GTR Test Accession:
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GTR000593432.2
Last updated in GTR: 2024-05-13
View version history
GTR000593432.2, last updated: 2024-05-13
GTR000593432.1, last updated: 2021-07-23
Last annual review date for the lab: 2024-06-03
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At a Glance
Test purpose:
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Diagnosis;
Mutation Confirmation;
Pre-symptomatic
Conditions (1):
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Tubulointerstitial kidney disease, autosomal dominant, 2
Genes (1):
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MUC1 (1q22)
Methods (1):
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Molecular Genetics - Targeted variant analysis: MALDI-TOF mass spectrometry
Target population: Help
Individuals with a diagnosis of tubulointerstitial kidney disease leading to …
Clinical validity:
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PPV = 100%, NPV = 100%
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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MKD
Specimen Source:
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- Isolated DNA
- View specimen requirements
Who can order: Help
- Health Care Provider
Lab contact:
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Diana Toledo, PhD, MS, CGC, Lab Associate Director
dtoledo@broadinstitute.org
dtoledo@broadinstitute.org
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.
Test service:
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Clinical Testing/Confirmation of Mutations Identified Previously
Test development:
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Test developed by laboratory (no manufacturer test name)
Informed consent required:
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Decline to answer
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,
How to Order,
Test strategy
Conditions
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Total conditions: 1
| 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: 1
Method Category
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Test method
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Instrument *
Targeted variant analysis
MALDI-TOF mass spectrometry
* Instrument: Not provided
Clinical Information
Test purpose:
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Diagnosis;
Mutation Confirmation;
Pre-symptomatic
Clinical validity:
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PPV = 100%, NPV = 100%
View citations (1)
- Blumenstiel B, DeFelice M, Birsoy O, Bleyer AJ, Kmoch S, Carter TA, Gnirke A, Kidd K, Rehm HL, Ronco L, Lander ES, Gabriel S, Lennon NJ. Development and Validation of a Mass Spectrometry-Based Assay for the Molecular Diagnosis of Mucin-1 Kidney Disease. J Mol Diagn. 2016;18(4):566-71. doi:10.1016/j.jmoldx.2016.03.003. Epub 2016 May 05. PMID: 27157321.
Clinical utility:
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Establish or confirm diagnosis
View citations (1)
- Bleyer AJ, Kmoch S, Antignac C, Robins V, Kidd K, Kelsoe JR, Hladik G, Klemmer P, Knohl SJ, Scheinman SJ, Vo N, Santi A, Harris A, Canaday O, Weller N, Hulick PJ, Vogel K, Rahbari-Oskoui FF, Tuazon J, Deltas C, Somers D, Megarbane A, Kimmel PL, Sperati CJ, Orr-Urtreger A, Ben-Shachar S, Waugh DA, McGinn S, Bleyer AJ, Hodanová K, Vylet'al P, Živná M, Hart TC, Hart PS. Variable clinical presentation of an MUC1 mutation causing medullary cystic kidney disease type 1. Clin J Am Soc Nephrol. 2014;9(3):527-35. doi:10.2215/CJN.06380613. Epub 2014 Feb 07. PMID: 24509297.
Target population:
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Individuals with a diagnosis of tubulointerstitial kidney disease leading to chronic kidney failure, or individuals with a known family history of tubulointerstitial kidney disease.
Recommended fields not provided:
What is the protocol for interpreting a variation as a VUS?,
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?,
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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See PMID: 27157321 for specifics regarding the development and validation of this method.
View citations (1)
- Blumenstiel B, DeFelice M, Birsoy O, Bleyer AJ, Kmoch S, Carter TA, Gnirke A, Kidd K, Rehm HL, Ronco L, Lander ES, Gabriel S, Lennon NJ. Development and Validation of a Mass Spectrometry-Based Assay for the Molecular Diagnosis of Mucin-1 Kidney Disease. J Mol Diagn. 2016;18(4):566-71. doi:10.1016/j.jmoldx.2016.03.003. Epub 2016 May 05. PMID: 27157321.
Test Platform:
Agena Bioscience
Test Confirmation:
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Each sample is run in duplicate on different plates for confirmation.
Test Comments:
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This test is validated to detect a single-base insertion/duplication of a cytosine residue within a variable number tandem repeat (VNTR) region of the MUC1 gene. This duplication lies within a GC-rich region of the gene, which is difficult to assess by standard next-generation sequencing methods. Therefore, this MALDI-TOF MS method …
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Availability:
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Tests performed
Interpretation performed in-house
Report generated in-house
Specimen preparation performed at an outside lab
Wet lab work performed in-house
Test performance comments
We accept only already extracted DNA for this assay.
Interpretation performed in-house
Report generated in-house
Specimen preparation performed at an outside lab
Wet lab work performed in-house
Test performance comments
We accept only already extracted DNA for this assay.
Analytical Validity:
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288 total samples assayed during validation. Fail rate: 1% (3/288) Inconclusive rate: 3.5% (10/285) Precision: 100% (two independent technologists, six replicate runs across three days, no discrepant conclusive calls) Accuracy: 100% (275/275 conclusive calls with no false negatives or false positives against the known reference) Analytical Sensitivity: 100% Analytical Specificity: …
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View citations (1)
- Blumenstiel B, DeFelice M, Birsoy O, Bleyer AJ, Kmoch S, Carter TA, Gnirke A, Kidd K, Rehm HL, Ronco L, Lander ES, Gabriel S, Lennon NJ. Development and Validation of a Mass Spectrometry-Based Assay for the Molecular Diagnosis of Mucin-1 Kidney Disease. J Mol Diagn. 2016;18(4):566-71. doi:10.1016/j.jmoldx.2016.03.003. Epub 2016 May 05. PMID: 27157321.
Assay limitations:
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This is a Lab-Developed Test (LDT) and has not been cleared by the FDA. The FDA has determined that such clearance or approval is not necessary. This test was validated for a specific Cytosine reside duplication/insertion in a specific VNTR region.
Proficiency testing (PT):
Is proficiency testing performed for this test?
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Yes
Method used for proficiency testing: Help
Alternative Assessment
PT Provider: Help
Internal Proficiency Testing
Description of PT method: Help
Alternative proficiency testing of de-identified internal samples and blinding laboratory technicians to sample results. Performed bi-annually.
Yes
Method used for proficiency testing: Help
Alternative Assessment
PT Provider: Help
Internal Proficiency Testing
Description of PT method: Help
Alternative proficiency testing of de-identified internal samples and blinding laboratory technicians to sample results. Performed bi-annually.
Recommended fields not provided:
Citations to support assay limitations,
Description of internal test validation method,
Major CAP category, CAP category, CAP test list
Regulatory Approval
FDA Review:
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Not provided
Additional Information
Clinical resources:
Molecular resources:
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