[Date]
[Medicare Administrative Contractor (MAC) Name]
[Address]
[City, State, Zip code]
RE:
Accurate Gapfilling for Cytogenomic Microarray Analysis under the 2013 Clinical Laboratory
Fee Schedule (CLFS)
Dear Sir/Madam,
On November 6, 2012, the Centers for Medicare and Medicaid Services (CMS) announced that the Tier 1
and Tier 2 molecular pathology (MoPath) CPT®1 codes (81201-81408) will be gapfilled for Medicare
reimbursement under the Clinical Laboratory Fee Schedule (CLFS) in 2013. This includes the following
Tier 1 codes for cytogenomic microarray analysis:
81228 Cytogenomic constitutional (genome-wide) microarray analysis; interrogation of
genomic regions for copy number variants (e.g., Bacterial Artificial Chromosome [BAC] or
oligo-based comparative genomic hybridization [CGH] microarray analysis)
81229 Interrogation of genomic regions for copy number and single nucleotide
polymorphism (SNP) variants for chromosomal abnormalities
These codes are differentiated by the types of genetic variants interrogated – CPT 81228 describes the
use of oligonucleotide probes to detect copy number variants (CNVs), whereas CPT 81229 describes the
former in addition to the use of single nucleotide polymorphism (SNP) probes to determine zygosity
status.
The following clinical vignettes issued by the American Medical Association (AMA) provide examples of
common patient scenarios in which each type of test/code may be performed/billed2:
CPT
Clinical Vignette
81228 An 18-month–old male presents to his physician with unexplained developmental delay. The
patient has a normal karyotype and his diagnostic evaluation is otherwise unrevealing. A
sample of anticoagulated peripheral blood is submitted to the laboratory for cytogenomic
constitutional (genome-wide) microarray analysis.
81229 A newborn female is determined to have multiple congenital anomalies by the attending
physician. The patient has a normal karyotype and her diagnostic evaluation is otherwise
unrevealing. The parents indicate they are both from the same ethnic background.
A sample of anticoagulated peripheral blood is submitted to the laboratory for cytogenomic
constitutional (genome-wide) microarray analysis.
1
CPT is a registered trademark of the American Medical Association. ©2012 American Medical Association. All
rights reserved.
2
© American Medical Association 2011. All rights reserved.
While cytogenomic microarray analysis is not a high-volume test within the Medicare patient
population, Medicare payment determinations are influential and often used as a benchmark by other
payers in developing rates for new CPT codes. Therefore, it is critical that [MAC Name] utilizes the
appropriate information and inputs in the gapfiiling process in order to derive accurate payment rates
for these codes.
Background on Cytogenomic Microarray Analysis
Cytogenomic microarray analysis (CMA) can be used to identify large structural variations throughout an
individual’s genome, including single nucleotide polymorphisms (SNPs) and copy number variations
(CNVs) that are linked to genetic disorders.
The American College of Medical Genetics (ACMG) guidelines recommend CMA testing for CNV as a
first-line test in the initial post-natal evaluation of individuals with the following multiple anomalies not
specific to a well-delineated genetic syndrome, apparently nonsyndromic developmental delay and/or
intellectual disability, or autism spectrum disorders3.
Supporting the Gapfilling Process for Cytogenomic Microarray Analysis
To ensure that [MAC Name] has the necessary information to make accurate payment determinations
for CPT codes 81228–81229, [Lab Name] is providing the following materials that reflect our own
experience in providing these tests (please see enclosed):
[Select only the materials that will be provided to the MAC]

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Submitted charges and routine discounts to charges
Analysis of the costs of resources required to perform the test
Payment rates provided by other payers [specify which payers]
Previously billed CPT code stacks
Although we are glad to share this information with [MAC Name] to support the gap-filling process, we
would like to request that it be kept strictly confidential at this time.
[Lab Name] believes that inaccurate rate setting for the cytogenomic microarray analysis codes under
the Medicare gapfilling process could lead to similarly inaccurate rates being set by Medicaid and other
payers, which would ultimately impede patient access to this medically necessary service. Therefore, we
ask that [MAC Name] consider the information provided here and adopt an appropriate methodology
that will ensure accurate payment rates for these codes.
3
Manning M, Hudgins L, Professional Practice and Guidelines Committee. Array-based technology and
recommendations for utilization in medical genetics practice for detection of chromosomal abnormalities. Genet
Med 2010; 12:742.
In summary:


Although cytogenomic microarray analysis is not ordered in high volumes for Medicare patients,
the outcome of Medicare gapfilling for the relevant CPT codes is likely to influence Medicaid and
private payer rate-setting as well.
Therefore, accurate Medicare rate setting for CPT 81228–81229 will be critical to ensuring
sustainable reimbursement by other payers, and therefore continued patient access to
cytogenomic microarray analysis when medically necessary.
[Lab Name] appreciates the opportunity to submit this information to [MAC Name] to support the gapfilling process for CPT codes 81228–81229, and will be glad to assist if any questions arise.
Yours sincerely,
[Name]
[Title]
[Phone Number]
[Email Address]