PAX6 gene mutation analysis - Clinical Genetic Test - GTR

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PAX6 gene mutation analysis

Clinical Genetic Test

offered by

Genetics and Molecular Pathology

View lab's test page

GTR Test Accession: GTR000562609.1

OPHTHALMOLOGYINHERITED DISEASENERVOUS SYSTEM ... View more

Last updated in GTR: 2019-02-19

Last annual review date for the lab: 2024-01-08

At a Glance

Test purpose:

Diagnosis; Mutation Confirmation

Conditions (7):

Congenital ocular coloboma; Aniridia 1; Autosomal dominant keratitis; ...

Genes (1):

PAX6 (11p13)

Methods (2):

Molecular Genetics - Sequence analysis of select exons: Multiplex Ligation-dependent Probe Amplification (MLPA); ...

Target population:

Indviduals with a personal and/or family history of symptoms consistent …

Clinical validity:

Not provided

Clinical utility:

Establish or confirm diagnosis; Guidance for management; Lifestyle planning; ...

Ordering Information

Offered by:

Genetics and Molecular Pathology
View lab's website
View lab's test page

Specimen Source:

Amniotic fluid
Buccal swab
Buffy coat
Chorionic villi
Isolated DNA
Peripheral (whole) blood
Saliva
View specimen requirements

Who can order:

Genetic Counselor
Licensed Physician

Test Order Code:

PAX6

Lab contact:

Andrew Dubowsky, Lab Director
andrew.dubowsky@sa.gov.au
61 8 8204 6447

Contact Policy:

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:

Refer to our website; standard laboratory test request form. Contact the laboratory directly for further details
Order URL

Test service:

Clinical Testing/Confirmation of Mutations Identified Previously
Confirmation of research findings
Custom Sequence Analysis
Genetic counseling
Result interpretation

Test additional service:

Custom Prenatal Testing

Test development:

Test developed by laboratory (no manufacturer test name)

Informed consent required:

Based on applicable state law

Test strategy:

Testing of the entire gene is available for patients symptomatic of aniridia. Cascade testing offered to family members for Class 4 and 5 variants, segregation studies offered for Class 3 variants.

Pre-test genetic counseling required:

Yes

Post-test genetic counseling required:

Yes

Conditions

Total conditions: 7

Condition/Phenotype	Identifier

Test Targets

Genes

Total genes: 1

Gene	Associated Condition	Germline or Somatic	Allele (Lab-provided)	Variant in NCBI

Methodology

Total methods: 2

Method Category

Test method

Instrument

Sequence analysis of select exons

Multiplex Ligation-dependent Probe Amplification (MLPA)

Sequence analysis of the entire coding region

Bi-directional Sanger Sequence Analysis

Applied Biosystems 3730 capillary sequencing instrument

Clinical Information

Test purpose:

Diagnosis; Mutation Confirmation

Clinical utility:

Establish or confirm diagnosis
Guidance for management
Lifestyle planning
Reproductive decision-making

Target population:

Indviduals with a personal and/or family history of symptoms consistent with aniridia

Variant Interpretation:

What is the protocol for interpreting a variation as a VUS?
Review clinical importance described in ClinVar, HGMD, LOVD, and literature. Assessment of classification criteria specified by ACMG and clinical review team meeting.

Are family members with defined clinical status recruited to assess significance of VUS without charge?
No. "Referral to a clinical genetics service is recommended. Predictive testing is currently NOT recommended using this variant for assessing disease risk. Sanger sequencing to confirm this variant and analysis of parental samples may help to further elucidate the clinical significance of this variant. If required, please send the parental samples … View more

Will the lab re-contact the ordering physician if variant interpretation changes?
Yes. Communication by way of patient specific written formal intepretive report

Research:

Is research allowed on the sample after clinical testing is complete?
Yes, and only if formal written consent has been provided.

Recommended fields not provided:

Clinical validity, Sample negative report, Sample positive report

Technical Information

Test Procedure:

DNA is extracted from the patient specimen, PCR amplification and sequence analysis of the entire coding region/ or indicated exons plus additional flanking intronic or other non-coding sequence. Sanger sequencing is carried out and the sequence is visualised on a capillary sequencer. Sequencing is performed separately in both the forward … View more

Test Confirmation:

Second independently collected specimen recommended for positive diagnostic tests.

Test Comments:

Bi-directional DNA sequencing of the intron exon boundarys of the entire PAX6 gene and MLPA / copy number analysis performed in parallel.

Availability:

Tests performed
Entire test performed in-house

Analytical Validity:

Proficiency Testing, both external and internal. Sanger of PCR fragments at an the error rate is less than 0.01% (99.99% accuracy). Technical specificity for all methods used in our lab estimated at > 99.5% and technical sensitivity > 99.5%. Mutation detection reproducibility for Sanger sequencing is 100%.

Assay limitations:

Large genomic rearrangements, small deletions and point mutations that remove a primer site.

Proficiency testing (PT):

Is proficiency testing performed for this test?
Yes

Method used for proficiency testing:
Formal PT program

PT Provider:
European Molecular Genetics Quality Network, EMQN

Description of PT method:
General module for PCR amplification and bidirectional sequencing of samples provided - NB gene not specific.

VUS:

Software used to interpret novel variations
Alamut Visual, plus supplemented with a number of online tools.

Laboratory's policy on reporting novel variations
Detailed interpretative report provided for Class 3, 4, and 5, however Class 3 (VUS) only reported where patient has elected to know about identification of VUS. Class 1 and 2 variants are not reported.

Recommended fields not provided:

Citations to support assay limitations, Description of internal test validation method, Citations for Analytical validity, Major CAP category, CAP category, CAP test list

Regulatory Approval

FDA Review:

Not provided

Additional Information

Reviews:

PubMed Clinical Queries

Clinical resources:

Consumer resources:

MedlinePlusGenetics (GHR)

MedlinePlus

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.