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Comparison of quasispecies diversity of HCV between chronic hepatitis c and hepatocellular carcinoma by Ultradeep pyrosequencing.

Park CW, Cho MC, Hwang K, Ko SY, Oh HB, Lee HC - Biomed Res Int (2014)

Bottom Line: Shannon's indices for quasispecies diversity in HCV E1 were significantly lower in patients with HCC than in those with CHC. 14 amino acid positions differed significantly between two groups.Shannon's indices in 14 amino acid positions were found to differentiate between patients with CHC and those with HCC.Our data propose that degree of HCV quasispecies measured by UDPS might be useful to predict progression of HCC in chronic HCV patients.

View Article: PubMed Central - PubMed

Affiliation: Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul 138-736, Republic of Korea.

ABSTRACT

Backgrounds: Hepatitis C virus (HCV) exists as population of closely related genetic variants known as quasispecies. HCV quasispecies diversity is strongly influenced by host immune pressure on virus. Quasispecies diversity is expected to decline as host immune response to HCV decreases over natural course of progressing from chronic hepatitis C (CHC) to hepatocellular carcinoma (HCC).

Methods: Ultradeep pyrosequencing (UDPS) was used to evaluate degree of quasispecies diversity in 49 patients infected with HCV including 26 with CHC and 23 with HCC. Whole structural protein of HCV genome was subjected to UDPS.

Results: Shannon's indices for quasispecies diversity in HCV E1 were significantly lower in patients with HCC than in those with CHC. 14 amino acid positions differed significantly between two groups. Area under curve of ROC analysis for differentiating HCC from CHC was >0.8 for all of 14 amino acid positions.

Conclusion: HCV quasispecies diversity as indicator of declining host immune functions was easily assessed by UDPS technology. Shannon's indices in 14 amino acid positions were found to differentiate between patients with CHC and those with HCC. Our data propose that degree of HCV quasispecies measured by UDPS might be useful to predict progression of HCC in chronic HCV patients.

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Related in: MedlinePlus

A summary of ultradeep pyrosequencing (UDPS) results. (a) Number of reads and aligned reads of each sample. (b) Average read length of each sample. (c) Hepatitis C virus (HCV) genome coverage by ultradeep pyrosequencing. The dots represent minimum, 25% quartile, 75% quartile, and maximum coverage of reads of samples at each amino acid position of HCV protein. HVR: hypervariable region.
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fig2: A summary of ultradeep pyrosequencing (UDPS) results. (a) Number of reads and aligned reads of each sample. (b) Average read length of each sample. (c) Hepatitis C virus (HCV) genome coverage by ultradeep pyrosequencing. The dots represent minimum, 25% quartile, 75% quartile, and maximum coverage of reads of samples at each amino acid position of HCV protein. HVR: hypervariable region.

Mentions: A total of 1,822,601 sequence reads were obtained from 49 samples using UDPS in the average number of sequence reads as 37,196 (range 4,996–94,180) per sample. Of those, UDPS sequence reads that can be aligned with standard sequence were 35,311 in average per sample, accounting for 94% of total reads (Figure 2(a)), and the average read length was 350 bp per each sample (Figure 2(b)). The number of reads at each position in HCV genome (HCV genome coverage) was nearly 2,000 to 10,000 (Figure 2(c)).


Comparison of quasispecies diversity of HCV between chronic hepatitis c and hepatocellular carcinoma by Ultradeep pyrosequencing.

Park CW, Cho MC, Hwang K, Ko SY, Oh HB, Lee HC - Biomed Res Int (2014)

A summary of ultradeep pyrosequencing (UDPS) results. (a) Number of reads and aligned reads of each sample. (b) Average read length of each sample. (c) Hepatitis C virus (HCV) genome coverage by ultradeep pyrosequencing. The dots represent minimum, 25% quartile, 75% quartile, and maximum coverage of reads of samples at each amino acid position of HCV protein. HVR: hypervariable region.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4066718&req=5

fig2: A summary of ultradeep pyrosequencing (UDPS) results. (a) Number of reads and aligned reads of each sample. (b) Average read length of each sample. (c) Hepatitis C virus (HCV) genome coverage by ultradeep pyrosequencing. The dots represent minimum, 25% quartile, 75% quartile, and maximum coverage of reads of samples at each amino acid position of HCV protein. HVR: hypervariable region.
Mentions: A total of 1,822,601 sequence reads were obtained from 49 samples using UDPS in the average number of sequence reads as 37,196 (range 4,996–94,180) per sample. Of those, UDPS sequence reads that can be aligned with standard sequence were 35,311 in average per sample, accounting for 94% of total reads (Figure 2(a)), and the average read length was 350 bp per each sample (Figure 2(b)). The number of reads at each position in HCV genome (HCV genome coverage) was nearly 2,000 to 10,000 (Figure 2(c)).

Bottom Line: Shannon's indices for quasispecies diversity in HCV E1 were significantly lower in patients with HCC than in those with CHC. 14 amino acid positions differed significantly between two groups.Shannon's indices in 14 amino acid positions were found to differentiate between patients with CHC and those with HCC.Our data propose that degree of HCV quasispecies measured by UDPS might be useful to predict progression of HCC in chronic HCV patients.

View Article: PubMed Central - PubMed

Affiliation: Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul 138-736, Republic of Korea.

ABSTRACT

Backgrounds: Hepatitis C virus (HCV) exists as population of closely related genetic variants known as quasispecies. HCV quasispecies diversity is strongly influenced by host immune pressure on virus. Quasispecies diversity is expected to decline as host immune response to HCV decreases over natural course of progressing from chronic hepatitis C (CHC) to hepatocellular carcinoma (HCC).

Methods: Ultradeep pyrosequencing (UDPS) was used to evaluate degree of quasispecies diversity in 49 patients infected with HCV including 26 with CHC and 23 with HCC. Whole structural protein of HCV genome was subjected to UDPS.

Results: Shannon's indices for quasispecies diversity in HCV E1 were significantly lower in patients with HCC than in those with CHC. 14 amino acid positions differed significantly between two groups. Area under curve of ROC analysis for differentiating HCC from CHC was >0.8 for all of 14 amino acid positions.

Conclusion: HCV quasispecies diversity as indicator of declining host immune functions was easily assessed by UDPS technology. Shannon's indices in 14 amino acid positions were found to differentiate between patients with CHC and those with HCC. Our data propose that degree of HCV quasispecies measured by UDPS might be useful to predict progression of HCC in chronic HCV patients.

Show MeSH
Related in: MedlinePlus