Proposal form for the evaluation of a genetic test for NHS Service Gene Dossier/Additional Provider

Transcription

1 Proposal form for the evaluation of a genetic test for NHS Service Gene Dossier/Additional Provider TEST DISEASE/CONDITION POPULATION TRIAD Submitting laboratory: London North East RGC GOSH Approved: September Disease/condition approved name and symbol as published on the OMIM database (alternative names will be listed on the UKGTN website) Deafness, X-Linked 2; DFNX2 2. OMIM number for disease/condition Disease/condition please provide a brief description of the characteristics of the disease/condition and prognosis for affected individuals. Please provide this information in laymen s terms. DFNX2 is a mixed type of deafness with conductive hearing loss resulting from stapes fixation, and progressive sensorineural deafness. It is associated with perilymphatic gusher at stapes surgery and unique developmental abnormalities of the ear. 4. Disease/condition mode of inheritance X-linked recessive 5. Gene approved name(s) and symbol as published on HUGO database (alternative names will be listed on the UKGTN website) POU class 3 homeobox 4; POU3F4 6. OMIM number for gene(s) Gene description(s) The POU3F4 gene encodes a member of the POU-III class of neural transcription factors that is expressed in the developing inner ear, brain, kidney and neural tube. POU3F4 maps to chromosome Xq b. Number of amplicons to provide this test 7c. MolU/Cyto band that this test is assigned to 8. Mutational spectrum for which you test including details of known common mutations Analysis involves Sanger sequencing the large single coding exon in 4 overlapping amplicons and MLPA. MolU Band D 2012/13 GenUs Band E 2103/14 Point mutations and small deletions / insertions and nonsense mutations are detected by sequence analysis. Large deletions and duplications are detected by MLPA. Specific deletions proximal to the POU3F4 gene affect highly conserved non-coding regions that are required for gene expression. MLPA is used to detect these commonly deleted regions. Naranjo et al (2010) Human Genetics 128(4): Technical method(s) Direct sequencing of the coding exon and intron/exon boundaries. Multiplex ligation-dependent probe amplification (MLPA) of the exon and upstream regions of the gene.

2 10. Validation process Please explain how this test has been validated for use in your laboratory Direct sequencing is a standard analytical method used in the laboratory for a range of diagnostic services requiring mutation detection. All primers used are validated and regularly checked for single nucleotide polymorphisms (SNPs). 11a. Are you providing this test already? Yes The MLPA kit (P163) is supplied by MRC-Holland, The Netherlands and the reaction carried out according to the manufacturer s protocols. MLPA is a commonly used technique within the laboratory and is validated for use with a number of additional disease genes. The laboratory participates in all relevant technical EQA schemes that are available through UKNEQAS and EMQN: 2011: In progress 2007 Genotypes correctly assigned in 3/3 sequencing EQA samples 2006 Genotypes correctly assigned in 3/3 sequencing EQA samples Genotypes correctly assigned in 3/3 sequencing EQA samples Genotypes correctly assigned in 4/4 sequencing EQA samples 35 cases with suspected X-linked deafness or a family history have been used to validate POU3F4 sequence and MLPA analysis 11b. If yes, how many reports have you produced? 35 including family members 11c. Number of reports mutation positive 14/16 probands tested exhibited the cardinal phenotype (see testing criteria). For 2/16 patients radiological data was not available and one of these was subsequently shown to have Pendred syndrome with two SLC26A4 mutations. Of the 14 patients with a consistent radiological phenotype 13 had a POU3F4 mutation detected by this testing strategy. 1/14 had no mutation detected. 11d. Number of reports mutation negative 3 (see above) 12. For how long have you been providing this service? 13a. Is there specialised local clinical/research expertise for this disease? 6 months Yes

3 13b. If yes, please provide details Dr Maria Bitner-Glindzicz, Consultant Clinical Geneticist, Level 4 York House, Great Ormond Street NHS Trust, London WC1N 3BH 14. Are you testing for other genes/diseases/conditions closely allied to this one? Branchio-oto-renal syndrome: EYA1, SIX1 and SIX5 genes; Pendred Syndrome: SLC26A4 gene; Connexin 26: GJB2 gene Please give details Your current activity If applicable - How many tests do you currently provide annually in your laboratory? 15a. Index cases 10 15b. Family members where mutation is known 20 Your capacity if Gene Dossier approved How many tests will you be able to provide annually in your laboratory if this gene dossier is approved and recommended for NHS funding? 16a. Index cases 50 16b. Family members where mutation is known Based on experience how many tests will be required nationally (UK wide) per annum? Please identify the information on which this is based 17a. Index cases Based on referrals into the Research Study at the Institute of Child Health. 17b. Family members where mutation is known 18. National activity (England, Scotland, Wales & Northern Ireland) If your laboratory is unable to provide the full national need please could you provide information on how the national requirement may be met. For example, are you aware of any other labs (UKGTN members or otherwise) offering this test to NHS patients on a local area basis only? This question has been included in order to gauge if there could be any issues in equity of access for NHS patients. It is appreciated that some laboratories may not be able to answer this question. If this is the case please write unknown. 20 This laboratory will be able to provide a National Service.

4 EPIDEMIOLOGY 19. Estimated prevalence of condition in the general UK population Please identify the information on which this is based Less than 1 in 100,000 based on the contribution of this gene to genetic deafness and the prevalence of congenital deafness 20. Estimated gene frequency (Carrier frequency or allele frequency) Please identify the information on which this is based 21. Estimated penetrance Please identify the information on which this is based Fully penetrant in males. Information comes from research studies in families segregating this type of deafness. Females are normal in the majority of cases although some may show mild hearing loss (again based on family studies in the research setting); we have detected two fully penetrant cases in females. 22. Estimated prevalence of condition in the target population. The target population is the group of people that meet the minimum criteria as listed in the Testing Criteria. The target population is clinically defined by patients exhibiting cardinal symptoms listed in the mutation testing criteria INTENDED USE 23. Please tick the relevant clinical purpose of testing Diagnosis Yes No Treatment Yes No Prognosis & management Yes No Presymptomatic testing Yes No Carrier testing for family members Yes No Prenatal testing Yes No

5 TEST CHARACTERISTICS 24. Analytical sensitivity and specificity This should be based on your own laboratory data for the specific test being applied for or the analytical sensitivity and specificity of the method/technique to be used in the case of a test yet to be set up. Direct Sanger sequencing has a high sensitivity in this laboratory using Big Dye chemistry with ABI analysers (3130XL, 3730XL). Data analysis is carried out using Mutation Surveyor software. We participate and perform successfully in EQA programmes for sequence analysis (see above). Bidirectional sequence analysis has specificity approaching 100% although large insertions/deletions and deep intronic mutations will not be detected by this method. The deafness MLPA kit (provided by MRC-Holland) detects whole exon deletion plus specific 5 deletions proximal to the POU3F4 gene as referenced in Naranjo et al (2010) Human Genetics 128(4): Clinical sensitivity and specificity of test in target population The clinical sensitivity of a test is the probability of a positive test result when condition is known to be present; the clinical specificity is the probability of a negative test result when disease is known to be absent. The denominator in this case is the number with the disease (for sensitivity) or the number without condition (for specificity). In all the patients analysed so far with what we consider to be the cardinal phenotype (N=14) all except one have had a positive test result. This is individual is known to have a balanced inversion outside the coding region of the gene which would be unlikely to be detected by this strategy. We therefore estimate the clinical sensitivity to be approximately 95% The clinical specificity is estimated to be 100% based on our results so far (N=10) research and clinical laboratory. 26. Clinical validity (positive and negative predictive value in the target population) The clinical validity of a genetic test is a measure of how well the test predicts the presence or absence of the phenotype, clinical condition or predisposition. It is measured by its positive predictive value (the probability of getting the condition given a positive test) and negative predictive value (the probability of not getting the condition given a negative test). As above, in patients exhibiting the cardinal symptoms, we would expect a very high PPV (close to 100%. Similarly in patients with a normal test result, the likelihood of these patients having DFNX2 is very low. Thus the NPV is also close to 100% 27. Testing pathway for tests where more than one gene is to be tested Please include your testing strategy if more than one gene will be tested and data on the expected proportions of positive results for each part of the process. Please illustrate this with a flow diagram. Only one gene will be tested. Direct sequencing analysis of the single coding exon and its intron/exon boundaries by PCR of four overlapping fragments MLPA analysis of the single exon and of three areas of large deletions/rearrangements CLINICAL UTILITY 28. How will the test add to the management of the patient or alter clinical outcome? 1. Molecular testing confirms the diagnosis of DFNX2 in patients with the cardinal phenotype or thought to have the cardinal phenotype. This type of deafness is also associated with the rare complication of perilymphatic gusher of cerebrospinal fluid at surgery; whilst this complication might be predicted from CT/MRI scan appearances this is not always the case, especially where surgeons and radiologists may never have seen a case before. Cochlear implant can be performed in such cases but should be approached with caution and patients counselled that prolonged recovery after gusher is a possibility. 2. Molecular testing may also suggest the possibility/confirm the presence, of a contiguous gene deletion syndrome. Deletions of contiguous probes would prompt further clinical evaluation of the child for choroideraemia (a rare and variable X-linked visual problem) and global developmental delay. 29. How will the availability of this test impact on patient and family life? 1) The major value of molecular analysis is in testing at risk female members of the family e.g. a proband s mother to determine recurrence risk, or sister to determine offspring risk. In small families without an obvious X-linked pattern of inheritance, molecular testing is the only accurate means of determining genetic risk. 2) In patients with a contiguous gene deletion syndrome and choroideraemia there are implications for the educational placement since it is likely that a child would eventually become visually impaired as well as deaf, and have significant learning difficulties. We have seen two such cases.

6 30. Benefits of the test Please provide a summary of the overall benefits of this test. The benefits of the test relate mainly to family members of the proband as accurate genetic risk determination becomes possible. Prior knowledge of a POU3F4 gene defect will help to direct surgical and cochlear implant intervention due to the greater risk of complications with these procedures. Additional clinical presentations such as developmental delay may be explained by a large deletion of the POU3F4 region. In the case of a point mutation, additional phenotypes indicate a need for further investigation. 31. Is there an alternative means of diagnosis or prediction that does not involve molecular diagnosis? If so (and in particular if there is a biochemical test), please state the added advantage of the molecular test. In males, MRI and CT scans are vital in making the diagnosis but the condition is very rare and not all radiologists would recognise it especially where they do not specialise in inner ear appearances. Scanning cannot be used with any accuracy to determine whether females are carriers of the condition. 32. Please describe any specific ethical, legal or social issues with this particular test. None 33. The Testing Criteria must be completed where Testing Criteria are not already available. If Testing Criteria are available, do you agree with them Yes/ No If No: Please propose alternative Testing Criteria AND please explain here the reasons for the changes. 34. Savings or investment per annum in the diagnostic pathway based on national expected activity, cost of diagnostics avoided and cost of genetic test. Please show calculations. Further genetic testing of the proband will be unnecessary once the molecular diagnosis has been made. GJB2 250 m.1555a>g 125 SLC26A4 450 TOTAL 825 For 20 patients per annum additional genetic testing would no longer be required: 16,500 (20 x 825) ERG ( 300) and ECG ( 25) testing would no longer be required. For 20 patients costs of these tests would be: 6,500 (20 x 325) Annual savings = 16, = 23, (costs of genetic test) = List the diagnostic tests/procedures that would no longer be required with costs. Costs and type of imaging procedures Costs and types of laboratory pathology tests (GJB2 + m.1555a>g+ SLC26A4) (other than molecular/cyto genetic proposed in this gene dossier) Costs and types of physiological tests (e.g. ECG) ERG ECG Cost and types of other investigations/procedures (e.g. biopsy) Total cost tests/procedures no longer required

7 36. REAL LIFE CASE STUDY In collaboration with the clinical lead, describe a real case example to illustrate how the test would improve patient experience. We were recently asked to test a young male child with speech and language delay secondary to profound deafness, together with motor delay. The radiologist queried the possibility of DFNX2 based on scan appearances but was not sure. There was no family history of deafness but the proband s mother had no brothers (only sisters) in her family. As time went on, the child appeared to develop features on the autistic spectrum. The mother requested a recurrence risk for deafness as she wished to have more children. A risk could not be given with certainty because of the slightly unusual clinical features (autism) and the hesitation of the radiologist. A risk of around 10% was given with the caveat that it could be up to 25% (with a 50% risk if the child was a male). Molecular testing has now shown that the child does have a point mutation in POU3F4 and that this is not present in his mother i.e. it is de novo. The recurrence risk is therefore reduced to that of gonadal mosaicism (probably less than 1% as this has not yet been reported). In the light of this information about risk the mother went on to have two further children who have normal hearing. Her sisters are not at risk of having affected children. The proband s autistic features remain and he is having investigations for this. Testing has clarified the diagnosis, provided accurate genetic counselling to the family, and indicated that further investigations are needed for another developmental problem. 37. For the case example, if there are cost savings, please provide these below: For the case example, the cost of some investigations (see 35. above) could have been avoided had the molecular test been available earlier in the child s management. PRE GENETIC TEST Costs and type of imaging procedures Costs and type of laboratory pathology tests: CX26 (GJB2), PS (SLC26A4), m.1555a>g 825 (see (other than molecular/cyto genetic proposed in this gene dossier) above) Costs and type of physiological tests (e.g. ECG): ERG, ECG 325 (see above) Cost and type of other investigations/procedures (e.g. biopsy) Cost outpatient consultations (genetics and non genetics) 350 Total cost pre genetic test 1500 POST GENETIC TEST Costs and type of imaging procedures Costs and types laboratory pathology tests (other than molecular/cyto genetic proposed in this gene dossier) Cost of genetic test proposing in this gene dossier 450 Costs and type of physiological tests (e.g. ECG) Cost and type of other investigations/procedures (e.g. biopsy) Cost outpatient consultations (genetics and non genetics) 350 Total cost post genetic test Estimated savings for case example described 700 See 35. above

8 UKGTN Testing Criteria Approved name and symbol of disease/condition(s): Deafness, X-Linked 2; DFNX2 Approved name and symbol of gene(s): POU class 3 homeobox 4; POU3F4 OMIM number(s): OMIM number(s): Patient name: Patient postcode: Date of birth: NHS number: Name of referrer: Title/Position: Lab ID: Referrals will only be accepted from one of the following: Referrer Clinical Geneticist Consultant Audiologist Tick if this refers to you. Minimum criteria required for testing to be appropriate as stated in the Gene Dossier: Criteria Sensorineural or mixed hearing loss AND MRI/CT scan findings: Dilatation of internal acoustic canal (bulbous) and deficiency of the lamina cribrosa, between the basal turn of the cochlea and the IAM. At risk family members where familial mutation is known Tick if this patient meets criteria Supportive features: Clear or possible X-linked inheritance (not necessary but would be highly suggestive) Possible choroideraemia (not necessary but would be highly suggestive) If the sample does not fulfil the clinical criteria or you are not one of the specified types of referrer and you still feel that testing should be performed please contact the laboratory to discuss testing of the sample