Proteogenomic Testing for Patients With Cancer

POLICY NUMBER

A.2.04.140

DESCRIPTION

Proteogenomics refers to the integration of genomic information with proteomic and transcriptomic information to provide a more complete picture of genome function. The current focus of proteogenomics is primarily on the diagnostic, prognostic, and predictive potential of proteogenomics in various cancers. One commercial proteogenomic test is available, the GPS Cancer test.

This policy provides an overview of the emerging field of proteogenomics, with an emphasis on the currently available proteogenomic test, the GPS Cancer test. In addition to focusing on the GPS Cancer test, this policy describes and outlines types of proteogenomic research currently reported in the literature and that have potential clinical applications.

Proteogenomics

The term proteome refers to the entire complement of proteins produced by an organism or cellular system, and proteomics refers to the large-scale comprehensive study of a specific proteome. Similarly, the term transcriptome refers to the entire complement of transcription products (messenger RNAs), and transcriptomics refers to the study of a specific transcriptome. Proteogenomics refers to the integration of genomic information with proteomic and transcriptomic information to provide a more complete picture of the function of the genome.

A system’s proteome is related to its genome and to genomic alterations. However, while the genome is relatively static over time, the proteome is more dynamic and may vary over time and/or in response to selected stressors. Proteins undergo a number of modifications as part of normal physiologic processes. Following protein translation, modifications occur by splicing events, alternative folding mechanisms, and incorporation into larger complexes and signaling networks. These modifications are linked to protein function and result in functional differences that occur by location and over time.

Some of the main potential applications of proteogenomics in medicine include:

• Identifying biomarkers for diagnostic, prognostic, and predictive purposes;

• Detecting cancer by proteomic profiles or “signatures;”

• Quantitating levels of proteins and monitoring levels over time for:

  • Cancer activity,

  • Early identification of resistance to targeted tumor therapy;

• Correlating protein profiles with disease states.

Proteogenomics is an extremely complex field due to the intricacies of protein architecture and function, the many potential proteomic targets that can be measured, and the numerous testing methods used. The types of targets currently being investigated and the testing methods used and under development are discussed next.

Proteomic Targets

A proteomic target can be any altered protein that results from a genetic variant. Protein alterations can result from germline and somatic genetic variants. Altered protein products include mutated proteins, fusion proteins, alternative splice variants, noncoding messenger RNAs, and posttranslational modifications.

Mutated Protein (Sequence Alterations)

A mutated protein has an altered amino acid sequence that arises from a genetic variant. A single amino acid may be replaced in a protein or multiple amino acids in the sequence may be affected. Mutated proteins can arise from germline or somatic genetic variants. Somatic variants can be differentiated from germline variants by comparison with normal and diseased tissue.

Fusion Proteins

Fusion proteins are the product of one or more genes that fuse together. Most fusion genes discovered have been oncogenic, and fusion genes have been shown to have clinical relevance in a variety of cancers.

Alternative Splice Events

Posttranslational enzymatic splicing of proteins results in numerous protein isoforms. Alternative splicing events can lead to abnormal protein isoforms with altered function. Some alternative splicing events have been associated with tumor-specific variants.

Noncoding RNAs

Noncoding portions of the genome serve as the template for noncoding RNA (ncRNA), which plays various roles in the regulation of gene expression. There are two classes of ncRNA: shorter ncRNAs, which include microRNAs and related transcript products, and longer ncRNAs, which are thought to be involved in cancer progression.

Posttranslational Modifications

Posttranslational modifications of histone proteins occur in normal cells and are genetically regulated. Histone proteins are found in the nuclei and play a role in gene regulation by structuring the DNA into nucleosomes. A nucleosome is composed of a histone protein core surrounded by DNA. Nucleosomes are assembled into chromatin fibers composed of multiple nucleosomes assembled in a specific pattern. Posttranslational modifications of histone proteins include a variety of mechanisms, including methylation, acetylation, phosphorylation, glycosylation, and related modifications.

Proteogenomic Testing Methods

Proteogenomic testing involves isolating, separating, and characterizing proteins from biologic samples, followed by correlation with genomic and transcriptomic data. Isolation of proteins is accomplished by trypsin digestion and solubilization. The soluble mix of protein isolates is then separated into individual proteins. This is generally done in multiple stages using high-performance liquid chromatography ion-exchange chromatography, 2-dimensional gel electrophoresis, and related methods. Once individual proteins are obtained, they may be characterized using various methods and parameters, some of which are described below. There is literature addressing the analytic validity of these testing techniques.

Immunohistochemistry and Fluorescence in situ Hybridization

Immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) are standard techniques for isolating and characterizing proteins. Immunohistochemistry identifies proteins by using specific antibodies that bind to the protein. Therefore, this technique can only be used for known proteins and protein variants because it relies on the availability of a specific antibody. This technique also can only test a relatively small number of samples at once.

There are a number of reasons why IHC and FISH are not well-suited for large-scale proteomic research. They are semiquantitative techniques and involve subjective interpretation. They are considered low-throughput assays that are time-consuming and expensive, and require a relatively large tissue sample. Some advances in IHC and FISH have addressed these limitations, including tissue microarray and reverse phase protein array.

• Tissue microarrays can be constructed that enable simultaneous analysis of up to 1000 tissue samples.

• Reverse phase protein array, a variation on tissue microarrays, allows for a large number of proteins to be quantitated simultaneously.

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. The development of technology that led to the application of MS to biological samples has advanced the field of proteogenomics rapidly. However, the application of MS to clinical medicine is in its formative stages. There are currently several types of mass spectrometers and a lack of standardization in the testing methods. Additionally, MS equipment is expensive and currently largely restricted to tertiary research centers.

The potential utility of MS lies in its ability to provide a wide range of proteomic information efficiently, including:

• Identification of altered proteins;

• Delineation of protein or peptide profiles for a given tissue sample;

• Amino acid sequencing of proteins or peptides;

• Quantitation of protein levels;

• 3-dimensional protein structure and architecture; and

• Identification of posttranslational modifications.

Mass Spectrometry Sampling Applications

“Top-down” MS refers to identification and characterization of all proteins in a sample without prior knowledge of which proteins are present. This method provides a profile of all proteins in a system, including documentation of posttranslational modifications and other protein isoforms. This method, therefore, provides a protein “profile” or “map” of a specific system. Following the initial analysis, intact proteins can be isolated and further analyzed to determine amino acid sequences and related information.

“Bottom-up” MS refers to identification of known proteins in a sample. This method identifies peptide fragments that indicate the presence of a specific protein. This method depends on having peptide fragments that can reliably identify a specific protein. Selective reaction monitoring MS is a bottom-up modification of MS that allows for direct quantification and specific identification of low-abundance proteins without the need for specific antibodies. This method requires the selection of a peptide fragment or “signature” that is used to target the specific protein. Multiplex assays have also been developed to quantitate the epidermal growth factor receptor, human epidermal growth factor receptors 2 and 3, and insulin-like growth factor-1 receptor.

Bioinformatics

Due to the complexity of proteomic information, the multiple tests used, and the need to integrate this information with other genomic data, a bioinformatics approach is necessary to interpret proteogenomic data. Software programs integrate and assist in the interpretation of the vast amounts of data generated by proteogenomics research. One software platform that integrates genomic and proteomic information is PARADIGM, which is used by The Cancer Genome Atlas (TCGA) project for data analysis. Other software tools currently available include the following:

• The Genome Peptide Finder matches the amino acid sequence of peptides predicted de novo with the genome sequence.

• The Proteogenomic Mapping Tool is an academic software for mapping peptides to the genome.

• Peppy is an automated search tool that generates proteogenomic data from translated databases and integrates this information for analysis.

• VESPA is a software tool that integrates data from various platforms and provides a visual display of integrated data.

Ongoing Proteogenomic Database Projects

The table below lists some of the ongoing databases being constructed for proteogenomic research.

There are also networks of researchers coordinating their activities in this field. The Clinical Proteomic Tumor Analysis Consortium is a coordinated project among 8 sites sponsored by the National Cancer Institute. This project seeks to characterize the genomic and transcriptomic profiles of common cancers systematically. This consortium has cataloged proteomic information for several types of cancers including breast, colon, and ovarian cancers. All project data are freely available.

Many existing genomic databases have begun to incorporate proteomic information. TCGA intends to profile changes in the genomes of 33 different cancers. As part of its analysis, messenger RNA expression is used to help define signaling pathways that are either upregulated or deregulated in conjunction with genetic variations. Currently, TCGA has published comprehensive molecular characterizations of multiple cancers, including breast, colorectal, lung, gliomas, renal, and endometrial cancers.

Proteogenomic Databases

CPTAC: Clinical Proteomic Tumor Analysis Consortium; TCGA: The Cancer Genome Atlas.

GPS Cancer Test

The GPS Cancer test is a commercially available proteogenomic test intended for patients with cancer. The test includes whole-genome sequencing, whole transcriptome (RNA) sequencing, and quantitative proteomics by mass spectrometry. The test is intended to inform personalized treatment decisions for cancer, and treatment options are provided when available, although treatment recommendations are not. Treatment options may include U.S. Food and Drug Administration-approved targeted drugs with potential for clinical benefit, active clinical trials of drugs with potential for clinical benefit, and/or available drugs to which the cancer may be resistant.

Clinical laboratories may develop and validate tests in-house and market them as a laboratory service; laboratory-developed tests (LDTs) must meet the general regulatory standards of the Clinical Laboratory Improvement Act (CLIA). The GPS Cancer test (NantHealth) is available under the auspices of the CLIA. Laboratories that offer LDTs must be licensed by the CLIA for high-complexity testing. To date, the U.S. Food and Drug Administration has chosen not to require any regulatory review of this test.

POLICY

Proteogenomic testing (see Policy Guidelines section) of individuals with cancer (including, but not limited to the GPS Cancer test) is considered investigational for all indications.

POLICY EXCEPTIONS

Federal Employee Program (FEP) may dictate that all FDA-approved devices, drugs or biologics may not be considered investigational and thus these devices may be assessed only on the basis of their medical necessity.

POLICY GUIDELINES

The coverage guidelines outlined in the Medical Policy Manual should not be used in lieu of the Member's specific benefit plan language.

Proteogenomic testing involves the integration of proteomic, transcriptomic, and genomic information. Proteogenomic testing can be differentiated from proteomic testing, in that proteomic testing can refer to the measurement of protein products alone, without integration of genomic and transcriptomic information. When protein products alone are tested, this is not considered proteogenomic testing.

Genetics Nomenclature Update

The Human Genome Variation Society nomenclature is used to report information on variants found in DNA and serves as an international standard in DNA diagnostics. It is being implemented for genetic testing medical evidence review updates starting in 2017 (see Table 1). The Society’s nomenclature is recommended by the Human Variome Project, the Human Genome Organization, and by the Human Genome Variation Society itself.

The American College of Medical Genetics and Genomics and the Association for Molecular Pathology standards and guidelines for interpretation of sequence variants represent expert opinion from both organizations, in addition to the College of American Pathologists. These recommendations primarily apply to genetic tests used in clinical laboratories, including genotyping, single genes, panels, exomes, and genomes. Table 2 shows the recommended standard terminology - “pathogenic,” “likely pathogenic,” “uncertain significance,” “likely benign,” and “benign” - to describe variants identified that cause Mendelian disorders.

Table 1. Nomenclature to Report on Variants Found in DNA

Table 2. ACMG-AMP Standards and Guidelines for Variant Classification

ACMG: American College of Medical Genetics and Genomics; AMP: Association for Molecular Pathology.

Genetic Counseling

Genetic counseling is primarily aimed at individuals who are at risk for inherited disorders, and experts recommend formal genetic counseling in most cases when genetic testing for an inherited condition is considered. The interpretation of the results of genetic tests and the understanding of risk factors can be very difficult and complex. Therefore, genetic counseling will assist individuals in understanding the possible benefits and harms of genetic testing, including the possible impact of the information on the individual's family. Genetic counseling may alter the utilization of genetic testing substantially and may reduce inappropriate testing. Genetic counseling should be performed by an individual with experience and expertise in genetic medicine and genetic testing methods.

Investigative is defined as the use of any treatment procedure, facility, equipment, drug, device, or supply not yet recognized as a generally accepted standard of good medical practice for the treatment of the condition being treated and; therefore, is not considered medically necessary. For the definition of Investigative, “generally accepted standards of medical practice” means standards that are based on credible scientific evidence published in peer-reviewed medical literature generally recognized by the relevant medical community, and physician specialty society recommendations, and the views of medical practitioners practicing in relevant clinical areas and any other relevant factors. In order for equipment, devices, drugs or supplies [i.e, technologies], to be considered not investigative, the technology must have final approval from the appropriate governmental bodies, and scientific evidence must permit conclusions concerning the effect of the technology on health outcomes, and the technology must improve the net health outcome, and the technology must be as beneficial as any established alternative and the improvement must be attainable outside the testing/investigational setting.

POLICY HISTORY

11/17/2016: Approved by Medical Policy Advisory Committee.

02/23/2018: Policy description updated regarding proteogenomic databases. Policy statement unchanged. Policy Guidelines updated regarding genetics nomenclature update.

07/19/2018: Policy title changed from "Proteogenomic Testing for Patients With Cancer (GPS Cancer™ Test)" to "Proteogenomic Testing for Patients With Cancer." Policy description updated regarding genetics nomenclature and proteogenomic databases. Policy statement unchanged. Policy Guidelines updated regarding genetic counseling.

07/16/2019: Policy reviewed; no changes.

07/14/2020: Policy reviewed. Policy statement unchanged. Policy Guidelines updated to remove genetics nomenclature and genetic counseling information.

08/26/2021: Policy description updated regarding proteogenomic databases. Policy statement unchanged.

07/13/2022: Policy reviewed. Policy statement updated to change "patients" to "individuals." Policy Guidelines updated to add genetics nomenclature update and genetic counseling information.

08/01/2023: Policy description updated. Policy statement unchanged. Policy Guidelines updated to change "patients" to "individuals."

07/22/2024: Policy description updated regarding proteogenomic databases. Policy statement unchanged.

08/21/2025: Policy reviewed; no changes.

SOURCE(S)

Blue Cross Blue Shield Association policy # 2.04.140

CODE REFERENCE

This may not be a comprehensive list of procedure codes applicable to this policy.

Investigational Codes

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