Journal: PLOS One

Article Title: SERS-based detection of DNA methylation for cancer diagnosis: Cation-mediated adsorption to silver nanoparticles

doi: 10.1371/journal.pone.0325539

Figure Lengend Snippet: (A) SERS spectra presented as mean and standard deviation of six genomic DNA (gDNA) samples (10 ng/µL) with 5-methylcytosine (5mC) levels ranging from 0.16 to 0.91%. The silver colloidal solution was supplemented with 5x10 -4 M Ca 2+ . (B) Positive correlation between intensity of cytosine SERS band at 790 cm -1 and the levels of 5mC. Boxes represent average; whiskers represent standard deviation (C) The SERS spectra (mean and standard deviation) of a double-stranded DNA sequence of 180 bp from the promoter region of SEPT9 gene with 0%, 50% and 100% methylation levels. (D) The correlation between the levels of 5mC and the intensity of the SERS band at 790 cm -1 . Boxes represent average; whiskers represent standard deviation.

Article Snippet: SEPT9 , Short sequence, double-straned, size = 180 bp (three methylation levels) , GenScript.

Techniques: Standard Deviation, Sequencing, Methylation

Journal: Pharmacoeconomics

Article Title: Health Economic Evidence and Modeling Challenges for Liquid Biopsy Assays in Cancer Management: A Systematic Literature Review

doi: 10.1007/s40273-023-01292-5

Figure Lengend Snippet: Overview of study characteristics, clinical applications, evaluated strategies, and overall judgement

Article Snippet: 10 , Deibel et al. (2021) [ ] , CEA/CUA (USA) , Screening and early detection General population from birth until either mortality or reaching the upper age limit of 100 years , Methylated SEPT9 DNA , Epi proColon (methylated SEPT9 DNA) Other strategies (no screening, colonoscopy, FIT, ColoGuard, and PolypDx) , Cost-effective Epi proColon was cost-effective compared with no screening, with a 100% adherence scenario; Epi proColon was cost-effective compared with no screening, colonoscopy, or FIT (2 years), with real-world adherence scenario; Epi proColon was dominated compared with ColoGuard in both scenarios..

Techniques: Biomarker Discovery, Selection, Clinical Proteomics, Mutagenesis, Methylation, Adjuvant, Marker, Imaging, Spectroscopy

Journal: Clinical Epigenetics

Article Title: Comparison of quantification algorithms for circulating cell-free DNA methylation biomarkers in blood plasma from cancer patients

doi: 10.1186/s13148-017-0425-4

Figure Lengend Snippet: Training cohort. Methylation levels of SEPT9 , SHOX2 , and mean SEPT9 / SHOX2 in plasma of HNSCC ( n = 137) and control ( n = 170) patients in relative quantification, genome equivalents (absolute quantification), and quasi-digital PCR with sensitivity (sens.), specificity (spec.), and cutoffs. Receiver Operating Characteristics with AUCs of HNSCC and control patients

Article Snippet: DD has been an employee and is a consultant of Epigenomics AG, a company that aims to commercialize the DNA methylation biomarkers SEPT9 and SHOX2 .

Techniques: Methylation, Clinical Proteomics, Control, Quantitative Proteomics, Digital PCR

Journal: Clinical Epigenetics

Article Title: Comparison of quantification algorithms for circulating cell-free DNA methylation biomarkers in blood plasma from cancer patients

doi: 10.1186/s13148-017-0425-4

Figure Lengend Snippet: Testing cohort. Methylation levels of SEPT9 , SHOX2 , and mean SEPT/SHOX2 in plasma of HNSCC ( n = 141) and control ( n = 102) patients in relative quantification, genome equivalents (absolute quantification), and quasi-digital PCR with sensitivity (sens.), specificity (spec.), and cutoffs. ROC curves with AUCs of HNSCC and control patients

Article Snippet: DD has been an employee and is a consultant of Epigenomics AG, a company that aims to commercialize the DNA methylation biomarkers SEPT9 and SHOX2 .

Techniques: Methylation, Clinical Proteomics, Control, Quantitative Proteomics, Digital PCR

Journal: Clinical Epigenetics

Article Title: Comparison of quantification algorithms for circulating cell-free DNA methylation biomarkers in blood plasma from cancer patients

doi: 10.1186/s13148-017-0425-4

Figure Lengend Snippet: Training cohort. Kaplan-Meier analysis of overall survival in HNSCC patients ( n = 129). Patients are stratified according to SHOX2 and SEPT9 plasma methylation levels. Plasma methylation levels were quantified using relative, absolute quantification, and quasi-digital PCR and dichotomized based on cutoffs that resulted in specificities and sensitivities as seen in Figs. and . Cutoff values for positive (above cutoff) and negative (below cutoff) classification: SEPT9 , SHOX2 , and mean SEPT9/SHOX2 . Cutoffs for relative quantification were SEPT9 = 0.055%, SHOX2 = 0.281%, and mean SEPT9/SHOX2 = 0.118%; for absolute quantification SEPT9 = 4.68 pg, SHOX2 = 22.7 pg, and mean SEPT9/SHOX2 = 14.3 pg; for quasi-digital PCR for SEPT9 > 2, for SHOX2 > 4 and for mean SEPT9/SHOX2 > 2 positive PCR reactions

Article Snippet: DD has been an employee and is a consultant of Epigenomics AG, a company that aims to commercialize the DNA methylation biomarkers SEPT9 and SHOX2 .

Techniques: Clinical Proteomics, Methylation, Quantitative Proteomics, Digital PCR

Journal: Clinical Epigenetics

Article Title: Comparison of quantification algorithms for circulating cell-free DNA methylation biomarkers in blood plasma from cancer patients

doi: 10.1186/s13148-017-0425-4

Figure Lengend Snippet: Testing cohort. Kaplan-Meier analysis of overall survival in HNSCC patients ( n = 137). Patients are stratified according to SHOX2 and SEPT9 plasma methylation levels. Plasma methylation levels were quantified using relative, absolute quantification and quasi-digital PCR and dichotomized based on cutoffs established in the training cohort. Cutoff values for positive (above cutoff) and negative (below cutoff) classification: SEPT9 , SHOX2 , and mean SEPT9/SHOX2 . Cutoffs for relative quantification were SEPT9 = 0.055%, SHOX2 = 0.281%, and mean SEPT9/SHOX2 = 0.118%; for absolute quantification SEPT9 = 4.68 pg, SHOX2 = 22.7 pg, and mean SEPT9/SHOX2 = 14.3 pg; for quasi-digital PCR for SEPT9 > 2, for SHOX2 > 4, and for mean SEPT9/SHOX2 > 2 positive PCR reactions

Article Snippet: DD has been an employee and is a consultant of Epigenomics AG, a company that aims to commercialize the DNA methylation biomarkers SEPT9 and SHOX2 .

Techniques: Clinical Proteomics, Methylation, Quantitative Proteomics, Digital PCR

Journal: Clinical Epigenetics

Article Title: Comparison of quantification algorithms for circulating cell-free DNA methylation biomarkers in blood plasma from cancer patients

doi: 10.1186/s13148-017-0425-4

Figure Lengend Snippet: Diagnostic and prognostic performance of SHOX2 and SEPT9 hypermethylation

Article Snippet: DD has been an employee and is a consultant of Epigenomics AG, a company that aims to commercialize the DNA methylation biomarkers SEPT9 and SHOX2 .

Techniques: Diagnostic Assay, Biomarker Discovery