Summary & Overview

CPT 0160U: mRNA Sequence Analysis of MSH6 (Ambry CustomNext® + RNA)

CPT code 0160U designates a Proprietary Laboratory Analyses (PLA) test — the CustomNext® + RNA: MSH6 assay from Ambry Genetics® — used for mRNA sequence analysis of the MSH6 gene alongside a primary full sequence analysis. As a PLA code, 0160U applies to a single manufacturer-specific laboratory test and signals a targeted molecular diagnostic service relevant to hereditary cancer evaluation and genomic medicine.

This publication covers national payer coverage and benchmarking context for major payers including Aetna, Blue Cross Blue Shield, Cigna Health, UnitedHealthcare, and Medicare. Readers will find an overview of typical sites of service and service type, a concise explanation of the clinical purpose of the assay, and which payers are included in comparative tables.

The report presents operational benchmarks, coding and billing notes tied to PLA designation, and policy updates that affect proprietary laboratory tests. Clinical context explains when MSH6 mRNA analysis is used in conjunction with full sequence analysis, and the implications for test ordering and claims reporting. Data availability and payer-specific policy details are summarized for a national audience to support coding, billing, and administrative decisions.

AetnaBlue Cross Blue ShieldCigna HealthUnitedHealthcareMedicare0160UCPTProprietary Laboratory AnalysesmRNA sequencingMSH6 genemolecular diagnosticsgenetic testinglaboratory billing

Billing Code Overview

CPT code 0160U is a Proprietary Laboratory Analyses (PLA) code for the CustomNext® + RNA: MSH6 test from Ambry Genetics®. The code is reported for mRNA sequence analysis of the MSH6 gene performed in conjunction with the primary code for full sequence analysis.

Service type: Molecular diagnostic laboratory test — targeted mRNA sequencing

Typical site of service: Clinical diagnostic laboratory

Clinical & Coding Specifications

Clinical Context

A typical patient is an adult referred for hereditary cancer genetic testing after a personal or family history suggesting Lynch syndrome or other mismatch repair-related cancer risk. The ordering clinician (often a geneticist, oncologist, or genetic counselor) requests comprehensive MSH6 analysis using Ambry Genetics® CustomNext® + RNA: MSH6 to evaluate both DNA sequence variants and RNA splicing consequences. The clinical workflow: the clinician documents the indication in the medical record, obtains informed consent for genetic testing, and collects a blood or saliva specimen at an outpatient laboratory, clinic, or hospital. The specimen is sent to the performing laboratory (Ambry Genetics®) where DNA full sequence analysis is performed as the primary test and adjunctive mRNA sequence analysis using the CustomNext® + RNA assay is performed to assess variants of uncertain significance for effects on splicing. Results are reported to the ordering provider and genetic counselor for interpretation and patient management discussions. Typical site of service: outpatient laboratory or clinic; typical service type: proprietary laboratory analysis (PLA) – specialized molecular diagnostic testing.

Coding Specifications

Modifier	Description	When to Use
`26`	Professional component	When reporting only the professional interpretation component if technical component billed separately.
`TC`	Technical component	When reporting only the laboratory technical component when professional interpretation billed separately.
`59`	Distinct procedural service	Data not available in the input.
`52`	Reduced services	When the lab performs a reduced or partial testing service relative to the full PLA.
`53`	Discontinued procedure	When testing is started but discontinued for patient-related or technical reasons.
`22`	Increased procedural services	When the test requires substantially greater effort or resources than typical.
`78`	Unplanned return to facility for related procedure	When an additional specimen collection or repeat testing is required emergently.
`80`	Assistant surgeon	Not typically applicable to lab testing; included if a supervising clinician provides direct procedural assistance during specimen collection.
`82`	Assistant surgeon (when qualified resident not available)	Rarely applicable; analogous use as `80` when needed.
`QK`	Medical direction of two or more assistants	Not typically applicable to lab PLA but included when multiple assisting providers are directed during specimen procurement.

Taxonomy Code	Specialty	Notes
207Q00000X	Clinical Geneticist	Providers who order and interpret hereditary cancer gene testing.
208D00000X	Medical Oncologist	Clinicians ordering testing for cancer risk assessment and treatment planning.
2080P0002X	Pathology/Laboratory Medicine	Laboratory directors overseeing molecular diagnostics.
363L00000X	Genetic Counselor	Professionals coordinating testing and counseling patients.
207L00000X	Clinical Molecular Geneticist	Specialists in molecular test interpretation.

Related Diagnoses

ICD-10 Code	Description	Clinical Relevance
`Z15.09`	Genetic susceptibility to other malignant neoplasm	Used when testing for hereditary cancer predisposition such as Lynch syndrome.
`Z80.0`	Family history of malignant neoplasm of digestive organs	Indicates family history prompting MSH6 testing for Lynch-associated colorectal cancer risk.
`Z80.9`	Family history of malignant neoplasm, unspecified	General family cancer history leading to hereditary testing.
`C18.9`	Malignant neoplasm of colon, unspecified	Personal colorectal cancer history that may trigger germline MSH6 analysis.
`C54.9`	Malignant neoplasm of corpus uteri, unspecified	Endometrial cancer history associated with Lynch syndrome prompting MSH6 evaluation.

Related CPT Codes

CPT Code	Description	Relationship to This Procedure
`81479`	Unlisted molecular pathology procedure	Used when additional custom or non-specific molecular testing is performed alongside the PLA if no specific CPT exists.
`81291`	MSH2 (MSH2 gene) analysis, full sequence	Often performed in parallel for comprehensive mismatch repair gene panel testing.
`81292`	MSH6 analysis, full sequence (DNA)	Primary code for the full sequence analysis of MSH6; `0160U` is reported in conjunction with the primary code for the mRNA component.
`81445`	Hereditary colorectal cancer panel (e.g., Lynch syndrome related genes)	Panel testing that may include MSH6 and is part of the broader diagnostic evaluation.
`88360`	Immunohistochemistry, per specimen; multiple antibodies	Performed on tumor tissue to assess mismatch repair protein expression and guide germline testing decisions.