The community-based screening pattern and strategy study for colorectal cancer
Ontology highlight
ABSTRACT:
DISEASE(S): Coloractal Cancer
PROVIDER: 2694882 | ecrin-mdr-crc |
REPOSITORIES: ECRIN MDR
Similar Datasets
Project description:Background and Aims: RNA biomarkers derived from sloughed enterocytes would provide an ideal, non-invasive method for early detection of colorectal cancer (CRC) and precancerous adenomas. To realize this goal, a highly reliable method to isolate preserved human RNA from stool samples is needed. Here we develop a protocol to identify RNA biomarkers associated with CRC to assess the use of these biomarkers for noninvasive screening of disease. Methods: Stool samples were collected from 454 patients prior to a colonoscopy. A nucleic acid extraction protocol was developed to isolate human RNA from 330 stool samples and transcript abundances were estimated by microarray analysis. This 330-patient cohort was split into a training set of 265 individuals to develop a machine learning model and a testing set of 65 individuals to determine the model’s ability to detect colorectal neoplasms. Results: Analysis of the transcriptome from 265 individuals identified 200 transcript clusters as differentially expressed (p<0.03). These transcripts were used to build a Support Vector Machine (SVM) based model to classify 65 individuals within the testing set. This SVM algorithm attained a 95% sensitivity for precancerous adenomas and a 65% sensitivity for CRC (stage I-IV). The machine learning algorithm attained a specificity of 59% for healthy individuals and an overall accuracy of 72.3%. Conclusions: We developed an RNA-based neoplasm detection model that is sensitive for CRC and precancerous adenomas. The model allows for non-invasive assessment of tumors and could potentially be used to provide clinical guidance for individuals within the screening population for colorectal cancer.
2019-02-25 | GSE99573 | GEO
Project description:Fecal immunochemical tests (FIT) detecting hemoglobin in stool are widely used for non-invasive colorectal cancer (CRC) screening, but their sensitivity leaves room for improvement. Our aim is to identify novel protein biomarkers in stool that outperform or complement hemoglobin in detecting CRCs and advanced adenomas (AAs). Stool samples (one series of 12 CRCs and 10 controls, and a second series of 81 CRCs, 40 AAs, 43 non-advanced adenomas and 129 controls) were analyzed by mass-spectrometry and searched for human proteins. Classification and regression tree and logistic regression analyses were performed to identify protein combinations that differentiated CRCs and/or AAs from controls. Antibody-based assays for four selected proteins were performed on an independent series of FIT samples (14 CRCs, 16 AAs, 18 non-advanced adenomas and 24 controls) Results: In total, 834 human proteins were identified, of which 29 were significantly enriched in CRCs versus controls in both stool sample series. Combinations of four proteins reached sensitivities of 80% and 45% for detecting CRCs and AAs, at 95% specificity, which was higher than hemoglobin alone.
2020-05-26 | PXD007767 | Pride
Project description:The primary objective is to determine sensitivity, specificity, positive predictive value and negative predictive value of a bi-target stool DNA testing (the methylation status of SDC2 and SFRP2) for colorectal cancer and advanced precancerous neoplasm(including advanced adenoma and advanced serrated lesions) screening, using colonoscopy as the reference method. Lesions will be confirmed as malignant or precancerous by histopathologic examination.
The secondary objective is to compare the performance of the bi-target stool DNA testing to a commercially available fecal immunochemical test (FIT) assay, both with respect to cancer and advanced precancerous neoplasm. Lesions will be confirmed as malignant or precancerous by colonoscopy and histopathologic examination.
| 2348965 | ecrin-mdr-crc
Project description:The spatiotemporal structure of the human microbiome, proteome, and metabolome reflects and determines regional intestinal physiology and may have implications for disease. Yet, we know little about the distribution of microbes, their environment, and their biochemical activity in the gut because of reliance on stool samples and limited access to only some regions of the gut using endoscopy in fasting or sedated individuals. To address these deficiencies, we developed and evaluated a safe, ingestible device that collects samples from multiple regions of the human intestinal tract during normal digestion and maintains the viability of microbes from these locations. The collection of 240 intestinal samples from 15 healthy individuals using the device and subsequent multi-omics analyses revealed significant differences between microbes, phages, host proteins, and metabolites present in the intestines versus stool. Certain microbial taxa and gene classes were differentially enriched, and prophage induction was more prevalent in the intestines than in stool. The host proteome and bile acid profiles varied along the intestines and were highly distinct from those of stool. Correlations between gradients in bile acid concentrations and microbial abundancepredicted species that altered the bile acid pool through deconjugation. Furthermore,microbially conjugated bile acids displayed amino acid-dependent trends in concentration that were not apparent in stool. Overall, non-invasive longitudinal profilingof microbes, proteins, and bile acids along the intestinal tract under physiological conditions can help elucidate the roles of the gut microbiome and metabolome in humanphysiology and disease.
2023-01-18 | PXD038906 | Pride
Project description:A cross sectional study using data collected at the time of liver biopsy, the final eligibility assessment for participation in iWITH (NCT01638559), an immunosuppression withdrawal trial. Microarrays were used to understand the gene expression profile differences among the three histological clusters (Cluster 1, Cluster 2 and Cluster 3)
2018-11-13 | GSE118587 | GEO
Project description:The primary objective is to compare the performance of Stool-based SDC2 DNA Methylation Test and commercially available Fecal Immunochemical Test(FIT) , on the detection rate of advanced adenomatous polyps and colorectal cancer in Chinese population. Subjects with positive results in either test will receive colonoscopy. Lesions will be confirmed as malignant or precancerous by colonoscopy and histopathologic examination.
| 2326441 | ecrin-mdr-crc
Project description:Colorectal cancer (CRC) screening has been demonstrated to reduce long term disease burden and costs. Unfortunately, less than 65 % of age-eligible persons in the US are actually screened for CRC. The leading methods, colonoscopy and FIT (fecal immunochemical test) testing, both have patient-associated barriers that reduce their use. The combination of bowel preparation and procedure time are barriers to colonoscopy, while stool handling as part of the sampling protocol reduces FIT usage.
It has been hypothesized and supported by a variety of preference studies that the availability of a blood-based assay for CRC screening would increase patient participation and adherence to CRC screening by reducing barriers that prevent participation.
This study is designed to investigate the relative participation in CRC screening in average risk, screening eligible patients with demonstrated non-adherence to guideline-recommended screening modalities. Participation with the fecal immunochemical test (FIT) and the blood-based Epi proColon test will be examined. Screening eligible average-risk patients identified as non-adherent by medical record will be eligible for the study. Potential subjects will be recruited to participate in a study via mailing and/or at a clinic visit. All study subjects will be enrolled at a clinic visit and will be randomized in two study arms. Those assigned to Arm 1 will be offered a FIT test kit for home use. Those assigned to Arm 2 will be offered a blood draw for the Epi proColon test. Rates of adherence will be compared between those that accept and complete the blood test and those that accept and complete the FIT test. A passive control, usual care arm will comprise subjects meeting eligibility criteria, but not recruited for or participating in the study.
In conjunction with published data (Johnson et al, 2014), the relative utilization of the blood test will be compared to the screening participation via FIT. Increased participation with the Epi proColon blood test could increase screening rates in the non-adherent population. Additionally, for those testing positive in the trial, the rate of adherence to colonoscopy will be determined.
| 2175283 | ecrin-mdr-crc
Project description:The primary objective is to determine the sensitivity and specificity of two Colorectal Cancer (CRC) screening methods, including stool DNA test and blood mRNA test, for colorectal cancer in Chinese population, with colonoscopy as reference method. Lesions will be confirmed as malignant or precancerous by colonoscopy and histopathologic examination.
The secondary objective is to compare the performance of these two CRC screening methods to a commercially available FIT assay, both with respect to cancer and advanced adenoma. Lesions will be confirmed as malignant or precancerous by colonoscopy and histopathologic examination.
| 2264226 | ecrin-mdr-crc
Project description:201B7 cells were cultured on iMatrix-511 for 4 days after cell seeding in Stem Fit AK03 medium or CTS Essential 8 medium (2 samples each), and separately, different 201B7 cells (2 samples each) were cultured in Stem Fit AK03 medium or gelatin solution (10%) + MFGE 8 (2 µg/mL) in CTS Essential 8 medium for 4 days from cell seeding. A hierarchical cluster analysis of the 10 cell types is shown (Figure 2A). The 5,919 probes with variable expression are shown in a heatmap. Comparisons between samples based on 'human ES cell' were made using a hierarchical cluster analysis, and 4,825 probes with variable expression in each of the four comparisons are shown in the heatmap (Figure 2B). Comparisons between samples based on 'human iPSC N116213' were performed using a hierarchical cluster analysis, and 4,886 probes with variable expression in each of the four comparisons are also shown in a heatmap (Figure 2C).
2023-04-20 | GSE230084 | GEO