Journal: Oncotarget

Article Title: Comprehensive profiling and quantitation of oncogenic mutations in non small-cell lung carcinoma using single molecule amplification and re-sequencing technology

doi: 10.18632/oncotarget.10464

Figure Lengend Snippet: Patient demographics and clinical information versus EGFR mutation status

Article Snippet: ARMS-PCR for detection of 29 hot spot EGFR mutations ( ) was performed using the Human EGFR Gene Mutations Fluorescence Polymerase Chain Reaction (PCR) Diagnostic Kit (Amoy Diagnostics, Xiamen, Fujian) as previously described [ ].

Techniques: Mutagenesis, Significance Assay

Journal: Oncotarget

Article Title: Comprehensive profiling and quantitation of oncogenic mutations in non small-cell lung carcinoma using single molecule amplification and re-sequencing technology

doi: 10.18632/oncotarget.10464

Figure Lengend Snippet: A total of 25 patients were studied with either activating EGFR or ALK mutations identified in the original tumour specimens. All non-tumour tissues were negative but low levels of new mutations were identified in four cases. Closed symbols represent the level of activating mutation in the tumour tissue whereas open symbols represent the level of activating or new mutations in the non-tumour tissue.

Article Snippet: ARMS-PCR for detection of 29 hot spot EGFR mutations ( ) was performed using the Human EGFR Gene Mutations Fluorescence Polymerase Chain Reaction (PCR) Diagnostic Kit (Amoy Diagnostics, Xiamen, Fujian) as previously described [ ].

Techniques: Mutagenesis

Journal: Oncotarget

Article Title: Comprehensive profiling and quantitation of oncogenic mutations in non small-cell lung carcinoma using single molecule amplification and re-sequencing technology

doi: 10.18632/oncotarget.10464

Figure Lengend Snippet: Concordance of SMART and ARMS-PCR assay for detection of EGFR mutations

Article Snippet: ARMS-PCR for detection of 29 hot spot EGFR mutations ( ) was performed using the Human EGFR Gene Mutations Fluorescence Polymerase Chain Reaction (PCR) Diagnostic Kit (Amoy Diagnostics, Xiamen, Fujian) as previously described [ ].

Techniques:

Journal: Diagnostic Pathology

Article Title: Quality assessment of a clinical next-generation sequencing melanoma panel within the Italian Melanoma Intergroup (IMI)

doi: 10.1186/s13000-020-01052-5

Figure Lengend Snippet: Clinical characteristics of the metastatic melanoma patients

Article Snippet: All specimens had already been screened for the presence of BRAF codon 15 mutations by SS approach and Real Time PCR assay (PNAClampTM BRAF Mutation Detection Kit; Panagene, Daejeon, Korea) or TherascreenTM BRAF Pyro assay (Qiagen, Valencia, CA) for molecular diagnostic purposes.

Techniques: Mutagenesis

Journal: Diagnostic Pathology

Article Title: Quality assessment of a clinical next-generation sequencing melanoma panel within the Italian Melanoma Intergroup (IMI)

doi: 10.1186/s13000-020-01052-5

Figure Lengend Snippet: Primer sequences and PCR amplification conditions for Sanger Sequencing (SS) validation

Article Snippet: All specimens had already been screened for the presence of BRAF codon 15 mutations by SS approach and Real Time PCR assay (PNAClampTM BRAF Mutation Detection Kit; Panagene, Daejeon, Korea) or TherascreenTM BRAF Pyro assay (Qiagen, Valencia, CA) for molecular diagnostic purposes.

Techniques: Amplification, Sequencing

Journal: Diagnostic Pathology

Article Title: Quality assessment of a clinical next-generation sequencing melanoma panel within the Italian Melanoma Intergroup (IMI)

doi: 10.1186/s13000-020-01052-5

Figure Lengend Snippet: Variants called by the three NGS systems with a coverage of at least 200x and a VAF ≥10%

Article Snippet: All specimens had already been screened for the presence of BRAF codon 15 mutations by SS approach and Real Time PCR assay (PNAClampTM BRAF Mutation Detection Kit; Panagene, Daejeon, Korea) or TherascreenTM BRAF Pyro assay (Qiagen, Valencia, CA) for molecular diagnostic purposes.

Techniques:

Journal: Biomicrofluidics

Article Title: Recent advances in microfluidic methods in cancer liquid biopsy

doi: 10.1063/1.5087690

Figure Lengend Snippet: Summary of previously reported microfluidics devices for isolation and characterization of cfNA.

Article Snippet: 221 Chip-based digital PCR (dPCR) mutational analyses of CTCs (captured in lung cancer patients with the GILUPI CellCollector) revealed mutations in the KRAS and EGFR genes relevant to treatment decisions, and were confirmed in the primary tumors of CRC patients.

Techniques: Isolation, Biomarker Discovery, Spectroscopy, Control, Hybridization, Mutagenesis, Microarray, Digital PCR, DNA Methylation Assay, SPR Assay, Lysis, Electrophoresis, Filtration, Imaging

Journal: Oncotarget

Article Title: Development, validation, and comparison of gene analysis methods for detecting EGFR mutation from non-small cell lung cancer patients-derived circulating free DNA

doi: 10.18632/oncotarget.26951

Figure Lengend Snippet: Patient characteristics

Article Snippet: Samples were amplified with BNA Real-time PCR Mutation Detection Kit for EGFR (Riken Genesis, Tokyo, Japan).

Techniques: Mutagenesis

Journal: Oncotarget

Article Title: Development, validation, and comparison of gene analysis methods for detecting EGFR mutation from non-small cell lung cancer patients-derived circulating free DNA

doi: 10.18632/oncotarget.26951

Figure Lengend Snippet: ( A ) There was a significant negative correlation between the cfDNA amounts and the PFSs of all kind of regimens administered immediately after cfDNA isolation ( N = 44; P < 0.01, Spearman’s rank correlation test). ( B ) There was a significant negative correlation between the cfDNA amounts and the PFSs of EGFR-TKI administered immediately after cfDNA isolation ( P < 0.01, Spearman’s rank correlation test), but not those of cytotoxic agents (data not shown).

Article Snippet: Samples were amplified with BNA Real-time PCR Mutation Detection Kit for EGFR (Riken Genesis, Tokyo, Japan).

Techniques: Isolation

Journal: Oncotarget

Article Title: Development, validation, and comparison of gene analysis methods for detecting EGFR mutation from non-small cell lung cancer patients-derived circulating free DNA

doi: 10.18632/oncotarget.26951

Figure Lengend Snippet: The concordance, sensitivity and specificity of activating EGFR mutation status between plasma cfDNA and tumor DNA

Article Snippet: Samples were amplified with BNA Real-time PCR Mutation Detection Kit for EGFR (Riken Genesis, Tokyo, Japan).

Techniques: Mutagenesis, Clinical Proteomics, Real-time Polymerase Chain Reaction

Journal: Oncotarget

Article Title: Development, validation, and comparison of gene analysis methods for detecting EGFR mutation from non-small cell lung cancer patients-derived circulating free DNA

doi: 10.18632/oncotarget.26951

Figure Lengend Snippet: Appearance of EGFR T790M mutation by each cfDNA detection method from 45 NSCLC patients harboring activating EGFR mutations

Article Snippet: Samples were amplified with BNA Real-time PCR Mutation Detection Kit for EGFR (Riken Genesis, Tokyo, Japan).

Techniques: Mutagenesis, Real-time Polymerase Chain Reaction

Journal: Oncotarget

Article Title: Development, validation, and comparison of gene analysis methods for detecting EGFR mutation from non-small cell lung cancer patients-derived circulating free DNA

doi: 10.18632/oncotarget.26951

Figure Lengend Snippet: Concordance among four cfDNA-based high-performance assays to detect EGFR mutations

Article Snippet: Samples were amplified with BNA Real-time PCR Mutation Detection Kit for EGFR (Riken Genesis, Tokyo, Japan).

Techniques:

Journal: Oncotarget

Article Title: Development, validation, and comparison of gene analysis methods for detecting EGFR mutation from non-small cell lung cancer patients-derived circulating free DNA

doi: 10.18632/oncotarget.26951

Figure Lengend Snippet: The concordance, sensitivity and specificity of EGFR mutation status by high-performance assays between plasma cfDNA and re-biopsy tisssue-derived tumor DNA in eight NSCLC patients who were performed re-biopsy

Article Snippet: Samples were amplified with BNA Real-time PCR Mutation Detection Kit for EGFR (Riken Genesis, Tokyo, Japan).

Techniques: Mutagenesis, Clinical Proteomics, Real-time Polymerase Chain Reaction

Journal: Oncotarget

Article Title: Development, validation, and comparison of gene analysis methods for detecting EGFR mutation from non-small cell lung cancer patients-derived circulating free DNA

doi: 10.18632/oncotarget.26951

Figure Lengend Snippet: The concordance, sensitivity and specificity of EGFR mutation status by high-performance assays between plasma cfDNA and initial biopsy tisssue-derived tumor DNA in 29 NSCLC patients who were not performed re-biopsy

Article Snippet: Samples were amplified with BNA Real-time PCR Mutation Detection Kit for EGFR (Riken Genesis, Tokyo, Japan).

Techniques: Mutagenesis, Clinical Proteomics, Real-time Polymerase Chain Reaction

Journal: Heliyon

Article Title: Functional analysis of a novel intronic variant of MCPH1 with autosomal recessive primary microcephaly

doi: 10.1016/j.heliyon.2024.e30285

Figure Lengend Snippet: Minigene assay for MCPH1 c.233+2T > G mutation and schematic diagram of the splicing pattern. A, The construction of a Minigene trapping vector. B, Results from gel electrophoresis of RT-PCR demonstrated the presence of bands for wild-type and mutant-type. The agarose gel electrophoresis results showed that the PCR product of pMini-CopGFP-WT exhibited a band at 362 bp, whereas pMini-CopGFP-MT displayed a band at 762 bp. C, Analysis of the minigene product through sequencing showed that the wild-type minigene formed a normal mRNA, but the c.233+2T > G substitution of MCPH1 caused a splicing abnormality, which eliminated the Intron 3 canonical splice site, leading to a 400bp insertion. D, The schematic diagram showed the splicing pattern of wild-type and mutant-type.

Article Snippet: The specific PCR primers for the MCPH1 mutation were designed by the Primer 5.0 software and synthesized by Sangon Biotech.

Techniques: Mini Gene Assay, Mutagenesis, Plasmid Preparation, Nucleic Acid Electrophoresis, Reverse Transcription Polymerase Chain Reaction, Agarose Gel Electrophoresis, Sequencing

Journal: Heliyon

Article Title: Functional analysis of a novel intronic variant of MCPH1 with autosomal recessive primary microcephaly

doi: 10.1016/j.heliyon.2024.e30285

Figure Lengend Snippet: Pedigree and sequence analysis of the proband . A, The pedigree of the Family. The arrows indicate the probands; B,C,D,The mutation c.233+2T > G of MCPH1 was identified in the proband (Ⅱ: 3), his father (Ⅰ: 1), and mother (Ⅰ: 2). The proband has a genotype of GG, while both his father and mother have a genotype of TG.

Article Snippet: The specific PCR primers for the MCPH1 mutation were designed by the Primer 5.0 software and synthesized by Sangon Biotech.

Techniques: Sequencing, Mutagenesis

Journal: Heliyon

Article Title: Functional analysis of a novel intronic variant of MCPH1 with autosomal recessive primary microcephaly

doi: 10.1016/j.heliyon.2024.e30285

Figure Lengend Snippet: The MCPH1 c.233+2T > G mutation resulting in truncated proteins. A, Locations of c.233+2T > G in the MCPH1 gene and protein structure. Red arrows indicate the positions of the mutation. B, Predicted wild-type protein; C, Predicted mutant-type protein.

Article Snippet: The specific PCR primers for the MCPH1 mutation were designed by the Primer 5.0 software and synthesized by Sangon Biotech.

Techniques: Mutagenesis

Journal: Heliyon

Article Title: Functional analysis of a novel intronic variant of MCPH1 with autosomal recessive primary microcephaly

doi: 10.1016/j.heliyon.2024.e30285

Figure Lengend Snippet: Mutations in the MCPH1 gene with MCPH.

Article Snippet: The specific PCR primers for the MCPH1 mutation were designed by the Primer 5.0 software and synthesized by Sangon Biotech.

Techniques:

Journal: Journal of Comparative Effectiveness Research

Article Title: Variant analysis of SARS-CoV-2 strains with phylogenetic analysis and the Coronavirus Antiviral and Resistance Database

doi: 10.2217/cer-2021-0208

Figure Lengend Snippet: The neighbor-joining tree construction method and Jukes-Cantor nucleotide distance measures were carried out with other sequences from all reference lineages from GISAID using CLC Sequence Viewer 8.0 (Qiagen, Aarhus A/S, Denmark) software. Bootstrap values are arranged as 1000 replicates. Because of numerous samples, the phylogenetic tree has been constructed as circular and rooted. The GISAID accession numbers of SARS-CoV-2 lineages are: alpha B.1.1.7-1 (EPI_ISL_3098706), alpha B.1.1.7-2 (EPI_ISL_3098709), delta B.1.617.1-1 (EPI_ISL_ 3066844), delta B.1.617.1-2 (EPI_ISL_ 3066436), delta B.1.617.2-1 (EPI_ISL_3098714), delta B.1.617.2-2 (EPI_ISL_3098716), beta B.1.351-1 (EPI_ISL_3098444), beta B.1.351-2 (EPI_ISL_3098450), eta B.1.525-1 (EPI_ISL_3089259), eta B.1.525-2 (EPI_ISL_3089260), gamma P.1-1 (EPI_ISL_3091694), gamma P.1-2 (EPI_ISL_3092082), lota B.1.526-1 (EPI_ISL_3092079), lota B.1.526-2 (EPI_ISL_3098714., WT: Wild type (EPI_ISL_3049390). The GenBank accession number of SARS-CoV-2 Wuhan-Hu-1 isolate: MN908947.3.

Article Snippet: Two variant-specific screening PCR kits (BioSpeedy SARS-CoV-2 N501Y/variant plus kit, Bioeksen Inc., İstanbul, Turkey and Diagnovital SARS-CoV-2 N501Y, delHV 69-70, E484K mutation detection kit, RTA Laboratories Inc., Istanbul, Turkey) were used in this study.

Techniques: Sequencing, Software, Construct

Journal: Journal of Comparative Effectiveness Research

Article Title: Variant analysis of SARS-CoV-2 strains with phylogenetic analysis and the Coronavirus Antiviral and Resistance Database

doi: 10.2217/cer-2021-0208

Figure Lengend Snippet: The distribution of distinct and missense mutations using phylogenetic analysis and the Coronavirus Antiviral and Resistance Database.

Article Snippet: Two variant-specific screening PCR kits (BioSpeedy SARS-CoV-2 N501Y/variant plus kit, Bioeksen Inc., İstanbul, Turkey and Diagnovital SARS-CoV-2 N501Y, delHV 69-70, E484K mutation detection kit, RTA Laboratories Inc., Istanbul, Turkey) were used in this study.

Techniques: Mutagenesis