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Pediatric and Adult (Postnatal) SNP Microarray and 5 Cell Chromosome Analysis

Single nucleotide polymorphism (SNP) based chromosomal microarray (CMA) is a powerful cytogenomic tool for detecting both copy number variation (deletions or duplications) and copy-neutral structural variants such as regions of homozygosity (ROH) and uniparental disomy (UPD). Detection of submicroscopic abnormalities, including microdeletions and microduplication, may be missed by standard chromosome analysis.  The addition of a 5 cell chromosome analysis evaluates chromosomes for balanced rearrangements such as inversions and translocations.
Features of the Infinium® CytoSNP-850K BeadChip Array
  • High resolution array containing 850,000 SNPs with ~15x redundancy of each marker
  • Follows the International Collaboration for Clinical Genomics (ICCG) guidelines for chip design
  • Probes spaced ~1.8 kb along genome for a resolution of ~10kb
  • Targets microdeletion/microduplication syndrome regions with enriched coverage for more than 3,200 known disease genes
  • Regions of homozygosity (ROH) evaluated for possible uniparental disomy (UPD) and recent shared ancestry
A consensus statement by International Collaboration for Clinical Genomics (ICCG) recommends that CMA should be the first tier test for individuals with developmental disabilities, intellectual disabilities, autism spectrum disorders, or multiple congenital anomalies. CMA testing is also indicated for individuals with seizures and other developmental problems for which a genomic basis is suspected.
Standard cytogenetic evaluation will help detect abnormal structural rearrangements in the chromosomes, such as translocations and inversions, identifying possible balanced translocation carriers. 
Patient DNA is obtained by extraction from peripheral white blood cells.  The CytoSNP-850K assay utilizes an amplification step for the DNA and hybridizes this to the BeadChip. The assay then uses a labeling process to provide allele and intensity data. BeadChips are scanned using a two-channel high-resolution laser imager and analyzed using Illumina software.
For reporting of copy number variations (CNVs), thresholds are ≥200 kb for deletions and ≥400 kb for duplications with reporting of smaller findings in clinically significant regions. Common CNVS listed in the Database of Genomic Variants are not reported. While NOT diagnostic, SNP data allows for detection of regions of homozygosity (ROH) suggestive of UPD (isodisomy) or shared ancestry (consanguinity) with possible implications in the context of recessive disorders. ROH is evaluated at ≥5 Mb with a reporting threshold of ~10 MB. Total percentage of ROH is reported when ≥5%.
For the cytogenetic analysis, a minimum of 5 metaphases are examined and 2 karyotypes are prepared at >550 band level.
CMA will not detect balanced rearrangements (i.e., inversions, translocations), heterodisomy, or very low level mosaicism. It will not detect single gene mutations such as single nucleotide mutations/polymorphisms. Abnormalities that are smaller than the resolution of the array may not be detected.
The 5 cell standard cytogenetic analysis will not detect very subtle chromosomal rearrangements and will not adequately detect possible mosaicism.
Specimen Requirements
Peripheral blood
  • Submit peripheral blood in two tubes: a minimum of 2 ml in an EDTA purple top tube and a minimum of 3 ml in a sodium heparin green top tube.
  • When 5 ml of peripheral blood cannot be obtained (e.g., in babies), 3 ml peripheral blood in a sodium heparin, green top tube alone is acceptable.
  • Label specimen tubes with patient's name and a second identifier.
  • Hold specimen at room temperature and transport to the Colorado Genetics Laboratory as soon as possible.
Sample must be accompanied by a completed Test Request Form.  Indicate chromosomal microarray testing, and include all pertinent medical and family history and/or a completed Pediatric/Adult Chromosomal Microarray Clinical Information Form.
Interpretation Services
     Detailed written report provided with genetic counseling phone consultation available to medical providers.
     Autism referrals cross-referenced with current autism database(s) for up-to-date copy number associations.
Follow-Up Testing
Colorado Genetics Laboratory recommends that parental/familial testing be considered when a genomic imbalance is detected by chromosomal microarray.  Please see current policy – Familial Follow-up After Abnormal Microarray Effective June 1, 2014.
Microarray Billing Policy Effective June 1, 2014
When the new molecular CPT codes became effective January 1, 2013, insurance companies subsequently revised their medical policies regarding medical necessity for chromosomal microarray.  Because of the variability among these policies, waivers for microarray testing have been implemented for all insurance carriers, except Colorado Medicaid.  
Please have your patient complete and sign the Waiver for CytoSNP-850K Microarray form below, and submit it with the specimen for microarray testing.  If the patient’s insurance denies the charges, the patient will be billed at a discounted rate.
Waiver for CytoSNP-850K Microarray
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. 86:749-64, 2010.