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Table 1 RT-PCR analysis for selected genes in chromosomal regions of deletion or amplification/duplication in primary RCC tumours and associated normal tissue

From: Methylation profiling and evaluation of demethylating therapy in renal cell carcinoma

Deletions

Chromosome

Potential tumour specifically inactivated genes

 

Tum Exp. Lost/Tum. Exp. Down-regulated/Tum. Exp. Normal or Up-regulated (Percentage of lost/down-regulated)

 

Chromosome 1

CHD5

TNFRSF1B

KIF17

UQCRH

GPX7

0/1/14 (6.7%)

0/0/15 (0.0%)

0/0/15 (0.0%)

0/0/15 (0.0%)

0/0/15 (0.0%)

TTC22

PDE4DIP

RGS7

TRIM58

 

1/1/13 (13.3%)

0/0/15 (0.0%)

3/4/8 (46.7%)

0/2/13 (13.1%)

 

Chromosome 6

GCM2

HIST1H3G

HIST1H4H

  

8/0/2 (80.0%)

0/0/15 (0.0%)

0/0/15 (0.0%)

  

Chromosome 8p

GATA4

NEFM

   

1/0/8 (11.1%)

1/2/12 (20.0%)

   

Chromosome 14q

EFS

PTGDR

C14orf39

FLRT2

 

0/1/14 (6.7%)

0/1/14 (6.7%)

1/0/8 (11.1%)

0/1/14 (6.7%)

 

Amplifications

Chromosome

Potential tumour specifically inactivated genes

 
 

(Percentage of tumours in which gene expression is lost or down-regulated in brackets)

 

Chromosome 1

TWIST1

HOXA11

AEBP1

KLF14

 
 

1/0/13 (7.1%)1

0/2/13 (13.3%)

3/0/12 (20.0%)

0/2/13 (13.3%)

 

Chromosome 8p

SOX17

CA3

ANGPT1

TMEM74

 
 

0/2/13 (13.3%)

0/3/12 (20.0%)

0/0/15 (0.0%)

4/3/8 (46.7%)

 
  1. 1Key= Tumour Expression Lost/Tumour Expression Down-regulated/Tumour Expression Normal or Up-regulated (Percentage of lost/down-regulated).
  2. Genes in bold type (GCM2, RGS7 and NEFM) demonstrated complete loss or downregulation of expression in at least 20% of RCC tumours and were located in regions of deletion.