Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gastric adenocarcinoma HER2 mass spectrometry-based quantification

ABSTRACT: In this study, we presented a new HER2 protein detection method based on mass spectrometry selected reaction monitoring (MS-SRM), determined the upper and lower limits of HER2 expression detection, and validated the method. We conducted a retrospective study on 118 formalin-fixed paraffin-embedded (FFPE) tissues from patients with advanced gastric adenocarcinoma in northern China.

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Tianjin Yunjian Medical Laboratory Co., Ltd.

PROVIDER: PXD041613 | JPOST Repository | Tue Apr 18 00:00:00 BST 2023

REPOSITORIES: jPOST

ACCESS DATA

Json Xml

Similar Datasets

Transcriptome of tumor biopsy sample of patient with non-small-cell lung adenocarcinoma, ALK rearrangement positive

Project description:We profiled gene expression in formalin-fixed, paraffin-embedded (FFPE) tumor biopsy sample of the patient with non-small-cell lung adenocarcinoma, ALK rearrangement positive.

2019-07-02 | GSE133605 | GEO

Identification of HER2 peptides for quantification in formalin-fixed paraffin-embedded breast cancer tissues

Project description:The ability to accurately quantify proteins in formalin-fixed paraffin-embedded (FFPE) tissues using targeted mass spectrometry opens exciting perspectives for biomarker discovery. We have developed and evaluated a selected reaction monitoring (SRM) assay for the human receptor tyrosine-protein kinase erbB-2 (HER2) in FFPE breast tumors. Peptide candidates were identified using an untargeted mass spectrometry approach in relevant cell lines. A selected reaction monitoring (SRM) assay was developed for the six best candidate peptides and evaluated for linearity, precision and lower limit of quantification. The six HER2 peptides of interest were then quantified by SRM in a cohort of 40 archival formalin-fixed paraffin-embedded tumor tissues from women with invasive breast carcinomas, showing different levels of HER2 gene amplification. Finally, the agreement was tested between data generated by SRM and data generated using standard clinical pathology methods, namely immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH). The high agreement observed indicates that SRM is a suitable method to quantify peptides from FFPE material, and therefore represents a powerful approach for biomarker discovery studies.

2015-07-16 | PXD002281 | Pride

Gene expression profiling of FFPE kidney cancer samples

Project description:We used Illumina microarrays to profile RNA expression in formalin-fixed paraffin-embedded (FFPE) samples of 22 metastatic or advanced RCC cases.

2021-07-28 | GSE180925 | GEO

SnFFPE-Seq: towards scalable single nucleus RNA-seq of formalin-fixed paraffin-embedded (FFPE) tissues

Project description:Profiling cellular heterogeneity in formalin-fixed paraffin-embedded (FFPE) tissues is key to characterizing clinical specimens for biomarkers, therapeutic targets, and drug responses. Here, we optimize methods for isolating intact nuclei and single nucleus RNA-seq from FFPE tissues in the mouse brain, and demonstrate a pilot application to a human clinical specimen of lung adenocarcinoma. Our method opens the way to broad applications of snRNA-Seq to archival tissues, including clinical samples.

2022-08-31 | GSE211797 | GEO

Expanding epigenomics to archived FFPE tissues: An evaluation of DNA repair methodologies

Project description:A study to evaluate techniques for repairing DNA from formalin-fixed paraffin-embedded (FFPE) tissue samples by direct comparison of FFPE DNA repair methods prior to analysis on genome-wide methylation array to matched fresh frozen (FF) tissues. Formalin-fixed paraffin-embedded tissue from three colon adenocarcinoma samples were subjected to different FFPE-oriented DNA repair approaches and sequences, then compared with corresponding fresh frozen tissues. All samples were hybridized to the Illumina Infinium 450k Human Methylation BeadChip.

2014-12-17 | E-GEOD-59038 | biostudies-arrayexpress

Comparison of microarray and RNA sequencing platforms for profiling microRNAs in formalin-fixed, paraffin-embedded human lung adenocarcinoma specimens

Project description:MicroRNAs are useful biomarkers for various disease states, and their preservation in formalin-fixed, paraffin-embedded (FFPE) tissue makes them particularly useful for clinicogenetic studies. Although global microRNA expression in FFPE samples is routinely measured with microarrays, the utility of RNA sequencing for such profiling has yet to be established. In this study, to appraise the suitability of RNA sequencing, microRNAs in RNA from pathologic stage I lung adenocarcinoma FFPE samples were quantified with 8x60K Agilent® SurePrint™ G3 Human miRNA 8x60k (release 16.0) microarray and Illumina® HiSeq™ 2000 sequencing platforms.

2014-12-31 | GSE57835 | GEO

Exon-array profiling of squamous cell carcinoma and adenocarcinoma in human cervical FFPE samples

Project description:Degradation and chemical modification of RNA in formalin-fixed paraffin-embedded (FFPE) samples hamper their use in expression profiling studies. In this study, we investigated the feasibility of gene expression signature generation from archival FFPE materials. Nineteen cervical squamous cell carcinoma (SCC) and nine adenocarcinoma (AC) 10~16-year-old FFPE samples were profiled using Affymetrix Exon 1.0 ST arrays. A comparison of the global gene expression changes between SCC and AC revealed 1217 differentially expressed genes. Of these, 1062 showed significantly higher expression levels in SCC relative to AC, and 155 genes were found to be specifically upregulated in AC. When the 1217-gene signature was tested on a fresh-frozen human non-small cell lung cancer (NSCLC) series, it correctly separated the 58 NSCLC samples into SCC and AC. In conclusion, our results showed that clinically and biologically relevant gene expression profiles can be derived from FFPE samples with Exon array profiling.

2011-02-17 | GSE27388 | GEO

Project description:Formalin-fixed, paraffin-embedded (FFPE) from prostate cancer patients

2016-11-30 | GSE90463 | GEO

Project description:Formalin-fixed, paraffin-embedded (FFPE) from prostate cancer patients

2016-11-30 | GSE89193 | GEO

Project description:Formalin-fixed, paraffin-embedded (FFPE) from prostate cancer patients

2016-11-30 | GSE88808 | GEO