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Chromosomal Microarray
Clinical Genetic Test
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offered by
Genetics Laboratory
GTR Test Accession: Help GTR000521543.3
CAP
INHERITED DISEASENERVOUS SYSTEMDYSMORPHOLOGY ... View more
Last updated in GTR: 2023-02-08
View version history
Last annual review date for the lab: 2023-02-08 Past due LinkOut
At a Glance
Test purpose: Help
Diagnosis
Conditions (7): Help
Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing; Global developmental delay; Intellectual disability more...
Chromosomal regions/ Mitochondria (1): Help
All chromosomal regions except the regions with high degree of repetative seqquences such as centromeric regions and the short ams of acrocentric chromosomes.
Methods (2): Help
Molecular Genetics - Deletion/duplication analysis: Microarray; ...
Target population: Help
Chromosomal Microarray testing is recommended as a first-line test in …
Clinical validity: Help
The whole-genome coverage platform has a sensitivity and specificity of …
Clinical utility: Help
Establish or confirm diagnosis
Ordering Information
Offered by: Help
Genetics Laboratory
View lab's website
Test short name: Help
SNP Microarray
Manufacturer's name: Help
Affymetrix CytoScan® HD
Specimen Source: Help
  • Amniocytes
  • Chorionic villi
  • Cord blood
  • Fetal blood
  • Fibroblasts
  • Fresh tissue
  • Frozen tissue
  • Isolated DNA
  • Peripheral (whole) blood
  • Product of conception (POC)
Who can order: Help
  • Genetic Counselor
  • Health Care Provider
  • Licensed Physician
  • Nurse Practitioner
  • Physician Assistant
Test Order Code: Help
Microarray
CPT codes: Help
**AMA CPT codes notice

Copyright: 2023 American Medical Association. All rights reserved.

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
Samples should be submitted with the appropriate requisition form (DNA test request form). Samples are received Monday through Saturday. Blood should be collected in EDTA or ACD tubes; cultured prenatal samples.
Test service: Help
Clinical Testing/Confirmation of Mutations Identified Previously
Genetic counseling
Prenatal tesing
FISH Analysis
Drug Metabolism testing
Cytogenetics Analysis
Maternal Serum Screening
Uniparental Disomy (UPD) Testing
X-Chromosome Inactivation Studies
Test development: Help
Manufactured (research use only; not FDA-reviewed)
Informed consent required: Help
No
Pre-test genetic counseling required: Help
No
Post-test genetic counseling required: Help
No
Recommended fields not provided:
Lab contact for this test, Test strategy
Conditions Help
Total conditions: 7
Condition/Phenotype Identifier
Test Targets
Chromosomal regions/Mitochondria Help
Total chromosomal regions/mitochondria: 1
Chromosomal region/Mitochondrion Associated condition
Methodology
Total methods: 2
Method Category Help
Test method Help
Instrument
Deletion/duplication analysis
Microarray
Illumina iScan Microarray Scanner
Detection of homozygosity
Microarray
Illumina iScan Microarray Scanner
Clinical Information
Test purpose: Help
Diagnosis
Clinical validity: Help
The whole-genome coverage platform has a sensitivity and specificity of approximately 99% for copy number changes >400kb.
View citations (1)
  • www.affyemtrix.com
Clinical utility: Help
Establish or confirm diagnosis
View citations (1)
  • The clinical utility of molecular karyotyping using high-resolution array-comparative genomic hybridization. Tzetis M, et al. Expert Rev Mol Diagn. 2012;12(5):449-57. doi:10.1586/erm.12.40. PMID: 22702362.

Target population: Help
Chromosomal Microarray testing is recommended as a first-line test in the evaluation of individuals with developmental delay/intellectual disability, autism spectrum disorder and multiple anomalies not specific to a well-defined genetic syndrome.
View citations (1)
  • South ST, Lee C, Lamb AN, Higgins AW, Kearney HM, . ACMG Standards and Guidelines for constitutional cytogenomic microarray analysis, including postnatal and prenatal applications: revision 2013. Genet Med. 2013;15(11):901-9. doi:10.1038/gim.2013.129. Epub 2013 Sep 26. PMID: 24071793.
Variant Interpretation:
What is the protocol for interpreting a variation as a VUS? Help
ACMG Guidelines. Genet Med. 2011 Jul;13(7):680-5. doi: 10.1097/GIM.0b013e3182217a3a

Will the lab re-contact the ordering physician if variant interpretation changes? Help
Yes.
Recommended fields not provided:
Are family members with defined clinical status recruited to assess significance of VUS without charge?, Is research allowed on the sample after clinical testing is complete?, Sample negative report, Sample positive report
Technical Information
Test Procedure: Help
http://support-docs.illumina.com/ARR/Inf-Global-Diversity-PGx-Checklist/Content/ARR/GlobalDiversity/Checklist.htm
Test Platform:
Infinium Global Diversity Array with Enhanced PGx-8
Test Comments: Help
FISH confirmation or copy-number-PCR may be recommended for parents' and/or proband's specimen if variants with uncertain significance are concerned to be relevant to proband's clinical presentations, or if microarray results are indicative for chromosomal structure rearrangements (translocation or inversion, etc.).
Availability: Help
Tests performed
Entire test performed in-house
Analytical Validity: Help
This assay identifies DNA copy number gains and losses associated with chromosomal imbalances; aneuploidy, deletions, and duplications of the loci represented on the array; loss of heterozygosity (LOH), uniparental isodisomy (UPD), regions of the genome that are identical-by-descent. This assay detects across the genome gains/losses and LOH at or above … View more
Assay limitations: Help
Microarray will not detect balanced alterations (reciprocal translocations, Robertsonian translocations, inversions, and balanced insertions). It will not detect imbalances smaller than the resolution of this array, point mutations or low level mosaicism (usually less than 5%).
Proficiency testing (PT):
Is proficiency testing performed for this test? Help
Yes

Method used for proficiency testing: Help
Formal PT program

PT Provider: Help
American College of Medical Genetics / College of American Pathologists, ACMG/CAP
VUS:
Software used to interpret novel variations Help
ChAS

Laboratory's policy on reporting novel variations Help
ACMG Guidelines. Genet Med. 2011 Jul;13(7):680-5. doi: 10.1097/GIM.0b013e3182217a3a
Recommended fields not provided:
Test Confirmation, Citations to support assay limitations, Description of internal test validation method, Citations for Analytical validity, Description of PT method, Major CAP category, CAP category, CAP test list
Regulatory Approval
FDA Review: Help
Category: FDA exercises enforcement discretion
Additional Information
Consumer resources:

IMPORTANT NOTE: NIH does not independently verify information submitted to GTR; it relies on submitters to provide information that is accurate and not misleading. NIH makes no endorsements of tests or laboratories listed in GTR. GTR is not a substitute for medical advice. Patients and consumers with specific questions about a genetic test should contact a health care provider or a genetics professional.