SNP based chromosomal microarray
GTR Test Accession: Help GTR000569041.2
Last updated in GTR: 2019-10-10
Last annual review date for the lab: 2023-07-05 LinkOut
At a Glance
Diagnosis; Mutation Confirmation
Autism spectrum disorder; Congenital chromosomal disease; Epilepsy; ...
Molecular Genetics - Deletion/duplication analysis: SNP Detection; ...
Not provided
The array consists of 1.95 million non-polymorphic markers and around …
Establish or confirm diagnosis
Ordering Information
Offered by: Help
Al Jalila Children's Genomics Center
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View lab's test page
Specimen Source: Help
Who can order: Help
  • Genetic Counselor
  • Health Care Provider
  • Licensed Dentist
  • Licensed Physician
  • Nurse Practitioner
  • Physician Assistant
  • Registered Nurse
Test Order Code: Help
CPT codes: Help
**AMA CPT codes notice
Contact Policy: Help
Laboratory can only accept contact from health care providers. Patients/families are encouraged to discuss genetic testing options with their health care provider.
How to Order: Help
Informed consent required: Help
Based on applicable state law
Pre-test genetic counseling required: Help
Decline to answer
Post-test genetic counseling required: Help
Decline to answer
Recommended fields not provided:
Conditions Help
Total conditions: 5
Condition/Phenotype Identifier
Test Targets
Chromosomal regions/Mitochondria Help
Total chromosomal regions/mitochondria: 1
Chromosomal region/Mitochondrion Associated condition
Total methods: 3
Method Category Help
Test method Help
Instrument *
Deletion/duplication analysis
SNP Detection
Detection of homozygosity
SNP Detection
Uniparental disomy study (UPD)
SNP Detection
* Instrument: Not provided
Clinical Information
Test purpose: Help
Diagnosis; Mutation Confirmation
Clinical validity: Help
The array consists of 1.95 million non-polymorphic markers and around 750,000 single-nucleotide polymorphism (SNP) markers, with an average genome-wide probe spacing of 1.1 kb, and an average intra-genic probe spacing of 880bp. The assay covers (25 markers/100Kb) 100% ISCA constitutional genes (n=3,483), 100% OMIM morbid genes (n=3,561) and 98% RefSeq … View more
Clinical utility: Help
Establish or confirm diagnosis
View citations (1)
  • Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Miller DT, et al. Am J Hum Genet. 2010;86(5):749-64. doi:10.1016/j.ajhg.2010.04.006. PMID: 20466091.

Variant Interpretation:
What is the protocol for interpreting a variation as a VUS? Help
Variants are interpreted according to the 2015 ACMG variant interpretation standards and guidelines

Are family members with defined clinical status recruited to assess significance of VUS without charge? Help

Will the lab re-contact the ordering physician if variant interpretation changes? Help
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Technical Information
Test Platform:
Affymetrix CytoScan HD Array
Availability: Help
Tests performed
Entire test performed in-house
Analytical Validity: Help
Assay-validation performed in-house have shown 100% sensitivity for genome-wide CNV losses 200kb in length and involving ≥25 markers, and gains 400Kb in length involving ≥50 markers. In addition, this assay has shown 100% sensitivity for small CNV losses >25Kb gains >50Kb in clinically relevant regions with dense probe-coverage.
Assay limitations: Help
This microarray platform cannot detect balanced chromosomal rearrangements, including translocations, insertions, inversions, point mutations, certain polyploidy states, DNA methylation abnormalities, or genomic imbalances of regions that are not represented on the microarray. Mosaicism below 30% may not be detected by this microarray. Repeat expansion disorders are not detected using this … View more
Proficiency testing (PT):
Is proficiency testing performed for this test? Help

Method used for proficiency testing: Help
Formal PT program

PT Provider: Help
American College of Medical Genetics / College of American Pathologists, ACMG/CAP
Laboratory's policy on reporting novel variations Help
Anything that is classified as a VUS or higher according to the 2015 ACMG guidelines is reported.
Recommended fields not provided:
Regulatory Approval
FDA Review: Help
Not provided
Additional Information

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