Circulating biomarkers for early detection and clinical management of colorectal cancer.

The SEPT9 gene methylation assay is the first FDA-approved blood assay for colorectal cancer (CRC) screening. Fecal immunochemical test (FIT), FIT-DNA test and CEA assay are also in vitro diagnostic (IVD) tests used in CRC screening. This meta-analysis aims to review the SEPT9 assay performance and compare it with other IVD CRC screening tests. By searching the Ovid MEDLINE, EMBASE, CBMdisc and CJFD database, 25 out of 180 studies were identified to report the SEPT9 assay performance. 2613 CRC cases and 6030 controls were included, and sensitivity and specificity were used to evaluate its performance at various algorithms. 1/3 algorithm exhibited the best sensitivity while 2/3 and 1/1 algorithm exhibited the best balance between sensitivity and specificity. The performance of the blood SEPT9 assay is superior to that of the serum protein markers and the FIT test in symptomatic population, while appeared to be less potent than FIT and FIT-DNA tests in asymptomatic population. In conclusion, 1/3 algorithm is recommended for CRC screening, and 2/3 or 1/1 algorithms are suitable for early detection for diagnostic purpose. The SEPT9 assay exhibited better performance in symptomatic population than in asymptomatic population.

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The performance of the SEPT9 gene methylation assay and a comparison with other CRC screening tests: A meta-analysis.

Diagnostic Accuracy of Methylated SEPT9 for Blood-based Colorectal Cancer Detection: A Systematic Review and Meta-Analysis

Diagnostic Accuracy of Methylated SEPT9 for Blood-based Colorectal Cancer Detection: A Systematic Review and Meta-Analysis.

Colorectal cancer (CRC) is still a leading cause of cancer death worldwide. Less than half of cases are diagnosed when the cancer is locally advanced. CRC is a heterogenous disease associated with a number of genetic or somatic mutations. Diagnostic markers are used for risk stratification and early detection, which might prolong overall survival. Nowadays, the widespread use of semi-invasive endoscopic methods and feacal blood tests characterised by suboptimal accuracy of diagnostic results has led to the detection of cases at later stages. New molecular noninvasive tests based on the detection of CRC alterations seem to be more sensitive and specific then the current methods. Therefore, research aiming at identifying molecular markers, such as DNA, RNA and proteins, would improve survival rates and contribute to the development of personalized medicine. The identification of “ideal” diagnostic biomarkers, having high sensitivity and specificity, being safe, cheap and easy to measure, remains a challenge. The purpose of this review is to discuss recent advances in novel diagnostic biomarkers for tumor tissue, blood and stool samples in CRC patients.

https://www.mdpi.com/1422-0067/23/2/852/pdf?version=1642147067

Novel Diagnostic Biomarkers in Colorectal Cancer

In recent years, detection of cell-free tumour DNA (ctDNA) or liquid biopsy has emerged as an attractive noninvasive methodology to detect cancer-specific genetic aberrations in plasma, and numerous studies have reported on the feasibility of ctDNA in advanced cancer. In particular, ctDNA assays can capture a more 'global' portrait of tumour heterogeneity, monitor therapy response, and lead to early detection of resistance mutations. More recently, ctDNA analysis has also been proposed as a promising future tool for detection of early cancer and/or cancer screening. As the average proportion of mutated DNA in plasma is very low (0.4% even in advanced cancer), exceedingly sensitive techniques need to be developed. In addition, as tumours are genetically heterogeneous, any screening test needs to assay multiple genetic targets in order to increase the chances of detection. Further research on the genetic progression from normal to cancer cells and their release of ctDNA is imperative in order to avoid overtreating benign/indolent lesions, causing more harm than good by early diagnosis. More knowledge on the sources and elimination of cell-free DNA will enable better interpretation in older individuals and those with comorbidities. In addition, as white blood cells are the major source of cell-free DNA in plasma, it is important to distinguish acquired mutations in leukocytes (benign clonal haematopoiesis) from an upcoming haematological malignancy or other cancer. In conclusion, although many studies report encouraging results, further technical development and larger studies are warranted before applying ctDNA analysis for early cancer detection in the clinic.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/joim.12897

Cell-free tumour DNA testing for early detection of cancer - a potential future tool.

BACKGROUND/AIMS Colonoscopy screening has been accepted broadly to evaluate the risk and incidence of colorectal cancer (CRC) during health examination in outpatients. However, the intrusiveness, complexity and discomfort of colonoscopy may limit its application and the compliance of patients. Thus, more reliable and convenient diagnostic methods are necessary for CRC screening. Genome instability, especially copy-number variation (CNV), is a hallmark of cancer and has been proved to have potential in clinical application. METHODS We determined the diagnostic potential of chromosomal CNV at the arm level by whole-genome sequencing of CRC plasma samples (n = 32) and healthy controls (n = 38). Arm level CNV was determined and the consistence of arm-level CNV between plasma and tissue was further analyzed. Two methods including regular z score and trained Support Vector Machine (SVM) classifier were applied for detection of colorectal cancer. RESULTS In plasma samples of CRC patients, the most frequent deletions were detected on chromosomes 6, 8p, 14q and 1p, and the most frequent amplifications occurred on chromosome 19, 5, 2, 9p and 20p. These arm-level alterations detected in plasma were also observed in tumor tissues. We showed that the specificity of regular z score analysis for the detection of colorectal cancer was 86.8% (33/38), whereas its sensitivity was only 56.3% (18/32). Applying a trained SVM classifier (n = 40 in trained group) as the standard to detect colorectal cancer relevance ratio in the test samples (n = 30), a sensitivity of 91.7% (11/12) and a specificity 88.9% (16/18) were finally reached. Furthermore, all five early CRC patients in stages I and II were successfully detected. CONCLUSION Trained SVM classifier based on arm-level CNVs can be used as a promising method to screen early-stage CRC.

/pdf/a-novel-method-to-detect-early-colorectal-cancer-based-on-2kns5sw0sc.pdf

A Novel Method to Detect Early Colorectal Cancer Based on Chromosome Copy Number Variation in Plasma.

Objective
To explore the role of detecting the methylation status of gene Septin9 (SEPT9) in plasma for colorectal cancer screening in Chinese population.


Methods
Patients were collected from Beijing Military General Hospital since September 2013 to February 2014. The performance of SEPT9 assay was validated in a single-blind study of 80 cases with colonoscopy and pathologically verified colorectal cancer and 52 normal controls. The detection of Septin9 gene methylation in peripheral blood was performed by fluorescence quantitative polymerase chain reaction (PCR). And immunoassay fecal occult blood test was conducted to compare the superiority of methylated Septin9 for screening colorectal cancer.


Results
The Septin9 assay successfully identified 75.0%(95%CI: 64.7%-83.6%) of cancers at a specificity of 98.1%(95%CI: 90.9%-99.9%). And it was superior to fecal occult blood screening for colorectal cancer (sensitivity 79.5% vs 53.8%, P<0.05).


Conclusion
Determination of SEPT9 methylation status is an innovative non-invasive plasma screening test for colorectal cancer.


Key words: 
Colorectal neoplasms; DNA methylation; Genes, Septin9

Significance of Septin9 gene methylation detection of plasma circulation DNA in colorectal cancer screening

The invention discloses a detection method and a detection device of gene deletion mutation. The method comprises the following steps: sequencing exon libraries of a sample to be detected and a comparison sample to acquire sequencing data of the sample to be detected and the comparison sample; respectively calculating sequencing numbers of the sample to be detected and the comparison sample on all windows in a form of dividing the sequencing data into several windows to acquire first sequencing numbers of the sample to be detected and the comparison sample on all the windows; performing homogenization on the first sequencing numbers of the sample to be detected and the comparison sample on all the windows to acquire second sequencing numbers of the sample to be detected and the comparison sample on all windows; dividing the second sequencing number of the sample to be detected on the windows by a median which is acquired from the second sequencing number of the comparison sample on all the windows to acquire a specific value; performing gene deletion mutation in the windows if the specific value is smaller than a set value. According to the method, the median in the comparison sample is used as a comparison standard, and compared with an average value or a standard difference, false positive can be relatively easily differentiated, and the result is relatively accurate.

Detection method and device of gene deletion mutation

The invention provides a novel index for analyzing chromosome variation and application thereof in tumor early stage screening. The main content comprises extracting subject sample DNA, analyzing the chromosome variation index thereof, comparing the chromosome variation index with a constructed normal people chromosome variation index, and therefore determining whether tumor load is present in the subject. Compared with other tumor markers, various early stage tumors can be found by the index with high sensitivity and high specificity, and therefore the effects of tumor early warning and later period clinic treatment guidance are achieved.

Qian Kang

Papers

A Novel Method to Detect Early Colorectal Cancer Based on Chromosome Copy Number Variation in Plasma.

Significance of Septin9 gene methylation detection of plasma circulation DNA in colorectal cancer screening

Detection method and device of gene deletion mutation

Novel early stage tumor marker and application based on chromosome variation index