CPT 0069U, 81229, 81327, 81407 - Miscellaneous Genetic and Molecular Diagnostic Tests

Code Description CPT

0069U Oncology (colorectal), microrna, rt-pcr expression profiling of mir-31-3p, formalinfixed paraffin-embedded tissue, algorithm reported as an expression score

81229 Cytogenomic constitutional (genome-wide) microarray analysis; interrogation of genomic regions for copy number and single nucleotide polymorphism (SNP) variants for chromosomal abnormalities

81327 SEPT9 (Septin9) (eg, colorectal cancer) methylation analysis

81407 Molecular pathology procedure, Level 8 (eg, analysis of 26-50 exons by DNA sequence analysis, mutation scanning or duplication/deletion variants of >50 exons, sequence analysis of multiple genes on one platform)

81479 Unlisted molecular pathology procedure

84999 Unlisted chemistry procedure

Miscellaneous Genetic and Molecular Diagnostic Tests


There are many genetic tests. High-quality medical studies show certain genetic tests are helpful when diagnosing some conditions or guiding treatment. However, not all genetic tests have been well studied. In some cases, studies have shown that genetic tests aren’t useful in making a diagnosis or changing care. This policy lists a number of genetic tests where there is not enough evidence in published medical studies to show that they bring health benefits. These tests are considered unproven. 

Note:   The Introduction section is for your general knowledge and is not to be taken as policy coverage criteria. The rest of the policy uses specific words and concepts familiar to medical professionals. It is intended for providers. A provider can be a person, such as a doctor, nurse, psychologist, or dentist. A provider also can be a place where medical care is given, like a hospital, clinic, or lab. This policy informs them about when a service may be covered.

Test Name Investigational

* Celiac PLUS * ColonSentry® * ColoVantage® * Crohn’s Prognostic * DecisionDx-Thymoma * DNA Methylation
Pathway Profile * Epi proColon®  * GI Effects® (Stool) * IBD sgi Diagnostic™  * ImmunoGenomic® Profile * Know Error™ * ResponseDX®: Colon * SEPT9 methylated DNA * TransPredict Fc gamma 3a


All of the tests listed in this policy are considered investigational and grouped according to the categories of genetic testing as outlined in Medical Policy 12.04.91 (General Approach to Genetic Testing; see Related Policies above): * Testing of an affected (symptomatic) individual’s germline to
benefit the individual (excluding reproductive testing) * Diagnostic testing * Prognostic testing * Therapeutic testing  Testing an asymptomatic individual to determine future risk of disease is considered investigational.  

Note: See Table 1 in Evidence Review for additional information about test names listed at the left.

Related Information

Genetic testing is considered investigational when criteria are not met, including when there is insufficient evidence to determine whether the technology improves the net health outcome.

Genetic Counseling

Genetic counseling is primarily aimed at patients 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.

Evidence Review


There are numerous commercially available genetic and molecular diagnostic, prognostic, and therapeutic tests for individuals with certain diseases and or asymptomatic individuals with a future risk. This medical policy evaluates miscellaneous genetic and molecular diagnostic tests not addressed in a separate review. If a separate medical policy exists, then conclusions reached there supersede conclusions in this policy. The main criterion for inclusion in this policy is the limited evidence on the clinical validity for the test. As a result, these tests do not have clinical utility and the evidence is insufficient to determine the effect on health outcomes. The lack of

clinical utility of these tests is based on criteria outlined in a separate medical policy (see Related Policies).


Tests that are assessed in this medical policy are listed in Table 1. Excluding reproductive testing, there are primarily three reasons why genetic and molecular tests might be useful to a person with a disease: diagnostic testing, prognostic testing, and therapeutic testing. A fourth reason would be testing that is done on an asymptomatic person to determine his/her future risk of developing the disease. 

Diagnostic Tests

Multiple Conditions

Single-nucleotide variants (SNVs) are the most common type of genetic variation, and each SNV represents a difference in a single nucleotide in the DNA sequence. Most commonly, SNVs are found in the DNA between genes and can act as biologic markers of genes and disease association. When SNVs occur within a gene or a gene regulatory region, they can play a more direct role in disease by affecting the gene’s function. SNVs may predict an individual’s response to certain drugs, susceptibility to environmental factors, and the risk of developing certain diseases.
DNA specimen provenance assays can be used to confirm that tissue specimens are correctly matched to the patient of origin. Specimen provenance errors may occur in up to 1% to 2% of pathology tissue specimens  and have serious negative implications for patient care if the error is not corrected. Analysis of DNA microsatellites from tissue specimens can be performed by analyzing long tandem repeats (LTR) and comparing the LTRs of the tissue specimen with LTRs from a patient sample.

Test Description: DNA Methylation Pathway Profile

The DNA Methylation Pathway Profile (Great Plains Laboratory) analyzes SNVs associated with certain biochemical processes, including methionine metabolism, detoxification, hormone imbalances, and vitamin D function. Intended uses for the test include clarification of a diagnosis suggested by other testing and as an indication for supplements and diet modifications.

Test Description: Know Error DNA Specimen Provenance Assay

The Know Error test (Strand Diagnostics) compares the LTRs of tissue samples with LTRs from a buccal swab of the patient. The intended use of the test is to confirm tissue of origin and avoid specimen provenance errors due to switching of patient samples, mislabeling, or sample contamination.

Celiac Disease 

Previously called sprue, celiac sprue, gluten-sensitive enteropathy, gluten intolerance, nontropical sprue, or idiopathic steatorrhea, celiac disease is an immune-based reaction to gluten (water insoluble proteins in wheat, barley, rye) that primarily affects the small intestine. Celiac disease occurs almost exclusively in patients who carry at least 1 human leukocyte antigen DQ2 or DQ8; the negative predictive value of having neither allele exceeds 98%.

 Serum antibodies to tissue transglutaminase, endomysium, and deamidated gliadin peptide (DGP) support a diagnosis of celiac disease, but diagnostic confirmation requires duodenal biopsy taken when patients are on a gluten-containing diet.

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