Additional file 1: of Performance of 6 HCV genotyping 9G test for HCV genotyping in clinical samples

Table S1. Comparison of 6 HCV Genotyping 9G Test and LiPA 2.0 with the sequencing in 46 discordant samples. Table S2. TP, TN, FP, and FN results of 6 HCV Genotyping 9G Test and LiPA 2.0 with the sequencing in 274 samples. Table S3. TP, TN, FP, and FN results of 6 HCV Genotyping 9G Test (n = 274). (DOCX 86 kb

Additional file 1: of A robust model of natural hepatitis C infection using hepatocyte-like cells derived from human induced pluripotent stem cells as a long-term host

Primer sets and conditions used in quantitative real-time PCR (qPCR). (DOCX 15 kb

Detected SNPs in HA gene fragment from sample #VIROAF1 (“AF1_HA.csv”).

<p>Each line describes the SNPs at each position in the HA gene fragment of VIROAF1. For instance, position 51 of the HA gene in VIROAF1 is G while the reference allele is A.</p><p>Detected SNPs in HA gene fragment from sample #VIROAF1 (“AF1_HA.csv”).</p

Demographic and Baseline Characteristics of 265 Treatment-Naïve HIV-Infected Patients.

<p>Demographic and Baseline Characteristics of 265 Treatment-Naïve HIV-Infected Patients.</p

Factors Associated with Undetectable HIV RNA at 6 Months after ART Initiation, by Univariate Logistic Regression.

<p>Factors Associated with Undetectable HIV RNA at 6 Months after ART Initiation, by Univariate Logistic Regression.</p

Carrier frequency of inherited genetic disorders in Thai population: implication for designing expanded carrier screening panel.

<strong>Background: Expanded carrier screening (ECS) is the process of screening individuals for hundreds of autosomal recessive (AR) and X-linked recessive (XLR) diseases. ECS result is beneficial for couples who want to make an informed reproductive choice. Though next-generation sequencing allows thousand of genes to be sequenced at once, the ideal ECS gene panel should only include diseases that its carriers are common in the population (1% or higher), and the prenatal diagnosis of the disease is allowed. However, designing the ECS panel for Thais can be difficult because the carrier frequency for most genetic diseases is unknown. Therefore, we retrospectively review our exome sequencing data from Thai patient to get an estimation of the carrier frequency. Method: Variants in 540 genes associated with AR and XLR from exome sequencing data of 178 unrelated Thai patients are filtered and matched against known pathogenic mutations in reputable mutation databases (OMIM, Clinvar, and HGMD). Result: Pathogenic mutations in SLC26A4 gene associated with Pendred syndrome has the highest carrier frequency of 2.81%. Usher syndrome (USH2A) are the second-most common with the carrier frequency of 2.25%. 1.69% of the patients also have pathogenic mutations in the gene related to impaired vision and impaired hearing such as OCA2 OTOF CLCN1 BSND and AHI1. Only 1.12% or less are the carrier of severe diseases such as myotonia congenita (CLCN1), lactic acidosis (POLG) and molybdenum cofactor deficiency (MOCS1). Conclusion: Inherited diseases that involved the impairment of hearing and vision is somewhat common among Thais. The ethical issue could arise when these diseases are included the ECS panel because they are not severe enough to allow for prenatal diagnosis. More discussion about ethics of ECS and more data on carrier frequency is needed to offer ECS ethically.</strong

Prevalence of primary HIV drug resistance mutations, from short reverse transcriptase genotypic resistance assay.

<p>Prevalence of primary HIV drug resistance mutations, from short reverse transcriptase genotypic resistance assay.</p

Comparison of Clinical Characteristics, Laboratory Investigations, and Clinical Outcomes between Patients with and without Primary HIV Drug Resistance.

<p>Comparison of Clinical Characteristics, Laboratory Investigations, and Clinical Outcomes between Patients with and without Primary HIV Drug Resistance.</p

The SNPs composition output chart of three HA sequences from three IFV subpopulations.

<p>Each circle represents the number of SNPs of VIROAF1 (sp1), VIROAF2 (sp2) and VIROAF6 (sp3) for the HA fragment; universal SNPs; unique SNPs; and likely common SNPs.</p

The outputs of SNPer for the eight fragments of the three different IFVs (“summary.csv”).

<p>Each row shows the number of SNPs of VIROAF1 (sp1), VIROAF2 (sp2) and VIROAF6 (sp3) for each fragment after comparison by SNPer. For example, in the first row, the HA fragment contains 27 SNPs in VIROAF1, 22 SNPs in VIROAF2 and 29 SNPs in VIROAF6. Twelve universal SNPs are in VIROAF1, VIROAF2, and VIROAF6. There are six SNPs in only VIROAF1, 10 SNPs in only VIROAF2 and eight SNPs in only VIROAF6. Only nine SNPs exist in both VIROAF6 and VIROAF1.(1)</p><p>The outputs of SNPer for the eight fragments of the three different IFVs (“summary.csv”).</p