CytoScan HD Microarray

Clinical Info

The Affymetrix CytoScan HD platform allows for genome-wide detection of copy number gains and losses. In addition to detection of copy number variations (CNVs), this SNP array also allows for the analysis of loss of heterozygosity (LOH) which can be useful in identifying uniparental disomy (UPD) as well as autozygosity (identity by descent). This platform features:

  • 2.67 million markers.
    • Backbone coverage of 1 marker per 1,737 bases
    • 750,000 SNPs
    • 1.9 million non-polymorphic probes
  • Gene coverage is 1 marker per 1100 bases for more than 36,000 RefSeq genes
Indications Microarrrays are a useful diagnostic tool for a variety of clinical indications including:
  • Individuals with a suspicion of a chromosomal abnormality or microduplication/deletion syndrome with a normal karyotype
  • Determining the size of duplication/deletion involved in an unbalanced translocation
  • Assessing possible cryptic duplications/deletions in an individual with an apparently balanced karyotype, but with phenotypic abnormalities
  • Individuals with suspected UPD
  • Individuals with possible long contiguous stretches of homozygosity to determine the degree of relatedness by identity-by-descent (autozygosity)
Specimen Requirements 3-5ml peripheral blood collected in an EDTA (lavender top) tube
Transport The specimen should be kept at room temperature and delivered via overnight shipping. Do not freeze.
Turnaround time 26 days
CPT Codes 81229

Whole Genome SNP Microarray:  $1950

Cell pellet from green top (if sent): $240

If chromosomes not previously done, recommend high resolution 'short study': $620

FISH to determine if duplication is in tandem (must be requested by the physician): $536

Parental Studies

For any copy number variants of unknown clinical significance (and findings <200 kb), there will not be a charge for parent studies.

Parental qPCR studies for pathogenic CNVs and CNVs greater than 200 kb will be charged.

     1 parent submitted: $200 

     2 parents submitted simultaneously: $300

     Other family members after parent studies: $150

     CPT Code: 81479

Contact For further information contact one of our This email address is being protected from spambots. You need JavaScript enabled to view it. at 1-800-473-9411.

Cytogenetics Lab

The Cytogenetics Lab provides high quality analysis for the detection of both constitutional chromosomal aberrations as well as abnormalities related to hematological malignancies

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