The characteristics of hepatitis B virus sequence
with virology and clinical pathology
Yi-Chun Lin
aKoun-Tem Sun
bWen-Chun Lin
cTing-Tsung Chang
dYueh-Min Huang
aa
Department of Engineering Science cInstitute of Molecular Medicine dInstitute of Basic Medical Sciences, acd
National Cheng Kung University ; bDepartment of Information and Learning Technology, Nation University of Tainan, Tainan, Taiwan
Abstract
The hepatitis B virus infection is the invisible killer of pathological changes of liver, and endangered people's health for a long time. Recently, related studies have found that difficult genotypes and HBsAg seroconversion effect the pathological change of liver. In this paper, we explored the variation of hepatitis B virus (HBV) on different genotypes and the HBsAg seroconversion in patients. Then, we develop a technique for association rules to solve thisproblem.
1. Samples and data preprocessing
To investigate the HBV DNA sequences, we collected analyzing samples form routine diagnostic blood specimens amount to twenty-two patients and obtained the amino acid sequences amount to three hundred and fifty-eight from NCBI database.
Figure 1. The flow chart of data preprocessing
2. Mining specific positions of HBV sequence
Of particular interest in study is employed association analysis to find the specific positions of HBV sequence and which have relation
.
Then, we further prune the discovered associations to remove those insignificantassociations and find a set of useful rules.
3.1 Association rules of distinguish genotypes
We discovered that the rules related to genotyping appear in p gene, S gene, PreS1 gene,respectively.
Table 1.The specific positions in p gene and s gene
Experimentally, the genotype A is classified according to that when position_104 shows “K” of P gene, position_47 shows “L” and position_59 shows N of S gene at the same time. Therefore, we can corollary the following rules.
1. {position_104=K, position_49=L, position_59=N} => Genotype A.
2. {position_199=P, position_47=V, position_59=S}=> Genotype B.
3. {position_104 =R, position_199=Q } => Genotype C. 4. {position_199 =Q, position_47=V, position_49=L} =>
Genotype D.
5. {position_104 =K, position_199=H, position_584=N} => Genotype E.
6. {position_104 =L, position_234=N} => Genotype F. 7. {position_104=K,position_199=Q,position_234=R,
position_47=V,position_49=P } => Genotype G. 8. {position_199=A, position_234=N, position_584=A} =>
Genotype H.
Number Gene Association rules
rule1 P {position_104=N,position_234=G,positio n_584=H,position_199=P} rule3 S {position_8=L,position_47=Vposition_4 9=L,position_56=Q,position_57=I,positi on_59=S,position_64=C,position_77=-,p osition_85=C} rule7 PreS1 {position_10=K,position_35=K,position_ 39=E,position_45=L,position_48=H,posi tion_51=N,position_54=D,position_57= K} M0052
