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Brief Your Billing & Coding Staff on New Medicare HCPCS & CLIA Code Changes

by | May 17, 2023

To avoid claims denials and improper billings, ensure billing and coding staff is aware of, and has adjusted to, all recent coding changes.

Several significant coding changes in the Healthcare Common Procedure Coding System (HCPCS) and Clinical Laboratory Improvement Amendments (CLIA) that may affect your Medicare reimbursements have taken effect since the start of 2022. To avoid claims denials and improper billings, lab compliance officers and managers need to ensure billing and coding staff is aware of, and has adjusted to, all recent coding changes. These changes are summarized in the Centers for Medicare & Medicaid Services (CMS) transmittal, “HCPCS Codes & Clinical Laboratory Improvement Amendments Edits: April 2023, MLN Matters Number: MM13024.”1 Here’s a quick briefing of all the essential changes that you can share with your billing staff:

What’s At Stake

Under CLIA regulations, labs must be appropriately certified for each test they perform. CMS edits each claim for a test that’s considered a CLIA laboratory test for a HCPCS code at the lab’s CLIA certificate level to ensure that Medicare pays only for lab tests that are performed in appropriately certified facilities. If the HCPCS code is for a test that’s not appropriate for the lab of that CLIA certification level to perform, the edit will reject the claim.

Discontinued HCPCS Codes

The new CMS MM13024 transmittal lists HCPCS codes that have recently been discontinued and should no longer be used.

Discontinued HCPCS Codes

HCPCS CodeDate of DiscontinuanceTest
0097UMarch 31, 2022Test for detection of gastrointestinal disease-causing organism using amplified probe
0151UMarch 31, 2022Test for detection of respiratory disease-causing organisms in sputum or respiratory tract specimen, 33 target organismal and antibiotic resistance
0012USeptember 30, 2022Gene analysis for germline disorder
0013USeptember 30, 2022Gene analysis of solid organ tumor tissue
0014USeptember 30, 2022DNA test for detecting gene abnormality associated with blood and lymphatic system cancer in blood or bone marrow
0056USeptember 30, 2022Whole genome sequencing in blood or bone marrow for acute myelogenous leukemia

New HCPCS Codes

MM13024 also lists new HCPCS codes that are subject to CLIA edits. According to CMS, for these HCPCS code tests to be payable by Medicare, the lab must have one of the following:

  • CLIA certificate of registration (certificate type code 9)
  • CLIA certificate of compliance (certificate type code 1)
  • CLIA certificate of accreditation (certificate type code 3)

New HCPCS Codes Subject to CLIA Edits

HCPCS CodeDate of AdditionTest
87913February 21, 2022Genotype analysis of severe acute respiratory syndrome coronavirus 2 (COVID-19) by nucleic acid (DNA or RNA) for identification of mutations in targeted regions
0306UApril 1, 2022Initial baseline gene analysis for minimal residual disease in cancer, next-generation targeted sequencing analysis of cell-free DNA, to determine patient-specific panel for future comparisons
0307UApril 1, 2022Subsequent gene analysis for minimal residual disease in cancer, next-generation targeted sequencing analysis of cell-free DNA, to determine patient-specific panel for future comparisons
0308UApril 1, 2022Analysis of three proteins (high sensitivity [hs] troponin, adiponectin, and kidney injury molecule-1 [KIM-1]) in plasma specimen, algorithm reported as risk score for obstructive coronary artery disease
0309UApril 1, 2022Analysis of four proteins (NT-proBNP, osteopontin, tissue inhibitor of metalloproteinase-1 [TIMP-1], and kidney injury molecule-1 [KIM-1]) in plasma specimen, algorithm reported as risk score for major adverse heart event
0310UApril 1, 2022Analysis of three biomarkers (NT-proBNP, C-reactive protein, and T-uptake) for Kawasaki disease (KD) in plasma specimen, algorithm reported as risk score for KD
0311UApril 1, 2022Measurement of bacterial susceptibility to antibiotics, reported as phenotypic minimum inhibitory concentration (MIC) for each organism identified
0312UApril 1, 2022Analysis of eight IgG autoantibodies and two cell-bound complement activation products associated with autoimmune disease, using enzyme-linked immunosorbent immunoassay (ELISA), flow cytometry, and indirect immunofluorescence in serum specimen or plasma and whole blood specimen, individual components reported along with algorithmic systemic lupus erythematosus-likelihood assessment
0313UApril 1, 2022DNA and mRNA next-generation sequencing (NGS) analysis of 74 genes and analysis of CEA (CEACAM5) gene expression in pancreatic cyst fluid specimen, algorithm reported as negative, low probability of cancer of pancreas, or positive with high probability of cancer of pancreas
0314UApril 1, 2022mRNA gene expression profiling by real-time polymerase chain reaction (RT-PCR) of 35 genes (32 content and 3 housekeeping) associated with melanoma of skin in formalin-fixed paraffin-embedded (FFPE) tissue specimen, algorithm reported as benign, intermediate, or malignant
0315UApril 1, 2022mRNA gene expression profiling by real-time polymerase chain reaction (RT-PCR) of 40 genes (34 content and 6 housekeeping) associated with squamous cell carcinoma of skin in formalin-fixed paraffin-embedded (FFPE) tissue specimen, algorithm reported as benign, intermediate, or malignant
0316UApril 1, 2022Evaluation of outer surface protein A (OspA) of Borrelia burgdorferi (Lyme disease) in urine specimen
0317UApril 1, 2022Four-probe fluorescence in situ hybridization (FISH) (3q29, 3p22.1, 10q22.3,10cen) assay of whole blood specimen, predictive algorithm-generated evaluation reported as decreased or increased risk for lung cancer
0318UApril 1, 2022Whole genome methylation analysis by microarray for 50 or more genes associated with congenital epigenetic disorders in blood specimen
0319UApril 1, 2022RNA gene expression profiling by select transcriptome sequencing in peripheral blood specimen taken before kidney transplant, algorithm reported as risk score for early acute rejection
0320UApril 1, 2022RNA gene expression profiling by select transcriptome sequencing in peripheral blood specimen taken after kidney transplant, algorithm reported as risk score for acute cellular rejection
0321UApril 1, 2022Detection test by nucleic acid (DNA or RNA) multiplex amplified probe technique for identification of 20 bacterial and fungal organisms associated with genital or urinary tract infection and identification of 16 associated antibiotic-resistance genes
0322UApril 1, 2022Measurement of 14 acyl carnitines and microbiome-derived metabolites associated with autism spectrum disorders by liquid chromatography with tandem mass spectrometry (LC-MS/MS) in plasma specimen, results reported as negative or positive for risk of metabolic subtypes associated with autism spectrum disorders
0323UJuly 1, 2022DNA and mRNA next-generation sequencing (NGS) analysis in cerebrospinal fluid specimen for detection of organisms causing disease in central nervous system
0324UJuly 1, 2022Culture of spheroid ovarian cancer cells for evaluation of four drugs (carboplatin, doxorubicin, gemcitabine, paclitaxel), result reported as tumor chemotherapy response prediction for each drug
0325UJuly 1, 2022Culture of spheroid ovarian cancer cells for evaluation of poly (ADP-ribose) polymerase (PARP) inhibitors (niraparib, olaparib, rucaparib, velparib), result reported as tumor chemotherapy response prediction for each drug
0326UJuly 1, 2022Targeted genomic sequence analysis of 83 or more genes in cell-free circulating DNA for detection of abnormalities associated with solid organ cancers
0327UJuly 1, 2022DNA sequence analysis of selected regions for detection of abnormal fetal chromosome number (trisomy 13, 18, and 21) in maternal plasma specimen, algorithm reported as risk score for each trisomy, includes sex reporting, if performed
0328UJuly 1, 2022Definitive drug testing for 120 or more drugs and metabolites in urine specimen
0329UJuly 1, 2022Exome and transcriptome sequence analysis of DNA and RNA from tumor with DNA from normal blood or saliva for subtraction, report of clinically significant mutations with therapy associations
0330UJuly 1, 2022Amplified nucleic acid probe for identification of 27 vaginal disease agents in vaginal swab specimen
0331UJuly 1, 2022Optical genome mapping of DNA from blood or bone marrow specimen, report of clinically significant alterations associated with blood or lymph system cancers
87593July 26, 2022Infectious agent detection by nucleic acid (DNA or RNA) of orthopoxvirus (e.g., monkeypox virus, cowpox virus, vaccinia virus), amplified probe technique, each
0332UOctober 1, 2022Genetic profiling of eight epigenetic markers to evaluate probability of responding to immune checkpoint-inhibitor therapy for cancer
0333UOctober 1, 2022Surveillance for liver cancer in high-risk patients using algorithm
0334UOctober 1, 2022Targeted genomic sequence analysis of 84 or more genes for detection of abnormalities associated with cancer of body organ
0335UOctober 1, 2022Whole genome sequence analysis of fetal sample for detection of abnormalities associated with rare constitutional/heritable diseases
0336UOctober 1, 2022Whole genome sequence analysis of comparator genome (parent) for detection of abnormalities associated with rare constitutional/heritable diseases
0337UOctober 1, 2022Evaluation of plasma cells for detection of abnormalities associated with plasma cell disorders and myeloma
0338UOctober 1, 2022Evaluation of circulating solid tumor cells in peripheral blood
0339UOctober 1, 2022mRNA expression profiling of genes associated with high-grade prostate cancer
0340UOctober 1, 2022DNA assays for detection of minimal residual disease in cancer
0341UOctober 1, 2022Fetal DNA sequencing of products of conception for detection of abnormal chromosome number
0342UOctober 1, 2022Multiplex immunoassay for markers of pancreatic cancer in serum
0343UOctober 1, 2022Exosome-based analysis of 442 small noncoding RNAs in urine to evaluate risk of prostate cancer
0344UOctober 1, 2022Evaluation of 28 lipid markers for risk of nonalcoholic fatty liver disease
0345UOctober 1, 2022Genomic analysis panel of 15 genes for detection of abnormalities associated with mental health disorders
0346UOctober 1, 2022Evaluation of beta-amyloid AB40 and AB42 ratio
0347UOctober 1, 2022DNA analysis of 16 genes involved in drug metabolism or processing
0348UOctober 1, 2022DNA analysis of 25 genes involved in drug metabolism or processing
0349UOctober 1, 2022DNA analysis of 27 genes involved in drug metabolism or processing, report including gene-drug interactions
0350UOctober 1, 2022DNA analysis of 27 genes involved in drug metabolism or processing, analysis and reported phenotypes
0351UOctober 1, 2022Biochemical assays for markers of bacterial infection
0352UOctober 1, 2022Detection of bacteria causing vaginosis and vaginitis by multiplex amplified nucleic acid probe technique
0353UOctober 1, 2022Detection of Chlamydia trachomatis and Neisseria gonorrhoeae by multiplex amplified DNA probe technique
0354UOctober 1, 2022Human papillomavirus (HPV) by quantitative polymerase chain reaction (qPCR)
0355UJanuary 1, 2023APOL1 (apolipoprotein L1) (e.g., chronic kidney disease), risk variants (G1, G2)
0356UJanuary 1, 2023Oncology (oropharyngeal), evaluation of 17 DNA biomarkers using droplet digital PCR (ddPCR) and cell-free DNA, algorithm reported as a prognostic risk score for cancer recurrence
0357UJanuary 1, 2023Oncology (melanoma), artificial intelligence (AI)-enabled quantitative mass spectrometry analysis of 142 unique pairs of glycopeptide and product fragments, plasma, prognostic, and predictive algorithm reported as likely, unlikely, or uncertain benefit from immunotherapy agents
0358UJanuary 1, 2023Neurology (mild cognitive impairment), analysis of β-amyloid 1-42 and 1-40, chemiluminescence enzyme immunoassay, cerebral spinal fluid, reported as positive, likely positive, or negative
0359UJanuary 1, 2023Oncology (prostate cancer), analysis of all prostate-specific antigen (PSA) structural isoforms by phase separation and immunoassay, plasma, algorithm reports risk of cancer
0360UJanuary 1, 2023Oncology (lung), enzyme-linked immunosorbent assay (ELISA) of seven autoantibodies (p53, NY-ESO-1, CAGE, GBU4-5, SOX2, MAGE A4, and HuD), plasma, algorithm reported as a categorical result for risk of malignancy
0361UJanuary 1, 2023Neurofilament light chain, digital immunoassay, plasma, quantitative
0362UJanuary 1, 2023Oncology (papillary thyroid cancer), gene-expression profiling via targeted hybrid capture-enrichment RNA sequencing of 82 content genes and 10 housekeeping genes, formalin-fixed paraffin embedded (FFPE) tissue, algorithm reported as one of three molecular subtypes
0363UJanuary 1, 2023Oncology (urothelial), mRNA, gene expression profiling by real-time quantitative PCR of five genes (MDK, HOXA13, CDC2 [CDK1], IGFBP5, and CXCR22), utilizing urine, algorithm incorporates age, sex, smoking history, and macrohematuria frequency, reported as a risk score for urothelial carcinoma
81418January 1, 2023Genomic sequence analysis panel of at least six genes associated with drug metabolism
81441January 1, 2023Gene sequence analysis panel of at least 30 genes associated with inherited bone marrow failure syndromes
81449January 1, 2023Targeted genomic sequence analysis panel of RNA of five-50 genes associated with solid organ neoplasm
81451January 1, 2023Targeted genomic sequence analysis panel of RNA of five-50 genes associated with blood and lymphatic system disorders
81456January 1, 2023Targeted genomic sequence analysis panel of RNA of 51 or greater genes associated with blood and lymphatic system disorders
84433January 1, 2023Evaluation of thiopurine S-methyltransferase (TPMT)
87467January 1, 2023Measurement of Hepatitis B surface antigen (HBsAg)
87468January 1, 2023Detection of Anaplasma phagocytophilum by amplified nucleic acid probe technique
87469January 1, 2023Detection of Babesia microtim by amplified nucleic acid probe technique
87478January 1, 2023Detection of Borrelia miyamotoi by amplified nucleic acid probe technique
87484January 1, 2023Detection of Ehrlichia chaffeensis by amplified nucleic acid probe technique

Takeaway

The lists don’t include new HCPCS codes for waived tests or provider-performed microscopy procedures. Rule: The listed tests aren’t payable to a facility that doesn’t have a valid, current, CLIA certificate, or that only has a current CLIA certificate of waiver (certificate type code 2) or a current CLIA certificate for provider-performed microscopy procedures (certificate type code 4). Exception: A facility with a current certificate type code 2 or 4 may be paid if it bills the appropriate HCPCS service code with a QW modifier.

Bottom Line: It’s up to you to ensure that the HCPCS codes you’ve billed to Medicare since February 2022 are in line with your CLIA certification. CMS notes that Medicare Administrative Contractors (MACs) won’t search their files either to retract payment for claims already paid, or to pay claims retroactively. However, MACs will adjust any claims that you bring to their attention.

References:

  1. https://www.cms.gov/files/document/mm13024-hcpcs-codes-clinical-laboratory-improvement-amendments-edits-april-2023.pdf

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