GTR Test Accession:
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GTR000554057.5
CAP
Last updated in GTR:
2022-01-12
View version history
GTR000554057.5,
last updated:
2022-01-12
GTR000554057.4,
last updated:
2021-01-11
GTR000554057.3,
last updated:
2018-03-28
GTR000554057.2,
last updated:
2017-08-23
GTR000554057.1,
registered in GTR:
2017-06-22
Last annual review date for the lab: 2024-07-17
LinkOut
At a Glance
Test purpose:
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Diagnosis;
Mutation Confirmation;
Pre-symptomatic; ...
Conditions (3):
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Alpha-1-antitrypsin deficiency;
Bronchiectasis;
Chronic obstructive pulmonary disease
Genes (1):
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SERPINA1 (14q32.13)
Methods (2):
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Molecular Genetics - Deletion/duplication analysis: Multiplex Ligation-dependent Probe Amplification (MLPA); ...
Target population: Help
All individuals with COPD regardless of age or ethnicity should …
Clinical validity:
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Not provided
Clinical utility:
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Establish or confirm diagnosis;
Lifestyle planning;
Predictive risk information for patient and/or family members
Ordering Information
Offered by:
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Test short name:
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SERPINA1
Specimen Source:
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- Buccal swab
- Buffy coat
- Cell culture
- Cord blood
- Fibroblasts
- Fresh tissue
- Frozen tissue
- Isolated DNA
- Peripheral (whole) blood
- Plasma
- Saliva
- Skin
Who can order: Help
- Genetic Counselor
- Health Care Provider
- Licensed Physician
Test Order Code:
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SERPINA1 sequencing
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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This laboratory is located in Ontario, Canada and cannot accept specimens from the USA. Out of province tests are available through arrangement with the laboratory manager. Properly labeled peripheral blood in EDTA with a completed requisition are required. This includes the patient's measured serum alpha-1 antitrypsin activity level and reasons …
Order URL
Test service:
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Clinical Testing/Confirmation of Mutations Identified Previously
Confirmation of research findings
Custom Deletion/Duplication Testing
Custom Sequence Analysis
Result interpretation
Confirmation of research findings
Custom Deletion/Duplication Testing
Custom Sequence Analysis
Result interpretation
Test additional service:
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Custom mutation-specific/Carrier testing
Test development:
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Test developed by laboratory but exempt from FDA oversight (eg. NYS CLEP approved, offered within a hospital or clinic)
Informed consent required:
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Decline to answer
Test strategy:
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Sanger sequencing. MLPA available as needed.
Pre-test genetic counseling required:
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Decline to answer
Post-test genetic counseling required:
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Decline to answer
Conditions
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Total conditions: 3
| Condition/Phenotype | Identifier |
|---|
Test Targets
Genes
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Total genes: 1
| 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
Multiplex Ligation-dependent Probe Amplification (MLPA)
Other
Sequence analysis of the entire coding region
Bi-directional Sanger Sequence Analysis
Applied Biosystems 3130, 3500
Clinical Information
Test purpose:
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Diagnosis;
Mutation Confirmation;
Pre-symptomatic;
Predictive
Clinical utility:
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Establish or confirm diagnosis
Lifestyle planning
Predictive risk information for patient and/or family members
View citations (1)
- Balduyck M, Odou MF, Zerimech F, Porchet N, Lafitte JJ, Maitre B. Diagnosis of alpha-1 antitrypsin deficiency: modalities, indications and diagnosis strategy. Rev Mal Respir. 2014;31(8):729-45. doi:10.1016/j.rmr.2014.06.001. Epub 2014 Jul 03. PMID: 25391508.
Lifestyle planning
View citations (1)
- Bernhard N, Lepper PM, Vogelmeier C, Seibert M, Wagenpfeil S, Bals R, Fähndrich S. Deterioration of quality of life is associated with the exacerbation frequency in individuals with alpha-1-antitrypsin deficiency - analysis from the German Registry. Int J Chron Obstruct Pulmon Dis. 2017;12:1427-1437. doi:10.2147/COPD.S130925. Epub 2017 May 12. PMID: 28553095.
Predictive risk information for patient and/or family members
View citations (1)
- Abboud RT, Nelson TN, Jung B, Mattman A. Alpha1-antitrypsin deficiency: a clinical-genetic overview. Appl Clin Genet. 2011;4:55-65. doi:10.2147/TACG.S10604. Epub 2011 Mar 31. PMID: 23776367.
Target population:
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All individuals with COPD regardless of age or ethnicity should be tested for AATD. All individuals with unexplained chronic liver disease should be tested for AATD. All individuals with necrotizing panniculitis, granulomatosis with polyangiitis, or unexplained bronchiectasis should be tested for AATD. Parents, siblings, and children, as well as extended …
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View citations (1)
- Sandhaus RA, Turino G, Brantly ML, Campos M, Cross CE, Goodman K, Hogarth DK, Knight SL, Stocks JM, Stoller JK, Strange C, Teckman J. The Diagnosis and Management of Alpha-1 Antitrypsin Deficiency in the Adult. Chronic Obstr Pulm Dis. 2016;3(3):668-682. doi:10.15326/jcopdf.3.3.2015.0182. Epub 2016 Jun 06. PMID: 28848891.
Variant Interpretation:
What is the protocol for interpreting a variation as a VUS?
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Variant interpretation protocol is as per ACMG consensus recommendations, Genet. Med. 2015; 17(5):405-424
Variant interpretation protocol is as per ACMG consensus recommendations, Genet. Med. 2015; 17(5):405-424
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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Not provided. It is expected that patients have received adequate counselling regarding potential for changes in variant interpretation over time. Patients should keep in touch with their counselling service with regard to this potential. Re-interpretation is performed at no additional cost, upon request.
Not provided. It is expected that patients have received adequate counselling regarding potential for changes in variant interpretation over time. Patients should keep in touch with their counselling service with regard to this potential. Re-interpretation is performed at no additional cost, upon request.
Recommended fields not provided:
Clinical validity,
Will the lab re-contact the ordering physician if variant interpretation changes?,
Is research allowed on the sample after clinical testing is complete?,
Sample negative report,
Sample positive report
Technical Information
Test Procedure:
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Test uses the MRC Holland MLPA P459 SERPINA1 probemix following the company's recommended procedures.
Test Platform:
ABI3130, ABI3500
Test Confirmation:
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Positive results are used in the context of other, independent factors (patient phenotype, second mutation, enzyme activity level).
Availability:
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Tests performed
Entire test performed in-house
Entire test performed in-house
Analytical Validity:
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Bidirectional Sanger sequencing has nearly 100% analytical sensitivity and specificity for detection of germ line sequence variants in the targeted regions.
View citations (1)
- Graham RP, Dina MA, Howe SC, Butz ML, Willkomm KS, Murray DL, Snyder MR, Rumilla KM, Halling KC, Highsmith WE. SERPINA1 Full-Gene Sequencing Identifies Rare Mutations Not Detected in Targeted Mutation Analysis. J Mol Diagn. 2015;17(6):689-94. doi:10.1016/j.jmoldx.2015.07.002. Epub 2015 Aug 28. PMID: 26321041.
Assay limitations:
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Limitations, including allele dropout due to exon deletion or SNP underlying the PCR primers represent less than 1% of cases.
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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SIFT, Polyphen, Align GVGD, NNSPLICE, MaxEntScan, SSF, Human Splicing Finder
Laboratory's policy on reporting novel variations Help
Novel variations are communicated typically by routine report with telephone support as needed.
SIFT, Polyphen, Align GVGD, NNSPLICE, MaxEntScan, SSF, Human Splicing Finder
Laboratory's policy on reporting novel variations Help
Novel variations are communicated typically by routine report with telephone support as needed.
Recommended fields not provided:
Citations to support assay limitations,
Description of internal test validation method,
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:
Practice guidelines:
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.