Summary & Overview
CPT 0249U: Theralink RPPA Assay for Breast Tumor Protein Analysis
CPT code 0249U represents a Proprietary Laboratory Analyses (PLA) code for the Theralink® Reverse Phase Protein Array (RPPA) assay, a laboratory-developed test that quantifies and assesses activation of 32 phosphoproteins and cell-surface receptor proteins in breast tumor tissue and delivers an algorithmic interpretive report. As a PLA code tied to a single manufacturer's assay, 0249U signals a specific, high-complexity molecular diagnostic service with potential impact on targeted therapy selection and precision oncology workflows nationally. Key payers covered in this analysis include Aetna, Blue Cross Blue Shield, Cigna Health, UnitedHealthcare, and Medicare. Readers will learn what CPT code 0249U denotes clinically and operationally, how payers approach coverage and billing for proprietary molecular assays, and the clinical context in which RPPA-based reports may inform treatment decisions. The publication summarizes typical sites of service and service type, lists common modifier usage where applicable, and points to the PLA nature of the code for contract and prior authorization considerations. Data not available in the input for associated taxonomies, ICD-10 diagnoses, related codes, and service-line level detail are noted where relevant.
Billing Code Overview
CPT code 0249U is a Proprietary Laboratory Analyses (PLA) code for the Theralink® Reverse Phase Protein Array (RPPA) assay by Theralink® Technologies Inc. The test evaluates a breast tumor tissue sample for the quantity and activation of 32 phosphoproteins and proteins that are cell surface receptors targeted by most cancer therapy drugs. The service includes algorithmic analysis and an interpretive report intended to help guide clinical treatment decisions.
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Service type: Laboratory molecular diagnostic assay with algorithmic interpretation
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Typical site of service: Clinical laboratory or reference diagnostic laboratory processing tumor tissue specimens
Clinical & Coding Specifications
Clinical Context
A 58-year-old woman with recently diagnosed invasive ductal carcinoma of the breast undergoes primary tumor biopsy or surgical resection. Her medical oncologist orders the Theralink® Reverse Phase Protein Array (RPPA) assay (0249U) on formalin-fixed, paraffin-embedded (FFPE) tumor tissue to quantify and evaluate activation state of 32 proteins and phosphoproteins, including cell surface receptors targeted by systemic therapies. The clinical workflow: tissue is selected and macrodissected in the pathology lab, a representative tumor block is sent to Theralink® Technologies Inc. or an authorized lab, the laboratory performs the RPPA analysis and algorithmic interpretation, and a report is returned to the ordering oncologist. The report is used as an adjunctive tool during multidisciplinary tumor board review to inform selection of targeted agents or clinical trial eligibility. Typical site of service is a hospital outpatient clinic, hospital-based pathology laboratory, or a commercial reference laboratory. Specimen collection and handling occur in surgical pathology or interventional radiology settings; the testing itself is performed in the performing laboratory.
Coding Specifications
| Modifier | Description | When to Use |
|---|---|---|
00 | Unspecified — not a standard CMS modifier for professional/technical separation | Data not typically used; included per input list |
26 | Professional component | Use when billing only the professional interpretation component if lab separates professional/technical components and payer requires split billing |
TC | Technical component | Use when billing only the laboratory/technical component of the test |
QK | Reserved for CLIA waived tests (laboratory director) | Rarely applicable; not routinely used for complex PLA tests |
QX | Ordering/servicing practitioner billing with CLIA waiver absence (modifier for labs) | Rarely applicable for complex reference lab testing |
QY | Ordering provider certified laboratory director | Not typically applicable for proprietary reference lab reporting |
AS | Physician assistant, nurse practitioner, or clinical nurse specialist services for Medicare Part B patients | Use when advanced practice clinician is the ordering/authorized clinician per payer rules |
FY | Ordering physician role in specimen collection/processing (specific payor-driven) | Use when a distinct reporting requirement by payer requires this modifier |
82 | Assistant surgeon (when no qualified resident available) | Use only when an assistant surgeon performed a relevant surgical procedure tied to specimen collection and billing requires documentation |
52 | Reduced services | Use if a limited or partial version of the test is performed with documentation of limitation |
| Taxonomy Code | Specialty | Notes |
|---|---|---|
| 207RH0000X | Hematopathology | Pathologists who coordinate specimen selection and send-out testing |
| 207L00000X | Anatomic Pathology | Surgical pathologists handling tumor block selection and test ordering |
| 2085P0200X | Medical Oncology | Medical oncologists ordering the assay to guide systemic therapy |
| 208000000X | Radiation Oncology | Radiation oncologists participating in multidisciplinary decisions where protein activation informs radiosensitizer selection |
| 208000000X-APP* | Advanced Practice Provider | Nurse practitioners/physician assistants who may order tests under supervision |
Related Diagnoses
| ICD-10 Code | Description | Clinical Relevance |
|---|---|---|
C50.911 | Malignant neoplasm of unspecified site of right female breast | Primary breast cancer diagnosis commonly associated with ordering tumor protein profiling |
C50.912 | Malignant neoplasm of unspecified site of left female breast | Primary breast cancer diagnosis commonly associated with ordering tumor protein profiling |
C50.919 | Malignant neoplasm of unspecified site of unspecified female breast | Used when laterality is not specified at time of order |
C79.81 | Secondary malignant neoplasm of breast | Used when evaluating metastatic deposits in breast tissue or recurrent tumor |
Z85.3 | Personal history of malignant neoplasm of breast | Relevant for recurrence risk assessment and consideration of targeted therapy |
Related CPT Codes
| CPT Code | Description | Relationship to This Procedure |
|---|---|---|
88305 | Level IV surgical pathology, gross and microscopic examination | Used by pathology to evaluate and report the tumor specimen and to select appropriate tissue for send-out molecular testing |
88172 | Cytopathology, cell block preparation | May be used when cell block from fine needle aspiration is prepared and sent for proteomic testing |
0003U | (Example PLA) — Molecular/Proteomic assay (proprietary) | Other proprietary molecular or proteomic tests that may be ordered in parallel for comprehensive profiling |
88342 | Immunohistochemistry, per single antigen/antibody stain | Performed when confirmatory protein expression by IHC complements RPPA results |
81225 | BRCA1 gene analysis, full sequence (example) | Genetic testing commonly performed in breast cancer workup and may be ordered alongside proteomic profiling |