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Is DNA sequencing enough to recommend personalized treatments for cancer patients? In a article published in Nature Reviews Clinical Oncology, CPTAC investigators and colleagues from the Fred Hutch, Baylor College of Medicine, and University of Washington Medicine make the case for proteogenomics - analysis of the genomic and proteomic changes in cancer tumors.
CPTAC is a comprehensive and coordinated effort to accelerate the understanding of the molecular basis of cancer through the application of robust, quantitative, proteomic technologies and workflows. The overarching goal of CPTAC is to improve our ability to diagnose, treat and prevent cancer.
"Big data" is a term to describe data sets so large or complex that traditional data processing strategies are inadequate. As continued advancements in biomedical technologies generate an increasing amount of patient data, administration of patient-centered care will depend, in part, on the ability to harness relevant insights from this data.
In February 2019, the precisionFDA and the National Cancer Institute’s (NCI) Clinical Proteomic Tumor Analysis Consortium (CPTAC) (in coordination with DREAM Challenges) proudly announced the best performers in the first-ever Crowdsourced Multi-omics Sample Mislabeling Big Data Challenge.
It is no coincidence that one cellular process is mentioned time and time again in discussions of cell-signaling pathways in cancer - that is phosphorylation. Since its discovery, it has come to be recognized as a global regulator of many intracellular processes such as growth, proliferation, and cell division.
In biomedical research, sample mislabeling, or incorrect annotation has been a long-standing problem that contributes to irreproducible results and invalid conclusions. These problems are particularly prevalent in large scale multi-omics studies where human errors could arise during sample transferring, sample tracking, large-scale data generation, and data sharing/management.
University of Michigan Rogel Cancer Center researchers Arul Chinnaiyan, Alexey Nesvizhskii and colleagues have recently teamed up to catalog circular RNA (circRNA) in multiple cancers and conducted initial research that suggests these stable structures could serve as cancer markers in blood or urine.
Integrative proteogenomic methods use mass spectrometry (MS)-based proteomic database for identifying new genomic alterations and validating novel protein sequences as potential disease biomarkers or therapeutic targets. The customized database approach is time consuming and not feasible for real-time web applications.
Built on a continuous partnership between National Cancer Institute’s (NCI’s) Cancer Imaging Program and the Clinical Proteomic Tumor Analysis Consortium (CPTAC), NCI’s The Cancer Imaging Archive (TCIA) releases a newly improved CPTAC histopathology interface. The interface hosts histopathology imaging generated by CPTAC, with matched radiology imaging in TCIA. Significant performance improvements have been made to the platform in response to feedback from the community, providing enhanced functionalities to query pathology report details, download, share and view slide images from approved...
Built on a continuous partnership between National Cancer Institute (NCI) and the University of Victoria Genome British Columbia Proteomics Centre, NCI’s CPTAC Assay Portal releases 660 mouse multiple reaction monitoring-mass spectrometry (MRM-MS) plasma assays to the community.
The incidence of early-onset gastric cancer (EOGC), a type of cancer that occurs in younger patients and found throughout the stomach, is markedly elevated in the Republic of Korea. As a country with the highest rates worldwide in both sexes, there is a need to identify molecular signatures that can be used to diagnose and treat EOGC.
Claudin-Low (CLOW) tumors are classified as a subset of triple-negative breast cancers and account for a minority of breast cancer cases. But until now, there has been little study of their unique biological features. Understanding the biology of CLOW tumors is important for designing targeted therapeutic agents to treat highly aggressive breast cancers.
The NCI-CPTAC Multi-omics Enabled Sample Mislabeling Correction Challenge sub-challenge 2 closes on December 19 at 07:59:59 UTC. Just four days left to submit your computational algorithms. Remember, if you did not participate in sub-challenge 1, you can still participate in sub-challenge 2. Thank you for your participation and please continue to post any questions or concerns on the discussion forum.
CAR T-cells, which are immune cells reprogrammed to fight cancer, are promising novel cancer therapies to treat certain types of tumors. But, the underlying biological pathways that lead to remission or toxicity are not fully understood. In a study published in Science Signaling, CPTAC investigator (part of the Proteogenomic Translational Research Centers) Dr. Amanda Paulovich, her team, and fellow researchers at Fred Hutchinson Cancer Research Center used proteomics t...
The NCI-CPTAC Multi-omics Enabled Sample Mislabeling Correction Challenge sub-challenge 2 closes on December 19 at 07:59:59 UTC. Just two weeks left to submit your compuational algorithms. Remember, if you did not participate in sub-challenge 1, you can still participate in sub-challenge 2.
The second data release for the NCI-CPTAC Multi-omics Enabled Sample Mislabeling Correction Challenge has launched! If you did not participate in sub-challenge 1 (submission 1), you can still participate in sub-challenge 2 (submission 2).
Several ongoing Phase I clinical trials are assessing the safety and tolerability of ATM (ataxia-telangiectasia mutated) and ATR (ataxia-telangiectasia and Rad3-Related) inhibitors when administered alone or in combination with existing therapies. ATM and ATR are attractive therapeutic targets in oncology due to defective DNA damage response (DDR) mechanisms found in many human cancers and are thought to resolve DNA damage in cancer cells and promote tumor regression.
The security of precisionFDA users’ personal information and data is of critical importance. To strengthen the safeguards already in place, precisionFDA will be introducing several changes to achieve compliance with the FedRAMP and FISMA Moderate security standards. These changes will take effect during a service outage on the site between 5PM October 31 and 5PM EDT November 1.
The Clinical Proteomic Tumor Analysis Consortium (CPTAC) is releasing the latest proteomic discovery datasets for Uterine Corpus Endometrial Carcinoma (UCEC) and Clear Cell Renal Cell Carcinoma (ccRCC). CPTAC has previously demonstrated how proteogenomics reveals new insights into cancer biology. Because of the scientific progress already made by the program, CPTAC is leveraging its investment in proteogenomics by characterizing UCEC and ccRCC and providing publicly available proteomic data for these latest tumor types.
In addition, CPTAC has also released data on the NCI-7 cell line...
Fanconi anemia (FA) is a rare inherited disorder characterized by progressive bone marrow failure and an increased risk of developing certain types of cancer. The FA pathway consists of a network of 21 proteins that is specialized for repairing DNA inter-strand cross-links. Identification of monoubiquitylation (or similar) defects in this network provides an opportunity for therapeutic targeting with a high-throughput, quantitative mechanism. CPTAC investigator...