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Test Code CH-SNP Cytogenetics SNP Array

Clinical System Name

Cytogenetics SNP Array Request


CMA Array
Cytoscan Array
Single Nucleotide Polymorphism
SNP Array



This test is appropriate for an individual with any of the following findings:

  • Developmental delay or intellectual disability
  • Dysmorphic features and/or congenital abnormality(ies)
  • Individuals with strong suspicion of a cytogenetic abnormality who have had a normal Karyotype, normal BAC or CGH array.

Sample Requirements

Specimen: Whole blood, cord blood

Container(s): Lavender/EDTA

Preferred Vol: 3-5 mL

Minimum Vol: 1-2 mL


Note: For infants <24 months, 2 full lavender top microtainers are acceptable.

Note:  For patients who have had a whole blood transfusion, wait 10 days post transfusion to draw for Cytogenetics.  No wait time is necessary if the patient received red cells or plasma. 


Specimen: Extracted DNA

Minimum: 250ng

Note: DNA concentration minimum 50 ng/ul: using a quantitation method specific to dsDNA

Processing Instructions

Reject due to: Heparin (call the SNP array lab first)

Spin: N

Aliquot: N

Temp: RT

Storage location:  Days: Transport specimen, requistion, and labels to 10th floor Cytogenetics (station #180). 

Eves/Nights: Store specimen, copy of requisition, and labels in the Cytogenetics box in CPA.


Off-site collection:  Ship overnight at RT. Samples received Mon-Fri: 8:00 am - 5:00 pm.


Temperature Time
Room temp 5 days
Refrigerated 5 days
Frozen No



STAT Performed TAT
N Daily 21 days


Performing Laboratory

Seattle Children's Hospital


Department: Molecular Genetics/Array Laboratory 

Phone number: 206-987-6233


Lab Client Services: 206-987-2617,


Lab Genetic Counselors:





The Affymetrix Cytoscan DX array contains 1.9 million non-polymorphic markers and 750,000 SNP markers which gives the following coverage:


  • Covering >36,000 RefSeq genes with one/880 bases
  • Backbone (non-gene) coverage of one marker/1,700 bases
  • X-chromosome genes (one marker/486 bases)
  • Covering 12,000 OMIM genes (~one marker/659 bases)

CPT Codes


Clinical Utility

A chromosome SNP (single nucleotide polymorphism) array is a genetic test that is able to detect changes in a person’s chromosomes, such as gains (duplications) or losses (deletions). These gains or losses result in extra or missing copies of genetic material. Changes in a person’s chromosomes may be associated with known genetic conditions or may cause problems with health and development.


The SNP array can also detect genetic similarity (regions of homozygosity). Genetic similarity is an area of the chromosome that does not show the normal differences we expect to see between the material passed down (inherited) from the mother and the father. If multiple regions of genetic similarity are found by the SNP array, that person’s parents might be more closely related than originally thought (called consanguinity). For example, the parents might be related like cousins. If a region of genetic similarity is found, it could provide a clue to a specific genetic condition and more genetic testing may be recommended.


The SNP array test does not detect all differences in the chromosomes or DNA. For example, it cannot detect rearrangements in the chromosomes that do not result in extra or missing copies of genetic material (balanced chromosome rearrangements) and cannot detect small changes in the DNA (point mutations).


Those providing pre-test counseling must be aware that our lab could report copy number changes involving deletions and duplications of loci that can cause or predispose to adult-onset disorders and some cancer predisposition syndromes.