GTR Test Accession:
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GTR000607890.2
Last updated in GTR: 2024-05-15
View version history
GTR000607890.2, last updated: 2024-05-15
GTR000607890.1, last updated: 2023-05-30
Last annual review date for the lab: 2024-05-28
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At a Glance
Test purpose:
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Diagnosis
Conditions (46):
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Reticular dysgenesis;
3-Methylglutaconic aciduria type 2;
3-methylglutaconic aciduria, type VIIA
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Genes (30):
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Methods (2):
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Molecular Genetics - Deletion/duplication analysis: Next-Generation (NGS)/Massively parallel sequencing (MPS); ...
Target population: Help
Providing a genetic evaluation for patients with a personal or …
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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Test short name:
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SCCNP
Specimen Source:
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- Fibroblasts
- Peripheral (whole) blood
- Skin
- View specimen requirements
Who can order: Help
- Genetic Counselor
- Health Care Provider
- Licensed Dentist
- Licensed Physician
- Nurse Practitioner
- Physician Assistant
- Public Health Mandate
- Registered Nurse
Lab contact:
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Elyse Love, MS, CGC, Certified Genetic counselor, CGC, Genetic Counselor
gcmolgen@mayo.edu
1-800-533-1710
gcmolgen@mayo.edu
1-800-533-1710
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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https://www.mayocliniclabs.com/test-catalog/Overview/619872#Specimen
Order URL
Order URL
Test development:
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Manufactured (research use only; not FDA-reviewed)
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:
Test strategy
Conditions
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Total conditions: 46
Condition/Phenotype | Identifier |
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Test Targets
Genes
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Total genes: 30
Gene | Associated Condition | Germline or Somatic | Allele (Lab-provided) | Variant in NCBI |
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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)
Illumina NovaSeq 6000
Sequence analysis of the entire coding region
Next-Generation (NGS)/Massively parallel sequencing (MPS)
Illumina NovaSeq 6000
Clinical Information
Test purpose:
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Diagnosis
Clinical utility:
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Establish or confirm diagnosis
View citations (7)
- Dale DC, Makaryan V. -Related Neutropenia. 2002 Jun 17 [updated 2018 Aug 23]. In: Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE, Amemiya A, editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2024. PMID: 20301705.
- Skokowa J, Dale DC, Touw IP, Zeidler C, Welte K. Severe congenital neutropenias. Nat Rev Dis Primers. 2017;3:17032. doi:10.1038/nrdp.2017.32. Epub 2017 Jun 08. PMID: 28593997.
- A Novel Homozygous HAX1 Mutation in a Child With Cyclic Neutropenia: A Case Report and Review. Tayal A, et al. J Pediatr Hematol Oncol. 2022;44(2):e420-e423. doi:10.1097/MPH.0000000000002110. PMID: 33633030.
- Fadeel B, Garwicz D, Carlsson G, Sandstedt B, Nordenskjöld M. Kostmann disease and other forms of severe congenital neutropenia. Acta Paediatr. 2021;110(11):2912-2920. doi:10.1111/apa.16005. Epub 2021 Jun 29. PMID: 34160857.
- Tangye SG, Al-Herz W, Bousfiha A, Cunningham-Rundles C, Franco JL, Holland SM, Klein C, Morio T, Oksenhendler E, Picard C, Puel A, Puck J, Seppänen MRJ, Somech R, Su HC, Sullivan KE, Torgerson TR, Meyts I. Human Inborn Errors of Immunity: 2022 Update on the Classification from the International Union of Immunological Societies Expert Committee. J Clin Immunol. 2022;42(7):1473-1507. doi:10.1007/s10875-022-01289-3. Epub 2022 Jun 24. PMID: 35748970.
- Chandra S, Bronicki L, Nagaraj CB, et al: WAS-related disorders. In: Adam MP, Everman DB, Mirzaa GM, et al, eds. GeneReviews [Internet]. University of Washington, Seattle; 2004. Updated September 22, 2016. Accessed January 19, 2023. Available at https://www.ncbi.nlm.nih.gov/books/NBK1178/
- https://www.ncbi.nlm.nih.gov/books/NBK1533
Target population:
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Providing a genetic evaluation for patients with a personal or family history suggestive of severe congenital neutropenia and/or cyclic neutropenia
Establishing a diagnosis of an inherited congenital neutropenia and, in some cases, allowing for appropriate management and surveillance for disease features based on the gene involved
View citations (7)
- Dale DC, Makaryan V. -Related Neutropenia. 2002 Jun 17 [updated 2018 Aug 23]. In: Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE, Amemiya A, editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2024. PMID: 20301705.
- Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL, . Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17(5):405-24. doi:10.1038/gim.2015.30. Epub 2015 Mar 05. PMID: 25741868.
- Skokowa J, Dale DC, Touw IP, Zeidler C, Welte K. Severe congenital neutropenias. Nat Rev Dis Primers. 2017;3:17032. doi:10.1038/nrdp.2017.32. Epub 2017 Jun 08. PMID: 28593997.
- A Novel Homozygous HAX1 Mutation in a Child With Cyclic Neutropenia: A Case Report and Review. Tayal A, et al. J Pediatr Hematol Oncol. 2022;44(2):e420-e423. doi:10.1097/MPH.0000000000002110. PMID: 33633030.
- Fadeel B, Garwicz D, Carlsson G, Sandstedt B, Nordenskjöld M. Kostmann disease and other forms of severe congenital neutropenia. Acta Paediatr. 2021;110(11):2912-2920. doi:10.1111/apa.16005. Epub 2021 Jun 29. PMID: 34160857.
- Tangye SG, Al-Herz W, Bousfiha A, Cunningham-Rundles C, Franco JL, Holland SM, Klein C, Morio T, Oksenhendler E, Picard C, Puel A, Puck J, Seppänen MRJ, Somech R, Su HC, Sullivan KE, Torgerson TR, Meyts I. Human Inborn Errors of Immunity: 2022 Update on the Classification from the International Union of Immunological Societies Expert Committee. J Clin Immunol. 2022;42(7):1473-1507. doi:10.1007/s10875-022-01289-3. Epub 2022 Jun 24. PMID: 35748970.
- Chandra S, Bronicki L, Nagaraj CB, et al: WAS-related disorders. In: Adam MP, Everman DB, Mirzaa GM, et al, eds. GeneReviews [Internet]. University of Washington, Seattle; 2004. Updated September 22, 2016. Accessed January 19, 2023. Available at https://www.ncbi.nlm.nih.gov/books/NBK1178/
Variant Interpretation:
What is the protocol for interpreting a variation as a VUS?
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All detected variants are evaluated according to the most recent American College of Medical Genetics and Genomics (ACMG) and Association for Molecular Pathology (AMP) recommendations. Variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance.
All detected variants are evaluated according to the most recent American College of Medical Genetics and Genomics (ACMG) and Association for Molecular Pathology (AMP) recommendations. Variants are classified based on known, predicted, or possible pathogenicity and reported with interpretive comments detailing their potential or known significance.
Are family members with defined clinical status recruited to assess significance of VUS without charge?
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Contact lab for details
Contact lab for details
Will the lab re-contact the ordering physician if variant interpretation changes?
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Not provided. The laboratory encourages health care providers to contact the laboratory at any time to learn how the status of a particular variant may have changed over time.
Not provided. The laboratory encourages health care providers to contact the laboratory at any time to learn how the status of a particular variant may have changed over time.
Research:
Is research allowed on the sample after clinical testing is complete?
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Research testing is only performed under IRB approved protocol with an opt-out policy in place.
Research testing is only performed under IRB approved protocol with an opt-out policy in place.
Recommended fields not provided:
Clinical validity,
Are family members with defined clinical status recruited to assess significance of VUS without charge?,
Will the lab re-contact the ordering physician if variant interpretation changes?,
Sample negative report,
Sample positive report
Technical Information
Test Procedure:
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Next-generation sequencing (NGS) and/or Sanger sequencing are performed to test for the presence of variants in coding regions and intron/exon boundaries of the genes analyzed, as well as some other regions that have known disease-causing variants. The human genome reference GRCh37/hg19 build was used for sequence read alignment. At least …
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Availability:
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Tests performed
Entire test performed in-house
Entire test performed in-house
Analytical Validity:
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At least 99% of the bases are covered at a read depth >30X. Sensitivity is estimated at >99% for single nucleotide variants, >94% for indels up to 39 base pairs, >95% for deletions up to 75 base pairs and insertions up to 47 base pairs.
Assay limitations:
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Clinical Correlations: Test results should be interpreted in the context of clinical findings, family history, and other laboratory data. Misinterpretation of results may occur if the information provided is inaccurate or incomplete. If testing was performed because of a clinically significant family history, it is often useful to first test …
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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
Platform PT performed
Description of internal test validation method: Help
This test was laboratory developed, and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements
Yes
Method used for proficiency testing: Help
Platform PT performed
Description of internal test validation method: Help
This test was laboratory developed, and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements
VUS:
Software used to interpret novel variations
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Variants may be analyzed using any combination of the following: Alamut, REVEL, Polyphen-2, SIFT, AGVGD, MutationTaster, SpliceSiteFinder-like, MaxEntScan, NNSPLICE, GeneSplicer, SpliceAI, gene-specific online databases, ISCA, UCSC Genome Browser
Laboratory's policy on reporting novel variations Help
All novel alterations and copy number variants are evaluated for potential pathogenicity and included in the written report, accordingly.
Variants may be analyzed using any combination of the following: Alamut, REVEL, Polyphen-2, SIFT, AGVGD, MutationTaster, SpliceSiteFinder-like, MaxEntScan, NNSPLICE, GeneSplicer, SpliceAI, gene-specific online databases, ISCA, UCSC Genome Browser
Laboratory's policy on reporting novel variations Help
All novel alterations and copy number variants are evaluated for potential pathogenicity and included in the written report, accordingly.
Recommended fields not provided:
Test Confirmation,
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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Category:
FDA exercises enforcement discretion
Additional Information
Reviews:
Clinical resources:
Molecular resources:
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.