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HelpTest Code LAB3623 Family Study Chromosomal SNP Microarray
Clinical System Name
Family Study Chromosomal SNP Microarray
Synonyms
Parental Follow Up Study Array
CH FAMS
Description
This test is appropriate for testing of parents and siblings of a child with an uncertain or abnormal result by traditional cytogenetic testing (karyotype, FISH) or chromosomal microarray (SNP array, array CGH). Based on the results of the child's testing, one of the following cytogenetic follow-up tests can be performed: SNP array, interphase or metaphase FISH, qPCR, or limited karyotype. The appropriate follow-up test is typically indicated on the child's test report.
Please contact the Laboratory Genetic Counselors (987-5400) if you have questions.
Sample Requirements
Specimen: Whole Blood
Container(s): Lavender/EDTA AND Dark Green/Sodium Heparin (no serum separator)
Preferred Vol: 3-5 mL per tube
Minimum Vol: TWO tubes: Lavender/EDTA and Dark Green/Sodium Heparin (no gel separator), 3 mL PER TUBE
Note: Keep sample at room temperature; deliver to the lab promptly. Samples received after 3 pm will be set up the following day.
DNA is not an acceptable specimen type for many Family Study tests, exceptions may be reviewed & approved by the Lab Genetic Counselors.
Processing Instructions
Reject due to:
Spin: N
Aliquot: N
Temp: RT
Storage location:
Days: Transport specimen, requisition, and labels to 4th floor Cytogenetics (station #181).
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.
Stability
| Specimen Type | Temperature | Time |
|---|---|---|
| Whole blood | Room temp | 3 days |
Availability
| STAT | Performed | TAT |
|---|---|---|
| N | Weekly | 21 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
Chromosomes are the packages within cells that contain a person’s genetic information (called “genes” or “DNA”). This genetic information tells a person’s body how to develop and function properly. Gains (duplications) or losses (deletions) result in extra or missing copies of genetic material. These types of changes in a person’s chromosomes may be associated with known genetic conditions or may cause problems with health and development, such as birth defects or cognitive impairment.
This test is appropriate for testing of parents and siblings of a child with an uncertain or abnormal result by traditional cytogenetic testing (karyotype, FISH) or chromosomal microarray (SNP array, array CGH). Based on the results of the child’s testing, one of the following cytogenetic follow-up tests can be performed: SNP array, interphase or metaphase FISH, qPCR, or limited karyotype. The appropriate follow-up test is typically indicated on the child’s test report.
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.