Table 2.

Selected gene loci, gene IDs, cytoband and genomic annotation of the amplicons used for QPCR validation.

Gene	Gene-ID	Cytoband	Amplicon position (NCBI Build 35.1 [hg17])	Amplicon position (hg18)
S100A8	6279	1q21	chr1:150,175,956–150,176,071	chr1:151,629,507–151,629,622
FN1	2335	2q34	chr2:216,112,380–216,112,466	chr2:215,995,119–215,995,205
RAF1	5894	3p25	chr3:12,635,039–12,635,148	Identical
DAB2	1601	5p13	chr5:39,418,493–39,418,602	identical
CSPG2	1462	5q14.3	chr5:82,821,732–82,821,832	identical
E2F3	1871	6p22	chr6:20,598,410–20,598,516	identical
SFRP1	6422	8p12-p11.1	chr8:41,285,606–41,285,686	identical
TUSC3	7991	8p22	chr8:15,524,970–15,525,081	identical
EDD1	51366	8q22	chr8:103,366,989–103,367,080	identical
MYC	4609	8q24.12-q24.13	chr8:128,822,158–128,822,287	identical
CDKN2A	1029	9p21	chr9:21,957,845–21,957,973	identical
KLF4	9314	9q31	chr9:107,331,117–107,331,240	chr9:109,291,383–109,291,506
MDM2	4193	12q14.3-q15	chr12:67,519,751–67,519,858	Identical
RB1	5925	13q14.2	chr13:47,853,426–47,853,564	Identical
TP53	7157	17p13.1	chr17:7,520,091–7,520,236	Identical

Loci were selected based on the frequency of alterations in the total SNP material, and on bladder cancer relevance according to literature and our own gene expression analyses [22]. Loci are not referring to the (insignificant) relative changes characterizing progressing tumors listed on Table 3, except SFRP1 (8p11). Primer sets leading to amplicons of 80–120 basepairs were designed using the Primer3 software http://frodo.wi.mit.edu/cgi-bin/primer3/primer3.cgi. The QPCR primer sequences are listed in Additional File 6.