GTR Test Accession:
Help
GTR000558593.7
Last updated in GTR: 2020-09-11
View version history
GTR000558593.7, last updated: 2020-09-11
GTR000558593.6, last updated: 2020-09-09
GTR000558593.5, last updated: 2018-07-03
GTR000558593.4, last updated: 2018-02-23
GTR000558593.3, last updated: 2018-02-06
GTR000558593.2, last updated: 2017-12-20
GTR000558593.1, last updated: 2017-12-08
Last annual review date for the lab: 2024-05-20
LinkOut
At a Glance
Test purpose:
Help
Diagnosis;
Mutation Confirmation;
Pre-symptomatic; ...
Conditions (11):
Help
Hyper-IgM syndrome type 2;
Ataxia-telangiectasia syndrome;
Ataxia-telangiectasia-like disorder
more...
Genes (11):
Help
Methods (3):
Help
Molecular Genetics - Deletion/duplication analysis: Next-Generation (NGS)/Massively parallel sequencing (MPS); ...
Target population: Help
HIGM is hallmarked by recurrent respiratory infections within the first …
Clinical validity:
Help
Not provided
Clinical utility:
Help
Not provided
Ordering Information
Offered by:
Help
Specimen Source:
Help
- Cell culture
- Fetal blood
- Fibroblasts
- Fresh tissue
- Isolated DNA
- Peripheral (whole) blood
- White blood cell prep
- View specimen requirements
Who can order: Help
- Genetic Counselor
- Health Care Provider
- Licensed Physician
Test Order Code:
Help
How to Order:
Help
Please visit Lab website for details. Additional specimen types may be acceptable based on method. Please contact us about prenatal cases.
Order URL
Order URL
Test service:
Help
Clinical Testing/Confirmation of Mutations Identified Previously
OrderCode: 2689
Custom Deletion/Duplication Testing
OrderCode: 2689
Custom Sequence Analysis
OrderCode: 100, 200, 300
Maternal cell contamination study (MCC)
OrderCode: 800
OrderCode: 2689
Custom Deletion/Duplication Testing
OrderCode: 2689
Custom Sequence Analysis
OrderCode: 100, 200, 300
Maternal cell contamination study (MCC)
OrderCode: 800
Test additional service:
Help
Custom Prenatal Testing
OrderCode: 990
OrderCode: 990
Test development:
Help
Test developed by laboratory but exempt from FDA oversight (eg. NYS CLEP approved, offered within a hospital or clinic)
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,
Contact policy,
Test strategy
Conditions
Help
Total conditions: 11
Condition/Phenotype | Identifier |
---|
Test Targets
Genes
Help
Total genes: 11
Gene | Associated Condition | Germline or Somatic | Allele (Lab-provided) | Variant in NCBI |
---|
Methodology
Total methods: 3
Method Category
Help
Test method
Help
Instrument
Deletion/duplication analysis
Next-Generation (NGS)/Massively parallel sequencing (MPS)
Other
Sequence analysis of the entire coding region
Next-Generation (NGS)/Massively parallel sequencing (MPS)
Other
Targeted variant analysis
Bi-directional Sanger Sequence Analysis
Applied Biosystems 3730 capillary sequencing instrument
Clinical Information
Test purpose:
Help
Diagnosis;
Mutation Confirmation;
Pre-symptomatic;
Risk Assessment;
Screening
Target population:
Help
HIGM is hallmarked by recurrent respiratory infections within the first years of life. Laboratory findings consistent with HIGM include normal or heightened IgM and reduced IgG, IgA and IgE levels, lack of antibody response to protein or polysaccharide antigens, reduced memory (CD27+) B cells and absence of switched memory (IgD-CD27+) …
View more
View citations (4)
- Etzioni A, Ochs HD. The hyper IgM syndrome--an evolving story. Pediatr Res. 2004;56(4):519-25. doi:10.1203/01.PDR.0000139318.65842.4A. Epub 2004 Aug 19. PMID: 15319456.
- Primary B cell immunodeficiencies: comparisons and contrasts. Conley ME, et al. Annu Rev Immunol. 2009;27:199-227. doi:10.1146/annurev.immunol.021908.132649. PMID: 19302039.
- Davies EG, Thrasher AJ. Update on the hyper immunoglobulin M syndromes. Br J Haematol. 2010;149(2):167-80. doi:10.1111/j.1365-2141.2010.08077.x. Epub 2010 Feb 23. PMID: 20180797.
- Leven EA, Maffucci P, Ochs HD, Scholl PR, Buckley RH, Fuleihan RL, Geha RS, Cunningham CK, Bonilla FA, Conley ME, Ferdman RM, Hernandez-Trujillo V, Puck JM, Sullivan K, Secord EA, Ramesh M, Cunningham-Rundles C. Hyper IgM Syndrome: a Report from the USIDNET Registry. J Clin Immunol. 2016;36(5):490-501. doi:10.1007/s10875-016-0291-4. Epub 2016 May 17. PMID: 27189378.
Variant Interpretation:
What is the protocol for interpreting a variation as a VUS?
Help
The PreventionGenetics protocol for interpreting sequence variants has been carefully developed over a period of 10 years. We are conservative in our interpretations. We do not label a variant as pathogenic or benign without conclusive evidence. Although we use a variety of software to assist us in interpretation, we rely … View more
The PreventionGenetics protocol for interpreting sequence variants has been carefully developed over a period of 10 years. We are conservative in our interpretations. We do not label a variant as pathogenic or benign without conclusive evidence. Although we use a variety of software to assist us in interpretation, we rely … View more
Are family members with defined clinical status recruited to assess significance of VUS without charge?
Help
Yes. Please visit our website for details at https://www.preventiongenetics.com/forms.php for Targeted variant tests.
Yes. Please visit our website for details at https://www.preventiongenetics.com/forms.php for Targeted variant tests.
Will the lab re-contact the ordering physician if variant interpretation changes?
Help
Yes. Please visit our website for details http://preventiongenetics.com/
Yes. Please visit our website for details http://preventiongenetics.com/
Recommended fields not provided:
Clinical validity,
Clinical utility,
Is research allowed on the sample after clinical testing is complete?,
Sample negative report,
Sample positive report
Technical Information
Test Procedure:
Help
For the PGxome we use Next Generation Sequencing (NGS) technologies to cover the coding regions of targeted genes plus ~10 bases of non-coding DNA flanking each exon. As required, genomic DNA is extracted from patient specimens. Patient DNA corresponding to these regions is captured using Agilent Clinical Research Exome hybridization …
View more
Availability:
Help
Tests performed
Entire test performed in-house
Entire test performed in-house
Analytical Validity:
Help
As of March 2016, 6.36 Mb of sequence (83 genes, 1557 exons) generated in our lab was compared between Sanger and NextGen methodologies. We detected no differences between the two methods. The comparison involved 6400 total sequence variants (differences from the reference sequences). Of these, 6144 were nucleotide substitutions and …
View more
Proficiency testing (PT):
Is proficiency testing performed for this test?
Help
Yes
Method used for proficiency testing: Help
Intra-Laboratory
Yes
Method used for proficiency testing: Help
Intra-Laboratory
VUS:
Software used to interpret novel variations
Help
GeneSplicer, Human Splicing Finder, MaxEntScan, Mutation Taster, NNSPLICE, PolyPhen 2, SIFT and Splice Site Finder.
Laboratory's policy on reporting novel variations Help
Sequence variants found in our patients are contributed to ClinVar. Anonymous patient sequence data will also be shared with researchers for preparation of peer-reviewed publications.
GeneSplicer, Human Splicing Finder, MaxEntScan, Mutation Taster, NNSPLICE, PolyPhen 2, SIFT and Splice Site Finder.
Laboratory's policy on reporting novel variations Help
Sequence variants found in our patients are contributed to ClinVar. Anonymous patient sequence data will also be shared with researchers for preparation of peer-reviewed publications.
Recommended fields not provided:
Test Confirmation,
Assay limitations,
Description of 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:
Help
Category:
FDA exercises enforcement discretion
Additional Information
Reviews:
Clinical resources:
Molecular 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.