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Test Code CGSNPB Cytogenomic SNP Array, Peripheral Blood

Specimen Type

Blood, Arterial

Container

Sodium Heparin (Green Top) Tube and EDTA (Lavendar Top)

Preferred Volume

5 mL

Offsite Collection Instructions

Peripheral blood samples collected in sodium heparin (green top) and EDTA (lavendar top) transported at room temperature to Lab Services Center.

UCMC Collection Instructions

Peripheral blood samples collected in sodium heparin (green top) and EDTA (lavendar top) stored at room temperature or refrigerator. Samples should be sent within 24 hours to UCM Lab Services Center at ambient temperature.

Availability

Monday – Friday, 8:00am – 5:00pm

Turnaround Time

2-4 weeks

STAT Availability

Not Available

Test Usage

This Cytogenomic SNP array is a high-resolution method for detecting copy number changes (gains or losses) across the entire genome in a single assay. This platform is also capable of detecting regions of homozygosity related to uniparental disomy or identity by descent. Indications for ordering include the following: Individuals with developmental delay/intellectual disability (with or without dysmorphic features), multiple congenital anomalies, autism spectrum disorder/pervasive developmental disorder, epilepsy/seizures, heart defects, family history of a chromosomal abnormality resulting in a genomic imbalance. This test is also able to further characterize certain chromosomal abnormalities including marker or ring chromosomes, Deletions or duplications, Unbalanced translocations and Apparently balanced de-novo rearrangements in individuals with abnormal phenotypes.

Test Methodology

Cytogenomic SNP array uses the Affymetrix CytoScan HD platform. This array includes 2.67 million markers for copy number (CN) analysis including approximately 750,000 SNP probes, and 1.9 million non-polymorphic probes for whole genome coverage. This array provides an average intergenic probe density of one probe per 880 bases and an overall (gene and non-gene backbone) probe density of one probe every 1,148 bases. Analysis of data is based on the most recent human genome build (hg19). All reported base pair coordinates are estimated. Deletions larger than 200 kb and duplications larger than 400 kb will generally be reported. Smaller copy number changes may also be reported if they are considered clinically significant based on genomic information available at the time the report is issued. Benign copy number variants will not be reported but will be kept on file in the laboratory. Copy number changes resulting in carrier status for autosomal recessive disorders may not be reported unless concern for a specific disorder is communicated to the laboratory. If applicable, copy number changes will be confirmed using fluorescence in situ hybridization (FISH) or other appropriate methodologies. Long continuous stretches of homology (LCSH), which can result from uniparental disomy (UPD) or common descent, can also be detected using the CytoScan HD array. Reported regions of LCSH will not be confirmed but recommendations for further molecular testing may be made to confirm UPD or to identify recessive alleles possibly associated with the patient’s condition.

Additional Information

A referral to a clinical geneticist or counselor is appropriate for individuals and families to discuss results of this test.

CPT Code

CPT 81229-CONST GENE ARRYSNP COPY VAR

Test Includes

Whole genome analysis of losses >200 Kb and gains >400 Kb including all known microdeletion and microduplication syndrome regions. Recommendations for follow up testing when warranted and interpretative report provided.

Reference Range

Interpretive report will be provided.

Test Limitations

This test will not detect balanced chromosome rearrangements such as Robertsonian or other reciprocal translocations, inversions or balanced insertions. This test will not detect imbalances of regions not represented on the array. This test does not detect all types and instances of uniparental disomy. This test is not designed to detect mosaicism at low levels. Normal findings do not rule out the diagnosis of any disorder since some genetic abnormalities may be undetectable with this assay. Specifically, this test does not detect point mutations, small deletions or insertions below the resolution of this assay, or other types of mutations such as epigenetic changes. The results of this test may be of unclear clinical significance. In such cases, additional family studies may be necessary to interpret the results. CNVs detected by this platform may not be investigated or reported if they are devoid of relevent gene content or reported as common findings in the general population based on available database searches or are gains smaller than 400 Kb or losses smaller than 200 Kb.

STAT Turnaround Time

For rush requests contact Dr. Fitzpatrick (2-2922, pg 2548) or the Cytogenetic Fellow (2-6203).

Minimum Volume

2 mL

Fee Code

75223

Synonyms

Microarray, SNP, gen hyb, ACGH, Gene, Whole Gene, CGH