microarray-based dna re-sequencing  (NimbleGen Systems GmbH)

Journal: bioRxiv

Article Title: Epigenetic investigation of multifocal small intestinal neuroendocrine tumours reveals accelerated ageing of tumours and epigenetic alteration of metabolic genes

doi: 10.1101/2024.12.02.626017

Figure Lengend Snippet: In this study, genome-wide DNA methylation of 100 samples from 11 patients was assessed. Each patient had multiple primary small intestinal neuroendocrine tumours (ranging from 2-16 per patient), and a subset of 9 patients had a matched normal small intestinal epithelial sample assessed. A subset of 8 patients also had metastases originating from their SI-NETs (ranging from 1-2 per patient). DNA methylation data was used to assess differential methylation relating to the multifocal tumours, the epigenetic clock was used to assess the ‘timing’ of tumour development and metabolic traits predicted by DNA methylation were compared between samples.

Article Snippet: Genome-wide DNA methylation microarray data was generated on the Illumina iScan System using the Illumina Infinium MethylationEPIC BeadChip according to the manufacturer’s protocol.

Techniques: Genome Wide, DNA Methylation Assay, Methylation

Journal: bioRxiv

Article Title: Epigenetic investigation of multifocal small intestinal neuroendocrine tumours reveals accelerated ageing of tumours and epigenetic alteration of metabolic genes

doi: 10.1101/2024.12.02.626017

Figure Lengend Snippet: (A) Plot of age predictions for normal epithelia samples (green), primary tumours (purple) and metastatic tumours (blue). Chronological age is indicated with the orange points and patients are indicated in order of chronological age. (B) Boxplot of age acceleration difference for the skin and blood clock predictions. (C) Somatic mutation count from tumours correlates with DNA methylation age in the skin and blood clock (p=0.0007).

Article Snippet: Genome-wide DNA methylation microarray data was generated on the Illumina iScan System using the Illumina Infinium MethylationEPIC BeadChip according to the manufacturer’s protocol.

Techniques: Mutagenesis, DNA Methylation Assay

Journal: Frontiers in Public Health

Article Title: Prevalence of sexually transmitted infections and human papillomavirus in cervical samples from incarcerated women in São Paulo, Brazil: a retrospective single-center study

doi: 10.3389/fpubh.2024.1353845

Figure Lengend Snippet: Sociodemographic and sexual characteristics of the incarcerated women in São Paulo, Brazil.

Article Snippet: The STI prevalence was determined using a similar DNA microarray system, EUROArray STI (EUROIMMUN, Germany).

Techniques:

Journal: Frontiers in Public Health

Article Title: Prevalence of sexually transmitted infections and human papillomavirus in cervical samples from incarcerated women in São Paulo, Brazil: a retrospective single-center study

doi: 10.3389/fpubh.2024.1353845

Figure Lengend Snippet: Prevalence of STIs among the imprisoned women. The y-axis has been segmented in order to display all results. STIs for which all women were negative for have been excluded.

Article Snippet: The STI prevalence was determined using a similar DNA microarray system, EUROArray STI (EUROIMMUN, Germany).

Techniques:

Journal: BMC Cancer

Article Title: NQO1 overexpression is associated with poor prognosis in squamous cell carcinoma of the uterine cervix

doi: 10.1186/1471-2407-14-414

Figure Lengend Snippet: IHC staining of the NQO1 protein on tissue microarray of cervical lesions. (A) NQO1 protein was weakly positive in cervical SCC. (B) NQO1 protein showed diffuse and strong cytoplasmic-positive staining in cervical SCC. (C) NQO1 protein was negative in normal cervical epithelia. (D) NQO1 protein was positive in SCC.

Article Snippet: DNA was extracted from paraffin-embedded cervical lesion specimens using the High Pure PCR Template Preparation kit (Cat.11796828001, Roche, Penzberg, Germany), and HPV detection and genotyping were performed using a PCR-based HPV-DNA microarray system (Biomedlab, Seoul, South Korea).

Techniques: Immunohistochemistry, Microarray, Staining

Journal: Scientific Reports

Article Title: Analysis of the application of a gene chip method for detecting Mycobacterium tuberculosis drug resistance in clinical specimens: a retrospective study

doi: 10.1038/s41598-021-97559-y

Figure Lengend Snippet: The layout of the DNA microarray method module; each detection panel includes 4 detection modules, which can detect two specimens at the same time. Modules 1 and 3 are used to detect mutations in the rpoB gene, and modules 2 and 4 are used to detect mutations in the katG gene and inhA promoter. QC quality control probe; EC external control probe; BC blank control; NC negative control probe; IC internal control probe; WT wild-type.

Article Snippet: To meet the demand for the rapid and accurate detection of Mtb and drug resistance, CapitalBio developed a DNA microarray gene detection system.

Techniques: Microarray, Control, Negative Control

Journal: Scientific Reports

Article Title: Analysis of the application of a gene chip method for detecting Mycobacterium tuberculosis drug resistance in clinical specimens: a retrospective study

doi: 10.1038/s41598-021-97559-y

Figure Lengend Snippet: The drug susceptibility test was used as a standard method to evaluate the efficacy of the DNA microarray for detecting RIF and INH resistance and MDR-TB.

Article Snippet: To meet the demand for the rapid and accurate detection of Mtb and drug resistance, CapitalBio developed a DNA microarray gene detection system.

Techniques: Microarray

Journal: Scientific Reports

Article Title: Analysis of the application of a gene chip method for detecting Mycobacterium tuberculosis drug resistance in clinical specimens: a retrospective study

doi: 10.1038/s41598-021-97559-y

Figure Lengend Snippet: Comparison of the diagnostic efficacy of the DNA microarray method when sputum smear grades were ≤ 1 + and ≥ 2 +

Article Snippet: To meet the demand for the rapid and accurate detection of Mtb and drug resistance, CapitalBio developed a DNA microarray gene detection system.

Techniques: Comparison, Diagnostic Assay, Microarray

Journal: Scientific Reports

Article Title: Analysis of the application of a gene chip method for detecting Mycobacterium tuberculosis drug resistance in clinical specimens: a retrospective study

doi: 10.1038/s41598-021-97559-y

Figure Lengend Snippet: Specimen processing procedure: A total of 5,911 sputum smear-positive specimens were collected. After experimental processing, 4148 specimens that were positive with the DNA microarray method and DST were finally included in the study. NTM, nontuberculous mycobacteria ; DST, drug sensitivity test.

Article Snippet: To meet the demand for the rapid and accurate detection of Mtb and drug resistance, CapitalBio developed a DNA microarray gene detection system.

Techniques: Microarray

Journal: Scientific Reports

Article Title: Analysis of the application of a gene chip method for detecting Mycobacterium tuberculosis drug resistance in clinical specimens: a retrospective study

doi: 10.1038/s41598-021-97559-y

Figure Lengend Snippet: Pattern diagrams of several common drug-resistant gene mutations detected by the DNA microarray method. The white box is the detection site of the wild-type codon, and the red box is the site of the detected mutant codon. ( a ) rpoB gene Leu511Pro (CTG → CCG); ( b ) rpoB gene Asp516Tyr (GAC → TAC); ( c ) rpoB gene His526Tyr (CAC → TAC); ( d ) rpoB gene Ser531Trp (TCG → TGG); ( e ) rpoB gene Ser531Leu (TCG → TTG); ( f ) katG gene Ser315Thr (AGC → ACC); ( g ) katG gene Ser315Asn (AGC → AAC); ( h ) inhA gene promoter-15 (C → T).

Article Snippet: To meet the demand for the rapid and accurate detection of Mtb and drug resistance, CapitalBio developed a DNA microarray gene detection system.

Techniques: Microarray, Mutagenesis