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

Transcription

1 Proposal form for the evaluation of a genetic test for NHS Service Gene Dossier Submitting laboratory: Bristol RGC 1. Disorder/condition approved name and symbol as published on the OMIM database (alternative names will be listed on the UKGTN website) KBG SYNDROME; KBGS. 2. OMIM number for disorder/condition # a. Disorder/condition please provide, in laymen s terms, a brief (2-5 sentences) description of how the disorder(s) affect individuals and prognosis. KBG syndrome is a rare dominant genetic disorder characterized by distinctive features including a triangular-shaped face, widely-spaced eyes, drooping eyelids, thin upper lip, a low anterior hairline and prominent ears. There are abnormal teeth with very large upper central incisors, whilst the lower incisors may have extra serrations (supernumerary mamelons). The skeletal features include short stature, curved spine (scoliosis), short bones in the hands, curvature of the fifth fingers (clinodactyly), abnormalities of the ribs and sternum, unusual hip bones (short femoral necks) and delayed bone maturation. Neurological manifestations are variably present as developmental delay, seizures and intellectual disability. The clinical picture is recognisable but the diagnosis can be difficult to establish with certainty as the features may be subtle. The dental manifestations may not be apparent until the permanent teeth erupt in later childhood. It has been suggested that 4 out of 8 major criteria (large teeth, characteristic facies, neurological involvement, delayed bone age, short stature, hand findings, rib, sternum and hip abnormalities, and an affected first degree relative) are required for diagnosis. 3b. Disorder/condition if required please expand on the description of the disorder provided in answer to Q3a. There are a number of additional features which may occur in some patients. They include cutaneous syndactyly, webbed neck, cryptorchidism, hearing loss, cleft palate/bifid uvula, strabismus and congenital heart defects. Severity of presentation may vary within families, and it is likely that the condition is under diagnosed because many of its features are mild. Most cases are simplex and more males than females have been described. Inheritance has been described as autosomal dominant based on male to male inheritance in 2 families. The majority of diagnosed cases present in infancy with developmental delay, motor impairment is evident in early infancy specifically delay in walking unaided (median age >25 months). Language delay is common and persistent over time with deficits in verbal comprehension and especially in expressive skills. In the longer term, intellectual disability is present in all patients, usually to a mild to moderate degree. Smithson SF et al (2000), Clin. Dysmorphol. 9:87-91 Skjei K et al (2007), Am J of Med Genet 143A: Sirmaci et al (2011), Am J Hum Genet 89, Disorder/condition mode of inheritance If this submission is for a panel test, please complete the mode of inheritance for each condition in the table in appendix 1. Autosomal dominant due to de novo or inherited mutations in ANKRD11. Incomplete penetrance in females may account for the predominance of affected boys. Recently a microdeletion syndrome of chromosome 16q24.3 including ANKRD11 has been described, patients have features of KBG Syndrome and additional developmental problems (see below). Not all patients with clinical features of KBG have ANKRD11 mutations and it is likely to be a heterogeneous condition.

2 5. Gene approved name(s) and symbol as published on HGNC database (alternative names will be listed on the UKGTN website) ankyrin repeat domain 11; ANKRD11 6a. OMIM number(s) for gene(s) * b. HGNC number(s) for gene(s) If a panel test see 5. above HGNC a. Gene description(s) ANKRD11 chromosome location 16q24.3. The 223kb ANKRD11 gene has 13 exons, exons 3-13 code for the full length functional protein with 9.3kb mrna and a protein of 2662 amino acid residues. ANKRD11 contains two transcriptional repression domains located at the N and C terminals and an activation domain capable of stimulating transcription (Zang A et al (2007), Biochem.Biophys.Res Commun. 358: ). The ankyrin repeat- containing protein 11 (ANKRD11/ANCO-1) is a member of a family of ankyrin repeat containing cofactors, which have a role in transcriptional regulation through suppression of p160 receptor coactivators via recruitment of histone deacetylases(hdacs) that act to antagonize transcriptional activation by nuclear receptors eg transcription factors. (Zang A et al (2004), J Biol. Chem. 279: ). Mutations in ANKRD11 have been identified in around 50% of KBG patients ( analysis of 10 cases ) Sirmaci A et al (2011) Am J Hum Genet 89: indicating that this is likely to be a heterogeneous condition, however the possibility of variants in the regulatory regions of ANKRD11 remains. 7b. Number of amplicons to provide this test (molecular) or type of test (cytogenetic) 29 amplicons covering regions of interest within ANKRD11 gene comprising exons c. GenU band that this test is assigned to for index case testing. GenU band F 8. Mutational spectrum for which you test including details of known common mutations If this application is for a panel test to be used for different clinical phenotypes and/or various sub panel tests please contact the team for advice before completing a Gene Dossier Sanger sequence analysis of the entire coding regions of genes, splice sites and branch points for point mutations and small insertions and deletions. There are no common mutations in ANKRD11, variants are novel and predominantly nonsense mutations (80% of published cases) and splice site mutations Sirmaci A et al (2011) Am J Hum Genet 89: A contiguous gene deletion syndrome at 16q24.3 (the 16q24.3 microdeletion syndrome) resulting in haploinsufficiency of ANKRD11 has been recognised as a distinct entity. Affected patients have facial dysmorphism resembling KBG and additionally, autism, intellectual disability and brain abnormalities. Deletions of 16q24.3 (which have varied in size from 265kb to 2.07Mb) would be detected by acgh which will be undertaken prior to ANKRD11 gene testing. A strategy whereby we re-examine this region if we get a sequencing request (to exclude CNVs below our reporting threshold) is likely to be appropriate. Willemsen MH et al (2010) Euro J Hum Genet 18: a. Technical method(s) please describe the test. DNA Sanger sequencing High Throughput (HT) Automated sequence analysis. Gene screening by bidirectional automated HT sanger sequence analysis (Beckman NX/ABI3730), the standard platform used for gene screening at BGL and analysis of the results with Mutation Surveyor software.

3 9b. For panel tests, please specify the strategy for dealing with gaps in coverage. 9c. Does the test include MLPA? (For panel tests, please provide this information in appendix 1) No 9d. If NGS is used, does the lab adhere to the Association of Clinical Genetic Science Best Practice Guidelines for NGS? 10. Is the assay to be provided by the lab or is it to be outsourced to another provider? If to be outsourced, please provide the name of the laboratory and a copy of their ISO certificate or their CPA number. Assay to be provided by Bristol Genetics laboratory. 11. Validation process Please explain how this test has been validated for use in your laboratory or submit your internal validation documentation. If this submission is for a panel test, please provide a summary of evidence of: i) instrument and pipeline validation, and ii) panel verification for the test Please submit as appendices to the Gene Dossier (these will be included in the published Gene Dossier available on the website). Please note that the preferred threshold for validation and verification is 95% sensitivity with 95% Confidence Intervals. HT automated sequence analysis: This method is routinely used to screen for mutations at BGL and had been validated for many services. Beckman NX robotics /ABI 3730 capillary electrophoresis and mutation surveyor software analysis are routinely used in the laboratory. Positive and negative control samples are included. Primers (SNP checked) have been designed to cover the coding regions and intron-exon boundaries. BGL also participates in external quality assurance EMQN sequencing QA schemes (since the pilot scheme was introduced in 2002). The assay has been validated on known normal controls stored in the laboratory and a positive control sample with the mutation c.[2398_2401del], p.glu800asnfs*62. 12a. Are you providing this test already? No, assay is under final stages of validation and samples are in storage awaiting testing. The validation data for this assay should be complete by the end of the next calendar month. A validation can be provided once complete. 12b(i). If yes, how many reports have you produced? 12b(ii). Number of reports mutation positive? 12b(iii). Number of reports mutation negative?

4 12b(iv). Please provide the time period in which these reports have been produced and whether in a research or a full clinical diagnostic setting. 13a. Is there specialised local clinical/research expertise for this disorder? Yes 13b. If yes, please provide details Dr Sarah F. Smithson, Consultant in Clinical Genetics has a clinical research interest this condition and research collaborations with colleagues in Northwick Park and Guys Hospitals, London. Smithson SF et al (2000), Clin. Dysmorphol. 9: Based on experience what will be the national (UK wide) activity, per annum, for: Index cases: approximately 10 Family members where mutation is known: approximately 20 It is possible that over time more tests would be requested as this is an under-diagnosed condition. 15. If your laboratory does not have capacity to provide the full national need please suggest 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. If you are unable to answer this question please write unknown. There is capacity for testing for UK at BGL 16. If using this form as an Additional Provider application, please explain why you wish to provide this test as it is already available from another provider.

5 EPIDEMIOLOGY 17a. Estimated prevalence of conditions in the general UK population Prevalence is total number of persons with the condition(s) in a defined population at a specific time. Please identify the information on which this is based. For panel tests, please provide estimates for the conditions grouped by phenotypes being tested. Unknown. Likely to be rare but probably under-recognised clinically. 17b. Estimated annual incidence of conditions in the general UK population Incidence is total number of new cases in a year in a defined population. Please identify the information on which this is based. For panel tests, please provide for groups of conditions. Unknown, rare. 18. Estimated gene frequency (Carrier frequency or allele frequency) Please identify the information on which this is based. n/a for panel tests. Unknown, rare. 19. Estimated penetrance of the condition. Please identify the information on which this is based n/a for panel tests Likely to be penetrant, as observed in dominant families described in the literature. Reduced expression in females. 20. Estimated prevalence of conditions in the population of people that will be tested. n/a for panel tests. Target population patients with KBG phenotype (> 4/8 of the diagnostic criteria ) Mutations in ANKRD11 have been identified in around 50% of KBG patients (analysis of 10 cases) Sirmaci A et al (2011) Am J Hum Genet 89: The detection rate is probably higher that this but literature rate varies as most reports are small series with mutation positive cases. INTENDED USE (Please use the questions in Annex A to inform your answers) 21. Please tick either yes or no for each clinical purpose listed. Panel Tests: a panel test would not be used for pre symptomatic testing, carrier testing and pre natal testing as the familial mutation would already be known in this case and the full panel would not be required. Diagnosis Yes No Treatment Yes possible influence on medical management Yes possible No influence on medical management Prognosis & management Yes No Presymptomatic testing (n/a for Panel Tests) Yes No Carrier testing for family members (n/a for Panel Tests) Yes No Prenatal testing (n/a for Panel Tests) Yes possible No

6 TEST CHARACTERISTICS 22. 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. Please note that the preferred threshold for validation and verification is 95% sensitivity with 95% Confidence Intervals. High Throughput Semi Automated Sequence analysis. Sensitivity %. To the best of our knowledge, no variant has been missed using a bi-directional sequencing approach. SCOBEC validation of unidirectional sequencing indicates a sensitivity of 99%. The sensitivity for detecting mutations in ANKRD11 will be 99% based on the mutations reported so far. 16q24.3 microdeletion syndrome detected by acgh prior to request for ANKRD11 mutation screening Specificity > 99% 23. 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 disorder is known to be absent. The denominator in this case is the number with the disorder (for sensitivity) or the number without condition (for specificity). Please provide the best estimate. UKGTN will request actual data after two years service. Clinical sensitivity 50 % based on Sirmaci data (but numbers small so this is a likely underestimate) Clinical specificity : Presumed over 95%, depending on the basis of interpretation of sequence variants as consensus mutations, or as innocuous polymorphisms. For testing relatives: Clinical sensitivity and specificity: will both be 100% when the mutation is definitely pathogenic. 24. 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). Not currently requested for panel tests Clinical validity: In an index case, finding one pathogenic mutation confirms the diagnosis in the majority of cases. We estimate that for index cases- Positive predictive value (PPV) = 100% for consensus mutations Negative predictive value (NPV) = greater uncertainty but likely to approach 80%. However, for testing family members, PPV and NPV are both effectively 100% for carrier status using consensus mutations. Complete non-penetrance in KBG is unlikely but clinical variability has been observed according to published data. 25. Testing pathway for tests where more than one gene is to be tested sequentially 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 will be added to the published Testing Criteria. n/a for panel tests It is logical to undertake array CGH testing prior to mutation analysis. The genetic testing strategy will then include sequencing ANKRD11 followed by MLPA (future development) to exclude gross rearrangements or partial gene deletions too small to be detected by the array.

7 CLINICAL UTILITY 26. How will the test change the management of the patient and/or alter clinical outcome? Please describe associated benefits for patients and family members. If there are any cost savings AFTER the diagnosis, please detail them here. It is likely that KBG syndrome is under-recognised and may remain an uncertain clinical diagnosis because of subtle features and/or lack of clinician experience with the disorder. Molecular genetic confirmation of the diagnosis will provide accurate diagnosis and confirm whether KBG has arisen for the first time in the child or has been inherited. As it is a dominant disorder, a positive test result would enable family members to be tested and to receive accurate genetic counselling. For patients with KBG there is a 50% risk of their children being affected which is highly significant. Patients with KBG syndrome have often had a history of developmental delay and a constellation of congenital anomalies of unexplained origin. A precise diagnosis allows focused medical investigations and management, for example affected children should be referred to a paediatric dentist and they should have an echocardiogram. However the large head circumference is very unlikely to have detrimental effects and specific investigation of that may be avoided. The main saving is avoidance of on-going investigations (especially MRI brain scan, skeletal survey and testing of other genes associated with developmental delay and macrocephaly) if the diagnosis remains unknown. 27. If this test was not available, what would be the consequences for patients and family members? Lack of diagnosis and understanding of disorder. Parents may decide not to have another child if risk is ill-defined. 28. 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. Only clinical diagnosis which is difficult in this syndrome. 29a. What unexpected findings could this test show? For example, lung cancer susceptibility when testing for congenital cataract because ERCC6 gene (primarily associated with lung cancer) is included in a panel test for congenital cataract. 29b. Please list any genes where the main phenotype associated with that gene is unrelated to the phenotype being tested by the panel. 30. If testing highlights a condition that is very different from that being tested for, please outline your strategy for dealing with this situation. 31. If a panel test, is this replacing an existing panel/multi gene test and/or other tests currently carried out through UKGTN using Sanger sequencing? If so, please provide details below. 32. Please describe any specific ethical, legal or social issues with this particular test. The test is likely to enhance medical care of the child, but unlikely to bring about disadvantages. There are no obvious ethical issues.

8 IS IT A REASONABLE COST TO THE PUBLIC? 33. In order to establish the potential costs/savings that could be realised in the diagnostic care pathway, please list the tests/procedures that would be required in the index case to make a diagnosis if this genetic test was not available. Type of test Cost ( ) Costs and type of imaging procedures Skeletal survey 1957 MRI scan of brain Costs and types of laboratory pathology tests Biochemical tests (other than molecular/cyto genetic test proposed in this Gene Including white Dossier) cell enzymes Costs and types of physiological tests (e.g. ECG) EEG possible Included above Cost and types of other investigations/procedures (e.g. biopsy) Total cost of tests/procedures no longer required (please write n/a if the genetic test does not replace any other tests procedures in the diagnostic care pathway) Based on the expected annual activity of index cases (Q14), please calculate the estimated annual savings/investments based on information provided in Q33. Number of index cases expected annually (a) 10 Cost to provide tests for index cases if the (b) genetic test in this Gene Dossier was not available (see Q32) Total annual costs pre genetic test (a) x (b) = (c) Total annual costs to provide genetic test (a) x cost of genetic testing for index case = (d) (b) 10 x 550 = 5500 Additional savings for 100% positive rate for (d) (c) = (e) index cases Percentage of index cases estimated to be (f) ~50% ( likely underestimate ) negative Number of index cases estimated to be negative (f) x number of index cases = (g) 5 Costs to provide additional tests for index cases (g) x (b) = (h) testing negative Total costs for tests for index patient activity (e) + (h) = (i) Total costs for family members Costs for family member test x number of family members expected to test in a year (j) 190 x 20 = 3800 If there is a genetic test already available and some of the family testing is already being provided, please advise the cost of the family testing already available Total costs for family members minus any family member testing costs already provided Additional savings for all activity expected in a year Cost for family member testing already available x estimated number of tests for family members already provided (k) (j) (k) = (l) 3800 (i) + (j) or (i) + (l)

9 35. REAL LIFE CASE STUDY Please provide a case study that illustrates the benefits of this test A boy was referred with delayed development and dysmorphic features. His elder brother had been seen in the genetic clinic previously because of x-linked hypohydrotic ectodermal dysplasia and molecular testing confirmed that condition. The boy was referred to ask if he may have a different manifestation of this, but his developmental profile and physical appearance were different. Careful evaluation of his phenotype revealed features of KBG syndrome, but this was uncertain. The clinical situation was complicated by the fact that both children were subject to neglect and required social care followed by placement with a different family member. When the diagnosis of KBG syndrome was confirmed by identification of an ANKRD11 mutation, it was made clear that there were two different diagnoses in the brothers. The delay was attributed to KBG rather than solely to neglect, which informed his long term placement and educational requirements. Appropriate medical and dental referrals were made. Family members were able to access carrier testing and the ANKRD11 mutation was confirmed to be de novo thereby confirming/excluding risks. TESTING CRITERIA 36. Please only complete this question if there is previously approved Testing Criteria. Please contact the UKGTN office if you are unsure whether testing criteria is available. 36a. Do you agree with the previously approved Testing Criteria? Yes/No 36b. If you do not agree, please provide revised Testing Criteria on the Testing Criteria form and explain below the reasons for the changes.

10 UKGTN Testing Criteria Test name: KBG Syndrome Approved name and symbol of disorder/condition(s): KBG Syndrome; KBGS Approved name and symbol of gene(s): ankyrin repeat domain 11; ANKRD11 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 Tick if this refers to you. Consultant Clinical Geneticist Minimum criteria required for testing to be appropriate as stated in the Gene Dossier: Criteria Tick if this patient meets criteria Affected with developmental delay AND 4 or more of the following: Macrodontia characteristic facies neurological involvement delayed bone age short stature characteristic hand findings costovertebral anomalies an affected first degree relative AND Array CGH Normal 16q24.3 OR At risk family members where familial mutation is known. Additional Information: 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.