Underneath the CPT codes and billing guidelines for molecular pathology tier 1 procedures, genomic sequencing procedures, other molecular multianalyte assays and for multianalyste assays with algortitmic analyses.
Molecular Pathology Tier 1 Procedures
Any procedures required prior to cell lysis such as microdissection (CPT 88380, CPT 88381) are reported separately.
AMA instructs coders to use CPT 87149 – CPT 87153, CPT 87470 – CPT 87801, and CPT 87900 – CPT 87904 for any molecular testing done for microbial identification.
This means molecular testing for infectious agents, such as HPV are NOT reported in the molecular pathology section of the code book. You should look to the Microbiology section for those codes.
For in situ hybridization, use the CPT 88271 – CPT 88275 (when interpreted by scientist instead of pathologist) and CPT 88365-88368 when interpreted by a pathologist.
CPT Codes For Gene Specific And Genomic Procedures
The following are the CPT codes for gene-specific and genomic procedures. Molecular pathology codes include all analytical services performed in the test. This includes cell lysis, nucleic acid stabilization, extraction, digestion, amplification, and detection.
81170 CPT Code Description
CPT 81170 can be used to report ABL1 and is desribed as: ABL proto-oncogene 1, non-receptor tyrosine kinase. For example acquired imatinib tyrosine kinase inhibitor resistance. Variants in the kinase domain and gene analysis.
81162 CPT Code Description
CPT 81162 can be used to bill breast cancer 1 and 2 (BRCA1 & BRCA 2). Do not report this code in conjunction with CPT 81211, CPT 81213, CPT 81214 & CPT 81216.
The 81162 CPT code is described by the CPT manual as: breast cancer 1 and 2 (BRCA1 & BRCA2). For example hereditary breast and ovarian cancer. Gene analysis;
- full sequence analysis;
- full duplication; and/or
- full deletion analysis.
81218 CPT Code Description
CPT 81218 can be used to bill CEBPA and is described as: “CEBPA (CCAAT/enhancer binding protein [C/EBP], alpha) (for example: acute myeloid leukemia). Full gene sequence, gene analysis, .”
81219 CPT Code Description
CPT 81219 can be billed for a calreticulin (CALR) procedure and is described as:
“Calreticulin (CALR) (for example: myeloproliferative disorders). Gene analysis and common variants in exon 9.”
81272 CPT Code Description
CPT 81272 can be used for a KIT procedure and is defined as: “KIT (v-kit Hardy-Zukerman 4 feline sarcoma viral oncogene homolog).
For example: GIST (gastrointestinal stromal tumor). Melanoma, acute myeloid leukemia. Gene analysis and targeted sequence analysis. Examples are exon 8, exon 11, exon 13, exon 17 & exon 18).
81273 CPT Code Description
CPT 81273 can also be used for a KIT procedure and is defined as:
“v-kit Hardy-Zukerman 4 feline sarcoma viral oncogene homolog. For example mastocytosis). Gene analysis, D816 variant/variants.”
81276 CPT Code Description
CPT 81276 can be used for a KRAS procedure. This code is defined as:
“Kirsten rat sarcoma viral oncogene homolog. For example carcinoma gene analysis. Additional variant or variants. For example codon 146 and codon 61).”
81311 CPT Code Description
CPT 81311 can be used to bill the NRAS procedure. It is decribed as:
“Neuroblastoma RAS viral [v-ras] oncogene homolog. For example colorectal carcinoma). Gene analysis and variants in exon 3 (for example codon 61) and exon 2 (for example codons 13 & 12).”
81314 CPT Code Description
CPT 81314 can be used to report a PDGFRA procedure. This code is defined as:
“Platelet-derived growth factor receptor, alpha polypeptide. For example gastrointestinal stromal tumor [GIST]). Targeted sequence analysis (for example exon 12 and exon 18) and gene analysis.”
Genomic Sequencing Procedures And Other Molecular Multianalyte Assays
This section of genomic sequencing procedures (GSPs) are DNA or RNA sequence analysis methods that simultaneously assay multiple genes or genetic regions relevant to a clinical situation.
Most commonly referred to a “Next Gen Sequencing” (NGS) or “Massively Parallel Sequencing” (MPS) in the laboratory, are tests intended to evaluate the genetic material in totality or near totality.
CPT Codes For Genomic Sequencing Procedures
The CPT codes in this section should be used when the components of the descriptor(s) are met regardless of the technique used, unless specifically noted in the code descriptor.
The CPT codes listed below in are panels associated with various disorders where the testing is performed by genomic sequence analysis.
In each of the CPT panel codes the code descriptors define specifically what genes must be tested in that panel as well as the minimum number of genes that must be tested in order to assign that given CPT code.
If all the components are NOT performed, then you must assign code(s) in the Tier 1 or Tier 2 section or if they aren’t listed in the Tier codes, use the unlisted code
AMA provides two parenthetical statements after this introduction section:
For cytogenomic microarray analyses, see CPT 81228, CPT 81229, CPT 81405, CPT 81406.
For long QT syndrome gene analyses, see CPT 81280, CPT 81282 .
81412 CPT Code Description
CPT 81412 can be used to report Ashkenazi Jewish associated disorders. Examples are:
- Tay-Sachs disease;
- Cystic fibrosis;
- Fanconi anemia group C;
- Bloom syndrome;
- Gaucher disease;
- Canavan disease, and
- Familial dysautonomia.
Genomic sequence analysis panel must include sequencing of at least nine genes. Including:
- HEXA; and
81432 CPT Code Description
CPT 81432 can be used to bill hereditary breast cancer related disorders. Examples are:
- Hereditary ovarian cancer;
- Hereditary endometrial cancer; and
- Hereditary breast cancer.
Genomic sequence analysis panel must include sequencing of at least fourteen genes. The following are included:
- BRCA1; and
81433 CPT Code Description
CPT 81433 can be used to report Hereditary breast cancer related disorders. Examples are:
- Hereditary ovarian cancer;
- Hereditary breast cancer; and
- Hereditary endometrial cancer.
It can be used for duplication alalysis panel and deletion analysis panel. It must include analyses for:
- STK11; and
81434 CPT Code Description
CPT 81434 can be used to bill hereditary retinal disorders. Examples are:
- Leber congenital amaurosis;
- Retinitis pigmentosa; and
- Cone-rod dystrophy.
Genomic sequence analysis panel must include sequencing of at least fifteen genes, including:
- RHO; and
81437 CPT Code Description
CPT 81437 can be used for hereditary neuroendocrine tumor disorders. Examples are:
- parathyroid carcinoma;
- medullary thyroid carcinoma; or
- malignant pheochromocytoma.
Genomic sequence analysis panel must include sequencing of at least six genes, including:
- SDHC; and
81438 CPT Code Description
CPT 81438 can be used for hereditary neuroendocrine tumor disorders. Examples are:
- Parathyroid carcinoma;
- Medullary thyroid carcinoma; or
- malignant pheochromocytoma.
Deletion analysis panel or duplication analysis panel must include analyses for:
- VHL; and
81442 CPT Code Description
CPT 81442 can be used to report noonan spectrum disorders. Examples are:
- Noonan-like syndrome;
- Cardio Facio Cutaneous syndrome;
- Noonan syndrome;
- Leopard syndrome; and
- Costello syndrome.
Genomic sequenceanalysis panel must include sequencing of at least twelve genes, including:
- RIT1; and
Multianalyste Assays With Algortitmic Analyses
Multianalyte Assays with Algorithmic Analyses (MAAAs) are procedures that utilize multiple results derived from assays of various types, including molecular pathology assays, fluorescent in situ hybridization assays and nonnucleic acid based assays (eg, proteins, polypeptides, lipids, carbohydrates).
Algorithmic analysis using the results of these assays as well as other patient information, if used, is then performed and reported typically as a numeric score(s) or as a probability.
CPT Codes For Multianalyte Assays with Algorithmic Analyses
MAAAs are typically unique to a single clinical laboratory or manufacturer. The results of individual component procedure(s) that are inputs to the MAAAs may be provided on the associated laboratory report; however, these assays are not reported separately using additional codes.
For more information on these codes, please see the MAAA section of the CPT code book and Appendix O.
81490 CPT Code Description
CPT 81490 can be used to report rheumatoid arthritis (autoimmune) and is defined as:
“Prognostic algorithm reported as a disease activity score. Analysis of twelve biomarkers using immunoassays. Utilizing serum.“
Do not report CPT 81490 in conjunction with CPT 86140.
81493 CPT Code Description
CPT 81493 can be used to report coronary artery disease and is defined as:
“mRNA, utilizing whole peripheral blood. Gene expression profiling by real-time RT-PCR of 23 genes. Algorithm reported as a risk score.”
81525 CPT Code Description
CPT 81525 can be used to report oncology and is defined as:
“mRNA. Utilizing formalin-fixed paraffin-embedded tissue. Gene expression profiling by real-time RT-PCR of 12 genes. 7 content genes and 5 housekeeping genes. Algorithm reported as a recurrence score.“
81528 CPT Code Description
CPT 81528 can be used to report oncology (colorectal) screening. It is defined as:
“Quantitative real time target and signal amplification of 10 DNA markers. Utilizing stool. KRAS mutations, promoter methylation of BMP3 and NDRG4. Also fecal hemoglobin. Algorithm reported as a positive or negative result.”
Do not report CPT 81528 in conjunction with CPT 81275 and CPT 82274.
81535 CPT Code Description
CPT 81535 can be used to report oncology (gynecologic). It is defined as:
“Live tumor cell culture and chemotherapeutic response by DAPI stain and morphology. First single drug or drug combination.. Predictive algorithm reported as a drug response score.”
81536 CPT Code Description
CPT 81536 can be used as an add-on code to report oncology (gynecologic). It is defined as:
“Live tumor cell culture and chemotherapeutic response by DAPI stain and morphology. Each additional single drug or drug combination. Predictive algorithm reported as a drug response score.”
List separately in addition to code for primary procedure. Do not report CPT 81536 in conjunction with CPT 81535.
81538 CPT Code Description
CPT 81538 can be used to report oncology (lung) and is described as:
“Utilizing serum. Mass spectrometric 8-protein signature (including amyloid A). Prognostic and predictive algorithm reported as good versus poor overall survival.”
81540 CPT Code Description
CPT 81540 can be used to report oncology (tumor of unknown origin) and is defined as:
“mRNA. To classify tumor into main cancer type and subtype. Gene expression profiling by real-time RT-PCR of 92 genes. 87 content genes and 5 housekeeping genes. Algorithm reported as a probability of a predicted main cancer type and subtype. Utilizing formalin fixed paraffin embedded tissue.”
81545 CPT Code Description
CPT 81545 can be used to report oncology (thyroid) and is defined as:
“Utilizing fine needle aspirate. Gene expression analysis of 142 genes. Agorithm reported as a categorical result. For example (eg, suspicious or benign.
81595 CPT Code Description
CPt 81595 can be used for cardiology (heart transplant) and is defined as:
“mRNA. Utilizing subfraction of peripheral blood. Gene expression profiling by real-time quantitative PCR of 20 genes. 11 content genes and 9 housekeeping genes. Algorithm reported as a rejection risk score.”
0009M CPT Code Description
CPT 0009M can be used for fetal aneuploidy trisomy 18 and trisomy 21. It is defined as:
“Algorithm reported as a risk score for each trisomy. DNA sequence analysis of selected regions using maternal plasma.”
0010M CPT Code Description
CPT 0010M can be used to report oncology (high grade prostate cancer). It is defined as:
“Prognostic algorithm reported as a probability score. Biochemical assay of four proteins, including:
- Intact PSA;
- Free PSA;
- human kallikrein 2 [hK2]; and
- Total PSA.
Digital rectal examination status. Plus patient age. Utilizing plasma and no history of positive prostate biopsy.
Surgical Pathology (Immunofluorescence Stains)
Note in the parenthetical that the AMA specifically states to not report CPT 88346 and CPT 88350 when the stain performed is a multiplex immunofluorescence stain(s)… it directs to the coder to assign the miscellaneous code CPT 88399.
Note that CPT 88350 has a + sign denoting an add-on code and can only be billed when CPT 88346 is also billed.
88350 CPT Code Description
CPT 88350 is an add-on code for immunofluorescence stains. This code represents any additional stains that are performed above the initial first stain which is assigned CPT 88346.
The “unit of service” is defined as each additional “single antibody stain procedure” from that designated specimen.
It is not solely each additional stain performed, it has to be a separate stain procedure for that given stain, hence the descriptor “single antibody stain procedure.”
It is defined as: “Immunofluoroscence. Per specimen; each additional single antibody stain procedure.”
List the 88350 addon code separately in addition to code for primary procedure. Report CPT 88350 in conjunction with CPT 88346.
Do not report CPT 88346 and CPT 88350 for fluorescent in situ hybridization studies, see CPT 88364, CPT 88365, CPT 88366, CPT 88367, CPT 88368, CPT 88369, CPT 88373, CPT 88374, and CPT 88377.
Do not report CPT 88346 and v 88350 for multiplex immunofluorescence analysis, use CPT 88399.