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

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

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

Profile of chromosomal alterations in all HCC samples (n = 159).

<p><b>(a)</b>, heatmap of CNAs across all chromosomes. <b>(b)</b>, the frequencies of CNAs across all chromosomes. Copy number gain and loss events of chromosomal segments were determined using log2-transformed ratio thresholds of 0.141 and −0.136 derived from the k-means clustering analysis. The color brightness is directly proportional to the frequency of CNA. Color red represents copy number gain and color blue represents copy number loss. CNA: copy number alteration.</p

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

Correlations between significant chromosomal aberrations either located on the same (a) or different (b) chromosomes in all HCCs.

<p>Chromosomal segments with significant gain were highlighted in red and those with significant loss in blue. Spearman's rank correlation coefficient was calculated to assess the correlations between different chromosomal copy number gains and losses at the significant level of p<0.001.</p

Cumulative effects of risk genotypes.

<p>A) Overall recurrence free survival; B) Early recurrence free survival. Cumulative effects of risk genotypes groups were assessed by Kaplan-Meier curves (left panels) and estimated using Cox proportional hazards model by multivariate analysis (right panels). Individual SNPs with significant <i>P</i> values <0.05 were included to categorize the risk genotype groups.</p

The functional KEGG pathways enriched with genes located on the chromosomal segments with significant CNAs in all HCCs.

<p><b>Note:</b> The pathways that were significantly affected by the identfied CNAs were determined by Fisher' exact test.</p><p>KEGG, Kyoto Encyclopedia of Genes and Genomes; CNA, copy number alteration.</p

Information of 4 collected public datasets (n = 159).

*<p>Information of virus infection for individual samples is unavailable. HBV, hepatitis B virus; HCV, hepatitis C virus; HBx, hepatitis B virus X protein.</p