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Constitutional SNP Array Karyotyping, Constitutional Chromosome Microarray Analysis (CMA)

Microarray, genetic, array, SNP, GSNPC

Test Codes

EPIC: LAB6768

Department

Cytogenetics

Instructions

Test Limitations
CMA cannot detect:

1. Balanced chromosome rearrangements such as translocations, balanced insertions, or inversions.
2. Low-level mosaicism.
3. An abnormality in a region not represented on the array.

Specimen Collection Criteria

Collect: One Dark Green-top Sodium Heparin tube and one Lavender-top EDTA tube. (Minimum: 3.0 mL each tube)

Gently invert tubes to mix specimen.  

NOTE: A copy of the completed requisition must accompany the specimen which must include patient name, date of birth, requesting physician, clinical indication, test requested, and specimen source.

Physician Office/Draw Specimen Preparation

Do not freeze specimen. Store peripheral blood at room temperature (20-26°C or 68-78.8°F) prior to courier pickup. For delays in transport (greater than 24 hours from the time of collection), refrigerate (2-8°C or 36-46°F) the specimen.

Preparation for Courier Transport

Transport: One dark green-top sodium heparin tube and one lavender-top EDTA tube (Minimum: 3.0-6.0 ml each tube) at room temperature (20-26°C or 68-78.8°F).

Rejection Criteria

• Improperly labeled specimens.
• Frozen specimens.
• Cracked or compromised specimen tubes.
• Specimens received greater than 4 days past the time of collection.

In-Lab Processing

Specimens are processed immediately upon receipt in the Laboratory.

Storage

Specimen Stability for Testing:

Room Temperature (20-26°C or 68-78.8°F): 24 hours 
Refrigerated (2-8°C or 36-46°F): 72 hours
Frozen (-20°C/-4°F or below): Unacceptable

Specimen Storage in Department Prior to Disposal:

Refrigerated (2-8°C or 36-46°F): 7 days. Extracted DNA is maintained for one year.

Laboratory

Royal Oak Cytogenetics Laboratory

Performed

Monday – Friday, 8:00 am – 5:00 pm.
Results are available 10-14 days after the laboratory receives insurance pre-authorization. Additional time may be needed for reflex testing of abnormal results.

Reference Range

Positive or negative for chromosome abnormality. A comprehensive interpretative report will be provided.

Test Methodology

Affymetrix CytoScan® HD Single Nucleotide Polymorphism (SNP) Array.

Clinical Utility

Moderate to severe mental retardation occurs in approximately 1% of the population and has many causes, with one third to one-half of cases being idiopathic. Unbalanced chromosome abnormalities are the most common cause of mental retardation, accounting for approximately 10% of cases; however, the ability of traditional karyotype analysis and fluorescence in situ hybridization (FISH) to identify a pathogenetic chromosome abnormality is limited by the band resolution achieved in the study and by the need for some clinical information to choose the proper FISH probes to utilize. Since the resolution of conventional cytogenetic analysis is 5-10Mb (5-10 million base pairs), any rearrangement smaller than this would be missed. In addition to mental retardation and developmental delay, unbalanced chromosome abnormalities and aneuploidy are also identified in patients with autism/autism spectrum disorder, dysmorphic features, and multiple congenital anomalies. Chromosome microarray analysis (CMA) utilizes a “DNA chip” that provides a genome-wide assessment of copy number changes (deletions and duplications) at a resolution far greater than what is achievable with other cytogenetic methodologies. At Beaumont, this test utilizes the Affymetrix CytoScan HD single nucleotide polymorphism (SNP) array that provides the broadest coverage and highest performance for detecting constitutional chromosome abnormalities. CytoScan HD Array has greater than 99 percent sensitivity and can reliably detect 25-50 kb copy number changes across the genome. With more than two million copy number markers (akin to performing over two million simultaneous FISH experiments), including 750,000 SNPs, the Beaumont CytoScan Array offers high-density resolution of the entire genome, extending throughout promoter and miRNA regions for relevant aberration detection and reporting. The Beaumont SNP array can also provide genotype information that allows for detection of copy number neutral aberrations such as uniparental disomy and consanguinity which can provide evidence for candidate recessive disorders. SNP array analysis is similar to the previously offered oligonucleotide array; however, it has comparatively superior sensitivity with resolution as good as 880 base pairs between each marker. The Beaumont experience with CMA has demonstrated a pathogenetic copy number in over 20% of the nearly 400 children tested since 2008, many of whom had a previously "normal" karyotype. In addition to intellectual disability, CMA has been shown to detect a submicroscopic rearrangement in 7% of children with nonsyndromic autism, 27% of children with syndromic autism spectrum disorder, and 17% of neonates with birth defects. Thus, SNP chromosome microarray analysis should be considered as a front-line test to evaluate patients with a suspected genetic disorder.

Reference

1. Moeschler JB et al (2014).  Pediatrics 134(3): e903-e918.
2. Li MM and Andersson HC (2009):  J Pediatrics 155(3); 311-317.
3. Marshall CR et al (2008): Am J Hum Genet 82, 477-488.
4. Shevell MI et al (2008): AM J Med Genet 147B: 1101-1108.
5. Lu XY et al (2008): Pediatrics 122: 1310-1318; Sagoo GS et al (2009): Genet Med 11(3): 139-146.

CPT Codes

81229

NOTE: This test requires insurance preauthorization. The Laboratory will not accept the specimen without preauthorization. Also note that CMA is generally performed in the outpatient setting.

Contacts

Last Updated

12/30/2022