Journal: Journal of Clinical Medicine

Article Title: Frequency of BRAF Mutations in Dysplastic Nevi, Lentigo Maligna, and Melanoma In Situ

doi: 10.3390/jcm13164799

Figure Lengend Snippet: The frequency of BRAF mutations varies across diagnoses.

Article Snippet: Three reaction mixtures were prepared for each sample: (i) mix with Mutation Detection Assay for V600E mutation (BRAF_476_mu; Assay ID: Hs00000111_mu), (ii) mix with Mutation Detection Assay for V600K mutation (BRAF_473_mu; Assay ID: Hs00000769_mu), (iii) Reference Assay (BRAF_rf; Assay ID: Hs00000172_rf).

Techniques: Mutagenesis

Journal: Journal of Clinical Medicine

Article Title: Frequency of BRAF Mutations in Dysplastic Nevi, Lentigo Maligna, and Melanoma In Situ

doi: 10.3390/jcm13164799

Figure Lengend Snippet: Presence and frequency of BRAF mutation between patients with ND, MIS, and LM.

Article Snippet: Three reaction mixtures were prepared for each sample: (i) mix with Mutation Detection Assay for V600E mutation (BRAF_476_mu; Assay ID: Hs00000111_mu), (ii) mix with Mutation Detection Assay for V600K mutation (BRAF_473_mu; Assay ID: Hs00000769_mu), (iii) Reference Assay (BRAF_rf; Assay ID: Hs00000172_rf).

Techniques: Mutagenesis

Journal: Journal of Clinical Medicine

Article Title: Frequency of BRAF Mutations in Dysplastic Nevi, Lentigo Maligna, and Melanoma In Situ

doi: 10.3390/jcm13164799

Figure Lengend Snippet: Age distribution of patients with and without BRAF mutation.

Article Snippet: Three reaction mixtures were prepared for each sample: (i) mix with Mutation Detection Assay for V600E mutation (BRAF_476_mu; Assay ID: Hs00000111_mu), (ii) mix with Mutation Detection Assay for V600K mutation (BRAF_473_mu; Assay ID: Hs00000769_mu), (iii) Reference Assay (BRAF_rf; Assay ID: Hs00000172_rf).

Techniques: Mutagenesis

Journal: Journal of Clinical Medicine

Article Title: Frequency of BRAF Mutations in Dysplastic Nevi, Lentigo Maligna, and Melanoma In Situ

doi: 10.3390/jcm13164799

Figure Lengend Snippet: Correlation of BRAF mutation and localization.

Article Snippet: Three reaction mixtures were prepared for each sample: (i) mix with Mutation Detection Assay for V600E mutation (BRAF_476_mu; Assay ID: Hs00000111_mu), (ii) mix with Mutation Detection Assay for V600K mutation (BRAF_473_mu; Assay ID: Hs00000769_mu), (iii) Reference Assay (BRAF_rf; Assay ID: Hs00000172_rf).

Techniques: Mutagenesis

Journal: Journal of Clinical Medicine

Article Title: Frequency of BRAF Mutations in Dysplastic Nevi, Lentigo Maligna, and Melanoma In Situ

doi: 10.3390/jcm13164799

Figure Lengend Snippet: Tumor size distribution in patients with and without BRAF mutation. ∗ and ◦ represent outliers.

Article Snippet: Three reaction mixtures were prepared for each sample: (i) mix with Mutation Detection Assay for V600E mutation (BRAF_476_mu; Assay ID: Hs00000111_mu), (ii) mix with Mutation Detection Assay for V600K mutation (BRAF_473_mu; Assay ID: Hs00000769_mu), (iii) Reference Assay (BRAF_rf; Assay ID: Hs00000172_rf).

Techniques: Mutagenesis

Journal: Journal of Clinical Medicine

Article Title: Frequency of BRAF Mutations in Dysplastic Nevi, Lentigo Maligna, and Melanoma In Situ

doi: 10.3390/jcm13164799

Figure Lengend Snippet: Correlation between the presence of the BRAF mutation and a previous melanoma diagnosis.

Article Snippet: Three reaction mixtures were prepared for each sample: (i) mix with Mutation Detection Assay for V600E mutation (BRAF_476_mu; Assay ID: Hs00000111_mu), (ii) mix with Mutation Detection Assay for V600K mutation (BRAF_473_mu; Assay ID: Hs00000769_mu), (iii) Reference Assay (BRAF_rf; Assay ID: Hs00000172_rf).

Techniques: Mutagenesis, Biomarker Discovery

Journal: Oncology Letters

Article Title: Detection of EGFR and BRAF mutations by competitive allele-specific TaqMan polymerase chain reaction in lung adenocarcinoma

doi: 10.3892/ol.2017.7652

Figure Lengend Snippet: Patients with BRAF mutations (n=12).

Article Snippet: CastPCR Extracted DNA samples from FFPE tissues were analyzed by the following Taqman ® Mutation Detection Assay kits (Life Technologies; Thermo Fisher Scientific, Inc., Waltham, MA, USA): EGFR_reference (Catalog Number: 4465807, Assay ID: Hs00000173_rf) and BRAF_reference (Catalog Number: 4465807, Assay ID: Hs00000172_rf); EGFR_6223_mu (Catalog Number: 4465804, Assay ID: Hs00000156_mu), EGFR_6225_mu (Catalog Number: 4465804, Assay ID: Hs00000157_mu), EGFR_6224_mu (Catalog Number: 4465804, Assay ID: Hs00000102_mu) and EGFR_6240_mu (Catalog Number: 4465804, Assay ID: Hs00000106_mu) for detecting the 2235–2249 del, 2236–2250 del, L858R and T790M, respectively; BRAF_460_mu (Catalog Number: 4465804, Assay ID: Hs00001351_mu), BRAF_467_mu (Catalog Number: 4465804, Assay ID: Hs00000996_mu) and BRAF_475_mu (Catalog Number: 4465804, Assay ID: Hs00001384_mu) for detecting G469A, D594G and V600E, respectively.

Techniques: Mutagenesis

Journal: Oncology Letters

Article Title: Detection of EGFR and BRAF mutations by competitive allele-specific TaqMan polymerase chain reaction in lung adenocarcinoma

doi: 10.3892/ol.2017.7652

Figure Lengend Snippet: Association between BRAF incidence and clinicopathological features.

Article Snippet: CastPCR Extracted DNA samples from FFPE tissues were analyzed by the following Taqman ® Mutation Detection Assay kits (Life Technologies; Thermo Fisher Scientific, Inc., Waltham, MA, USA): EGFR_reference (Catalog Number: 4465807, Assay ID: Hs00000173_rf) and BRAF_reference (Catalog Number: 4465807, Assay ID: Hs00000172_rf); EGFR_6223_mu (Catalog Number: 4465804, Assay ID: Hs00000156_mu), EGFR_6225_mu (Catalog Number: 4465804, Assay ID: Hs00000157_mu), EGFR_6224_mu (Catalog Number: 4465804, Assay ID: Hs00000102_mu) and EGFR_6240_mu (Catalog Number: 4465804, Assay ID: Hs00000106_mu) for detecting the 2235–2249 del, 2236–2250 del, L858R and T790M, respectively; BRAF_460_mu (Catalog Number: 4465804, Assay ID: Hs00001351_mu), BRAF_467_mu (Catalog Number: 4465804, Assay ID: Hs00000996_mu) and BRAF_475_mu (Catalog Number: 4465804, Assay ID: Hs00001384_mu) for detecting G469A, D594G and V600E, respectively.

Techniques:

Journal: Oncology Letters

Article Title: Detection of EGFR and BRAF mutations by competitive allele-specific TaqMan polymerase chain reaction in lung adenocarcinoma

doi: 10.3892/ol.2017.7652

Figure Lengend Snippet: Patients with BRAF mutations (n=12).

Article Snippet: CastPCR Extracted DNA samples from FFPE tissues were analyzed by the following Taqman ® Mutation Detection Assay kits (Life Technologies; Thermo Fisher Scientific, Inc., Waltham, MA, USA): EGFR_reference (Catalog Number: 4465807, Assay ID: Hs00000173_rf) and BRAF_reference (Catalog Number: 4465807, Assay ID: Hs00000172_rf); EGFR_6223_mu (Catalog Number: 4465804, Assay ID: Hs00000156_mu), EGFR_6225_mu (Catalog Number: 4465804, Assay ID: Hs00000157_mu), EGFR_6224_mu (Catalog Number: 4465804, Assay ID: Hs00000102_mu) and EGFR_6240_mu (Catalog Number: 4465804, Assay ID: Hs00000106_mu) for detecting the 2235–2249 del, 2236–2250 del, L858R and T790M, respectively; BRAF_460_mu (Catalog Number: 4465804, Assay ID: Hs00001351_mu), BRAF_467_mu (Catalog Number: 4465804, Assay ID: Hs00000996_mu) and BRAF_475_mu (Catalog Number: 4465804, Assay ID: Hs00001384_mu) for detecting G469A, D594G and V600E, respectively.

Techniques: Mutagenesis

Journal: Oncology Letters

Article Title: Detection of EGFR and BRAF mutations by competitive allele-specific TaqMan polymerase chain reaction in lung adenocarcinoma

doi: 10.3892/ol.2017.7652

Figure Lengend Snippet: Association between BRAF incidence and clinicopathological features.

Article Snippet: CastPCR Extracted DNA samples from FFPE tissues were analyzed by the following Taqman ® Mutation Detection Assay kits (Life Technologies; Thermo Fisher Scientific, Inc., Waltham, MA, USA): EGFR_reference (Catalog Number: 4465807, Assay ID: Hs00000173_rf) and BRAF_reference (Catalog Number: 4465807, Assay ID: Hs00000172_rf); EGFR_6223_mu (Catalog Number: 4465804, Assay ID: Hs00000156_mu), EGFR_6225_mu (Catalog Number: 4465804, Assay ID: Hs00000157_mu), EGFR_6224_mu (Catalog Number: 4465804, Assay ID: Hs00000102_mu) and EGFR_6240_mu (Catalog Number: 4465804, Assay ID: Hs00000106_mu) for detecting the 2235–2249 del, 2236–2250 del, L858R and T790M, respectively; BRAF_460_mu (Catalog Number: 4465804, Assay ID: Hs00001351_mu), BRAF_467_mu (Catalog Number: 4465804, Assay ID: Hs00000996_mu) and BRAF_475_mu (Catalog Number: 4465804, Assay ID: Hs00001384_mu) for detecting G469A, D594G and V600E, respectively.

Techniques:

Journal: Oncotarget

Article Title: Mutational profile of skin lesions in hepatocellular carcinoma patients under tyrosine kinase inhibition: a repercussion of a wide-spectrum activity

doi: 10.18632/oncotarget.27891

Figure Lengend Snippet: Clinical and molecular features of control samples

Article Snippet: Detection and measurement of BRAF V600E (BRAF_476_mu: Hs00000111_mu; BRAF_rf: Hs00000172_rf), HRAS G12D (HRAS_484_mu: Hs00000778_mu; HRAS_ref: Hs00001018_rf), HRAS Q61K (HRAS_496_mu: Hs00000785_mu; HRAS_ref: Hs00001018_rf), HRAS Q61L (HRAS_498_mu: Hs00000786_mu; HRAS_ref: Hs00001018_rf) and KRAS G12D (KRAS_521_mu: Hs00000121_mu; KRAS_rf: Hs00000174_rf) somatic mutations was done by means of competitive allele-specific TaqManTM PCR technology (castPCRTM Technology).

Techniques: Control

Journal: Frontiers in Oncology

Article Title: Clinicopathological correlations in 38 cases of gastroenteropancreatic high-grade neuroendocrine neoplasms

doi: 10.3389/fonc.2024.1399079

Figure Lengend Snippet: Illustrates the distribution of BRAF V600E mutation in GEP HG-NENs. A statistically significant disparity (**p=0.0086) was observed between NET G3 and SCNEC (A) . The distribution of KRAS mutation in GEP HG-NENs is also shown in the figure (B) .

Article Snippet: In our study, the BRAF V600E mutation was identified in 32.4% of the HG-NEN cases.

Techniques: Mutagenesis

Journal: Epigenetics

Article Title: Reduced aquaporin-1 transcript expression in colorectal carcinoma is associated with promoter hypermethylation

doi: 10.1080/15592294.2019.1580112

Figure Lengend Snippet: AQP1 transcript expression in tissues from the combined TCGA-COAD and TCGA-READ datasets by clinicopathological characteristics.

Article Snippet: For tissues, RNA sequencing expression (median number of fragments per kilobase of exon per million reads, FPKM), Infinium HumanMethylation450 BeadChip (HM450) DNA methylation (beta-values), and BRAF mutation data were obtained from TCGA Research Network ( http://cancergenome.nih.gov/ ).

Techniques: Expressing, Mutagenesis

Journal: Epigenetics

Article Title: Reduced aquaporin-1 transcript expression in colorectal carcinoma is associated with promoter hypermethylation

doi: 10.1080/15592294.2019.1580112

Figure Lengend Snippet: Overall survival for the 453 patients with complete clinical data in the combined TCGA-COAD and TCGA-READ datasets.

Article Snippet: For tissues, RNA sequencing expression (median number of fragments per kilobase of exon per million reads, FPKM), Infinium HumanMethylation450 BeadChip (HM450) DNA methylation (beta-values), and BRAF mutation data were obtained from TCGA Research Network ( http://cancergenome.nih.gov/ ).

Techniques: Expressing, Mutagenesis

Journal: Molecular Diagnosis & Therapy

Article Title: Glioma 2021 WHO Classification: The Superiority of NGS Over IHC in Routine Diagnostics

doi: 10.1007/s40291-022-00612-3

Figure Lengend Snippet: Examples of the most common pathogenic variants detected by NGS. The black arrows show the position of the detected variant. Abnormalities were assessed using TIER 2017 Variant Classification and AMCG 2015. A TERT promoter upstream gene variant NC_000005.9: g.1295228G>A TIER I; pathogenic. B TERT promoter upstream gene variant NC_000005.9:g.1295250G>A TIER I; pathogenic. C IDH1 R132H missense variant NM_005896.2:c.395G>A (p.Arg132His) TIER I. D IDH1 R132S missense variant NM_005896.2:c.394C>A (p.Arg132Ser) TIER II; Likely pathogenic. E PIK3CA missense variant NM_006218.2:c.1633G>A (p.Glu545Lys) TIER I; pathogenic. F BRAF missense variant NM_004333.4:c.1799T>A (p.Val600Glu) TIER I; pathogenic. NGS next-generation sequencing

Article Snippet: The black arrows indicate mutations detected using next-generation sequencing (NGS Targeted Hotspot Panel, Entrogen), Sanger sequencing (Applied Biosystems SeqStudio Genetic Analyzer), and qPCR ( IDH1/2 Mutation Detection Kit, Entrogen), with a limit of detection of 5, 20, and 1%, respectively.

Techniques: Variant Assay, Next-Generation Sequencing

Journal: Molecular Diagnosis & Therapy

Article Title: Glioma 2021 WHO Classification: The Superiority of NGS Over IHC in Routine Diagnostics

doi: 10.1007/s40291-022-00612-3

Figure Lengend Snippet: Evaluation of IDH1 status obtained by non-reference center (IHC), with 3 molecular methods (NGS, qPCR, Sanger) obtained by reference oncology center

Article Snippet: The black arrows indicate mutations detected using next-generation sequencing (NGS Targeted Hotspot Panel, Entrogen), Sanger sequencing (Applied Biosystems SeqStudio Genetic Analyzer), and qPCR ( IDH1/2 Mutation Detection Kit, Entrogen), with a limit of detection of 5, 20, and 1%, respectively.

Techniques: Mutagenesis

Journal: Molecular Diagnosis & Therapy

Article Title: Glioma 2021 WHO Classification: The Superiority of NGS Over IHC in Routine Diagnostics

doi: 10.1007/s40291-022-00612-3

Figure Lengend Snippet: Evaluation of IDH1 status received from non-reference center (MLPA), with 3 molecular methods (NGS, qPCR, Sanger) received from reference oncology center

Article Snippet: The black arrows indicate mutations detected using next-generation sequencing (NGS Targeted Hotspot Panel, Entrogen), Sanger sequencing (Applied Biosystems SeqStudio Genetic Analyzer), and qPCR ( IDH1/2 Mutation Detection Kit, Entrogen), with a limit of detection of 5, 20, and 1%, respectively.

Techniques: Mutagenesis

Journal: Molecular Diagnosis & Therapy

Article Title: Glioma 2021 WHO Classification: The Superiority of NGS Over IHC in Routine Diagnostics

doi: 10.1007/s40291-022-00612-3

Figure Lengend Snippet: Examples of IHC and MLPA reports from different non-oncological reference centers versus NGS, qPCR, and Sanger sequencing results from the oncology reference center. Two false positives were detected by MLPA and IHC, and one false negative by IHC. Pathogenic variants detected by NGS were additionally validated by two independent methods: Sanger sequencing and qPCR. The black arrows indicate mutations detected using next-generation sequencing (NGS Targeted Hotspot Panel, Entrogen), Sanger sequencing (Applied Biosystems SeqStudio Genetic Analyzer), and qPCR ( IDH1/2 Mutation Detection Kit, Entrogen), with a limit of detection of 5, 20, and 1%, respectively. Two red curves represent (1) positive control and (2) amplicon with mutation detected ( arrow ). The patient no. 13 – MLPA report indicates IDH-wildtype, while NGS, qPCR, and Sanger sequencing confirmed mutation in the IDH1 gene. IHC immunohistochemistry, MLPA multiplex ligation-dependent probe amplification, NGS next-generation sequencing, qPCR quantitative polymerase chain reaction

Article Snippet: The black arrows indicate mutations detected using next-generation sequencing (NGS Targeted Hotspot Panel, Entrogen), Sanger sequencing (Applied Biosystems SeqStudio Genetic Analyzer), and qPCR ( IDH1/2 Mutation Detection Kit, Entrogen), with a limit of detection of 5, 20, and 1%, respectively.

Techniques: Sequencing, Next-Generation Sequencing, Mutagenesis, Positive Control, Amplification, Immunohistochemistry, Multiplex Assay, Ligation, Real-time Polymerase Chain Reaction

Journal: Molecular Diagnosis & Therapy

Article Title: Glioma 2021 WHO Classification: The Superiority of NGS Over IHC in Routine Diagnostics

doi: 10.1007/s40291-022-00612-3

Figure Lengend Snippet:

Article Snippet: The black arrows indicate mutations detected using next-generation sequencing (NGS Targeted Hotspot Panel, Entrogen), Sanger sequencing (Applied Biosystems SeqStudio Genetic Analyzer), and qPCR ( IDH1/2 Mutation Detection Kit, Entrogen), with a limit of detection of 5, 20, and 1%, respectively.

Techniques: Next-Generation Sequencing, Real-time Polymerase Chain Reaction

Journal: Journal of Pathology and Translational Medicine

Article Title: TERT mutations and aggressive histopathologic characteristics of radioiodine-refractory papillary thyroid cancer

doi: 10.4132/jptm.2024.07.29

Figure Lengend Snippet: Incidences of TERT -promoter mutations and BRAF V600E mutations in RI-refractory and RI-responsive PTCs

Article Snippet: Molecular assays included PNA-mediated clamping polymerase chain reaction amplification of mutated BRAF genes (Panagene, Daejeon, Korea) [ ] and pyrosequencing for TERT -promoter mutations, using established protocols and updated techniques reflecting recent advances in molecular diagnostics [ , ].

Techniques:

Journal: Journal of Pathology and Translational Medicine

Article Title: TERT mutations and aggressive histopathologic characteristics of radioiodine-refractory papillary thyroid cancer

doi: 10.4132/jptm.2024.07.29

Figure Lengend Snippet: Combined incidence of TERT -promoter mutations and BRAF V600E mutations

Article Snippet: Molecular assays included PNA-mediated clamping polymerase chain reaction amplification of mutated BRAF genes (Panagene, Daejeon, Korea) [ ] and pyrosequencing for TERT -promoter mutations, using established protocols and updated techniques reflecting recent advances in molecular diagnostics [ , ].

Techniques: Mutagenesis

Journal: Journal of Pathology and Translational Medicine

Article Title: TERT mutations and aggressive histopathologic characteristics of radioiodine-refractory papillary thyroid cancer

doi: 10.4132/jptm.2024.07.29

Figure Lengend Snippet: Relationship between clinicopathologic features and TERT -promoter mutation or BRAF V600E mutation in PTCs

Article Snippet: Molecular assays included PNA-mediated clamping polymerase chain reaction amplification of mutated BRAF genes (Panagene, Daejeon, Korea) [ ] and pyrosequencing for TERT -promoter mutations, using established protocols and updated techniques reflecting recent advances in molecular diagnostics [ , ].

Techniques: Mutagenesis, Biomarker Discovery

Journal: Journal of Pathology and Translational Medicine

Article Title: TERT mutations and aggressive histopathologic characteristics of radioiodine-refractory papillary thyroid cancer

doi: 10.4132/jptm.2024.07.29

Figure Lengend Snippet: Relationship between immunohistochemical results and expression of mutations of TERT and BRAF V600E

Article Snippet: Molecular assays included PNA-mediated clamping polymerase chain reaction amplification of mutated BRAF genes (Panagene, Daejeon, Korea) [ ] and pyrosequencing for TERT -promoter mutations, using established protocols and updated techniques reflecting recent advances in molecular diagnostics [ , ].

Techniques: Immunohistochemical staining, Expressing, Mutagenesis

Journal: Journal of Pathology and Translational Medicine

Article Title: TERT mutations and aggressive histopathologic characteristics of radioiodine-refractory papillary thyroid cancer

doi: 10.4132/jptm.2024.07.29

Figure Lengend Snippet: Sensitivity and specificity of histopathologic features and mutations in radioiodine-refractory PTCs

Article Snippet: Molecular assays included PNA-mediated clamping polymerase chain reaction amplification of mutated BRAF genes (Panagene, Daejeon, Korea) [ ] and pyrosequencing for TERT -promoter mutations, using established protocols and updated techniques reflecting recent advances in molecular diagnostics [ , ].

Techniques: Mutagenesis

Journal: Journal of Pathology and Translational Medicine

Article Title: TERT mutations and aggressive histopathologic characteristics of radioiodine-refractory papillary thyroid cancer

doi: 10.4132/jptm.2024.07.29

Figure Lengend Snippet: Logistic regression analysis on radioiodine-refractoriness in PTCs (n = 108)

Article Snippet: Molecular assays included PNA-mediated clamping polymerase chain reaction amplification of mutated BRAF genes (Panagene, Daejeon, Korea) [ ] and pyrosequencing for TERT -promoter mutations, using established protocols and updated techniques reflecting recent advances in molecular diagnostics [ , ].

Techniques: Mutagenesis, Selection