Chromosome Array (ACGH and SNP), Postnatal

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Pseudonyms: Microarray, Chromosomal Microarray, CMA, Constitutional Array, Array Comparative Genomic Hybridization, Array CGH, Whole Genome Array

TESTING METHODOLOGY: Array Comparative Genomic Hybridization
  • Collect: 3-5 mL peripheral blood in EDTA (purple) and 3-5 mL peripheral blood in sodium heparin (green) for children and adults; 2 mL EDTA and 2 mL sodium heparin for newborns
  • Min. Collection: 2 mL EDTA and 2 mL sodium heparin for children and adults; 1 mL EDTA and 1 mL sodium heparin for newborns
  • Transport: peripheral blood in EDTA (purple) and sodium heparin (green) at 20-25oC
  • Stability: Ambient: 24 hours; Refrigerated: 72 hours; Frozen: unacceptable
  • Unacceptable Conditions: Frozen or clotted specimens; specimens in anticoagulants other than EDTA and sodium heparin

A Cytogenetics Laboratory Test Requisition must accompany the specimen. Contact the Cytogenetics Laboratory at 918-502-1722 to obtain further information.

Test Summary: The microarray covers every region known to be involved in chromosome abnormalities, including 255 recognized genetic syndromes and over 980 gene regions of functional significance in human development. It also covers the sex chromosomes and the chromosomal regions most likely to be involved in unbalanced rearrangements (the pericentromeric regions and the subtelomeres). Microarray analysis is performed using an array which includes 108,000 oligonucleotide probes and 60,000 SNP probes. The oligonucleotide probes identify copy number variants (deletions and duplications). The SNP probes detect stretches of homozygosity in the genome. There is one copy number probe for every 10 kilobases in regions of clinical significance and one copy number probe in every 35 kilobases across the rest of the genome. The average SNP probe spacing is one probe every 49 kilobases across the genome. The data analysis is performed by an experienced clinical cytogeneticist using Genoglyphix® software. 
Methods: Microarray analysis using an array of 168,000 oligonucleotide probes to targeted genome regions and SNPs; abnormalities are confirmed by fluorescence in situ hybridization (FISH)
Interpretation: An abnormal (clinically significant) result is reported when an abnormality (gain or loss) is associated with a known Mendelian disorder, a recognized microdeletion or microduplication syndrome or an unbalanced chromosome rearrangement. The results of this test may also be of unclear clinical significance. In these cases, studies of parents may be required to assist in interpreting the results. Carrier status for autosomal recessive conditions is not reported unless the variation detected is consistent with the patient's reason for referral. Consultation with a genetic professional is recommended for test interpretation.
Unclear clinical significance:
Some test results may have unclear clinical significance, meaning that it is not clear whether the alterations detected are the cause of the clinical abnormalities in the patient. These cases may require studies of the parents to help with interpretation. Sometimes, even after family studies, it is still uncertain whether a copy number change causes the clinical abnormalities in the patient. In these cases, continued surveillance of the medical literature for new information regarding the alteration is recommended.
Data from SNP analysis:
Data from the SNP probes demonstrate either homozygosity (AA or BB) or heterozygosity (AB) at every SNP locus. Long regions of homozygosity (AOH) indicate findings of potential clinical significance. In evaluating SNP data for clinical significance, findings of AOH that are >5 megabases of DNA in size are considered. The finding of long regions of homozygosity aids in the diagnosis of autosomal recessive disease and uniparental disomy.
Test Limitations: 

• Balanced chromosome rearrangements (such as balanced translocations and inversions) will not be detected.
• Alteration of chromosome regions not represented on the microarray will not be detected.
• Some cases of mosaicism (particularly levels of mosaicism below 50%) may not be detected.
• DNA sequence alterations and single base pair mutations will not be detected.
• A normal result does not exclude the diagnosis of any of the disorders represented on the microarray since the percentage of patients who will demonstrate a copy number alteration varies depending on the locus.
• A normal result does not exclude the diagnosis of an imprinted gene disorder since some patients will have heterodisomy or another mechanism that can cause the disorder.
• A normal result does not exclude the diagnosis of an autosomal recessive disorder since mutations in both copies of a gene do not come from a common ancestor in some cases.
Test Variables: Turnaround time will average approximately 28 days if confirmation of an abnormality by FISH is necessary.
FDA Approval: This test is not approved by the FDA and it should used as an adjunct to other clinical information.
Indications for Use:

    Microarray analysis is recommended for patients with:
    • Autism spectrum disorders
    • Developmental delay/intellectual disability
    • Multiple congenital anomalies
    • Neurodevelopmental disorders
    • Neuromuscular disorders
    • Dysmorphic features
    • Seizure disorders
    • Imprinted gene disorders  due to uniparental disomy
    • Autosomal recessive disorders due to identity by descent
    Microarray analysis is used following conventional chromosome analysis to:
    • Determine the size and gene content of chromosome abnormalities such as marker chromosomes and unbalanced translocations
    • Determine the presence of cryptic chromosome imbalances for  chromosome rearrangements that appear to be balanced
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