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Table 2 Selected gene loci, gene IDs, cytoband and genomic annotation of the amplicons used for QPCR validation.

From: Chromosomal imbalance in the progression of high-risk non-muscle invasive bladder cancer

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

  1. 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.