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HelpTest Code LAB1803 Chromosomal SNP Microarray
Clinical System Name
Chromosomal SNP Microarray
Synonyms
Affymetrix
Array
CMA Array
Cytoscan Array
Microarray
Single Nucleotide Polymorphism
SNP
SNP Array
Cytogenetic SNP Array
Description
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 Blood: Lavender/EDTA
Preferred Blood Vol: 3-5 mL
Minimum Blood Vol: 1-2 mL; 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 from EDTA blood
Minimum: 2µg
Note: DNA concentration minimum 50 ng/µl: using a quantitation method specific to dsDNA; 260/280 ratio 1.70-2.00. Isolation of nucleic acids for clinical testing must be performed in a CLIA-certified laboratory or a laboratory meeting equivalent requirements as determined by the CAP and/or the CMS.
Specimen: Saliva collected using ORAgene Dx OGD-575/675 collection kit.
Container: ORAgene Dx OGD-575/675 collection kit.
Restrictions: The ORAgene Dx OGD575/675 kit is not for children under 6 months.
IMPORTANT NOTE: Manufacturer instructions must be followed. Please review link: How to Collect a Saliva Sample for Genetic Testing (Spanish). Contact the lab directly for more information or to obtain a kit - 206-987-2563, ReferenceLabTeam@seattlechildrens.org.
Processing Instructions
Blood:
Reject due to: call the SNP array lab first
Spin: N
Aliquot: N
Temp: RT
Storage location: Store specimen in the Cytogenetics room temp box in CPA.
Off-site collection: Ship overnight at RT. Samples received Mon-Fri: 8:00 am - 5:00 pm.
Saliva:
Reject due to: use of a kit that is not ORAgene Dx OGD-575/675
Spin: No
Aliquot: No
Temp: RT
Storage location: Store specimen in the Cytogenetics room temp box in CPA.
Off-site collection: Ship overnight at RT. Samples received Mon-Fri: 8:00 am - 5:00 pm
Stability
| Specimen Type | Temperature | Time |
|---|---|---|
| Whole blood, extracted DNA | RT | 3-5 d |
| Whole blood, extracted DNA | 2 - 8 C | 7 d |
|
Saliva, extracted from ORAgene Dx OGD-575/675 |
room temperature or refrigerated | up to 2 weeks |
| Extracted DNA | -20 C or -70 C | years |
Note: Whole blood samples > 7days may be submitted to be assessed by our lab for acceptability for testing.
Availability
| STAT | Performed | TAT |
|---|---|---|
| N | Daily | 28 days |
Performing Laboratory
Seattle Children's Hospital
Department
Department: Molecular Genetics/Array Laboratory
Phone number: 206-987-3872
Lab Client Services: 206-987-2617, labclientservices@seattlechildrens.org
Lab Genetic Counselors: LabGC@seattlechildrens.org
CPT Codes
81229
Methodology
Method:
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)
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.