title: Genotyping theGALNT14gene by joint analysis of two linked single nucleotide polymorphisms using liver tissues for clinical and geographical comparisons.
abstract: AGALNT14single nucleotide polymorphism, rs9679162, has recently been found to be capable of predicting chemotherapy responses in patients with far-advanced hepatocellular carcinoma (HCC). In the present study, a novel assay was designed and genotyping was performed on 244 surgically removed liver tissues. This assay employed two polymerase chain reaction (PCR)-generated restriction enzyme sites to simultaneously determine the genotypes of two adjacent single nucleotide polymorphisms (SNPs), rs9679162 and rs6752303, on theGALNT14gene. Genotypes determined by this assay reached 100% concordance with those detected by the direct sequencing method. Clinical analysis showed that the TT genotype of rs9679162 was lower in percentage among patients with virus-originated HCC compared with those with non-viral HCC (22.57 vs. 47.06%, respectively; P=0.023). The proportion of the TT genotype in the 244 HCC patients (24.18%) did not deviate significantly from those of two public-domain (HapMap) Chinese cohorts from Denver, Colorado, USA (28.44%) and Beijing, China (30.15%) (P>0.05). The proportion of the TT genotype was significantly higher in Japanese and African populations (42.11-54.55%; P<0.0001) but significantly lower in an Italian cohort (7.84%; P=0.0004). In conclusion, the novel PCR-generated double restriction enzyme sites method could correctly determine the genotypes of two target SNPs inGALNT14in liver tissues. The TT genotype was associated with the non-viral etiology of HCC. A marked variation in ethnicity was found for the distribution of this genotype.
authors.affiliation: Liver Research Center, Chang Gung Memorial Hospital, Taipei 10507, Taiwan, R.O.C.
authors.forename: Kung-Hao
authors.initials: KH
authors.lastname: Liang
authors.affiliation: Liver Research Center, Chang Gung Memorial Hospital, Taipei 10507, Taiwan, R.O.C.
authors.forename: Pei-Ching
authors.initials: PC
authors.lastname: Yang
authors.affiliation: Liver Research Center, Chang Gung Memorial Hospital, Taipei 10507, Taiwan, R.O.C. ; Molecular Medicine Research Center, Chang Gung University, Taoyuan 10507, Taiwan, R.O.C.
authors.forename: Chau-Ting
authors.initials: CT
authors.lastname: Yeh
keywords: glycosyltransferase; hepatocellular carcinoma; non-viral etiology; restriction enzyme; single nucleotide polymorphism