[Screening and analysis of coding SNPs of HLA-DQA1 gene involved in susceptibility for cervical cancer].
OBJECTIVE
Polymorphisms of human leukocyte antigen (HLA) gene play an important role in the development of cervical cancer. This study was to screen single nucleotide polymorphisms (SNPs) of HLA-DQA1 gene involved in susceptibility of cervical cancer by a bioinformatics approach, and analyze their correlations to abnormal gene functions.


METHODS
SNPs of HLA-DQA1 were screened from a public database dbSNP by SNPper software, and relevant FASTA subsequences were also obtained from dbSNP. PARSESNP software was used to analyze cSNPs.


RESULTS
Two SNPs, rs9272693 and rs9272703, which may induce mis-sense mutation, were identified in codon region of HLA-DQA1 gene. A PSSM difference>10 was used to predict deleterious mutation.


CONCLUSIONS
SNPper software in combination with PARSESNP software could be used to analyze SNPs of HLA-DQA1 gene and select the variants in a conserved region, and it provides an evaluation criterion. But the results need to be verified in cervical cancer patients and control populations.
Li
Yan-Yun
YY
Laboratory of Molecular Biology, Basic Medical Research Center, Tianjin Medical University, Tianjin 300070, P. R. China. yanyun_li@yeah.net
Xing
Jun
J
Zhao
Lin-Sheng
LS
Li
Yan-Ni
YN
Wang
Yu-Chuan
YC
Zhang
Wei-Ming
WM
D019992:Databases as Topic; D005260:Female; D020022:Genetic Predisposition to Disease; D006683:HLA-DQ Antigens / Q000235:genetics*; D059848:HLA-DQ alpha-Chains; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D012984:Software; D002583:Uterine Cervical Neoplasms / Q000235:genetics*
D006683:HLA-DQ Antigens; D059848:HLA-DQ alpha-Chains; C069050:HLA-DQA1 antigen