Since its first mention in the scientific literature in 2004 by Jaffe et al1, the term proteogenomics has been shrouded in mystery and thick technical language. It is a complex idea, but one that is gaining traction as its value to improve our understanding of cancer development and potentially...
Phosphorylation is a key process in the regulation of protein activity and has long been appreciated as an essential mechanism for the control of cellular function - tells a protein where to go, what to bind to and even when to die.
The Clinical Proteomic Tumor Analysis Consortium (CPTAC) is pleased to release its newest comprehensive dataset - deep proteomic/phosphoproteomic data and imaging data of Lung Adenocarcinoma (LUAD) patient tumors. The CPTAC Tumor Characterization Program uses proteogenomic analysis to systematic...
Riding the wave of the future requires scientists to move away from silo-thinking to an inclusive and collaborative mind set. By leveraging the power of crowdsourcing, precisionFDA and NCI-CPTAC teamed up to launch the Multi-omics Enabled Sample Mislabeling Correction Big Data Challenge. Over 500...
Analyzing both the entire set of genes and all the proteins produced by colon cancer tissues from patient samples has revealed a more comprehensive view of the tumor that points at novel cancer biological mechanisms and possible new therapeutic strategies.
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...
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 abili...
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...
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 transf...
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 ur...
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...
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 i...
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 signature...
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 th...
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. Than...
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 investigat...
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.