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BACKGROUND This study was performed to estimate the genetic effects of HtrA1 polymorphisms rs1049331 and rs11200638 on treatment response in stage III colon cancer patients receiving 5-FU-based chemotherapy. MATERIAL AND METHODS A total of 105 stage III colon cancer patients who received postoperative 5-FU based adjuvant chemotherapy were included in our study. Chemotherapy was performed in 3 cycles for the patients. HtrA1 rs1049331 and rs11200638 polymorphisms were genotyped via polymerase chain reaction with sequencing method. The treatment response was e