CPT 0046U: FLT3 ITD MRD by NGS Assay

Headline: New CPT code 0046U designates a proprietary NGS assay for FLT3 ITD MRD monitoring

Lead: CPT code 0046U identifies a Proprietary Laboratory Analyses (PLA) next-generation sequencing assay — the FLT3 internal tandem duplication (ITD) minimal residual disease (MRD) test developed and marketed by LabPMM LLC, an Invivoscribe Technologies, Inc. company. The test detects FLT3-ITD variants to inform disease monitoring and treatment decisions in hematologic malignancies such as acute myeloid leukemia. Nationally, molecular MRD testing is a growing component of precision oncology and hematology care.

Why it matters: A PLA CPT code signals a single-manufacturer laboratory test with a unique billing identifier, simplifying claims submission and tracking for payers and providers. The code supports consistent documentation of a clinically significant NGS assay used for MRD detection.

Key payers covered: Aetna, Blue Cross Blue Shield, Cigna Health, UnitedHealthcare, and Medicare.

What readers will learn: The publication provides benchmarks for code adoption and coverage patterns, a summary of payer policies and reimbursement considerations, clinical context for FLT3-ITD MRD testing by NGS, and coding guidance for laboratory billing teams. It also outlines common modifiers and considerations for technical and professional components where applicable.

Data notes: Data not available in the input for associated taxonomies, ICD-10 diagnoses, related codes, and detailed payer-specific policy language.

Billing Code Overview

CPT code 0046U is a Proprietary Laboratory Analyses (PLA) code for the FLT3 ITD MRD by NGS test performed by LabPMM LLC, an Invivoscribe Technologies, Inc. Company. The test detects internal tandem duplication (ITD) variants in the fms–related tyrosine kinase 3 (FLT3) gene to determine the presence of minimal residual disease (MRD), commonly used in monitoring conditions such as acute myeloid leukemia.

The service type is a molecular diagnostic next-generation sequencing (NGS) assay performed by a clinical molecular laboratory. The typical site of service is a clinical reference laboratory or specialized molecular diagnostics laboratory where trained laboratory analysts conduct the technical assay and report results to the ordering clinician.

Clinical Context

A 52-year-old patient with a history of acute myeloid leukemia (AML) in apparent morphologic remission presents for molecular surveillance following induction and consolidation therapy. The treating hematologist/oncologist orders a peripheral blood or bone marrow assay to detect minimal residual disease (MRD) targeting FLT3 internal tandem duplication (ITD) variants using a next-generation sequencing (NGS) assay. The specimen is collected in the outpatient infusion center or inpatient hematology unit and sent to LabPMM LLC (an Invivoscribe Technologies, Inc., Company). The laboratory performs the technical FLT3 ITD MRD by NGS test to detect and quantify FLT3 ITD alleles, producing results used by the clinician to guide prognosis, decisions about additional therapy (for example targeted therapy or stem cell transplant planning), and interval surveillance. Typical workflow steps: specimen collection and accessioning, DNA extraction, NGS library preparation and sequencing, bioinformatic analysis for FLT3 ITD detection, laboratory analyst review and technical reporting, and transmission of results to the ordering hematologist/oncologist. Typical sites of service are hospital inpatient labs, hospital outpatient labs, and independent clinical reference laboratories performing specialized molecular pathology testing.

Coding Specifications

Modifier	Description	When to Use
`26`	Professional component	Use when billing only the professional interpretation component for services when applicable (if separate professional component exists).

Taxonomy Code	Specialty	Notes
207RH0000X	Hematology & Oncology	Hematologists/oncologists order MRD testing and interpret results in context of AML management.
208M00000X	Pathology	Molecular pathology and clinical laboratory pathologists oversee validation and interpretation of molecular assays.
171M00000X	Molecular Genetic Pathology	Specialists who direct NGS-based molecular diagnostic testing and sign out reports.
208000000X	Clinical Pathology	Clinical pathologists who manage laboratory operations and quality assurance for high-complexity testing.

Related Diagnoses

ICD-10 Code	Description	Clinical Relevance
`C92.0`	Acute myeloblastic leukemia with minimal differentiation	AML subtypes with FLT3 ITD mutations can be monitored with FLT3 MRD testing.
`C92.01`	Acute myeloblastic leukemia with maturation	Used when FLT3 ITD MRD testing is needed for disease surveillance in this AML variant.
`C92.02`	Acute myeloblastic leukemia without mention of maturation	FLT3 mutation testing informs prognosis and MRD status.
`C92.10`	Acute myelomonocytic leukemia, not having remission	MRD testing may be performed during or after therapy to assess residual disease.
`D46.9`	Myelodysplastic syndrome, unspecified	When progression or transformation to AML is suspected, FLT3 MRD testing may be ordered.

Related CPT Codes

CPT Code	Description	Relationship to This Procedure
`0046U`	FLT3 ITD MRD by NGS (Proprietary Laboratory Analyses, specific to LabPMM LLC/Invivoscribe)	Primary code reported for the laboratory assay detecting FLT3 ITD variants for MRD assessment.
`81479`	Unlisted molecular pathology procedure	Used in rare cases for reporting molecular tests not otherwise specified by a PLA code, though `0046U` is the specific PLA code for this assay.
`88305`	Level IV surgical pathology, gross and microscopic exam (not typically used for molecular testing)	May be used if a concurrent morphologic bone marrow biopsy interpretation is billed by a pathologist alongside molecular MRD testing.
`81206`	KRAS gene analysis (example molecular test)	Representative of other gene mutation assays that may be ordered alongside FLT3 testing for comprehensive molecular profiling.
`81403`	Exome or targeted sequencing panel (tiered molecular panel code)	Used when broader NGS panels are performed that include FLT3 among multiple genes; indicates relationship when testing is performed as part of multi-gene panels.

OpenPayer

Summary & Overview