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The most frequently deleted area was 6q25.
Four candidate tumor suppressor genes RUNX3, ARID1A, ERRFI1 and mTOR, all located on this exclusively deleted area, are of interest.
The gene SLITRK6 was selected as a candidate gene for both gastric cancer cell lines, however only in the GP202 gastric cancer cell line this gene was located in a deleted area.
It is worth noting that the 6q deleted area was not considered as exclusively deleted since this genomic area showed a medium level of amplification.
Specific transcriptional profiles have been correlated with two subgroups of 13q deletion based on the size of deleted area (short/biallelic versus wide/monoallelic).
It appeared that the region encoded by the deleted area in the 72 and 174 bp deletion variants is highly conserved among different MLO proteins (Fig. 1c).
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Furthermore, we identified three frequently deleted areas of 1p.
Of these, 164 oligonucleotides, representing 134 different genes, were located in deleted areas.
Array CGH profiles of the cell lines GP202 and IPA220 were obtained to detect the deleted areas potentially harbouring tumour suppressor genes.
Fifteen polymorphic polymerase chain reaction (PCR) markers were used to identify the separately deleted areas and the findings were compared with clinicopathological variables and 5-year survival of the patients.
In addition we selected two genes potentially inactivated by nonsense mutation which were located outside deleted areas, but showed high log2 ratios and no known splice variants (CSTA for the GP202 and INHBB for the IPA220 gastric cancer cell lines).
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