Browse
Submit Data
Databases
API
Help

Dataset Information

6 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Peripheral Blood Monocytes as Predictive Marker for Colorectal Cancer Diagnosis: A Comparative Study of a Stool Based Versus Blood Based Screening Test

ABSTRACT: In this prospective study, the main goal is to evaluate the strength of Monomark -a monocyte-based transcriptomic test combined to a mathematical model- in patients with a positive FIT test. Therefore, in parallel to the routine FIT screening, blood samples will be harvested and the monocyte genetic profile will be determined. This fundamental study, will disclose the diagnostic power of a biomarker panel ("MonoMark") head to head with the well-established FIT diagnostic test, a core prerequisite for the routine use of this test as an alternative and more reliable CRC screening tool.

DISEASE(S): Colorectal Cancer,Colorectal Neoplasms

PROVIDER: 2268158 | ecrin-mdr-crc |

REPOSITORIES: ECRIN MDR

ACCESS DATA

Json Xml

Similar Datasets

Assessing the Effect of a Blood-based Colorectal Cancer Screening Test on Screening Adherence and Colonoscopy Completion

Project description:Objectives: Colonoscopy and stool-based testing are the two predominant colorectal cancer (CRC) screening tests used in the US, and both reduce colorectal cancer mortality. However, only 62% of Americans are up to date with screening, partly because many individuals find these two tests inconvenient or unacceptable for a variety of reasons. There is an unmet need for a non-invasive test that does not require bowel preparation or handling stool, and the Septin9 DNA blood test may be an alternative for those individuals who would otherwise remain unscreened. Aims: Aim 1: To measure screening uptake with a blood test in screen-resistant patients who have declined both colonoscopy and fecal immunochemical testing (FIT) at the Manhattan VA Medical Center * Sub-Aim 1a: To assess the proportion of those with a positive blood-based screening test who undergo diagnostic colonoscopy * Sub-Aim 1b: To describe the endoscopic findings on diagnostic colonoscopy Aim 2: To survey screen-resistant patients to understand their beliefs and attitudes about colorectal cancer screening and testing options We hypothesize that a substantial proportion of patients who have refused colonoscopy and FIT will accept the blood test. We hypothesize this will be driven by the convenience of the blood test. Methods: This will be randomized controlled trial of individuals who have refused colonoscopy and FIT within past 6 months. Eligible patients will be randomized 1:1 to the intervention or control group. Both groups will be invited to participate in navigated colonoscopy or FIT by letter and telephone call. The intervention group will also be invited to participate in the blood test if they refuse colonoscopy and FIT. We will enroll 180 participants in each group (total n=360).

| 2278536 | ecrin-mdr-crc

Diagnostic sensitivity analysis of the immunochemical fecal occult blood test for colorectal cancers

Project description:Interventions: Immunochemical fecal occult blood test (FIT) using OC sensor io (Eiken co) Primary outcome(s): Diagnostic sensitivity of immunochemical fecal occult blood test (FIT) for colorectal cancers based on the location, staging, tumor size and macroscopic types. Study Design: Single arm Non-randomized

| 2624966 | ecrin-mdr-crc

Rapid Identification of Bacterial Pathogens using a PCR- and Microarray-Based Assay

Project description:A method based on a modified broad-range PCR and an oligonucleotide microarray for the simultaneous detection and identification of 12 bacterial pathogens at the species level. The feasibility of this assay in routine diagnostic testing was evaluated using 146 blood culture positive and 40 blood culture negative samples. The processed data are composed of ORGANISM NAME or NEGATIVE answer depending if the pathogen is detected in the sample or not. See supplementary file linked below.

2010-06-24 | E-GEOD-17221 | biostudies-arrayexpress

Gene expression profiles from female BasL breast cancer patients

Project description:Diagnostic samples from routine analysis of female BasL breast cancer patients

2022-02-14 | GSE196723 | GEO

Blood based gene expression signature for diagnosis of epithelial ovarian cancer

Project description:Objective: The immune system is a key player in fighting cancer. Thus, we seeked to identify a molecular ‘immune response signature’ indicating the presence of epithelial ovarian cancer (EOC) and to combine this with a serum protein biomarker panel to increase the specificity and sensitivity for earlier detection of EOC. Methods: Comparing the expression of 32,000 genes in a leukocytes fraction from 48 EOC patients and 20 controls, three uncorrelated shrunken centroid models were selected, comprised of 7, 14, and 6 genes. A second selection step using RT-qPCR data and significance analysis of microarrays yielded 13 genes which were finally used in 343 samples (90 healthy, 6 cystadenoma, 8 low malignant potential tumor, and 239 EOC patients). Using new 65 controls and 224 EOC patients the abundances of six plasma proteins was determined and used in combination with the expression values from the 13 genes for diagnosis of EOC. Results: Combined diagnostic models using either each five gene expression and plasma protein abundance values or 13 gene expression and six plasma protein abundance values can discriminate controls from patients with EOC with Receiver Operator Characteristics Area Under the Curve values of 0.998 and bootstrap .632+ validated classification errors of 3.1% and 2.8%, respectively. The sensitivities were 97.8% and 95.6%, respectively, at a set specificity of 99.6%. Conclusion: The combination of expression based and plasma protein based biomarkers in one diagnostic model increases the sensitivity and the specificity significantly. Such a diagnostic test may allow earlier diagnosis of epithelial ovarian cancer. The expression of a blood cell fraction from 20 healthy controls and 48 patients with epithelial ovarian cancer was compared.

2011-09-01 | E-GEOD-31682 | biostudies-arrayexpress

Blood based gene expression signature for diagnosis of epithelial ovarian cancer

2011-09-02 | GSE31682 | GEO

Routine use of microarray-based gene expression profiling to identify patients with low cytogenetic risk acute myeloid leukemia: accurate results can be obtained even with suboptimal samples

Project description:This SuperSeries is composed of the following subset Series: GSE34577: Routine use of microarray-based gene expression profiling to identify patients with low cytogenetic risk acute myeloid leukemia: accurate results can be obtained even with suboptimal samples (training samples) GSE34714: Routine use of microarray-based gene expression profiling to identify patients with low cytogenetic risk acute myeloid leukemia: accurate results can be obtained even with suboptimal samples. (test samples) Refer to individual Series

2012-01-04 | E-GEOD-34823 | biostudies-arrayexpress

Fixed tissue ChIP-Seq (FiT-Seq) of archived clinical samples reveals chromatin dynamics and tumor-specific enhancer profiles

Project description:Analysis of cancer epigenomes has revealed important insights into key lineage determinants and oncogenic drivers. Chromatin immune-precipitation followed by next generation sequencing (ChIP-seq) has allowed the comprehensive mapping of transcription factor cistromes and histone modifications in fresh or frozen cells and tissues. It has not been possible, however, to apply ChIP-seq to the vast majority of clinical tissue samples, owing to the very extensive tissue fixation and cross-linking introduced during routine pathological processing. This severely limits the ability to study the most valuable, clinically annotated tissue resources. Here we describe Fixed-Tissue chromatin immune-precipitation sequencing (FiT-seq), which allows the epigenomic analysis of routine formalin-fixed paraffin-embedded (FFPE) tissue samples. FiT-seq enables reliable extraction of soluble chromatin from fixed tissues for accurate detection of histone marks and we verify high concordance between FiT-seq from FFPE and ChIP-seq from matched fresh frozen (FF) samples of the same tumors. We demonstrate the value of FiT-seq to investigate differences in chromatin states in normal and malignant colorectal epithelium and to identify robust correlations to methylated DNA, gene expression, and transcription factor activities. Using multiple histone marks we generate chromatin state maps and identify tissue- and tumor-specific cis-regulatory elements in clinical samples from various tumor types, readily distinguishing cancers by tissue of origin. Tumor specific enhancers and super-enhancers elucidated by FiT-seq are correlated with known biological drivers of cancer and can assist in understanding how chromatin state affects gene regulation.

2016-04-25 | GSE73398 | GEO

Diagnosis of Taenia solium infections based on “mail order” RNA-sequencing of single tapeworm egg isolates from stool samples

Project description:Combined community health programs aiming at health education, preventive antiparasitic chemotherapy, and vaccination of pigs have proven their potential to regionally reduce and even eliminate Taenia solium infections that are associated with a high risk of neurological disease through ingestion of T. solium eggs. Yet it remains challenging to target T. solium endemic regions precisely or to make exact diagnoses in individual patients. One major reason is that the widely available stool microscopy may identify Taenia ssp. eggs in stool samples as such, but fails to distinguish between invasive (T. solium) and less invasive Taenia (T. saginata, T. asiatica, and T. hydatigena) species. The identification of Taenia ssp. eggs in routine stool samples often prompts a time-consuming and frequently unsuccessful epidemiologic workup in remote villages far away from a diagnostic laboratory. Here we present “mail order” single egg RNA-sequencing, a new method allowing the identification of the exact Taenia ssp. based on a few eggs found in routine diagnostic stool samples. We provide first T. solium transcriptome data, which show extremely high mitochondrial DNA (mtDNA) transcript counts that can be used for subspecies identification. “Mail order” RNA-sequencing can be administered by health personnel equipped with basic laboratory tools such as a microscope, a Bunsen burner, and access to an international post office for shipment of samples to a next generation sequencing facility. Our suggested workflow combines traditional stool microscopy, RNA-extraction from single Taenia eggs with mitochondrial RNA-sequencing, followed by bioinformatic processing with a basic laptop computer. The workflow could help to better target preventive healthcare measures and improve diagnostic specificity in individual patients based on incidental findings of Taenia ssp. eggs in diagnostic laboratories with limited resources.

2021-11-06 | GSE175668 | GEO

Gene expression profiling in myeloproliferative neoplasms

Project description:Gene expression profiles were established for 50 MPNs samples. RNA extracted from 2 healthy people was used as control. All MPNs were screened for JAK2V617F mutation as part of routine diagnostic practice.

2011-12-31 | E-MTAB-510 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data