Biomarker discovery by proteomics-based approaches for early detection and personalized medicine in colorectal cancer

2017 ◽  
Vol 11 (5-6) ◽  
pp. 1600072 ◽  
Author(s):  
Claudia Corbo ◽  
Armando Cevenini ◽  
Francesco Salvatore
Keyword(s):  
Colorectal Cancer ◽  
Personalized Medicine ◽  
Early Detection ◽  
Biomarker Discovery ◽  
And Personalized Medicine

scholarly journals Identification of Novel Mutations in Colorectal Cancer Patients Using AmpliSeq Comprehensive Cancer Panel

2021 ◽  
Vol 11 (6) ◽  
pp. 535
Author(s):  
Bader Almuzzaini ◽  
Jahad Alghamdi ◽  
Alhanouf Alomani ◽  
Saleh AlGhamdi ◽  
Abdullah A. Alsharm ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Personalized Medicine ◽  
Cancer Patients ◽  
Biomarker Discovery ◽  
Local Population ◽  
Network Analyses ◽  
Functional Perspective ◽  
Novel Variants ◽  
Colorectal Cancer Patients ◽  
Cancer Panel

Biomarker discovery would be an important tool in advancing and utilizing the concept of precision and personalized medicine in the clinic. Discovery of novel variants in local population provides confident targets for developing biomarkers for personalized medicine. We identified the need to generate high-quality sequencing data from local colorectal cancer patients and understand the pattern of occurrence of variants. In this report, we used archived samples from Saudi Arabia and used the AmpliSeq comprehensive cancer panel to identify novel somatic variants. We report a comprehensive analysis of next-generation sequencing results with a coverage of >300X. We identified 466 novel variants which were previously unreported in COSMIC and ICGC databases. We analyzed the genes associated with these variants in terms of their frequency of occurrence, probable pathogenicity, and clinicopathological features. Among pathogenic somatic variants, 174 were identified for the first time in the large intestine. APC, RET, and EGFR genes were most frequently mutated. A higher number of variants were identified in the left colon. Occurrence of variants in ERBB2 was significantly correlated with those of EGFR and ATR genes. Network analyses of the identified genes provide functional perspective of the identified genes and suggest affected pathways and probable biomarker candidates. This report lays the ground work for biomarker discovery and identification of driver gene mutations in local population.

scholarly journals Gel-Based Proteomics of Clinical Samples Identifies Potential Serological Biomarkers for Early Detection of Colorectal Cancer

2019 ◽  
Vol 20 (23) ◽  
pp. 6082 ◽  
Author(s):  
Stine Thorsen ◽  
Irina Gromova ◽  
Ib Christensen ◽  
Simon Fredriksson ◽  
Claus Andersen ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Early Detection ◽  
Biomarker Discovery ◽  
Real Life ◽  
Clinical Samples ◽  
Plasma Samples ◽  
Healthy Individuals ◽  
Protein Biomarkers ◽  
2D Gel ◽  
Cancer Diseases

The burden of colorectal cancer (CRC) is considerable—approximately 1.8 million people are diagnosed each year with CRC and of these about half will succumb to the disease. In the case of CRC, there is strong evidence that an early diagnosis leads to a better prognosis, with metastatic CRC having a 5-year survival that is only slightly greater than 10% compared with up to 90% for stage I CRC. Clearly, biomarkers for the early detection of CRC would have a major clinical impact. We implemented a coherent gel-based proteomics biomarker discovery platform for the identification of clinically useful biomarkers for the early detection of CRC. Potential protein biomarkers were identified by a 2D gel-based analysis of a cohort composed of 128 CRC and site-matched normal tissue biopsies. Potential biomarkers were prioritized and assays to quantitatively measure plasma expression of the candidate biomarkers were developed. Those biomarkers that fulfilled the preset criteria for technical validity were validated in a case-control set of plasma samples, including 70 patients with CRC, adenomas, or non-cancer diseases and healthy individuals in each group. We identified 63 consistently upregulated polypeptides (factor of four-fold or more) in our proteomics analysis. We selected 10 out of these 63 upregulated polypeptides, and established assays to measure the concentration of each one of the ten biomarkers in plasma samples. Biomarker levels were analyzed in plasma samples from healthy individuals, individuals with adenomas, CRC patients, and patients with non-cancer diseases and we identified one protein, tropomyosin 3 (Tpm3) that could discriminate CRC at a significant level (p = 0.0146). Our results suggest that at least one of the identified proteins, Tpm3, could be used as a biomarker in the early detection of CRC, and further studies should provide unequivocal evidence for the real-life clinical validity and usefulness of Tpm3.

scholarly journals Cancer oriented biobanks: A comprehensive review

2018 ◽  
Author(s):  
Shankargouda Patil ◽  
Barnali Majumdar ◽  
Kamran Habib Awan ◽  
Gargi S. Sarode ◽  
Sachin C. Sarode ◽  
...  
Keyword(s):  
Cancer Research ◽  
Personalized Medicine ◽  
Biomarker Discovery ◽  
Review Paper ◽  
Comprehensive Review ◽  
Therapeutic Drugs ◽  
The World ◽  
And Personalized Medicine

Biobanks provide a platform for innovative biomedical research and has improvised translational and personalized medicine to a great extent. Time 2009 published 10 ideas changing the world right now with biobanks on the list emphasizing its role in discovery and development of new therapeutic drugs. They form the cornerstone, providing resources for future investigations and biomarker discovery to understand the effects of genetic, environmental and lifestyle factors on human morbidity, mortality and health. The aim of this review paper is to understand the role of biobanking in cancer research, the challenges faced and strategies to overcome these, for long term and sustainable research in the field of oncology.

MicroRNA in biofluids—Robust biomarkers for disease, toxicology, or injury studies: The case of minimally invasive colorectal cancer detection.

2012 ◽  
Vol 30 (30_suppl) ◽  
pp. 20-20
Author(s):  
Peter Mouritzen ◽  
Søren Jensby Nielsen ◽  
Maria Wrang Teilum ◽  
Thorarinn Blondal ◽  
Ditte Andreasen ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Early Detection ◽  
Biomarker Discovery ◽  
Expression Profiles ◽  
Minimal Invasive ◽  
Reference Ranges ◽  
Disease States ◽  
A Genome ◽  
New Biomarkers ◽  
Clinical Source

20 Background: MicroRNAs function as post-transcriptional regulators of gene expression. Their high relative stability in common clinical source materials (FFPE blocks, plasma, serum, urine, saliva, etc.) and the ability of microRNA expression profiles to accurately classify discrete tissue types and specific disease states have positioned microRNAs as promising new biomarkers for diagnostic application. Furthermore microRNAs have been shown to be rapidly released from tissues into the circulation with the development of pathology. Methods: Thousands of biofluid samples were profiled including blood derived plasma/serum and urine using a genome-wide LNA-based microRNA qPCR platform, which has unparalleled sensitivity and robustness even in biofluids with extremely low microRNA levels. Only a single RT reaction is required to conduct full miRNome profiling thereby facilitating high-throughput profiling without the need for pre-amplification. Results: Normal reference ranges for circulating microRNAs were determined in several biofluids, allowing development of qPCR arrays containing only relevant microRNA subsets present in various biofluids together with tissue specific microRNA markers. Procedures were developed to control pre-analytical variables, for quality checking and qualifying biofluid samples in particular serum and plasma but also urine and other biofluids. An extensive QC system was implemented in order to secure technical excellence and reveal any unwanted bias in the dataset. We currently screen and validate microRNAs biomarkers for cancer with the aim of developing minimal invasive tests to be applied in early detection population screens. Conclusions: The qPCR panels support development of robust biomarkers in disease, toxicology, and injury studies. We will demonstrate how panels may be quickly and robustly applied in biomarker discovery/validation projects using the specific case early detection of colorectal cancer in blood. Close attention is required on pre-analytical parameters. Hemolysis and cellular contamination affect miRNA profiles in biofluids and control is required.

scholarly journals New frontiers in metabolomics: from measurement to insight

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 1148 ◽  
Author(s):  
Eli Riekeberg ◽  
Robert Powers
Keyword(s):  
Statistical Analysis ◽  
Systems Biology ◽  
Personalized Medicine ◽  
Rapid Growth ◽  
Health Research ◽  
Biomarker Discovery ◽  
Complete Analysis ◽  
Analysis Techniques ◽  
Measurement And Analysis ◽  
And Personalized Medicine

Metabolomics is the newest addition to the “omics” disciplines and has shown rapid growth in its application to human health research because of fundamental advancements in measurement and analysis techniques. Metabolomics has unique and proven advantages in systems biology and biomarker discovery. The next generation of analysis techniques promises even richer and more complete analysis capabilities that will enable earlier clinical diagnosis, drug refinement, and personalized medicine. A review of current advancements in methodologies and statistical analysis that are enhancing and improving the performance of metabolomics is presented along with highlights of some recent successful applications.

Informatics Solutions for Biomarker Discovery and Personalized Medicine in Clinical Care

2019 ◽  
pp. 135-142
Author(s):  
Jan-Willem Boiten ◽  
Rita Azevedo ◽  
Marinel Cavelaars ◽  
André Dekker ◽  
Remond J. A. Fijneman ◽  
...  
Keyword(s):  
Personalized Medicine ◽  
Biomarker Discovery ◽  
Clinical Care ◽  
And Personalized Medicine
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