selection of microsatellite markers for bladder cancer diagnosis without the need for corresponding blood选择微卫星标记对膀胱癌诊断不需要相应的血液.pdfVIP

Selection of Microsatellite Markers for Bladder Cancer Diagnosis without the Need for Corresponding Blood 1 1 1 1 1 Angela A. G. van Tilborg , Lucie C. Kompier , Irene Lurkin , Ricardo Poort , Samira El Bouazzaoui , 1 1 2 2 3 Kirstin van der Keur , Tahlita Zuiverloon , Lars Dyrskjot , Torben F. Orntoft , Monique J. Roobol , Ellen C. Zwarthoff1* 1 Department of Pathology, Erasmus MC, Rotterdam, The Netherlands, 2 Aarhus University Hospital, Department of Clinical Biochemistry, Skejby, Denmark, 3 Department of Urology, Erasmus MC, Rotterdam, The Netherlands Abstract Microsatellite markers are used for loss-of-heterozygosity, allelic imbalance and clonality analyses in cancers. Usually, tumor DNA is compared to corresponding normal DNA. However, normal DNA is not always available and can display aberrant allele ratios due to copy number variations in the genome. Moreover, stutter peaks may complicate the analysis. To use microsatellite markers for diagnosis of recurrent bladder cancer, we aimed to select markers without stutter peaks and a constant ratio between alleles, thereby avoiding the need for a control DNA sample. We investigated 49 microsatellite markers with tri- and tetranucleotide repeats in regions commonly lost in bladder cancer. Based on analysis of 50 blood DNAs the 12 best performing markers were selected with few stutter peaks and a constant ratio between peaks heights. Per marker upper and lower cut off values for allele ratios were determined. LOH of the markers was observed in 59/104 tumor DNAs. We then determined the sensitivity of the marker panel for detection of recurr