GTR Test Accession:
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GTR000569041.2
CAP
Last updated in GTR: 2019-10-10
View version history
GTR000569041.2, last updated: 2019-10-10
GTR000569041.1, last updated: 2019-09-29
Last annual review date for the lab: 2023-07-05
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At a Glance
Test purpose:
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Diagnosis;
Mutation Confirmation
Conditions (5):
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Autism spectrum disorder; Congenital chromosomal disease; Epilepsy; ...
Human genome
Methods (3):
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Molecular Genetics - Deletion/duplication analysis: SNP Detection; ...
Target population: Help
Not provided
Clinical validity:
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The array consists of 1.95 million non-polymorphic markers and around …
Clinical utility:
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Establish or confirm diagnosis
Ordering Information
Offered by:
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Specimen Source:
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- Isolated DNA
- Peripheral (whole) blood
- View specimen requirements
Who can order: Help
- Genetic Counselor
- Health Care Provider
- Licensed Dentist
- Licensed Physician
- Nurse Practitioner
- Physician Assistant
- Registered Nurse
Test Order Code:
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CY001
CPT codes:
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Contact Policy:
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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:
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Informed consent required:
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Based on applicable state law
Pre-test genetic counseling required:
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Decline to answer
Post-test genetic counseling required:
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Decline to answer
Recommended fields not provided:
Lab contact for this test,
Test strategy,
Test development
Conditions
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Total conditions: 5
Condition/Phenotype | Identifier |
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Test Targets
Chromosomal regions/Mitochondria
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Total chromosomal regions/mitochondria: 1
Chromosomal region/Mitochondrion | Associated condition |
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Methodology
Total methods: 3
Method Category
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Test method
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Instrument *
Deletion/duplication analysis
SNP Detection
Detection of homozygosity
SNP Detection
Uniparental disomy study (UPD)
SNP Detection
* Instrument: Not provided
Clinical Information
Test purpose:
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Diagnosis;
Mutation Confirmation
Clinical validity:
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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 …
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Clinical utility:
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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?
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Variants are interpreted according to the 2015 ACMG variant interpretation standards and guidelines
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?
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Yes.
Yes.
Will the lab re-contact the ordering physician if variant interpretation changes?
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Yes.
Yes.
Recommended fields not provided:
Target population,
Is research allowed on the sample after clinical testing is complete?,
Sample negative report,
Sample positive report
Technical Information
Test Platform:
Affymetrix CytoScan HD Array
Availability:
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Tests performed
Entire test performed in-house
Entire test performed in-house
Analytical Validity:
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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:
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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 …
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Proficiency testing (PT):
Is proficiency testing performed for this test?
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Yes
Method used for proficiency testing: Help
Formal PT program
PT Provider: Help
American College of Medical Genetics / College of American Pathologists, ACMG/CAP
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:
Laboratory's policy on reporting novel variations
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Anything that is classified as a VUS or higher according to the 2015 ACMG guidelines is reported.
Anything that is classified as a VUS or higher according to the 2015 ACMG guidelines is reported.
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:
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Not provided
Additional Information
Clinical resources:
Practice guidelines:
Consumer resources:
IMPORTANT NOTE:
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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.