Proposal form for the evaluation of a genetic test for NHS Service Gene Dossier Test Disease Population Triad Disease name OMIM number for disease 147920 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 Kabuki syndrome KABUKI MAKE-UP SYNDROME; KMS NIIKAWA-KUROKI SYNDROME Kabuki syndrome is characterised by developmental delay / learning difficulties in association with a characteristic facial appearance, short stature and variable additional congenital malformations (e.g. cleft palate and congenital heart disease) and medical complications (e.g. neonatal hypoglycaemia, immune dysfunction and hypothyroidism). Autosomal dominant (usually de novo) Gene name(s) MLL2 OMIM number for gene(s) 602113 Gene alternative names ALR; MLL4; AAD10; KMT2B; KMT2D; TNRC21; CAGL114 Please provide any alternative names you wish listed Gene description(s) (including The MLL2 comprises 54 exons that are analysed in 78 amplicons number of amplicons) Mutational spectrum for which you test including details of known common mutations Point mutations and small insertions / deletions. No common mutations have been identified. At present it is unknown if large multi-exon deletions and duplications contribute significantly to the mutation spectrum of this gene. Technical Method (s) Bi-directional sequence analysis of MLL2. Analysis involves sequencing all exons and their intronic boundaries. Validation Process Note: please explain how this test has been validated for use in your laboratory Sequencing primers have been designed and optimised for all 78 amplicons. A panel of 60 individuals with suspected Kabuki syndrome and normal controls have been screened by sequence analysis. From this panel 35 / 60 (58%) have been found to have a mutation. This has also enabled us to identify common polymorphisms in MLL2. The laboratory also participates in all relevant technical EQA schemes that are available through UK NEQAS and EMQN: 2007 -Genotypes correctly assigned in 3/3 sequencing EQA samples 2006 - Genotypes correctly assigned in 3/3 sequencing EQA samples 2005 - Genotypes correctly assigned in 3/3 sequencing EQA samples 2004 - Genotypes correctly assigned in 4/4 sequencing EQA samples. 1
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, offered on a research basis in 2010 during the validation process. If : Number of reports issued: 50 Number of reports mutation positive: 35 Number of reports mutation negative:15 6 months Please provide details Dr. Richard Scott, Consultant Clinical Geneticist, NE Thames Regional Genetics Service. No Index cases: 40 Family members where mutation is known: 50 Index cases: 50 Family members where mutation is known: 100 Index cases: 50 cases per year. Based on estimated incidence of 1 in 32,000 (Niikawa et al Am J Med Genet 1988;31:565-89). Family members where mutation is known: 40-50 per year. Assuming 60-75% mutation detection rate (Ng et al. Nat Genet 2010;42:790-3 and Paulussen et al Hum Mutat Epub 2010) and potential unavailability of ~20% parents. Current practice would be to test both parents to confirm mutations are de novo. With additional experience, it may become unnecessary to test parents where the mutation is clearly pathogenic. The laboratory can provide a national service. We are aware that the Manchester Laboratory intends to offer this service to UKGTN. Together, our laboratories can meet the national requirement should it exceed the anticipated 50 index cases p.a. 2
Epidemiology Estimated prevalence of disease in the general UK population Estimated gene frequency (Carrier frequency or allele frequency) Estimated penetrance 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 1 in 32,000 (estimated from retrospective hospital-based study; Niikawa et al Am J Med Genet 1988;31:565-89) 1 in 50,000 (based on estimated prevalence and current 60-75% estimated mutation frequency MLL2 (Ng et al Nat Genet 2010;42:790-3; Paulussen et al Hum Mutat Epub 2010). 100% (Ng et al Nat Genet 2010;42:790-3; Paulussen et al Hum Mutat Epub 2010) Individuals with a probable diagnosis of Kabuki syndrome (see diagnostic criteria below) based on the presence of: 1. characteristic facial appearance suggestive of Kabuki Syndrome Long palpebral fissures with eversion of the lateral portion of the lower eyelid Broad, arched eyebrows with lateral sparseness Short columella with depressed nasal tip Large, prominent or cupped ears. AND 2. developmental delay OR In newborns only: a combination of congenital abnormalities such that Kabuki Syndrome is the most likely diagnosis. Greater than 90%, with mutation frequency >50%. Intended Use (Please use the questions in Annex A to inform your answers) Please tick the relevant clinical purpose of testing Diagnosis Treatment Prognosis & Management Presymptomatic testing Risk Assessment for family members Risk Assessment prenatal testing YES No NO 3
Test Characteristics Analytical sensitivity and s pecificity 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 Clinical utility of test in target population (Please refer to Appendix A) Please provide a description of the clinical care pathway. Direct sequencing has a high sensitivity in this laboratory. We use Big Dye chemistry, ABI analysers (3130XL, 3730XL) and analyse 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. Clinical sensitivity currently estimated to be 60-75%. Clinical specificity is likely to be ~100% (Ng et al Nat Genet 2010;42:790-3; Paulussen et al Hum Mutat Epub 2010). Positive predictive value ~100% (Ng et al Nat Genet 2010;42:790-3; Paulussen et al Hum Mutat Epub 2010). Negative predictive value not relevant as the test will be used principally to confirm a clinical diagnosis. Bi-directional sequencing of all coding exons of MLL2. Utility of a positive test result: It allows confirmation of the clinical diagnosis and provides an explanation for the parents. It confirms applicability of the management guidelines (www.dyscerne.org/dysc/digitalassets/0/264_kabuki_guidelin es.pdf and Adam and Hudgins Clin Genet 2004l;67:209-19) and can therefore affect management of the child e.g. screening for cardiac and renal abnormalities and 4
How will the test add to the management of the patient or alter clinical outcome? ophthalmological examination for anterior chamber abnormalities and delayed visual maturation. It can alert the doctors managing the child to the possibility of rare complications such a biliary atresia, episodic idiopathic thrombocytopenic purpura It facilitates accurate genetic counselling confirming the low recurrence risk for Kabuki syndrome in which many cases are due to de novo mutations. This can be reassuring for parents though small risk of gonadal mosaicism remains allowing the option of prenatal diagnosis. This can be useful when parents are making future reproductive decisions. It helps parents to access support for education and social care. In the UK there is an informal email network but an international organisation is based in Canada (www.kabukisyndrome.com) If the diagnosis is made it means that doctors can stop searching for other causes of learning disability and the patients are saved from having to undergo more investigations, many of which might be invasive In the case of KS there are specific benefits; It is an important early differential diagnosis of Rubinstein-Taybi syndrome. Also many patients with KS were previously investigated for chromosomal microdeletions with negative results or a rare recessive disorder such as Malpuech syndrome was considered. As a consequence they were given high/moderate recurrence risks for future pregnancies with no prospect of a test. Having the diagnosis of KS confirmed subsequently but excluded in the parents has meant that parents can be given very low recurrence risks and this can have a huge impact on reproductive decisions. Although this condition can be recognised clinically the phenotype is variable and often there is much discussion, even amongst experts, about mild cases or those with heights within the normal range. There are no other tests. Utility of a negative test result: will allow prioritisation of mutation negative cases for additional aetiological investigations including CGH array, other single gene analyses and research / exome studies aimed at identifying other genes causing Kabuki syndrome. In many cases of Kabuki syndrome, while the diagnosis is suspected, it cannot be made with certainty on clinical grounds. This often prevents the comprehensive application of the established clinical management guidelines (www.dyscerne.org/dysc/digitalassets/0/264_kabuki_guidelines.p df and Adam and Hudgins Clin Genet 2004l;67:209-19). This includes approaches that allow the identification of a number of associated disorders that might otherwise be missed (e.g. submucous cleft palate, hypothyroidism, immune dysfunction and subclinical hypoglycaemia). Molecular confirmation of the diagnosis in such cases will allow this. 5
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 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? In the case of positive test results, it will remove the need / cost of continued investigation of the underlying cause (including multiple clinical appointments, CGH array and other single gene analyses). It will also allow inclusion of affected individuals in tailored management guidelines (see above) and potentially reduce cost of follow-up of missed diagnosis of associated medical problems (www.dyscerne.org/dysc/digitalassets/0/264_kabuki_guidelines.p df and Adam and Hudgins Clin Genet 2004l;67:209-19). Failure to properly adhere to tailored management guidelines (see above) in clinically uncertain cases. This could lead to failure to identify associated medical disorders, e.g. submucous cleft palate, hypothyroidism, immune dysfunction and subclinical hypoglycaemia, and result in serious adverse outcomes. Confirms diagnosis that is often uncertain on clinical grounds. This allows (1) inclusion of clinically uncertain but proven cases in tailored management programme; (2) correct genetic counselling; (3) prenatal testing; (4) avoidance of unnecessary continued investigation of aetiology. No Diagnosis can be made clinically only in classical cases. N/A 6
UKGTN Testing Criteria Name of Disease(s): KABUKI SYNDROME 1; KABUK1 (147920) Name of gene(s): myeloid/lymphoid or mixed-lineage leukemia 2; MLL2 (602113) 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 Tick if this refers to you. Minimum criteria required for testing to be appropriate as stated in the Gene Dossier: Criteria Characteristic facial appearance suggestive of Kabuki Syndrome, e.g: Long palpebral fissures with eversion of the lateral portion of the lower eyelid Broad, arched eyebrows with lateral sparseness Short columella with depressed nasal tip Large, prominent or cupped ears. AND developmental delay OR In newborns only: a combination of congenital abnormalities such that Kabuki Syndrome is the most likely diagnosis. 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