title: Selection of microsatellite markers for bladder cancer diagnosis without the need for corresponding blood.
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 recurrent bladder cancer by assaying 102 urine samples of these patients. Sensitivity was 63% when patients were stratified for LOH in their primary tumors. We demonstrate that up-front selection of microsatellite markers obliterates the need for a corresponding blood sample. For diagnosis of bladder cancer recurrences in urine this significantly reduces costs. Moreover, this approach facilitates retrospective analysis of archival tumor samples for allelic imbalance.
authors.affiliation: Department of Pathology, Erasmus MC, Rotterdam, The Netherlands.
authors.forename: Angela A G
authors.initials: AA
authors.lastname: van Tilborg
authors.forename: Lucie C
authors.initials: LC
authors.lastname: Kompier
authors.forename: Irene
authors.initials: I
authors.lastname: Lurkin
authors.forename: Ricardo
authors.initials: R
authors.lastname: Poort
authors.forename: Samira
authors.initials: S
authors.lastname: El Bouazzaoui
authors.forename: Kirstin
authors.initials: K
authors.lastname: van der Keur
authors.forename: Tahlita
authors.initials: T
authors.lastname: Zuiverloon
authors.forename: Lars
authors.initials: L
authors.lastname: Dyrskjot
authors.forename: Torben F
authors.initials: TF
authors.lastname: Orntoft
authors.forename: Monique J
authors.initials: MJ
authors.lastname: Roobol
authors.forename: Ellen C
authors.initials: EC
authors.lastname: Zwarthoff
mesh_terms: D004247:DNA / Q000097:blood / Q000235:genetics / Q000652:urine; D018900:Dinucleotide Repeats / Q000235:genetics*; D006801:Humans; D008297:Male; D008875:Middle Aged; D016133:Polymerase Chain Reaction / Q000379:methods*; D012008:Recurrence; D015203:Reproducibility of Results; D018911:Trinucleotide Repeats / Q000235:genetics*; D001749:Urinary Bladder Neoplasms / Q000097:blood / Q000175:diagnosis* / Q000235:genetics* / Q000652:urine
chemical_list: D004247:DNA