Comparison of Hepatocellular Carcinoma miRNA Expression Profiling as Evaluated by Next Generation Sequencing and Microarray

<div><p>MicroRNA (miRNA) expression profiling has proven useful in diagnosing and understanding the development and progression of several diseases. Microarray is the standard method for analyzing miRNA expression profiles; however, it has several disadvantages, including its limited detection of miRNAs. In recent years, advances in genome sequencing have led to the development of next-generation sequencing (NGS) technologies, which significantly advance genome sequencing speed and discovery. In this study, we compared the expression profiles obtained by next generation sequencing (NGS) with the profiles created using microarray to assess if NGS could produce a more accurate and complete miRNA profile. Total RNA from 14 hepatocellular carcinoma tumors (HCC) and 6 matched non-tumor control tissues were sequenced with Illumina MiSeq 50-bp single-end reads. Micro RNA expression profiles were estimated using miRDeep2 software. As a comparison, miRNA expression profiles for 11 out of 14 HCCs were also established by microarray (Agilent human microRNA microarray). The average total sequencing exceeded 2.2 million reads per sample and of those reads, approximately 57% mapped to the human genome. The average correlation for miRNA expression between microarray and NGS and subtraction were 0.613 and 0.587, respectively, while miRNA expression between technical replicates was 0.976. The diagnostic accuracy of HCC, p-value, and AUC were 90.0%, 7.22×10⁻⁴, and 0.92, respectively. In summary, NGS created an miRNA expression profile that was reproducible and comparable to that produced by microarray. Moreover, NGS discovered novel miRNAs that were otherwise undetectable by microarray. We believe that miRNA expression profiling by NGS can be a useful diagnostic tool applicable to multiple fields of medicine.</p></div

Additional file 1: of The Alcohol Use Disorders Identification Test for Consumption (AUDIT-C) is more useful than pre-existing laboratory tests for predicting hazardous drinking: a cross-sectional study

Table S1. Alcohol Use Disorders Identification Test; the standardized questionnaire used to assess hazardous drinking. Table S2. Juso Alcohol Calculator (JAC); the method used to calculate alcohol consumption and grams based on patients’ reported alcohol consumption volume and type. (PPTX 79 kb

Clinical information of 14 HCC patients analyzed in this study.

<p>Abbreviations, moderately; moderately differentiated HCC, well; well differentiated HCC, poorly; poorly differentiated HCC, NI; no information, CH; chronic hepatitis, LC; liver cirrhosis, only HCC; only HCC was analyzed by NGS, both; both tumor and non-tumorous tissue were analyzed by NGS, neither; neither HCC nor non-tumorous tissue was not analyzed.</p><p>Clinical information of 14 HCC patients analyzed in this study.</p

Additional file 2: of Putting “sticky notes” on the electronic medical record to promote intra-hospital referral of hepatitis B and C virus-positive patients to hepatology specialists: an exploratory study

Detailed data about the patients (n = 6) who received anti-viral treatment in Period 2. (PPTX 54 kb

Transient Elastography-Based Liver Profiles in a Hospital-Based Pediatric Population in Japan

<div><p>Background & Aims</p><p>The utility of transient elastography (FibroScan) is well studied in adults but not in children. We sought to assess the feasibility of performing FibroScans and the characteristics of FibroScan-based liver profiles in Japanese obese and non-obese children.</p><p>Methods</p><p>FibroScan examinations were performed in pediatric patients (age, 1–18 yr) who visited Osaka City University Hospital. Liver steatosis measured by controlled attenuation parameter (CAP), and hepatic fibrosis evaluated as the liver stiffness measurement (LSM), were compared among obese subjects (BMI percentile ≥90%), non-obese healthy controls, and non-obese patients with liver disease.</p><p>Results</p><p>Among 214 children examined, FibroScans were performed successfully in 201 children (93.9%; median, 11.5 yr; range, 1.3–17.6 yr; 115 male). CAP values (mean±SD) were higher in the obese group (n = 52, 285±60 dB/m) compared with the liver disease (n = 40, 202±62, <i>P</i><0.001) and the control (n = 107, 179±41, <i>P</i><0.001) group. LSM values were significantly higher in the obese group (5.5±2.3 kPa) than in the control (3.9±0.9, <i>P</i><0.001), but there were no significant differences in LSM between the liver disease group (5.4±4.2) and either the obese or control group. LSM was highly correlated with CAP in the obese group (ρ = 0.511) but not in the control (ρ = 0.129) or liver disease (ρ = 0.170) groups.</p><p>Conclusions</p><p>Childhood obesity carries a high risk of hepatic steatosis associated with increased liver stiffness. FibroScan methodology provides simultaneous determination of CAP and LSM, is feasible in children of any age, and is a non-invasive and effective screening method for hepatic steatosis and liver fibrosis in Japanese obese children.</p></div

Additional file 1: of Putting “sticky notes” on the electronic medical record to promote intra-hospital referral of hepatitis B and C virus-positive patients to hepatology specialists: an exploratory study

Distribution of patients in non-hepatology departments who were referred to hepatologists in Period 2. (PPTX 51 kb

Boxplots of the expression of 11 miRNAs in HCC and non-tumorous tissue obtained by NGS, which were used for the differential analysis.

<p>P-values were computed using two-sided Wilcoxon Rank Sum test. Asterisk indicates a significant difference of p<0.05 (*).</p

Comparison between differential (K-177 vs. CU-087) logarithmic HCC miRNA expression in NGS (horizontal axis) and microarray (vertical) analysis.

<p>Pearson's correlation coefficient is 0.5555.</p

Performance of discrimination between 14 HCC samples and 6 normal tissue samples using miRNA expression obtained by NGS analysis.

<p>Performance of discrimination between 14 HCC samples and 6 normal tissue samples using miRNA expression obtained by NGS analysis.</p

Comparison between logarithmic HCC miRNA expression in NGS (horizontal axis) and microarray (vertical) analysis (K-177_1 means the first technical replicates of code No. K-177).

<p>One black circle showed one miRNA. Pearson's correlation coefficient is 0.6059.</p