Summary & Overview
CPT 0162U: CustomNext® + RNA Lynch mRNA Sequence Analysis
CPT code 0162U designates a Proprietary Laboratory Analyses (PLA) test: the CustomNext® + RNA: Lynch (MLH1, MSH2, MSH6, PMS2) mRNA sequencing assay from Ambry Genetics®. This code is used in conjunction with the primary full-sequence analysis code to report mRNA sequence analysis specific to the four Lynch syndrome genes. Nationally, PLA codes like 0162U matter because they identify manufacturer-specific molecular assays that can affect coding consistency, claims adjudication, and lab reporting.
Key payers in this analysis include Aetna, Blue Cross Blue Shield, Cigna Health, UnitedHealthcare, and Medicare. Readers will find an overview of what the code represents, typical clinical and laboratory contexts for use, and the payer landscape relevant to coverage and billing practices. The publication summarizes benchmarking points, common billing modifiers, and clinical context for Lynch syndrome mRNA testing, and highlights areas where policy updates or payer guidance commonly appear. Data not available in the input will be noted where applicable.
Billing Code Overview
CPT code 0162U is a Proprietary Laboratory Analyses (PLA) code for the CustomNext® + RNA: Lynch (MLH1, MSH2, MSH6, PMS2) test from Ambry Genetics®. The code applies to the mRNA sequence analysis of the four listed Lynch syndrome–associated genes when reported in conjunction with the primary code for full sequence analysis. This PLA designation indicates the code is specific to a single manufacturer or laboratory test.
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Service type: Molecular diagnostic laboratory testing for mRNA sequence analysis of Lynch syndrome genes
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Typical site of service: Clinical laboratory or outpatient laboratory setting
Data not available in the input.
Clinical & Coding Specifications
Clinical Context
A patient with a personal or family history suggestive of Lynch syndrome—such as early-onset colorectal or endometrial cancer, multiple Lynch-associated tumors, or a first-degree relative with confirmed pathogenic variants—undergoes comprehensive germline testing. The ordering clinician (typically a geneticist, oncologist, or colorectal surgeon) requests full sequence analysis of the four Lynch genes (MLH1, MSH2, MSH6, PMS2) and the laboratory performs mRNA (RNA) sequence analysis as an adjunct to DNA testing to detect splicing abnormalities or expression-level consequences of suspected variants. The workflow: the clinician obtains informed consent, collects a blood sample (or other validated specimen) and sends it to the lab with clinical indication and prior test results. The lab performs DNA full sequence analysis (primary test) and, when indicated by variant interpretation needs, runs the Ambry Genetics CustomNext® + RNA: Lynch test reported under 0162U for mRNA sequence analysis of MLH1, MSH2, MSH6, and PMS2. Results are reported back to the ordering provider for integration into genetic counseling, risk assessment, and management planning.
Coding Specifications
| Modifier | Description | When to Use |
|---|---|---|
26 | Professional component | When billing separately for the professional interpretation of the test if payer requires split billing between technical and professional components. |
TC | Technical component | When billing only the laboratory technical processing component (instrumentation, reagents) separately. |
52 | Reduced services | If the laboratory performs a reduced or limited version of the test compared to full protocol. |
59 | Data not available in the input. | Data not available in the input. |
62 | Two surgeons | Data not available in the input. |
78 | Return to OR for related procedure by same physician | Data not available in the input. |
80 | Assistant surgeon | Data not available in the input. |
82 | Assistant (when qualified resident not available) | Data not available in the input. |
22 | Unusual procedural services | When the test requires substantially greater effort or resources than typical (rarely used for PLA codes; applies if documentation supports higher complexity). |
53 | Discontinued procedure | When the specimen collection or processing was started but testing was discontinued before completion. |
| Taxonomy Code | Specialty | Notes |
|---|---|---|
207V00000X | Clinical Molecular Genetics Laboratory | Laboratories performing specialized molecular diagnostic testing including PLA tests. |
207L00000X | Laboratory Director | Laboratory directors overseeing high-complexity molecular testing workflows. |
207K00000X | Medical Genetics & Genomics | Clinical geneticists ordering and interpreting hereditary cancer testing. |
207P00000X | Pathology | Molecular pathology specialists involved in test interpretation and variant classification. |
Related Diagnoses
| ICD-10 Code | Description | Clinical Relevance |
|---|---|---|
Z15.09 | Genetic susceptibility to other malignant neoplasm | Used when testing is ordered for known family history or genetic susceptibility to cancers associated with Lynch syndrome. |
Z80.0 | Family history of malignant neoplasm of digestive organs | Captures family history prompting hereditary colorectal cancer testing. |
Z80.49 | Family history of malignant neoplasm of other female genital organs | Used when family history of endometrial or ovarian cancer prompts Lynch testing. |
C18.9 | Malignant neoplasm of colon, unspecified | Represents patients with colorectal cancer undergoing germline evaluation for Lynch syndrome. |
C54.9 | Malignant neoplasm of corpus uteri, unspecified | Represents patients with endometrial cancer in whom Lynch-associated testing is indicated. |
R19.5 | Other fecal abnormalities | May be present in symptomatic patients with colorectal disease leading to diagnosis and subsequent genetic testing. |
Related CPT Codes
| CPT Code | Description | Relationship to This Procedure |
|---|---|---|
81443 | Molecular pathology procedure; full gene sequence analysis, one gene (e.g., full sequence analysis of a single gene) | Often billed for full sequence analysis of individual Lynch genes as the primary DNA-based test; 0162U is reported in conjunction with the primary full sequence analysis when RNA analysis is performed. |
81479 | Unlisted molecular pathology procedure | May be used when a laboratory-specific RNA analysis or combined proprietary algorithm lacks a precise category; PLA 0162U supplants use of unlisted codes when applicable. |
G0452 | Pharmacogenomics testing (note: use varies by payer) | Not directly related but sometimes ordered in the same oncology/genetics workup for therapy guidance; included here as a commonly paired molecular code. |
0000U | Data not available in the input. | Data not available in the input. |
0143U | Data not available in the input. | Data not available in the input. |