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 HEMOCHROMATOSIS, TYPE 4; HFE4 OMIM number for disease # Disease alternative names please provide any alternative names you wish listed HEMOCHROMATOSIS, AUTOSOMAL DOMINANT HEMOCHROMATOSIS DUE TO DEFECT IN FERROPORTIN Disease please provide a brief description of the disease characteristics Type B: Autosomal dominant iron loading condition with similar clinical picture to HFE related hemochromatosis but without mutations in the HFE gene. Type A: Autosomal dominant iron loading condition with normal or low transferrin saturation. Patient may be anemic in early life. Biochemically the disease can be associated with normal or low serum transferrin saturation, despite high ferritin. Iron accumulation in the reticuloendothelial cells is characteristic of the disease. Patients showed a reduced tolerance to phlebotomy and became anaemic on therapy despite persistently elevated serum ferritin values. Disease - mode of inheritance Gene name(s) Autosomal dominant SOLUTE CARRIER FAMILY 40 (IRON-REGULATED TRANSPORTER), MEMBER 1; SLC40A1 OMIM number for gene(s) * Gene alternative names please provide any alternative names you wish listed Gene description(s) (including number of amplicons). IRON-REGULATED TRANSPORTER 1; IREG1 SOLUTE CARRIER FAMILY 11 (PROTON-COUPLED DIVALENT METAL ION TRANSPORTER), MEMBER 3, FORMERLY; SLC11A3. FERROPORTIN 1; FPN1 Exons: 8 Transcript length: 3,429 bps Translation length: 571 residues, 8 amplicons Mutational spectrum for which you test including details of known common mutations. Technical Method (s) Coding region and splice sites for all coding exons Common mutations; V162del; A77D; N144H/D/T DNA sequencing 1
2 Validation Process Note: please explain how this test has been validated for use in your laboratory 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 Activity If applicable - How many tests do you currently provide annually in your laboratory? Your Activity 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)? 4 patients with AD iron overload have been sequenced. Ferroportin mutations were identified in reports ( 8 pending) 7 pos/ 12 neg 5 years Yes Please provide details Prof TM Cox and Dr WJH Griffiths are international experts in this field Yes, common mutations in HFE1 and HFE2 10 Index cases: Previous workload 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. We will be able to provide a UK-wide service, currently not available. 2
3 Epidemiology Estimated prevalence of disease in the general UK population No studies performed but likely to be rare <1/1000 Estimated gene frequency (Carrier frequency or allele frequency) <1:1000 based on disease frequency Estimated penetrance Biochemical penetrance 100% based on published literature, clinical penetrance as yet undefined 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) Patients with typical HFE4 iron overload phenotype* +/- family history of non HFE haemochromatosis. *Phenotype is: high ferritin / normal transferrin sat / mild anaemia / macrophage iron loading / autosomal dominant transmission / absence of other cause for hyperferritinaemia Estimated prevalence of disease in the target population 70% 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 3
4 Test Characteristics 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. Bi-directional sequencing coupled with Mutation Surveyor software has a quoted sensitivity of >99% and specificity of >99% If more than one gene will be tested, please include your testing strategy and data on the expected proportions of positive results for each part of the process. Please illustrate this with a flow diagram. 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) Comprehensive data not available. As type 4 haemochromatosis is defined as mutations in SLC40A1, specificity is likely to be high, barring gross deletions of SLC40A1 which will not be detected by this method. Sensitivity depends on the inclusion criteria. It is likely to be 70% for patients with AD iron overload, and the biochemical and histopathological features of type 4 haemochromatosis. The test cannot be recommended for the diagnosis of raised ferritin without other features of type 4 haemochromatosis. 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). The positive predictive value is likely to be high if used in biochemically and histopathologically affected individuals and their family members. The negative predictive value is likely to be high if used for screening family members 4
5 Clinical utility of test in target population (Please refer to Appendix A) Please provide a description of the clinical care pathway. Hereditary iron overloading (haemochromatosis) can lead to extensive multi organ damage with considerable morbidity and mortality. The liver is usually the main site of iron induced damage: patients may require liver transplant, or may suffer hepatocellular carcinoma. However if detected early the condition is treatable by regular phlebotomy. The most common form of hereditary haeomchromatosis if association with HFE1. Once this condition has been excluded several other genetic loci contribute to the condition, which can present identically (HFE4 type B) or with slightly different clinical presentiation (HFE4 type A). How will the test add to the management of the patient or alter clinical outcome? This test will be used to provide a positive diagnosis of type 4 haemochromatosis in patients presenting with biochemical and histopathological features of this condition. In both type A and type B type 4 haemochromatosis the transmission is autosomal dominant. Type A patients have high serum ferritin with no obvious cause but normal transferrin saturation, a history of mild anaemia and predominantly macrophage iron loading. Type B patients will have been investigated for type 1 haemochromatosis due to iron induced hepatic damage but with high ferritin as well as transferrin saturation, but without the C282Y mutation in the HFE1 gene. These patients will typically present to hepatologists. 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? The aims of the genetic test are twofold: to establish a positive diagnosis, and therefore prevent further testing and to screen family members as this condition is treatable prior to clinical presentation. A poor response to phlebotomy can be predicted in Type A patients. 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? The condition can be suspected following liver biopsy, and with the typical phenotype. However, the disease can only be diagnosed by DNA testing in both pre-symptomatic and symptomatic forms. As the disease is potentially reversible in the preclinical phase missing this diagnosis in clinically affected subjects has major implications to family members. Due to the high penetrance of the clinical phenotype and the greatly improved prognosis once the condition is identified, there are no specific ethical, legal or social issues. Please complete the testing criteria form. 5
6 UKGTN Testing criteria Name of Disease(s): HEMOCHROMATOSIS, TYPE 4; HFE4 (606069) Name of gene(s): solute carrier family 40 (iron-regulated transporter), member 1;SLC40A1(604653) 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 Geneticists Consultant Hepatologist Tick if this refers to you. Minimum criteria required for testing to be appropriate as stated in the Gene Dossier: Criteria Proven family history of HEMOCHROMATOSIS, TYPE 4 with a known mutation OR Raised serum ferritin (300ug/L in men 200ug/L in women) with normal transferrin saturation (<60% in men and <50% in women). AND evidence of reticulo-endothelial iron staining on liver biopsy or splenic iron overload on MRI AND Homozygous C28Y mutation negative 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. 6
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