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Scientific Approaches

CPTAC employs two complementary scientific approaches, a "Targeting Genome to Proteome" (Targeting G2P) approach and a "Mapping Proteome to Genome" (Mapping P2G) approach, in order to address biological questions from data generated on a sample.

  • In a “Targeting G2P” approach, a genome dataset defines the protein sequences (candidates) to be targeted in proteomic measurements.  With this approach, labs detect and quantify protein products that correspond to genomic abnormalities including splice variants, mutations, insertions, deletions, rearrangements, copy number aberrations, or epigenomic changes detected at the genome level.
  • In a “Mapping P2G” approach, the integration of the genomic and proteomic datasets is postponed until after the completion of both types of measurements.  Advantage to this approach is that it allows a broader inventory of the detectable proteins in a tumor, including up- or down-regulation of protein abundance, and identification of post-translational modifications that may be critical to cell signaling pathways and networks.  In addition, this integrative approach can be used to improve the quality of genome annotations, as it provides confirmation of protein-coding genes (using proteomic information to annotate the genome).

The combination of these two approaches is anticipated to produce a more comprehensive inventory of the detectable proteins in a tumor and advance our understanding of cancer biology.  The targets identified are subsequently configured into multiplexed targeted assays that can be tested in relevant cohorts of biospecimens.

Rigor and Reproducibility

Commitment To Standards
CPTAC is committed to applying the highest analytical and computational standards, while providing resources and reagents to the public that enable cancer researchers to effectively and reproducibly use proteomic and proteogenomic approaches.  Developing standardized workflows lays the groundwork for future reproducible studies. This level of scientific rigor and transparency in conducting biomedical research is key to ensure quality data production and the successful application of knowledge toward improving health outcomes.

Commitment To Quality
CPTAC is committed to using the latest state-of-the-art technology to provide timely, accurate and reliable omic, and other types of data in cancer biology and related technologies.  To realize this, CPTAC employs a defined Quality Management System that guides our research network in fulfilling our mission, meeting all applicable requirements and ensuring continual improvement in all of our components.  The CPTAC Quality Management system manages and monitors all activities of the program and ensures that each component is equipped with the necessary materials data and information to meet or exceed the CPTAC program expectations.