BlueCross BlueShield of Tennessee Medical Policy Manual

Proteogenomic Testing for Individuals with Cancer


Proteogenomic testing (e.g. GPS Cancer™ Test) is intended for individuals with cancer. The test includes whole-genome sequencing (20,000 genes, 3 billion base pairs), whole transcriptome (RNA) sequencing, and quantitative proteomics by mass spectrometry. Mass spectrometry (MS) separates molecules by their mass to charge ratio and has been used as a research tool for studying proteins for many years. Proteogenomic testing can be differentiated from proteomic testing, in that proteomic testing can refer to the measurement of protein products only, without integration of genomic information. When protein products alone are tested, this is not considered proteogenomic testing.

The current focus of proteogenomics is primarily on the diagnostic and predictive potential of proteogenomics in various cancers. For proteogenomic testing in general, the research is at an early stage. There is a lack of standardization of testing methods, and uncertain accuracy for most proteogenomic technologies. Further research is needed to standardize and validate proteogenomic testing methods.




There is no published evidence on the clinical validity or clinical utility of proteogenomic testing (e.g., GPS Cancer™ Test) and only a few studies have provided information on validity for proteomic research in general. Further research is needed to adequately standardize and validate proteogenomic testing for clinical use.


American Society of Clinical Oncology (ASCO). (2014). American Society of Clinical Oncology Educational Book: Mass spectrometry-based proteomics: From cancer biology to protein biomarkers, drug targets, and clinical applications. (Vol 34, pg. 791).  Retrieved August 29, 2017 from

BlueCross BlueShield Association. Medical Policy Reference Manual. (6:2017). Proteogenomic testing for patients with cancer (GPS Cancer™ Test) (2.04.140). Retrieved August 28, 2017 from BlueWeb. (34 articles and/or guidelines reviewed)

Edwards, N. J., Oberti, M., Thangudu, R. R., Cai, S., McGarvey, P. B., Jacob, S., et al. (2015, June). The CPTAC data portal: A resource for cancer proteomics research. Journal of Proteome Research, 14 (6), 2707-2713. Abstract retrieved August 31, 2016 from PubMed database.

Gregorich, Z. R., & Ge, Y. (2014, May). Top-down proteomics in health and disease: challenges and opportunities. Proteomics, 14 (10), 1195-1210. (Level 4 evidence)

Mertins, P., Mani, D., Ruggles, K., Gillette, M., Clauser, K., Wang, P., et al. (2016, November). Proteogenomics connects somatic mutations to signalling in breast cancer. Nature, 534 (7605), 55-62. (Level 4 evidence)

Sheynkman, G., Shortreed, M., Cesnik, A., and Smith, L. (2016, June). Proteogenomics: integrating next-generation sequencing and mass spectrometry to characterize human proteomic variation. Annual Review of Analytical Chemistry, 9 (1), 521-545. (Level 4 evidence)

Zhang, H., Liu, T., Zhang, Z., Payne, S. H., Zhang, B., McDermott, J., et al. (2016, July). Integrated proteogenomic characterization of human high-grade serous ovarian cancer. Cell, 166 (3), 755-765. (Level 4 evidence)




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