Whole Genome SNP Microarray

Clinical Info
 The lab uses the Affymetrix Cytoscan HD platform. This thorough analysis of regions throughout the genome may identify the causes of numerous genetic conditions and cases of unexplained intellectual disabilities or other anomalies. This SNP array also allows for the analysis of loss of heterozygosity which can be useful in identifying uniparental disomy (UPD) as well as autozygosity (identity by descent). This array features...
  • 2.67 million markers.
    • 750,000 SNPs
    • 1.9 million non-polymorphic probes
  • Backbone coverage of 1 marker per 1,737 bases
  • Gene coverage is 1 marker per 880 bases for more than 36,000 RefSeq genes
  • Enriched Gene Coverage
    • 12,000 OMIM genes, 1 marker/659 bases
    • X chromosome genes, 1 marker/486 bases
    • Complete ISCA constitutional coverage,1 marker/384 bases
    • Cancer genes, 1 marker/553 bases
  • Enhanced ability to measure mosaicism
  • Characterization of LOH and UPD
  • SNP genotyping allows allele specific copy number and parent of origin analysis.
Indications
  • Individuals with unexplained intellectual disability, developmental delay, autism, dysmorphic features or other phenotypic anomalies
  • 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 for DNA isolation and 3-5mls peripheral blood collected in a sodium heparin (green top) tube for metaphase chromosome isolation. The lavendar top, EDTA tube is required. The green top, sodium heparin tube, is requested but not required. You may send the EDTA without the sodium heparin if necessary; however, additional sample in a green top may be requested at a later date.

If parental studies are recommended, an EDTA (lavender top) and sodium heparin (green top) tube are needed from the parents.
Transport The specimen should be kept at room temperature and delivered via overnight shipping. Do not freeze.
Turnaround time 26 days
In some cases, parental samples may be requested to clarify results
CPT Codes 81229
Cost Whole Genome SNP Microarray:  $1950

There may be additional charges for cell culture, FISH studies, and parental studies.
For a prenatal sample or tissue sample, there will be an additional charge for culture:

     Skin or other tissue: $342

     Amniotic fluid or CVS: $312

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
Contact For further information contact This email address is being protected from spambots. You need JavaScript enabled to view it. , MS, Lab Counselor or Barb DuPont, PhD, Cytogenetics Laboratory Director at 1-800-473-9411

Form Needed

Download ggc cyto-request-form - writable.pdf

Have Questions Need Support?

Contact our Laboratory Representative for assistance.
Kellie King, MS, CGC

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

Find out more