p53 sequence determination in gastric biopsy specimens by chip and conventional sequencing technology

Background: The mutation of p53 gene is play an important role in the pathogenesis of malignant diseases.

Aims: To find disease specific p53 gene mutations and to compare the traditional sequencing technique with DNA sequencing microarray technology and to compare the mutations in the blood cells and in the pathological tissues.

Materials and methods: After informed consent, peripheral blood was drawn and gastric biopsy samples were taken from the pathological and healthy part of the stomach. Genomic DNA was extracted from 25 biopsy and blood samples from patients with intestinal metaplasia. From the 11 exons of p53 ten (2–11) were amplified with PCR and examined with GeneChip p53 Assay (Affymetrix), and four (5–8) exons with traditional gel sequencing method (LICOR IR2).

Results: Both the isolated DNA from stabilized blood sample and from frozen biopsies have good quality and quantity. The results of conventional sequencing and DNA chip technology is nicely comparable. Though the number of the examined samples were low, genetic polymorphism can be found.

Conclusions: The DNA chip technology give a new and good opportunity for the genetic diagnosis. This technique is much faster and finally could be cheaper than traditional sequencing. The DNA demand of the chip technique is also smaller than the conventional method. This method give us opportunity to examine the malignant and premalignant alterations not just in the stomach but in the whole gastrointestinal tract.