Development and clinical evaluation of a microarray for hepatitis C virus genotyping.
The hepatitis C virus (HCV) genotype is the most important factor in predicting the outcome of chronic hepatitis C treatment. Therefore, convenient and accurate HCV genotyping methods for routine laboratory testing are needed. In this study, to identify the HCV genotypes, an oligonucleotide DNA chip was designed using 15 probes from the 5'-untranslated region. Reverse transcription was combined with asymmetric polymerase chain reaction (PCR) to obtain an amplified product for hybridization without the need for a denaturation step. In addition, a biotin-labeled PCR product and streptavidin-Cy3 conjugate were cohybridized simultaneously. Clinical sera from Korean and French patients (n=112) were used to compare the chip results with those obtained by direct sequencing. The DNA chip showed 100% accuracy for the commercial panels and had a lower detection limit of 2.8x10(2) IU/ml. Agreement levels between the chip and sequencing results at the genotype and subgenotype levels were 100% and 94.6% (106/112), respectively. By the combined reverse transcription-asymmetric PCR and cohybridization methods, the DNA chip reduced assay time and was convenient to use. This DNA chip may be useful for identifying HCV genotypes in clinical laboratories.
Park
Jae-Chan
JC
BioCore Institute of Biotechnology BioCore Co, 6F Ace Techno Tower 5(th), 197-22 Guro-dong, Guro-gu, Seoul, Republic of Korea.
Kim
Jong-Man
JM
Kwon
Oh-Joong
OJ
Lee
Kyoung-Ryul
KR
Chai
Young-Guy
YG
Oh
Heung-Bum
HB
D005602:France; D005838:Genotype; D016174:Hepacivirus / Q000145:classification* / Q000235:genetics*; D006526:Hepatitis C / Q000821:virology*; D006801:Humans; D046228:Microarray Analysis / Q000379:methods*; D009693:Nucleic Acid Hybridization / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D012367:RNA, Viral / Q000235:genetics*; D056910:Republic of Korea; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA; D044967:Serum / Q000821:virology; D013223:Statistics as Topic; D014773:Virology / Q000379:methods*
D012367:RNA, Viral