylation in isocitrate dehydrogenase mutant gliomas

doi: 10.1093/noajnl/vdac030

Figure Lengend Snippet: Overall survival (OS) outcomes of patients stratified by MGMT promoter methylation status. (A) OS of the entire patient cohort. (B) OS of patients diagnosed with glioblastoma multiforme (GBM). (C) OS of patients diagnosed with anaplastic astrocytoma (AA) and low-grade astrocytoma (LA). (D) OS of patients diagnosed with anaplastic oligodendroglioma (AO) and low-grade oligodendroglioma (LO). (E) OS of patients diagnosed with AA. (F) OS of patients diagnosed with LA. (G) OS of patients diagnosed with AO. (H) OS of patients diagnosed with LO.

Article Snippet: The majority of MGMT gene promoter methylation assays was performed by LabCorp or NeoGenomics Laboratories using bisulfite modification of tumor deoxyribonucleic acid (DNA) and polymerase chain reaction (PCR) to detect CpG methylation.

Techniques: Methylation

Journal: Neuro-oncology Advances

Article Title: Prognostic value of O 6 -methylguanine-DNA methyltransferase methylation in isocitrate dehydrogenase mutant gliomas

doi: 10.1093/noajnl/vdac030

Figure Lengend Snippet: Multivariate Analysis of OS in Various Pathological Subgroups

Article Snippet: The majority of MGMT gene promoter methylation assays was performed by LabCorp or NeoGenomics Laboratories using bisulfite modification of tumor deoxyribonucleic acid (DNA) and polymerase chain reaction (PCR) to detect CpG methylation.

Techniques:

Journal: Neuro-oncology Advances

Article Title: Prognostic value of O 6 -methylguanine-DNA methyltransferase methylation in isocitrate dehydrogenase mutant gliomas

doi: 10.1093/noajnl/vdac030

Figure Lengend Snippet: Progression-free survival (PFS) outcomes of patients stratified by MGMT promoter methylation status. (A) PFS of the entire patient cohort. (B) PFS of patients diagnosed with glioblastoma multiforme (GBM). (C) PFS of patients diagnosed with anaplastic astrocytoma (AA) and low-grade astrocytoma (LA). (D) PFS of patients diagnosed with anaplastic oligodendroglioma (AO) and low-grade oligodendroglioma (LO). (E) PFS of patients diagnosed with AA. (F) PFS of patients diagnosed with LA. (G) PFS of patients diagnosed with AO. (H) PFS of patients diagnosed with LO.

Article Snippet: The majority of MGMT gene promoter methylation assays was performed by LabCorp or NeoGenomics Laboratories using bisulfite modification of tumor deoxyribonucleic acid (DNA) and polymerase chain reaction (PCR) to detect CpG methylation.

Techniques: Methylation

Journal: Neuro-oncology Advances

Article Title: Prognostic value of O 6 -methylguanine-DNA methyltransferase methylation in isocitrate dehydrogenase mutant gliomas

doi: 10.1093/noajnl/vdac030

Figure Lengend Snippet: Multivariate Analysis of PFS in Various Pathological Subgroups

Article Snippet: The majority of MGMT gene promoter methylation assays was performed by LabCorp or NeoGenomics Laboratories using bisulfite modification of tumor deoxyribonucleic acid (DNA) and polymerase chain reaction (PCR) to detect CpG methylation.

Techniques: