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The aim of this study was to evaluate if Urine Cytology (UC) is an appropriate screening procedure for detecting urinary tract neoplasia at an early stage in persons at risk in Hereditary Non-Polyposis Colorectal Cancer families. Method In the National Danish HNPCC-register persons at risk were identified in three categories of HNPCC-families (1) families harbouring a disease causing mutation in a Mismatch repair gene (MMR), (2) families fulfilling the Amsterdam I or II criteria and (3) families suspected of HNPCC. In total 3,411 persons were identified and traced in Patobank—the National Danish Pathology database. All UC and UTC (Urinary Tract Tumours) were listed and evaluated. Results 977 persons had a total of 1,868 screening procedures performed. Two of these procedures (0.1%) lead to diagnosis of an asymptomatic urothelial tumour. In ten times as many procedures (22 persons) UC lead to a false positive screening diagnosis. During the study period fourteen persons (1.4%) developed a UTC and five of these were interval tumours. The sensitivity of UC in diagnosing asymptomatic UTC in HNPCC patients was 29%. Twelve of the tumours were found in persons from families with a proven MMR-mutation and eleven out of these were MSH2 mutations (92%, 95% cl 62–100%). Discussion UC is not a proper method of screening for UTC in HNPCC. However, the study can not reveal if screening for UTC in special families ought to be recommended. Consequently, further studies needs to be performed in order to evaluate an appropriate screening programme.