Overestimation and underestimation of hepatitis C virus RNA levels in a widely used real-time polymerase chain reaction-based method, Hepatology, vol.44, issue.1, pp.22-31, 2007. ,
DOI : 10.1002/hep.21656
Performance of Version 2.0 of the Cobas AmpliPrep/Cobas TaqMan Real-Time PCR Assay for Hepatitis B Virus DNA Quantification, Journal of Clinical Microbiology, vol.48, issue.10, pp.3641-3648, 2010. ,
DOI : 10.1128/JCM.01306-10
URL : https://hal.archives-ouvertes.fr/inserm-00529803
Performance of the Abbott Real-Time PCR Assay Using m2000sp and m2000rt for Hepatitis C Virus RNA Quantification, Journal of Clinical Microbiology, vol.47, issue.6, pp.1726-1758, 2009. ,
DOI : 10.1128/JCM.01300-08
URL : https://hal.archives-ouvertes.fr/inserm-00395281
Development of a Second Version of the Cobas AmpliPrep/Cobas TaqMan Hepatitis C Virus Quantitative Test with Improved Genotype Inclusivity, Journal of Clinical Microbiology, vol.49, issue.9, pp.3309-3324, 2011. ,
DOI : 10.1128/JCM.00602-11
An update on treatment of genotype 1 chronic hepatitis C virus infection: 2011 practice guideline by the American Association for the Study of Liver Diseases, Hepatology, vol.54, issue.suppl 1, pp.1433-1477, 2011. ,
DOI : 10.1002/hep.24641
Diagnosis, management, and treatment of hepatitis C: An update, Hepatology, vol.11, issue.Suppl 5, pp.1335-74, 2009. ,
DOI : 10.1002/hep.22759
Asian-Pacific consensus statement on the management of chronic hepatitis B: a 2008 update, Hepatology International, vol.47, issue.Suppl 1, pp.263-283, 2008. ,
DOI : 10.1007/s12072-008-9080-3
Chronic hepatitis B: Update 2009, Hepatology, vol.57, issue.RR-8, pp.661-663, 2009. ,
DOI : 10.1002/hep.23190
The effect of using lower limit of quantitation (LLQ) vs lower limit of detection (LLD) for the definition of undetectable HCV RNA: data from the RESPOND-2 and SPRINT-2 trials, Hepatology, vol.54, p.442, 2011. ,
Clinical relevance of detectable but not quantifiable hepatitis C virus RNA during boceprevir or telaprevir treatment, Hepatology, vol.5, issue.4, 2012. ,
DOI : 10.1002/hep.24791
Hepatitis B virus surface antigen levels: A guide to sustained response to peginterferon alfa-2a in HBeAg-negative chronic hepatitis B, Hepatology, vol.102, issue.Suppl, pp.1141-50, 2009. ,
DOI : 10.1002/hep.22760
Early serum HBsAg drop: A strong predictor of sustained virological response to pegylated interferon alfa-2a in HBeAg-negative patients, Hepatology, vol.37, issue.Suppl 2, pp.1151-1158, 2009. ,
DOI : 10.1002/hep.22744
Kinetics of hepatitis B surface antigen decline during 3 years of telbivudine treatment in hepatitis B e antigen-positive patients, Hepatology, vol.99, issue.Suppl. 1, pp.1611-1631, 2010. ,
DOI : 10.1002/hep.23905
Hepatitis B surface antigen quantification: Why and how to use it in 2011 ??? A core group report, Journal of Hepatology, vol.55, issue.5, pp.1121-1152, 2011. ,
DOI : 10.1016/j.jhep.2011.06.006
A comparison of two assays for quantification of Hepatitis B surface antigen in patients with chronic hepatitis B, J Clin Virol, vol.51, pp.175-183, 2011. ,
Analytical evaluation of HCV core antigen and interest for HCV screening in haemodialysis patients, Journal of Clinical Virology, vol.48, issue.1, pp.18-21, 2010. ,
DOI : 10.1016/j.jcv.2010.02.012
Analytical Performance Characteristics and Clinical Utility of a Novel Assay for Total Hepatitis C Virus Core Antigen Quantification, Journal of Clinical Microbiology, vol.48, issue.4, pp.1161-1169, 2010. ,
DOI : 10.1128/JCM.01640-09
Usefulness of dried blood samples for quantification and molecular characterization of HBV-DNA, Hepatology, vol.126, issue.1, pp.133-142, 2004. ,
DOI : 10.1002/hep.20275
Dried blood spot for hepatitis C virus serology and molecular testing, Hepatology, vol.68, pp.752-760, 2010. ,
DOI : 10.1002/hep.23407
Evaluation of the Abbott Real-Time HIV-1 quantitative assay with dried blood spot specimens, Clinical Microbiology and Infection, vol.15, issue.1, pp.93-100, 2009. ,
DOI : 10.1111/j.1469-0691.2008.02116.x
Genome-wide association studies: theoretical and practical concerns, Nature Reviews Genetics, vol.60, issue.2, pp.109-127, 2005. ,
DOI : 10.1093/jnci/djh075
Genomewide Association Studies and Human Disease, New England Journal of Medicine, vol.360, issue.17, pp.1759-68, 2009. ,
DOI : 10.1056/NEJMra0808700
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3422859
The pursuit of genome-wide association studies: where are we now?, Journal of Human Genetics, vol.461, issue.4, pp.195-206, 2010. ,
DOI : 10.1038/jhg.2010.19
RNA-Seq: a revolutionary tool for transcriptomics, Nature Reviews Genetics, vol.328, issue.1, pp.57-63, 2009. ,
DOI : 10.1038/nrg2484
Sequencing technologies ??? the next generation, Nature Reviews Genetics, vol.37, issue.1, pp.31-46, 2010. ,
DOI : 10.1038/nrg2626
Solexa Ltd, Pharmacogenomics, vol.5, issue.4, pp.433-441, 2004. ,
DOI : 10.1517/14622416.5.4.433
Genome sequencing in microfabricated high-density picolitre reactors, Nature, vol.2, pp.376-80, 2005. ,
DOI : 10.1016/0888-7543(88)90007-9
An integrated semiconductor device enabling non-optical genome sequencing, Nature, vol.475, pp.348-52, 2011. ,
Real-time DNA sequencing from single polymerase molecules, Science, vol.323, pp.133-141, 2009. ,
Evaluation of next generation sequencing platforms for population targeted sequencing studies, Genome Biology, vol.10, issue.3, p.32, 2009. ,
DOI : 10.1186/gb-2009-10-3-r32
Comparing Platforms for C. elegans Mutant Identification Using High-Throughput Whole-Genome Sequencing, PLoS ONE, vol.452, issue.12, p.4012, 2008. ,
DOI : 10.1371/journal.pone.0004012.t006
High throughput sequencing in mice: a platform comparison identifies a preponderance of cryptic SNPs, BMC Genomics, vol.10, issue.1, p.379, 2009. ,
DOI : 10.1186/1471-2164-10-379
Comparison of Sequence Reads Obtained from Three Next-Generation Sequencing Platforms, PLoS ONE, vol.5, issue.5, p.19534, 2011. ,
DOI : 10.1371/journal.pone.0019534.s003
Substantial biases in ultra-short read data sets from high-throughput DNA sequencing, Nucleic Acids Research, vol.36, issue.16, p.105, 2008. ,
DOI : 10.1093/nar/gkn425
Evaluation of Oligonucleotide Sequence Capture Arrays and Comparison of Next-Generation Sequencing Platforms for Use in Molecular Diagnostics, Clinical Chemistry, vol.56, issue.8, pp.1297-306, 2010. ,
DOI : 10.1373/clinchem.2010.145441
Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing, BMC Genomics, vol.23, issue.21, p.245, 2011. ,
DOI : 10.1093/bioinformatics/btm404
II. Error Probabilities, Genome Research, vol.8, issue.3, pp.186-94, 1998. ,
DOI : 10.1101/gr.8.3.186
???I. Accuracy???Assessment, Genome Research, vol.8, issue.3, pp.175-85, 1998. ,
DOI : 10.1101/gr.8.3.175
Estimation of Errors in ???Raw??? DNA Sequences: A Validation???Study, Genome Research, vol.8, issue.3 ,
DOI : 10.1101/gr.8.3.251
Managing and Analyzing Next-Generation Sequence Data, PLoS Computational Biology, vol.5, issue.6 ,
DOI : 10.1371/journal.pcbi.1000369
URL : http://doi.org/10.1371/journal.pcbi.1000369
Characterization of mutation spectra with ultra-deep pyrosequencing: Application to HIV-1 drug resistance, Genome Research, vol.17, issue.8, pp.1195-201, 2007. ,
DOI : 10.1101/gr.6468307
The Evolutionary Analysis of Emerging Low Frequency HIV-1 CXCR4 Using Variants through Time???An Ultra-Deep Approach, PLoS Computational Biology, vol.54, issue.12, p.1001022, 2010. ,
DOI : 10.1371/journal.pcbi.1001022.s001
Phylogenetic Analysis of Population-Based and Deep Sequencing Data to Identify Coevolving Sites in the nef Gene of HIV-1, Molecular Biology and Evolution, vol.27, issue.4, pp.819-851, 2010. ,
DOI : 10.1093/molbev/msp289
Detection of Minority Resistance during Early HIV-1 Infection: Natural Variation and Spurious Detection rather than Transmission and Evolution of Multiple Viral Variants, Journal of Virology, vol.85, issue.16, pp.8359-67, 2011. ,
DOI : 10.1128/JVI.02582-10
Ultra-deep pyrosequencing, a powerful new tool to study HBV Resistance to nucleoside/nucleotide analogues, identifies pre-existing HBV variants bearing resistance mutations and characterizes their on-treatment kinetics, Hepatology, vol.52, p.117, 2011. ,
67 MOLECULAR CHARACTERIZATION OF HCV RESISTANCE TO TELAPREVIR BY MEANS OF ULTRA-DEEP PYROSEQUENCING: PREEXISTING RESISTANT VARIANTS AND DYNAMICS OF RESISTANT POPULATIONS, Journal of Hepatology, vol.54, p.30, 2011. ,
DOI : 10.1016/S0168-8278(11)60069-X
HIV-1 coreceptor usage prediction by " ultra-deep pyrosequencing " increases the rate of patients treated with success by CCR5 antagonists, Antiviral Ther, vol.16, p.100, 2011. ,
Changes in Serum Levels of HBV DNA and Alanine Aminotransferase Determine Risk for Hepatocellular Carcinoma, Gastroenterology, vol.141, issue.4, pp.1240-1248, 2011. ,
DOI : 10.1053/j.gastro.2011.06.036
Hepatitis B virus DNA levels and outcomes in chronic hepatitis B, Hepatology, vol.48, issue.S5, pp.72-84, 2009. ,
DOI : 10.1002/hep.22884
The importance of HBV genotype in HBeAg-positive chronic hepatitis B patients in whom sustained response is pursued, Journal of Hepatology, vol.54, issue.2, pp.395-401, 2011. ,
DOI : 10.1016/j.jhep.2010.07.052
Is response to antiviral treatment influenced by hepatitis B virus genotype?, Journal of Hepatology, vol.52, issue.3, pp.441-450, 2010. ,
DOI : 10.1016/j.jhep.2009.12.014
Tenofovir and Entecavir Are the Most Effective Antiviral Agents for Chronic Hepatitis B: A Systematic Review and Bayesian Meta-analyses, Gastroenterology, vol.139, issue.4, pp.1218-1247, 2010. ,
DOI : 10.1053/j.gastro.2010.06.042
Entecavir treatment for chronic hepatitis B: Adaptation is not needed for the majority of na??ve patients with a partial virological response, Hepatology, vol.49, issue.5 Suppl., pp.443-51, 2011. ,
DOI : 10.1002/hep.24406
Virologic Monitoring of Hepatitis B Virus Therapy in Clinical Trials and Practice: Recommendations for a Standardized Approach, Gastroenterology, vol.134, issue.2, pp.405-420, 2008. ,
DOI : 10.1053/j.gastro.2007.11.036
Hepatitis C Virus (HCV) Genotype 1 Subtype Identification in New HCV Drug Development and Future Clinical Practice, PLoS ONE, vol.4, issue.12, p.8209, 2009. ,
DOI : 10.1371/journal.pone.0008209.t002
URL : https://hal.archives-ouvertes.fr/inserm-00443832
Host genomics and HCV treatment response, Journal of Gastroenterology and Hepatology, vol.364, issue.suppl. 1, pp.212-234, 2012. ,
DOI : 10.1111/j.1440-1746.2011.06918.x
Treatment failure and resistance with direct-acting antiviral drugs against hepatitis C virus, Hepatology, vol.53, issue.5, pp.1742-51, 2011. ,
DOI : 10.1002/hep.24262
8 EVOLUTION OF TREATMENT-EMERGENT RESISTANT VARIANTS IN TELAPREVIR PHASE 3 CLINICAL TRIALS, Journal of Hepatology, vol.54, p.4, 2011. ,
DOI : 10.1016/S0168-8278(11)60010-X
CA Real-time PCR Manual with High Pure System Viral Nucleic Acid Kit COBAS ® TaqMan 650 ?L 20 IU/mL 25 (1.4 Log10)- 3, ) IU/mL COBAS ® Ampliprep - COBAS ® TaqMan ® (CAP/CTM) HCV Test ,
Des Plaines, IL Real-time PCR m2000SP m2000RT 200 or 500 ?L 12 IU/mL (for 500?L) 30 IU/mL (for 200 ?L ,
Germany Real-time PCR QIAsymphony RGQ Rotor-Gene Q 1000 ?L 36 ,
Assay (kPCR) Siemens Medical Solutions Diagnostics, Tarrytown, NY Real-time PCR Sample Preparation (SP) Module Amplification and Detection (AD) Module 500 ?L 15 IU ,