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. 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

Hydrate occurrence in Europe: a review of available evidence

Large national programs in the United States and several Asian countries have defined and characterised their marine methane hydrate occurrences in some detail, but European hydrate occurrence has received less attention. The European Union-funded project “Marine gas hydrate – an indigenous resource of natural gas for Europe” (MIGRATE) aimed to determine the European potential inventory of exploitable gas hydrate, to assess current technologies for their production, and to evaluate the associated risks. We present a synthesis of results from a MIGRATE working group that focused on the definition and assessment of hydrate in Europe. Our review includes the western and eastern margins of Greenland, the Barents Sea and onshore and offshore Svalbard, the Atlantic margin of Europe, extending south to the northwestern margin of Morocco, the Mediterranean Sea, the Sea of Marmara, and the western and southern margins of the Black Sea. We have not attempted to cover the high Arctic, the Russian, Ukrainian and Georgian sectors of the Black Sea, or overseas territories of European nations. Following a formalised process, we defined a range of indicators of hydrate presence based on geophysical, geochemical and geological data. Our study was framed by the constraint of the hydrate stability field in European seas. Direct hydrate indicators included sampling of hydrate; the presence of bottom simulating reflectors in seismic reflection profiles; gas seepage into the ocean; and chlorinity anomalies in sediment cores. Indirect indicators included geophysical survey evidence for seismic velocity and/or resistivity anomalies, seismic reflectivity anomalies or subsurface gas escape structures; various seabed features associated with gas escape, and the presence of an underlying conventional petroleum system. We used these indicators to develop a database of hydrate occurrence across Europe. We identified a series of regions where there is substantial evidence for hydrate occurrence (some areas offshore Greenland, offshore west Svalbard, the Barents Sea, the midNorwegian margin, the Gulf of Cadiz, parts of the eastern Mediterranean, the Sea of Marmara and the Black Sea) and regions where the evidence is more tenuous (other areas offshore Greenland and of the eastern Mediterranean, onshore Svalbard, offshore Ireland and offshore northwest Iberia). We provide an overview of the evidence for hydrate occurrence in each of these regions. We conclude that around Europe, areas with strong evidence for the presence of hydrate commonly coincide with conventional thermogenic hydrocarbon provinces