Constitutional Chromosomal Microarray Analysis — Peripheral Blood and Buccal Swab

CPT Code(s): 81229

Service Code (IU Health): 53024030

Ordering Recommendation: Detection of submicroscopic chromosomal genetic imbalances and identification of cryptic deletions and/or duplications beyond the resolution of conventional karyotyping. Utilized as a first-tier test for unexplained developmental delay and autism spectrum disorder as well as multiple congenital anomalies that do not fall into a syndromic category.

Synonyms: CMA, Constitutional, CGH, SNP, Microarray

Methodology: Cytogenomic SNP microarray.

Performed: Monday through Friday

Reported: 10-14 days

Patient Preparation: None

Collect:

• Whole blood: (1) Green (Sodium Heparin) and (1) Lavender (EDTA).
• ORAcollect®-Dx, OCD-100. Follow kit instructions for collection. No eating or drinking for 30 minutes prior to collection. Buccal collection kits will be provided on request. Please call or email Kristen (317-274- 2243, klbennet@iu.edu) or Ronae (317-278-6528, rdw2@iu.edu) for assistance.

Specimen Volume:

• Blood: 3-5 mL (Green) and 3-5 mL (Lavender); for infants, 1 mL minimum (Lavender).
• Or buccal swab collection vial.

Storage/Transport: Room temperature. Do not freeze or expose to extreme temperatures.

Unacceptable Conditions: Frozen specimens. Clotted specimens.

Stability: Ambient: 48 hours; Refrigerated: 48 hours; Frozen: Unacceptable.

Characteristics:  Chromosomal microarray (CMA) analysis is a molecular cytogenetic technique that essentially scans the entire genome for gains and losses of genetic material. CMA is performed using the CytoScan™ HD microarray platform (ThermoFisher) with approximately 1.9 million non-polymorphic copy number probes and 743,000 single nucleotide polymorphism (SNP) probes. Each probe is designed to provide copy number information on a specific segment of the genome and/or SNP genotyping information. The aggregate of information supplied by each individual probe on the array enables genome-wide evaluation of copy number changes for thousands of genes simultaneously in just one test. The presence of SNP probes enables detection of long contiguous stretches of copy-neutral absence-of-heterozygosity (CNAOH) that may indicate uniparental isodisomy (UPD) or regions of the genome identical by descent. Accurate identification, assessment, and correlation of copy number variants (CNVs) with clinical phenotypes and disease requires significant expertise in a clinical genetics setting. 

Clinical sensitivity: CMA testing has been shown to detect genetic aberrations in 10-15% of individuals with unexplained intellectual disability, multiple congenital anomalies, or autism spectrum disorder.

Limitations: Does not detect balanced rearrangements such as translocations, insertions or inversions, single base pair mutations, very small deletions/duplications, or rearrangements of the mitochondrial genome. Low-level mosaicism may not be detected. Although detection of a large contiguous stretch of CN-AOH by this assay suggests UPD, further molecular analysis is necessary for UPD confirmation and determination of parent of origin. Failure to detect CN-AOH by this assay does not exclude the possibility of UPD. The observation of large contiguous regions of CN-AOH across multiple chromosomes encompassing more than 10% of the genome suggests a potential consanguineous relationship between the proband's parents. This assay is not designed to be a paternity test and should not be used definitively to assign a specific relationship between the parents of the proband.

Properly collected buccal swabs are an acceptable source of DNA and offer a simple and noninvasive alternative to a needle stick. However, buccal swabs are subject to greater variability in DNA quality and quantity than a traditional blood draw. For more consistent results, we prefer, whenever appropriate, to use peripheral blood as the source of DNA for CMA analysis. Note that FISH studies cannot be performed on buccal swab specimens. 

References:

1. Miller DT et al. Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet 2010 May 14;86(5):749-764

2. Manning M et al. 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(11):742-745

3. Kearney HM et al. Working Group of the American College of Medical Genetics Laboratory Quality Assurance Committee American College of Medical Genetics standards and guidelines for interpretation and reporting of postnatal constitutional copy number variants. Genet Med 2011;13(7):680-685

4. Kearney HM et al. Diagnostic implications of excessive homozygosity detected by SNP-based microarrays: consanguinity, uniparental disomy, and recessive single-gene mutations. Clin Lab Med 2011;31(4):595-613