Genotype-Specific Genomic Markers Associated with Primary Hepatomas, Based on Complete Genomic Sequencing of Hepatitis B Virus

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  author =       "Joseph J. Y. Sung and Stephen K. W. Tsui and 
                 Chi-Hang Tse and Eddie Y. T. Ng and Kwong-Sak Leung and 
                 Kin-Hong Lee and Tony S. K. Mok and Angeline Bartholomeusz and 
                 Thomas C. C. Au and Kelvin K. F. Tsoi and 
                 Stephen Locarnini and Henry L. Y. Chan",
  title =        "Genotype-Specific Genomic Markers Associated with
                 Primary Hepatomas, Based on Complete Genomic Sequencing
                 of Hepatitis B Virus",
  journal =      "Journal of Virology",
  year =         "2008",
  volume =       "82",
  number =       "7",
  pages =        "3604--611",
  month =        apr,
  keywords =     "genetic algorithms, genetic programming",
  DOI =          "doi:10.1128/JVI.01197-07",
  abstract =     "We aimed to identify genomic markers in hepatitis B
                 virus (HBV) that are associated with hepatocellular
                 carcinoma (HCC) development by comparing the complete
                 genomic sequences of HBVs among patients with HCC and
                 those without. One hundred patients with HBV-related
                 HCC and 100 age-matched HBV-infected non-HCC patients
                 (controls) were studied. HBV DNA from serum was
                 directly sequenced to study the whole viral genome.
                 Data mining and rule learning were employed to develop
                 diagnostic algorithms. An independent cohort of 132
                 cases (43 HCC and 89 non-HCC) was used to validate the
                 accuracy of these algorithms. Among the 100 cases of
                 HCC, 37 had genotype B (all subgenotype Ba) and 63 had
                 genotype C (16 subgenotype Ce and 47 subgenotype Cs)
                 HBV infection. In the control group, 51 had genotype B
                 and 49 had genotype C (10 subgenotype Ce and 39
                 subgenotype Cs) HBV infection. Genomic algorithms
                 associated with HCC were derived based on
                 genotype/subgenotype-specific mutations. In genotype B
                 HBV, mutations C1165T, A1762T and G1764A, T2712C/A/G,
                 and A/T2525C were associated with HCC. HCC-related
                 mutations T31C, T53C, and A1499G were associated with
                 HBV subgenotype Ce, and mutations G1613A, G1899A,
                 T2170C/G, and T2441C were associated with HBV
                 subgenotype Cs. Amino acid changes caused by these
                 mutations were found in the X, envelope, and
                 precore/core regions in association with HBV genotype
                 B, Ce, and Cs, respectively. In conclusion, infections
                 with different genotypes of HBV (B, Ce, and Cs) carry
                 different genomic markers for HCC at different parts of
                 the HBV genome. Different HBV genotypes may have
                 different virologic mechanisms of
  notes =        "PMID:",

Genetic Programming entries for Joseph J Y Sung Stephen K W Tsui Chi-Hang Tse Eddie Y T Ng Kwong-Sak Leung Kin-Hong Lee Tony S K Mok Angeline Bartholomeusz Thomas C C Au Kelvin K F Tsoi Stephen Locarnini Henry L Y Chan