Selection of microsatellite markers for bladder cancer diagnosis without the need for corresponding blood.

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....

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Autores principales:	Angela A G van Tilborg, Lucie C Kompier, Irene Lurkin, Ricardo Poort, Samira El Bouazzaoui, Kirstin van der Keur, Tahlita Zuiverloon, Lars Dyrskjot, Torben F Orntoft, Monique J Roobol, Ellen C Zwarthoff
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/0c4ca61dc0bf4194a0f747c3dda52fcb
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spelling	oai:doaj.org-article:0c4ca61dc0bf4194a0f747c3dda52fcb2021-11-18T07:08:01ZSelection of microsatellite markers for bladder cancer diagnosis without the need for corresponding blood.1932-620310.1371/journal.pone.0043345https://doaj.org/article/0c4ca61dc0bf4194a0f747c3dda52fcb2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22927958/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Microsatellite 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.Angela A G van TilborgLucie C KompierIrene LurkinRicardo PoortSamira El BouazzaouiKirstin van der KeurTahlita ZuiverloonLars DyrskjotTorben F OrntoftMonique J RoobolEllen C ZwarthoffPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 8, p e43345 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Angela A G van Tilborg Lucie C Kompier Irene Lurkin Ricardo Poort Samira El Bouazzaoui Kirstin van der Keur Tahlita Zuiverloon Lars Dyrskjot Torben F Orntoft Monique J Roobol Ellen C Zwarthoff Selection of microsatellite markers for bladder cancer diagnosis without the need for corresponding blood.
description	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.
format	article
author	Angela A G van Tilborg Lucie C Kompier Irene Lurkin Ricardo Poort Samira El Bouazzaoui Kirstin van der Keur Tahlita Zuiverloon Lars Dyrskjot Torben F Orntoft Monique J Roobol Ellen C Zwarthoff
author_facet	Angela A G van Tilborg Lucie C Kompier Irene Lurkin Ricardo Poort Samira El Bouazzaoui Kirstin van der Keur Tahlita Zuiverloon Lars Dyrskjot Torben F Orntoft Monique J Roobol Ellen C Zwarthoff
author_sort	Angela A G van Tilborg
title	Selection of microsatellite markers for bladder cancer diagnosis without the need for corresponding blood.
title_short	Selection of microsatellite markers for bladder cancer diagnosis without the need for corresponding blood.
title_full	Selection of microsatellite markers for bladder cancer diagnosis without the need for corresponding blood.
title_fullStr	Selection of microsatellite markers for bladder cancer diagnosis without the need for corresponding blood.
title_full_unstemmed	Selection of microsatellite markers for bladder cancer diagnosis without the need for corresponding blood.
title_sort	selection of microsatellite markers for bladder cancer diagnosis without the need for corresponding blood.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/0c4ca61dc0bf4194a0f747c3dda52fcb
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Selection of microsatellite markers for bladder cancer diagnosis without the need for corresponding blood.

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