Journal: Marine Drugs

Article Title: Emerging Trends in Genetic Engineering of Microalgae for Commercial Applications

doi: 10.3390/md20050285

Figure Lengend Snippet: Examples of genetic engineering of microalgae for carotenoid production.

Article Snippet: The construction of metabolic pathways and assembled transcriptome using next generation DNA pyrosequencing technology was applied to Dunaliella tertiolecta marine microalga [ ].

Techniques: CRISPR, Knock-Out, Mutagenesis, Cloning, Expressing, Over Expression, Transformation Assay, Gene Expression, Irradiation

Journal: Scientific Reports

Article Title: Predictive assessment in pharmacogenetics of Glutathione S-transferases genes on efficacy of platinum-based chemotherapy in non-small cell lung cancer patients

doi: 10.1038/s41598-017-02833-7

Figure Lengend Snippet: Characteristics of studies included in meta-analysis.

Article Snippet: Deng J.H. et al . , 2015 , China , Asian , 97 , NR , 40.20% , IIIB, IV , RECIST , ORR/DCR/PFS , DNA pyrosequencing , GSTP1 , 15.

Techniques: Sequencing, DNA Sequencing, Multiplex Assay

Journal: Scientific Reports

Article Title: Differences in DNA Methylation and Functional Expression in Lactase Persistent and Non-persistent Individuals

doi: 10.1038/s41598-018-23957-4

Figure Lengend Snippet: Pyrosequencing of DNA methylation at cg20242066. ( A ) Schematic of LCT proximal promoter with location of cg20242066 upstream of the first three exons of the gene. The genomic coordinate of cg20242066 is also given (genome build hg19). ( B) DNA methylation quantification in CC vs. C/T vs. TT individuals, as well as in ( C) Phenotypically Persistent (PER) and Non-persistent (NON-PER) individuals. Student’s T-test was calculated for inter-group comparisons (*p < 0.05; **p < 0.001). Number of individuals in each group is given in parenthesis. ( D) Correlation between DNA methylation at cg20242066 and lactase enzymatic activity (enzymatic activity data from Baffour-Awuah et al . ). ( E) Correlation between DNA methylation at cg20242066 and LCT gene expression ( LCT gene expression data from Baffour-Awuah et al . ).

Article Snippet: Figure 3 Pyrosequencing of DNA methylation at cg20242066. ( A ) Schematic of LCT proximal promoter with location of cg20242066 upstream of the first three exons of the gene.

Techniques: DNA Methylation Assay, Activity Assay, Gene Expression

Journal: Scientific Reports

Article Title: Differences in DNA Methylation and Functional Expression in Lactase Persistent and Non-persistent Individuals

doi: 10.1038/s41598-018-23957-4

Figure Lengend Snippet: Correlation between DNA methylation at the LCT enhancer and cg20242066. ( A ) Lactase enzymatic activity according to the genotype of the individual at −13910C > T (rs4988235). Student’s T-test was calculated for inter-group comparisons (*p < 0.05; **p < 0.001). ( B) Correlation between DNA methylation at the LCT promoter cg20242066 and LCT enhancer.

Article Snippet: Figure 3 Pyrosequencing of DNA methylation at cg20242066. ( A ) Schematic of LCT proximal promoter with location of cg20242066 upstream of the first three exons of the gene.

Techniques: DNA Methylation Assay, Activity Assay

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 pyrosequencing samples . ( A ) Frequency of positive results for all glioma samples above and below the cutoff value of VAF = 0.325. ( B ) Cumulative mean frequency of positive test results as a function of VAF. ( C ) Trends in cumulative mean MGMT promoter pyrosequencing score with increasing VAF. ( D ) Mean MGMT promoter pyrosequencing scores above and below VAF = 0.325. Similar results are shown for each tumor subtype, including IDH-wildtype glioblastoma ( E - H ), IDH-mutant astrocytoma ( I - L ) and IDH-mutant and 1p/19q co-deleted oligodendroglioma ( M - P ). (Horizontal dashed black lines: mean values for cohort; Horizontal solid red lines: MGMT positivity cutoff of 10.0%; Vertical dashed black lines: cutoff values identified by Cutoff Finder; Vertical dashed red lines: cutoff values identified by multi-part linear regression; Panels A, E, I, M: Fisher’s exact test; Panels D, H, L, P: unpaired Student’s T-test; pyroseq: pyrosequencing; *p < 0.05; ****p < 0.0001)

Article Snippet: Fig. 5 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)

Techniques: Methylation, Mutagenesis

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: Fig. 5 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)

Techniques: Methylation, DNA Methylation Assay, Mutagenesis

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: Fig. 5 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)

Techniques: Mutagenesis, Methylation, 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: Fig. 5 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)

Techniques: Methylation, DNA Methylation Assay, 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: Central hypothesis . MGMT promoter methylation is pathologic, and occurs only in tumor cells. Cellular glioma samples are rich in DNA from tumor cells, whereas paucicellular glioma samples contain a large fraction of DNA from non-tumor cells, which can “dilute” positive methylation signals from tumor cell DNA, leading to false-negative results

Article Snippet: Fig. 5 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)

Techniques: Methylation

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: Fig. 5 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)

Techniques: Pyrosequencing Assay, Methylation, Mutagenesis