Summary & Overview
CPT 0036U: EXaCT–1 Whole Exome Sequencing (WES)
CPT code 0036U designates EXaCT–1 whole exome sequencing (WES), a Proprietary Laboratory Analyses (PLA) molecular assay performed by the Lab of Oncology–Molecular Detection at Weill Cornell Medicine–Clinical Genomics Laboratory. As a PLA code, 0036U identifies a single, manufacturer- or laboratory-specific test that sequences the protein-coding regions of the genome, supporting diagnostic evaluation and genomic characterization in oncology and other clinical contexts. Nationally, PLA codes like 0036U matter because they represent lab-developed or proprietary tests with unique clinical utility and distinct coding and coverage considerations compared with generic or bundled genomic tests.
Key payers covered in this analysis include Aetna, Blue Cross Blue Shield, Cigna Health, UnitedHealthcare, and Medicare. Readers will find a concise summary of the code’s clinical scope, how the service is typically delivered, and the payer landscape addressed. The publication presents benchmarks where available, notes relevant policy and coverage considerations for proprietary molecular assays, and provides clinical context for WES utilization in specialty care. Data not provided in the input—such as specific coverage policies, reimbursement rates, associated taxonomies, ICD-10 pairings, and related codes—are identified as unavailable.
Billing Code Overview
CPT code 0036U is a Proprietary Laboratory Analyses (PLA) code that describes the EXaCT–1 whole exome testing performed by the Lab of Oncology–Molecular Detection, Weill Cornell Medicine–Clinical Genomics Laboratory. The test is a molecular assay that sequences the functional coding regions (exons) of the genome and is used for whole exome sequencing (WES).
Service type: Molecular diagnostic testing — whole exome sequencing (WES)
Typical site of service: Clinical molecular diagnostics laboratory; may be ordered in outpatient or inpatient clinical settings with specimen processing performed in a specialized laboratory
Clinical & Coding Specifications
Clinical Context
A typical patient is an adult or pediatric individual with a suspected genetic disorder unexplained by prior targeted testing, recurrent undiagnosed multisystem findings, or a cancer patient whose tumor or germline status requires comprehensive protein-coding region sequencing. The clinician (geneticist, oncologist, or pediatric neurologist) documents medical necessity and orders the EXaCT–1 whole exome sequencing (0036U) from the Lab of Oncology–Molecular Detection, Weill Cornell Medicine–Clinical Genomics Laboratory. The clinical workflow includes: pre-test counseling and consent, blood or saliva specimen collection at an outpatient clinic or hospital phlebotomy service, specimen shipment to the laboratory, laboratory processing with exome capture and high-throughput sequencing, bioinformatic variant calling and annotation, clinical interpretation by laboratory molecular pathologists/geneticists, and issuance of a clinical report. Post-test, the ordering clinician reviews results with the patient and documents the clinical impact on diagnosis, prognosis, or treatment selection. Typical site of service is outpatient clinics, hospital outpatient departments, or specialty genetics centers. Specimens may be collected in ambulatory phlebotomy, inpatient bedsides, or ambulatory surgery centers when relevant.
Coding Specifications
| Modifier | Description | When to Use |
|---|---|---|
00 | Default, no modifier | Rarely used on claims; indicates no special reporting modifier is appended |
11 | Office or outpatient service | Used when the ordering and specimen collection occur in an office/outpatient visit |
26 | Professional component | Applied when billing only the professional interpretation component separate from the technical testing |
TC | Technical component | Applied when billing only the laboratory technical component (sequencing and analysis) separate from interpretation |
22 | Increased procedural services | Used if unusually high laboratory interpretive effort or extensive additional analysis is documented by the laboratory |
52 | Reduced services | Used if testing was partially performed or limited compared with full EXaCT–1 assay |
53 | Discontinued procedure | Used if testing was started but discontinued for documented clinical reasons prior to completion |
62 | Two surgeons/dual physician involvement | Rare for this lab test; use if dual physician oversight is required and properly documented |
78 | Unplanned return to the operating/procedure room by the same physician | Not typical for this assay; included for completeness when applicable in perioperative genetic testing workflows |
80 | Assistant surgeon | Not typically applicable; include only if an assistant’s interpretive service is separately billed |
QX | CLIA/college of American Pathologists (CAP) compliance modifier for diagnostic lab personnel | Used when specific compliance or personnel qualifiers apply to the performing laboratory |
QY | Qualified nonphysician laboratory personnel | Used when a qualified nonphysician performs the interpretive laboratory tasks allowed under payer rules |
AD | Additional diagnostic test or service | Used when the laboratory performs an additional distinct diagnostic assay in conjunction with the EXaCT–1 |
AS | Physician assistant, nurse practitioner, or clinical nurse specialist services | Used when such clinicians provide billable professional services related to test interpretation |
| Taxonomy Code | Specialty | Notes |
|---|---|---|
207RG0100X | Medical Geneticist | Primary ordering and interpretation oversight for germline WES |
207RH0000X | Hematology/Oncology | Orders WES for tumor profiling or hereditary cancer predisposition |
208000000X | Neurology | Orders WES for neurodevelopmental or neuromuscular disorders |
208000000X | Pediatrics | Orders WES for congenital anomalies and undiagnosed pediatric disorders |
208D00000X | Pathology | Laboratory medical director and variant interpretation roles |
Related Diagnoses
| ICD-10 Code | Description | Clinical Relevance |
|---|---|---|
R62.0 | Delayed milestone in childhood | WES is commonly used for pediatric patients with global developmental delay or unexplained delays |
G40.9 | Epilepsy, unspecified | Unexplained epilepsy may prompt WES to identify genetic epilepsies |
Q87.8 | Other specified congenital malformation syndromes affecting multiple systems | Multisystem congenital anomalies often lead to WES for diagnosis |
C80.1 | Malignant neoplasm, primary site unknown | WES of tumor and/or germline can assist in identifying actionable mutations |
Z15.09 | Genetic susceptibility to other malignant neoplasms | Used when evaluating hereditary cancer predisposition with comprehensive sequencing |
Related CPT Codes
| CPT Code | Description | Relationship to This Procedure |
|---|---|---|
81161 | Exome (eg, large-scale sequencing of the coding regions of the genome) | A general CPT code for whole exome sequencing used when a PLA code is not applied; conceptually overlaps with 0036U |
81225 | BRCA1, full gene sequencing and duplication/deletion analysis | May be ordered before or instead of WES when a specific hereditary breast/ovarian cancer suspicion exists |
81416 | Targeted oncology sequence analysis panel (multiple genes) | May be ordered in parallel for focused tumor profiling or to complement exome findings |
88360 | Microscopic examination, surgical pathology; interpretation of molecular pathology results | Used when pathologist documents and interprets molecular findings in a pathology report |
99000 | Handling and/or conveyance of special services (example) | Ancillary billing for special specimen handling or courier services related to sending samples to the reference lab |