Journal: International Journal of Molecular Sciences

Article Title: A Liquid Biopsy in Bladder Cancer—The Current Landscape in Urinary Biomarkers

doi: 10.3390/ijms23158597

Figure Lengend Snippet: Table presenting data for methylation biomarkers.

Article Snippet: TERT , diagnostic , n = 60 (BCa (NMIBC) = 27, LG = 16, HG = 6; control group = 23; n = 10, tmr) , DNA was isolated from urine samples of 60 patients using QIAamp Circulating Nucleic Acid Kit (Qiagen GmbH, Hilden, Germany). The reference plasmids were created using pUC19 vector (cloning sites KpnI and HindIII). Forward primer and reverse primer were provided by Evrogen RU, AO. DNA isolated from liver cancer cells (originating from the HepG2 cell line; cat no. 85011430; MilliporeSigma) was used for amplification of the mutant C228T fragment. High-Fidelity DNA Polymerase (New England BioLabs Inc., Ipswich, MA, USA) was used to amplify the mutant insert. Quantification of DNA was performed using the QX200 ddPCR System (Bio-Rad Laboratories, Inc., Hercules, CA, USA). Detection of TERT promoter and mutations was achieved using TaqMan Liquid Biopsy dPCR Assays (TERT_C228T, Assay ID Hs000000092_rm and TERT_C250T, Assay ID Hs000000093_rm; Thermo Fisher Scientific Inc.). Data analysis performed with IBM SPSS Statistics 22.0 Software (IBM Corp., Armonk, NY, USA). , BCa detection , , AUC = 0.768, Se. = 55.56%, Sp. = 100% , retrospective , [ ] .

Techniques: Methylation, Diagnostic Assay, Real-time Polymerase Chain Reaction, Isolation, DNA Methylation Assay, Software, DNA Extraction, Modification, Sequencing, Amplification

Journal: International Journal of Molecular Sciences

Article Title: A Liquid Biopsy in Bladder Cancer—The Current Landscape in Urinary Biomarkers

doi: 10.3390/ijms23158597

Figure Lengend Snippet: Table presenting data for proteomics biomarkers.

Article Snippet: TERT , diagnostic , n = 60 (BCa (NMIBC) = 27, LG = 16, HG = 6; control group = 23; n = 10, tmr) , DNA was isolated from urine samples of 60 patients using QIAamp Circulating Nucleic Acid Kit (Qiagen GmbH, Hilden, Germany). The reference plasmids were created using pUC19 vector (cloning sites KpnI and HindIII). Forward primer and reverse primer were provided by Evrogen RU, AO. DNA isolated from liver cancer cells (originating from the HepG2 cell line; cat no. 85011430; MilliporeSigma) was used for amplification of the mutant C228T fragment. High-Fidelity DNA Polymerase (New England BioLabs Inc., Ipswich, MA, USA) was used to amplify the mutant insert. Quantification of DNA was performed using the QX200 ddPCR System (Bio-Rad Laboratories, Inc., Hercules, CA, USA). Detection of TERT promoter and mutations was achieved using TaqMan Liquid Biopsy dPCR Assays (TERT_C228T, Assay ID Hs000000092_rm and TERT_C250T, Assay ID Hs000000093_rm; Thermo Fisher Scientific Inc.). Data analysis performed with IBM SPSS Statistics 22.0 Software (IBM Corp., Armonk, NY, USA). , BCa detection , , AUC = 0.768, Se. = 55.56%, Sp. = 100% , retrospective , [ ] .

Techniques: Diagnostic Assay, DNA Extraction, Enzyme-linked Immunosorbent Assay, Mass Spectrometry, Western Blot, Expressing, Software, Multiplex Assay, Bead-based Assay

Journal: International Journal of Molecular Sciences

Article Title: A Liquid Biopsy in Bladder Cancer—The Current Landscape in Urinary Biomarkers

doi: 10.3390/ijms23158597

Figure Lengend Snippet: Table presenting data for mRNA biomarkers.

Article Snippet: TERT , diagnostic , n = 60 (BCa (NMIBC) = 27, LG = 16, HG = 6; control group = 23; n = 10, tmr) , DNA was isolated from urine samples of 60 patients using QIAamp Circulating Nucleic Acid Kit (Qiagen GmbH, Hilden, Germany). The reference plasmids were created using pUC19 vector (cloning sites KpnI and HindIII). Forward primer and reverse primer were provided by Evrogen RU, AO. DNA isolated from liver cancer cells (originating from the HepG2 cell line; cat no. 85011430; MilliporeSigma) was used for amplification of the mutant C228T fragment. High-Fidelity DNA Polymerase (New England BioLabs Inc., Ipswich, MA, USA) was used to amplify the mutant insert. Quantification of DNA was performed using the QX200 ddPCR System (Bio-Rad Laboratories, Inc., Hercules, CA, USA). Detection of TERT promoter and mutations was achieved using TaqMan Liquid Biopsy dPCR Assays (TERT_C228T, Assay ID Hs000000092_rm and TERT_C250T, Assay ID Hs000000093_rm; Thermo Fisher Scientific Inc.). Data analysis performed with IBM SPSS Statistics 22.0 Software (IBM Corp., Armonk, NY, USA). , BCa detection , , AUC = 0.768, Se. = 55.56%, Sp. = 100% , retrospective , [ ] .

Techniques: Diagnostic Assay, Expressing, Multiplex Assay, Software, Spectrophotometry, Concentration Assay, Purification, SYBR Green Assay, Amplification, Staining, Enzyme-linked Immunosorbent Assay, Reverse Transcription Polymerase Chain Reaction

Journal: International Journal of Molecular Sciences

Article Title: A Liquid Biopsy in Bladder Cancer—The Current Landscape in Urinary Biomarkers

doi: 10.3390/ijms23158597

Figure Lengend Snippet: Table presenting data for mutations biomarkers.

Article Snippet: TERT , diagnostic , n = 60 (BCa (NMIBC) = 27, LG = 16, HG = 6; control group = 23; n = 10, tmr) , DNA was isolated from urine samples of 60 patients using QIAamp Circulating Nucleic Acid Kit (Qiagen GmbH, Hilden, Germany). The reference plasmids were created using pUC19 vector (cloning sites KpnI and HindIII). Forward primer and reverse primer were provided by Evrogen RU, AO. DNA isolated from liver cancer cells (originating from the HepG2 cell line; cat no. 85011430; MilliporeSigma) was used for amplification of the mutant C228T fragment. High-Fidelity DNA Polymerase (New England BioLabs Inc., Ipswich, MA, USA) was used to amplify the mutant insert. Quantification of DNA was performed using the QX200 ddPCR System (Bio-Rad Laboratories, Inc., Hercules, CA, USA). Detection of TERT promoter and mutations was achieved using TaqMan Liquid Biopsy dPCR Assays (TERT_C228T, Assay ID Hs000000092_rm and TERT_C250T, Assay ID Hs000000093_rm; Thermo Fisher Scientific Inc.). Data analysis performed with IBM SPSS Statistics 22.0 Software (IBM Corp., Armonk, NY, USA). , BCa detection , , AUC = 0.768, Se. = 55.56%, Sp. = 100% , retrospective , [ ] .

Techniques: Diagnostic Assay, Spectrophotometry, Amplification, Sequencing, Software, Isolation, Plasmid Preparation, Clone Assay, Mutagenesis, DNA Sequencing, DNA Extraction

Journal: Genome Biology

Article Title: NT-seq: a chemical-based sequencing method for genomic methylome profiling

doi: 10.1186/s13059-022-02689-9

Figure Lengend Snippet: NT-seq detects both adenine and cytosine methylation in oligonucleotides. a The inverse of A to G ratio at adenine sites between unmodified control and 6mA modified oligo. b Linear regression between A to G frequency at 6mA site and the percentage of 6mA modified oligo. c The inverse of C to T ratio at cytosine sites between unmodified oligo and oligo modified by BamHI methyltransferase. d Linear regression between C to T frequency at 4mC position 39 and the percentage of 4mC modified oligo. e Linear regression between C to T frequency at 4mC position 42 and the percentage of 4mC modified oligo. f C to T ratio at cytosine sites between unmodified control and 5mC modified oligo. Modified adenine or cytosine sites are labeled in red. Adenine or cytosine sites inside the primer regions are not included. Dots represent the mean and error bars represent standard deviation. All samples were replicated three times. One replicate for 25%, 50%, and 100% of 4mC modified oligo samples was not used due to library prep and sequencing depth issues

Article Snippet: 4mC modified oligo (91bp) was generated by treating dsDNA oligo with BamHI methyltransferase (methylates GGATCC motif at the first cytosine base) according to the manufacturer’s instructions (NEB, M0223S).

Techniques: Methylation, Modification, Labeling, Standard Deviation, Sequencing