Cumulative incidence of HCC by the clinical cut-off values of baseline enzyme levels. HCC incidence by the clinical cut-off of baseline (A) ALT, (B) AST, (C) ALP, and (D) GGT.

<p>Cumulative incidence of HCC by the clinical cut-off values of baseline enzyme levels. HCC incidence by the clinical cut-off of baseline (A) ALT, (B) AST, (C) ALP, and (D) GGT.</p

Additional file 1 of Comparison of capture-based mtDNA sequencing performance between MGI and illumina sequencing platforms in various sample types

Additional file 1: Table S1. Sample and sequencing information. Table S2. A list of consensus haplotypes from all samples. Table S3. A complete list of mtDNA variants. Table S4. Homoplasmic/heteroplasmic fraction of mtDNA variants in fresh and FFPE tumor tissue

Supplementary Data from MicroRNA Expression Signatures in Barrett's Esophagus and Esophageal Adenocarcinoma

Supplementary Data from MicroRNA Expression Signatures in Barrett's Esophagus and Esophageal Adenocarcinom

Combined effects of GGT with other liver enzymes on HCC risk.

<p>Notes: ¹The cutoff values for ALT are: Normal, ALT ≤40.0 U/L for male or ≤31.0 U/L for female; Elevated, ALT >40.0 U/L for male or >31.0 U/L for female; the cutoff values for AST are: Normal, AST ≤37.0 U/L for male or ≤31.0 U/L for female; Elevated, AST >37.0 U/L for male or >31.0 U/L for female; the cutoff values for ALP are: Normal, ALP≤117.0 U/L for all patients; Elevated, ALP>117.0 U/L for all patients; the cutoff values for GGT are: Normal, GGT ≤51.0 U/L for male or GGT ≤33.0 U/L for female; Elevated, GGT >51.0 U/L for male or >33.0 U/L for female. Normal, both enzymes were at normal range; Elevated, both enzymes were at elevated levels.</p>2<p>HR adjusted for gender, age, smoking status, alcohol consumption, cirrhosis, and family cancer.</p>3<p>HR adjusted for gender, age, smoking status, alcohol consumption, and family cancer.</p

Profiles of etiology-related chromosomal aberrations in HCCs.

<p><b>(a).</b> the comparison of chromosomal aberration profiles between HBV-related HCCs and HCV-related HCCs. <b>(b)</b>, the comparison of chromosomal aberration profiles between virus-related HCCs and non-virus-related HCCs. Copy number gains and losses with a significant difference in frequencies were highlighted in red and blue, respectively.</p

Comparison of correlations among log2-transformed ratios of 159 samples from four independent datasets before (a) and after preprocessing (b).

<p>In triangle (a) and (b), color points dotted in rectangles represent PCC values of log2-transformed ratio between any two samples from different datasets, while color points dotted in small triangles represent those from same dataset. The brightness of color blue is directly proportional to the value (0 – 1) of Pearson correlation coefficient.</p

The association of serum liver enzyme levels within 1 year of follow-up and HCC risk in HBV-infected patients.

<p>Notes: ¹The cutoff values for ALT are: Normal, ALT ≤40.0 U/L for male or ≤31.0 U/L for female; Elevated, ALT >40.0 U/L for male or >31.0 U/L for female; the cutoff values for AST are: Normal, AST ≤37.0 U/L for male or ≤31.0 U/L for female; Elevated, AST >37.0 U/L for male or >31.0 U/L for female; the cutoff values for ALP are: Normal, ALP≤117.0 U/L for all patients; Elevated, ALP>117.0 U/L for adults and 117–390 for children (3–15 years); the cutoff values for GGT are: Normal, GGT ≤51.0 U/L for male or GGT ≤33.0 U/L for female; Elevated, GGT >51.0 U/L for male or >33.0 U/L for female.</p>2<p>HR adjusted for gender, age, smoking status, alcohol consumption, cirrhosis, and family cancer.</p>3<p>HR adjusted for gender, age, smoking status, alcohol consumption, and family cancer.</p

Characteristics of the study population by serum liver enzymes activity status at baseline.

<p>Notes: ¹The cutoff values for ALT are: Normal, ALT ≤40.0 U/L for male or ≤31.0 U/L for female; Elevated, ALT >40.0 U/L for male or >31.0 U/L for female;</p>2<p>the cutoff values for AST are: Normal, AST ≤37.0 U/L for male or ≤31.0 U/L for female; Elevated, AST >37.0 U/L for male or >31.0 U/L for female;</p>3<p>the cutoff values for ALP are: Normal, ALP≤117.0 U/L for all patients; Elevated, ALP>117.0 U/L for adults and 117–390 for children (3–15 years);</p>4<p>the cutoff values for GGT are: Normal, GGT ≤51.0 U/L for male or GGT ≤33.0 U/L for female; Elevated, GGT >51.0 U/L for male or >33.0 U/L for female.</p

Potential higher order gene—gene interactions among TCA pathway polymorphisms.

<p>A) Tree structure identifying subgroups of patients with different genetic backgrounds; B) Kaplan—Meier survival curves for patients based on survival tree analysis.</p

A High-Efficiency Capture-Based NGS Approach for Comprehensive Analysis of Mitochondrial Transcriptome

The transcription of the mitochondrial genome is pivotal for maintenance of mitochondrial functions, and the deregulated mitochondrial transcriptome contributes to various pathological changes. Despite substantial progress having been achieved in uncovering the transcriptional complexity of the nuclear transcriptome, many unknowns and controversies remain for the mitochondrial transcriptome, partially owing to the lack of a highly efficient mitochondrial RNA (mtRNA) sequencing and analysis approach. Here, we first comprehensively evaluated the influence of essential experimental protocols, including strand-specific library construction, two RNA enrichment strategies, and optimal rRNA depletion, on accurately profiling mitochondrial transcriptome in whole-transcriptome sequencing (WTS) data. Based on these insights, we developed a highly efficient approach specifically suitable for targeted sequencing of whole mitochondrial transcriptome, termed capture-based mtRNA seq (CAP), in which strand-specific library construction and optimal rRNA depletion were applied. Compared with WTS, CAP has a great decrease of required data volume without affecting the sensitivity and accuracy of detection. In addition, CAP also characterized the unannotated mt-tRNA transcripts whose expression levels are below the detection limits of conventional WTS. As a proof-of-concept characterization of mtRNAs, the transcription initiation sites and mtRNA cleavage ratio were accurately identified in CAP data. Moreover, CAP had very reliable performance in plasma and single-cell samples, highlighting its wide application. Altogether, the present study has established a highly efficient pipeline for targeted sequencing of mtRNAs, which may pave the way toward functional annotation of mtRNAs and mtRNA-based diagnostic and therapeutic strategies in various diseases