GTR Test Accession:
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GTR000553938.1
Registered in GTR:
2017-06-18
View version history
GTR000553938.1,
registered in GTR:
2017-06-18
Last annual review date for the lab: 2023-11-29
Past due
LinkOut
At a Glance
Test purpose:
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Diagnosis;
Pre-implantation genetic diagnosis
Conditions (4):
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1-22, X,Y;
16p11.2-p12.2
Methods (1):
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Molecular Genetics - Deletion/duplication analysis: Microarray
Target population: Help
Individuals with developmental delay/intellectual delay, multiple congenital anomaly, autism
Clinical validity:
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Not provided
Clinical utility:
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Establish or confirm diagnosis
Ordering Information
Offered by:
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Manufacturer's name:
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Affymetrix
Specimen Source:
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- Amniocytes
- Amniotic fluid
- Buffy coat
- Chorionic villi
- Cord blood
- Isolated DNA
- Peripheral (whole) blood
- Product of conception (POC)
Who can order: Help
- Health Care Provider
Lab contact:
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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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Specimen type: whole blood, tissue, etc.
Days that sample should be accepted: 72h for whole blood
Required forms: a paper Test Requisition Form and Consent Form
Order URL
Days that sample should be accepted: 72h for whole blood
Required forms: a paper Test Requisition Form and Consent Form
Order URL
Test service:
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Clinical Testing/Confirmation of Mutations Identified Previously
Confirmation of research findings
Custom Balanced Chromosome Rearrangement Studies
Custom Deletion/Duplication Testing
Marker Chromosome Identification
Preimplantation Genetic Diagnosis (PGD)
Uniparental Disomy (UPD) Testing
Confirmation of research findings
Custom Balanced Chromosome Rearrangement Studies
Custom Deletion/Duplication Testing
Marker Chromosome Identification
Preimplantation Genetic Diagnosis (PGD)
Uniparental Disomy (UPD) Testing
Test additional service:
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Custom mutation-specific/Carrier testing
Test development:
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Manufactured (research use only; not FDA-reviewed)
Informed consent required:
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Yes
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:
Test Order Code,
Test strategy
Conditions
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Total conditions: 4
| Condition/Phenotype | Identifier |
|---|
Test Targets
Chromosomal regions/Mitochondria
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Total chromosomal regions/mitochondria: 2
| Chromosomal region/Mitochondrion | Associated condition |
|---|
Methodology
Total methods: 1
Method Category
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Test method
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Instrument
Deletion/duplication analysis
Microarray
Affymetrix GeneChip Scanner 3000 7G Whole-Genome Association System
Clinical Information
Test purpose:
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Diagnosis;
Pre-implantation genetic diagnosis
Clinical utility:
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Target population:
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Individuals with developmental delay/intellectual delay, multiple congenital anomaly, autism
View citations (3)
- 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.
- Ellison JW, Ravnan JB, Rosenfeld JA, Morton SA, Neill NJ, Williams MS, Lewis J, Torchia BS, Walker C, Traylor RN, Moles K, Miller E, Lantz J, Valentin C, Minier SL, Leiser K, Powell BR, Wilks TM, Shaffer LG. Clinical utility of chromosomal microarray analysis. Pediatrics. 2012;130(5):e1085-95. doi:10.1542/peds.2012-0568. Epub 2012 Oct 15. PMID: 23071206.
- Riggs ER, Wain KE, Riethmaier D, Smith-Packard B, Faucett WA, Hoppman N, Thorland EC, Patel VC, Miller DT. Chromosomal microarray impacts clinical management. Clin Genet. 2014;85(2):147-53. doi:10.1111/cge.12107. Epub 2013 Feb 21. PMID: 23347240.
Variant Interpretation:
What is the protocol for interpreting a variation as a VUS?
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Joingenome includes VUSs in the result report according to ACMG guidelines. Factors that can increase the probability of a VUS being clinically relevant include: Variant is rare, de novo, predicted to be deleterious by computer models, and/or in a gene or region that is highly conserved during evolution.
Joingenome includes VUSs in the result report according to ACMG guidelines. Factors that can increase the probability of a VUS being clinically relevant include: Variant is rare, de novo, predicted to be deleterious by computer models, and/or in a gene or region that is highly conserved during evolution.
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. The Medical Director is responsible for systematically re-evaluation the previous interpretation results of the genetic testings over a period of one year.
Yes. The Medical Director is responsible for systematically re-evaluation the previous interpretation results of the genetic testings over a period of one year.
Recommended fields not provided:
Clinical validity,
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
Test Confirmation:
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MLPA/QF-PCR
Availability:
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Tests performed
Entire test performed in-house
Entire test performed in-house
Analytical Validity:
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Analytic sensitivity: 90.7%
Analytic specificity: 95.3%
Assay limitations:
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Could't be used to detect balanced rearrangement, point mutation, and low mosaicism
Proficiency testing (PT):
Is proficiency testing performed for this test?
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Yes
Method used for proficiency testing: Help
Inter-Laboratory
Description of internal test validation method: Help
MLPA/QF-PCR
Yes
Method used for proficiency testing: Help
Inter-Laboratory
Description of internal test validation method: Help
MLPA/QF-PCR
VUS:
Software used to interpret novel variations
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SIFT, PolyPhen2, CADD,REVEL,PROVEN, Mutation Taster
Laboratory's policy on reporting novel variations Help
Joingenome includes novel variant(s) in the result report when the gene is clinically relevant, predicted to be deleterious by computer models, and/or in a gene or region that is highly conserved during evolution, co-segregation with disease in the family.
SIFT, PolyPhen2, CADD,REVEL,PROVEN, Mutation Taster
Laboratory's policy on reporting novel variations Help
Joingenome includes novel variant(s) in the result report when the gene is clinically relevant, predicted to be deleterious by computer models, and/or in a gene or region that is highly conserved during evolution, co-segregation with disease in the family.
Recommended fields not provided:
Citations to support assay limitations,
Citations to support internal test validation method,
Citations for Analytical validity,
PT Provider,
Description of PT method,
Major CAP category, CAP category, CAP test list
Regulatory Approval
FDA Review:
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Not provided
Additional Information
Reviews:
Clinical resources:
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.