Clinical evaluation of a colorimetric oligonucleotide chip for genotyping hepatitis C virus.
BACKGROUND
Hepatitis C virus (HCV) is a major cause of chronic liver disease worldwide. It is associated with the development of end-stage liver disease and hepatocellular carcinoma. Studies have shown that determination of hepatitis C virus (HCV) genotypes is clinically important for prediction of the clinical course and the outcome of antiviral therapy. The aim of this study was to evaluate a colorimetric oligonucleotide chip, which can be used for the rapid and economical detection of the genotypes/subtypes of hepatitis C virus.


METHODS
A total of 860 serum specimens were tested by an oligonucleotide chip genotyping test. Partial genotype results were compared with those obtained by sequencing method and INNOLiPA HCV II assay. The relative sensitivities of the methods were assessed by using the 5'NCR amplicon from the HCV RNA fluorescent amplicor HCV tests and Light Cycler.


RESULTS
Of 860 serum specimens tested for their genotypes/subtypes by the oligonucleotide array, 607 HCV positive serum samples could be typed by the sequencing method and 60 of 607 HCV positive serum specimens were typed by INNOLiPA HCV II method. Identification of genotype/subtypes by nucleotide sequencing and INNOLiPA HCV II assay showed respective coincidence rates of 99.8% and 96.7% with the HCV oligonucleotide chip results. And the colorimetric method exhibited 99.8% of relative sensitivity compared with the fluorescent amplicor HCV tests.


CONCLUSIONS
To our knowledge this oligonucleotide chip genotyping method offers a fast and convenient way to determine the genotype in large-scale settings. The tests can be easily adapted by a clinical diagnostic laboratory.
Mao
Hongju
H
Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 865 Changning Road, Shanghai 200050, PR China. hjmao@mail.sim.ac.cn
Zhang
Honglian
H
Zhang
Hua
H
Zhao
Jianlong
J
Lu
Zhimeng
Z
Jin
Gendi
G
Gu
Shimin
S
Wang
Huimin
H
Wang
Yongzhong
Y
D003124:Colorimetry / Q000295:instrumentation* / Q000379:methods; D005838:Genotype; D016174:Hepacivirus / Q000235:genetics*; D019698:Hepatitis C, Chronic / Q000175:diagnosis / Q000188:drug therapy / Q000235:genetics / Q000821:virology; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation* / Q000379:methods