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

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1 Proposal form for the evaluation of a genetic test for NHS Service Gene Dossier Test Disease Population Triad Disease name Choroideremia OMIM number for disease Disease alternative names please provide any alternative names you wish listed Disease please provide a brief description of the disease characteristics Disease - mode of inheritance Gene name(s) OMIM number for gene(s) Gene alternative names please provide any alternative names you wish listed Gene description(s) (including number of amplicons) Mutational spectrum for which you test including details of known common mutations. Tapetochoroidal dystrophy Choroidal sclerosis Choroideremia is an X-linked ocular disorder that leads to the degeneration of the choriocapillaris, retinal pigment epithelium, and the retinal photoreceptor of the eye. Affected males suffer progressive loss of vision (reduction of central vision, constriction of visual fields, night blindness) beginning at an early age, and the choroid and retina undergo complete atrophy. Heterozygous females show little or no visual defect although many (not all) show funduscopic changes. X-Linked Recessive CHM gene, which encodes Rab escort protein-1 (REP1) CHM Rab escort protein 1 REP1 CHM is the only gene known to be associated with choroideremia. It has 15 coding exons across bp of genomic DNA. It has a transcript length of 2,115 bps which encodes for the 653 amino acid Rab escort protein 1 (REP1) protein. This gene is amplified in 15 amplicons (UKGTN MOLU Band D). There are no founder/common mutations. Our screen detects point mutations and small insertion deletion variants. Whole exon deletions can be detected in males but not in females. Technical Method (s) Validation Process Note: please explain how this test has been validated for use in your laboratory Bi-directional fluorescent Sanger sequencing for point mutations and indels. Multiplex PCR for exonic deletions in males. There are no reference materials available to act as validation controls. A series of patients ascertained through research testing have been repeat tested in developing the diagnostic system. We have screened 36 patients for the CHM gene. We found a total of 25 mutations. All mutations found were confirmed with two fresh dilutions. 1

2 Are you providing this test already? If yes, how many reports have you produced? Please give the number of mutation positive/negative samples you have reported For how long have you been providing this service? Is there specialised local clinical/research expertise for this disease? Are you testing for other genes/diseases closely allied to this one? Please give details Your Current Activity If applicable - How many tests do you currently provide annually in your laboratory? 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? Based on experience how many tests will be required nationally (UK wide)? 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. Yes Number of reports issued: 36 Number of reports mutation positive: 25 Number of reports mutation negative:11 2 Years Yes No Please provide details Close links are retained with the Regional Clinical Genetics Service, Manchester Royal Eye Hospital and Moorfields Eye Hospital. We currently offer testing for a wide range of ophthalmic genetic disorders. X-linked and dominant retinitis pigmentosa (gene dossiers accepted), Best disease, macular dystrophy, Leber congenital amaurosis (gene dossiers pending). See above we have to date tested 36 index cases in 24 months. We anticipate a workload of up to 40 index cases pa and a further 20 reflex tests (see below). We can meet this capacity in house. We are currently only receiving samples from two centres (Manchester and Moorfield s). We would expect this to rise if the dossier is accepted. Based upon current demand we anticipate perhaps 40 index cases pa. This will lead to reflex testing for up to 20 relatives pa. This is solely a linkage based service. Consequently we are the only laboratory offering a mutation scanning service. We feel we can continue to meet the national need. 2

3 Epidemiology Estimated prevalence of disease in the general UK population Estimated gene frequency (Carrier frequency or allele frequency) Estimated penetrance Prevalence is estimated to be 1:50,000. This estimation is supported by the assumption that if the prevalence of RP is 1:3500, and about 6% of individuals diagnosed with RP-related disorders actually have CHM [Heckenlively 1991], it is likely that approximately 1:58,000 individuals have CHM. Heckenlively JR. Choroideremia. In: Heckenlively JR, Arden GB (eds) Principles and Practice of Clinical Electrophysiology of Vision. Mosby Year Book, St. Louis, pp Whilst most affected individuals are male this disorder can affect females. Therefore it is not possible to accurately estimate carrier frequencies from the disease prevalence figures (above). The penetrance is high (100%) in males but can vary in females due to X-inactivation. Target Population Description of the population to which this test will apply (i.e. description of the population as defined by the minimum criteria listed in the testing criteria) Estimated prevalence of disease in the target population The target population is defined by the choroideremia phenotype, ie. only cases with a high index of suspicion (ascertained by clinical geneticists or collaborating ophthalmologists) and a high probability of carrying a CHM mutation are offered testing. Reflex testing (carrier and predictive) will be made available to family members in the context of appropriate genetic counselling. The test will be available to all UK inhabitants. Only individuals with a high prior likelihood of carrying a mutation (ie affected by choroideremia) will be tested. In the first two years of screening we identified causative mutations in 25 out of 36 index cases referred. Intended Use (Please use the questions in Annex A to inform your answers) Please tick the relevant clinical purpose of testing YES NO Diagnosis Treatment Prognosis & Management Presymptomatic testing Risk Assessment for family members Risk Assessment prenatal testing (see text) 3

4 Test Characteristics An alytical 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. Clinical sensitivity and specificity of test in target population The clinical sensitivity of a test is the probability of a positive test result when disease 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 disease (for specificity) 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 disease or predisposition. It is measured by its positive predictive value (the probability of getting the disease given a positive test) and negative predictive value (the probability of not getting the disease given a negative test). Testing pathway 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. This can be added to the document as a separate sheet if necessary. On the basis of re-sequencing of positive controls (and experiences with other services in the lab) we estimate that the analytical sensitivity and specificity of the techniques used (Sanger sequencing and multiplex PCR) will be greater than 98%. To date no other gene has been implicated in this disease. In our cohort a pathogenic variant has been found in 90% of males with a strong clinical suspicion of choroideremia So far all confirmed CHM mutations have been clearly pathogenic (frame-shift, nonsense, splice site) and interpretation has been straightforward. Missense changes of unknown clinical significance are rare (only one so far identified in our cohort). Given the very low number of UVs and the high penetrance in males the positive predictive value in males is almost 100%. The vast majority of females remain asymptomatic - there is a low positive predictive value in females. Similarly the negative predictive value in a family with a known mutation will be 100% in males. This is a single gene test. 4

5 Clinical utility of test in target population (Please refer to Appendix A) Please provide a description of the clinical care pathway. Choroideremia (CHM) is a severe form of retinal dystrophy. Males with the disease present in the first two decades of life and are significantly disabled by the condition during adulthood, however it can be challenging to distinguish CHM from other retinal dystrophies. Genetic testing for choroideremia has a large impact on the families in establishing the mode of inheritance and identifying or excluding carrier status in women (carriers often have a normal fundus in adult-hood). How will the test add to the management of the patient or alter clinical outcome? What impact will this test have on the NHS i.e. by removing the need for alternative management and/or investigations for this clinical population? Please provide evidence from your own service. The implications of CHM are similar to other X-linked disorders: Asymptomatic young females - in particular those with experience of their fathers/brothers with the disease, are often anxious to know their carrier status. Since this cannot be provided with 100% accuracy from clinical testing, carrier testing is often sought by these females. a. Asymptomatic young females, in whom carrier status is excluded are able to be discharged from follow-up. b. Females carrying a mutation may be offered PND. Asymptomatic males a. The age at which males should be tested is debatable however, families are often keen to ensure that boys are diagnosed early since this impacts upon education, training, life choices (e.g. career choices) and management. For this reason examination, or genetic testing, under the age of 5 may be requested and is considered. b. Males who have been reassured on clinical grounds are often anxious to have genetic confirmation later in life in order to demonstrate that they do not carry mutations. Symptomatic males Molecular confirmation has a positive impact on coping with this debilitating disease. CHM is associated with severe early onset visual disability and blindness secondary to retinal degeneration. The condition is therefore associated with a significant and progressive disability in the context of normal general health that is also progressive. The condition is X linked. Genetic counselling: Genetic testing for CHM mutations will provide a precise molecular diagnosis in over 95% of cases. This provides clearer information regarding carrier status (not all carriers are distinguishable clinically) and hence will provide choices (eg PND) that would not otherwise be available. This test will impact significantly on a significant number of families by offering options (carrier, pre-symptomatic and prenatal testing) where this has previously not been possible. It will benefit families in whom one or more individuals have a clinical diagnosis of choroideremia. 5

6 What are the consequences of not doing this genetic test. Commissioners have asked for specific information to support introduction of tests. Utility of test in the NHS In a couple of sentences explain the utility of this test for the disease(s) 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 Please describe any specific ethical, legal or social issues with this particular test? Denying this testing will severely limit the reproductive choices of patients thereby increasing significantly the emotional burden of the disease. Female carrier not being identified leading to males being born with severe visual impairments. This test identifies a severe inherited retinal dystrophy. It will make possible carrier, pre-symptomatic and first trimester prenatal diagnosis. Affected individuals are first identified by characteristic changes in the fundus on retinal examination. However this is not a reliable carrier test in females. None known 6

7 UKGTN Testing criteria Name of Disease(s): CHOROIDEREMIA; CHM (303100) Name of gene(s): choroideremia (Rab escort protein 1); CHM (300390) 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 Consultant Clinical Geneticist Consultant Ophthalmologist Tick if this refers to you. Minimum criteria required for testing to be appropriate as stated in the Gene Dossier: Criteria Males with progressive loss of vision (reduction of central vision, constriction of visual fields, night blindness) beginning at an early age AND Extinguished or severely reduced scotopic and photopic electroretinogram (ERG) AND Characteristic fundus appearance (choroid and retina undergo complete atrophy) OR At risk relatives in family with known mutation Tick if this patient meets criteria 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. 7

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