- Chromosomal SNP microarray
- Chromosomal 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 and high resolution 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.
If clinically relevant, common aneuploidies, such
as Down syndrome or Trisomy 18, should be ruled out by chromosome analysis or
fluorescence in situ hybridization before CMA testing is
If cytogenetic evaluation has not been performed previously, 5-cell chromosome analysis is a helpful addition to the microarray testing. In cases of a normal CMA, the abbreviated cytogenetic analysis will help detect balanced structural rearrangements in the chromosomes, such as translocations and inversions. In cases of imbalances detected by CMA, the cytogenetic analysis may further clarify the abnormal finding(s), such as confirming the presence of a derivative chromosome.
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 5-cell chromosome analysis, a minimum of 5 metaphases are examined and 3 karyotypes are prepared at ≥450-550 band level (standard resolution).
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
The 5-cell chromosome analysis will not detect very subtle chromosomal rearrangements and will not adequately detect possible mosaicism.
Submit peripheral blood in two tubes: a minimum
of 2 ml in a 4 ml EDTA (purple/lavender 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), submit 2 ml of blood in a sodium heparin tube.
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.
Samples must be accompanied by a completed Test Request Form. Indicate specific chromosomal microarray test option. Include all pertinent medical and family history and/or a completed Pediatric/Adult Chromosomal Microarray Clinical Information Form.
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.
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.
- Kearney HM, et al. American College of Medical Genetics standards and guidelines for interpretation and reporting of postnatal constitutional copy number variants. Genet Med. 13:680-5, 2011.
- 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.
- South ST, et al. ACMG Standards and Guidelines for constitutional cytogenomic microarray analysis, including postnatal and prenatal applications: revision 2013. Genet Med. 15:901-9, 2013.