PT  - JOURNAL ARTICLE
AU  - Yanyun Li
AU  - Jun Xing
AU  - Linsheng Zhao
AU  - Yanni Li
AU  - Yuchuan Wang
AU  - Weiming Zhang
TI  - Bioinformatics Analysis for Coding SNPs of the HLA-DQA1 Gene Involved in Susceptibility to Cervical Cancer
DP  - 2006 Feb 01
TA  - Chinese Journal of Clinical Oncology
PG  - 49--54
VI  - 3
IP  - 1
4099  - http://www.cancerbiomed.org/content/3/1/49.short
4100  - http://www.cancerbiomed.org/content/3/1/49.full
SO  - Cancer Biol Med2006 Feb 01; 3
AB  - OBJECTIVE To analyze coding SNPs of the HLA-DQA1 gene involved in susceptibility for cervical cancer by a bioinformatics approach, and to choose some SNPs that may have an association with cervical cancer.METHODS By a SNPper tool we extracted SNPs from a public database (dbSNP), exporting them in FASTA formats suitable for subsequent use. Then we used PARSESNP as a tool for the analysis of the cSNPs.RESULTS In the cSNPs of the HLA-DQA1 gene, we find that rs9272693 and rs9272703, are made up of missense mutations which convert a codon for one amino acid into a codon for a different amino acid. We chose a PSSM Difference >10 as a lower level for the scores of changes predicted to be deldterious.CONCLUSION We used a bioinformatics approach for cSNPs analysis of the HLA-DQA1 gene. This method can select the variants in a conserved region, and give a PSSM Difference score. But the results need to be verified in cervical cancer patients and a control population.