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Data were scanned and entered into SPSS files for analysis.

The resulting genotyping data were scanned and analyzed with the software ABI PRISM™ GeneScan 3.7 and Genotyper 3.7 software package (Applied Biosystems, Foster City, CA, USA), which displayed the AFLP fingerprints and quantified the polymorphic peaks.

The obtained data were scanned and extracted using GenePix, processed using R scripts for quality control and normalization (Lyne et al., 2003), and analyzed using GeneSpring GX3 (Agilent Technologies UK Ltd ,Wokingham, UK).

35 The questionnaire data were scanned, checked and verified using TeleForm TM scanning processes.

The quantitative data were scanned for completeness and responses were coded and entered into the computer using IBM® SPSS® for Windows Version 17.0.

The hybridization data were scanned for visible defects and then extracted using default settings and tabulated as CEL files using Affymetrix GeneChip Operating Software GCOSS 1.2).

Regions of interest from the tumour data were scanned for these CNPs and matches were removed from downstream analyses (Figure S2-B).

Data were scanned using Teleforms (Verity software) and analyzed using Stata (Stata Version 11).

Questionnaire data were scanned using Teleform® procedures and manually quality-checked; statistical analyses were performed using STATA v.9.

Tissues for rNO cases were obtained from the same institute as those for rUCs; their microarray data were scanned using the same facility and in roughly the same time period as data for rUC samples.

The data were scanned by a transmission-mode scanner and quantitated using Image J software.