GTR Test Accession:
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GTR000500225.9
CAP
Last updated in GTR: 2021-01-19
View version history
GTR000500225.9, last updated: 2021-01-19
GTR000500225.8, last updated: 2020-08-17
GTR000500225.7, last updated: 2019-08-13
GTR000500225.6, last updated: 2018-08-20
GTR000500225.5, last updated: 2016-10-17
GTR000500225.4, last updated: 2016-06-10
GTR000500225.3, last updated: 2015-11-13
GTR000500225.2, last updated: 2014-11-17
GTR000500225.1, last updated: 2013-11-20
Last annual review date for the lab: 2023-07-18
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At a Glance
Test purpose:
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Diagnosis;
Monitoring;
Mutation Confirmation; ...
Conditions (18):
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Microcephalic osteodysplastic primordial dwarfism type II; 3-M syndrome; DNA ligase IV deficiency; ...
Genes (32):
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ATR (3q23), CCDC8 (19q13.32), CDC45 (22q11.21), CDC6 (17q21.2), CDK5RAP2 (9q33.2), ...
Methods (2):
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Molecular Genetics - Deletion/duplication analysis: Next-Generation (NGS)/Massively parallel sequencing (MPS); ...
Target population: Help
The target population for this test is patients suspected of …
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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Specimen Source:
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- Buccal swab
- Cell culture
- Cord blood
- Fetal blood
- Fibroblasts
- Peripheral (whole) blood
- Saliva
- View specimen requirements
Who can order: Help
- Genetic Counselor
- Health Care Provider
- Licensed Physician
- Nurse Practitioner
- Physician Assistant
- Registered Nurse
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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All samples should be shipped via overnight delivery at room temperature.
No weekend or holiday deliveries.
Label each specimen with the patient’s name, date of birth and date sample collected.
Send specimens with complete requisition and consent form, otherwise, specimen processing may be delayed.
Order URL
No weekend or holiday deliveries.
Label each specimen with the patient’s name, date of birth and date sample collected.
Send specimens with complete requisition and consent form, otherwise, specimen processing may be delayed.
Order URL
Test service:
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Clinical Testing/Confirmation of Mutations Identified Previously
Confirmation of research findings
Confirmation of research findings
Test additional service:
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Custom Prenatal Testing
Custom mutation-specific/Carrier testing
Custom mutation-specific/Carrier testing
Test development:
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Test developed by laboratory (no manufacturer test name)
Informed consent required:
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No
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,
Lab contact for this test,
Test strategy
Conditions
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Total conditions: 18
| Condition/Phenotype | Identifier |
|---|
Test Targets
Genes
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Total genes: 32
| Gene | Associated Condition | Germline or Somatic | Allele (Lab-provided) | Variant in NCBI |
|---|
Methodology
Total methods: 2
Method Category
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Test method
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Instrument *
Deletion/duplication analysis
Next-Generation (NGS)/Massively parallel sequencing (MPS)
Sequence analysis of the entire coding region
Next-Generation (NGS)/Massively parallel sequencing (MPS)
* Instrument: Not provided
Clinical Information
Test purpose:
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Diagnosis;
Monitoring;
Mutation Confirmation;
Pre-symptomatic;
Risk Assessment;
Screening
Clinical utility:
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Establish or confirm diagnosis
View citations (1)
- Formate assay in body fluids: application in methanol poisoning. Makar AB, et al. Biochem Med. 1975;13(2):117-26. doi:10.1016/0006-2944(75)90147-7. PMID: 1. Klingseisen A, Jackson AP. Mechanisms and pathways of growth failure in primordial dwarfism. (2011) Genes Dev. 25:2011-24. 2. Faivre, L. Cormier-Daire, V. Seckel Syndrome. Orphanet encyclopedia, April 2005. http://www.orpha.net 3. Willems, M. et al., Molecular analysis of pericentrin gene (PCNT) in a series of 24 Seckel/microcephalic osteodysplastic primordial dwarfism type II (MOPDII) familes. (2010) J Med Genet. 47:797-802. 4. Abdel-Salam G. et al., Expanding the phenotypic and mutational spectrum in microcephalic osteodysplastic primordial dwarfism type I. (2012) Am J Med Genet A. 158A: 1455-1461. 5. O’Driscoll, M et al. A splicing mutation affecting expression of ataxia-telangiectasa and Rad3-related protein (ATR) results in Seckel syndrome. (2003) Nature Genet. 33:497-501. 6. Sir J et al. A primary microcephaly protein complex forms a ring around parental centrioles. (2011) Nat Genet. 43: 1147-53. 7. Al-Dosari, MS, et al. Novel CENPJ mutation causes Seckel syndro.
Target population:
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The target population for this test is patients suspected of having a diagnosis of primordial dwarfism.
Variant Interpretation:
What is the protocol for interpreting a variation as a VUS?
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Variants are identified and evaluated using a custom collection of bioinformatic tools and comprehensively interpreted by our team of directors and genetic counselors.
Variants are identified and evaluated using a custom collection of bioinformatic tools and comprehensively interpreted by our team of directors and genetic counselors.
Will the lab re-contact the ordering physician if variant interpretation changes?
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Yes.
Yes.
Research:
Is research allowed on the sample after clinical testing is complete?
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http://dnatesting.uchicago.edu/research-consent-form
http://dnatesting.uchicago.edu/research-consent-form
Recommended fields not provided:
Clinical validity,
Are family members with defined clinical status recruited to assess significance of VUS without charge?,
Sample negative report,
Sample positive report
Technical Information
Availability:
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Tests performed
Entire test performed in-house
Entire test performed in-house
Analytical Validity:
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Analytical Sensitivity 99-100%
Accuracy 100%
Precision 100%
Assay limitations:
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This assay covers the coding and immediate flanking regions of the included genes. Variants in the promoter region and in other non-coding regions will not be detected. Variants that occur within regions of high homology and/or repetitiveness may not be detected due to issues with alignment. The technical sensitivity of …
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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:
Software used to interpret novel variations
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A custom collection of bioinformatics tools
Laboratory's policy on reporting novel variations Help
The laboratory reports novel variations
A custom collection of bioinformatics tools
Laboratory's policy on reporting novel variations Help
The laboratory reports novel variations
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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Category:
FDA exercises enforcement discretion
Additional Information
Clinical resources:
Molecular resources:
IMPORTANT NOTE:
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Patients and consumers
with specific questions about a genetic test should contact a health care provider or a genetics professional.