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Diagnostic Services

Genetics Lab


Chromosome SNP Array

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 (runs 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 cause 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 will report copy number changes involving deletions and duplications of loci that can cause or predispose to adult-onset disorders and some cancer predisposition syndromes.

Test Name: Cytogenetics SNP Array
Test Code:
Test Description:
The Affymetrix Cytoscan HD array contains 1.7 million copy number markers and 750,000 SNP markers which gives the following coverage:
- ISCA constitutional gene coverage of one marker/384 bases
- 12,000 OMIM gene coverage with one marker/659 bases
- >36,000 RefSeq gene coverage with one marker/880 bases
- Backbone (non-gene) coverage of one marker/1737 bases
Affymetrix; Array; CMA Array; Cytoscan Array; Microarray; Single Nucleotide Polymorphism; SNP; 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 cytogenetic abnormality who have had normal BAC array CGH
Related Tests: Cytogenetics Familial Study  
This test is appropriate for parental testing of a child with an uncertain or abnormal array result.

Clinical Links: International Standards of Cytogenomic Arrays Consortium (ISCA)
OMIM: Online Mendelian Inheritance in Man
The Reference Sequence (RefSeq) collection
Drawn daily
Turnaround Time:
21 days
Affymetrix SNP Array
Reference Range:
Interpretive Report Provided
Consent Form:
Sample Requirements: Type
Whole Blood: Adults: 3-5ml
Infants: 1-2ml

EDTA (purple) tube.

Keep at room temperature

Ship overnight at room temperature
Samples Received:
Mon - Fri 8:00am - 5:00pm PST
Special Considerations:
Please e-mail Client Services or call at 206-987-2617 with any billing questions
CPT Code:
Please e-mail Client Services or call at 206-987-2617 with any billing questions