Table 1.
Characteristics of primary liver cancer patients.
Fig 1.
Workflow for chromosome data analysis.
ChAS data was transferred to Excel, arranged, and saved as CSV files. These files were imported into bioinformatics tools for analysis. A heatmap was generated to visualize the top 50 probe markers on each chromosome. The results were combined into a single CSV file and analyzed using Principal Component Analysis (PCA) to identify group differences. The heatmap was also used to analyze the top 50 regions across all chromosomes. Candidate chromosome abnormality regions were identified based on the top 10 log2 fold change, top 10 p-value, and top 5 prevalence of loss and gain in HCC and CCA patients.
Table 2.
Recurrence of chromosome abnormality in HCC.
Fig 2.
The karyoview analysis using ChAS software.
The figure presents an ideogram of all copy number variation in HCC cases (A) and (B) CCA cases. Blue bar represents gain; red bar represents loss.
Table 3.
Recurrence of chromosome abnormality in CCA.
Fig 3.
A heatmap clustering of chromosomal abnormality regions.
The x-axis represents the number of cases with hepatocellular carcinoma (HCC) and cholangiocarcinoma (CCA). The y-axis lists the top 50 chromosomal abnormality regions. Z-scored copy number variations (CNVs) range from -2 to 2. Red indicates CNV gains, while blue indicates CNV losses.
Table 4.
The differential copy number variations ratios between HCC and CCA in the top 10 chromosome region with the highest fold change.
Table 5.
Distinct chromosomal patterns in HCC and CCA: analysis of top 10 low p-value chromosome regions.
Fig 4.
Identification of HCC and CCA chromosome abnormality regions.
(A) A principal component (PC) scores plot of HCC and CCA patients. (B) The PC analysis of HCC and CCA. (C) A heatmap clustering chromosome region marker. The x-axis represents cases of HCC and CCA. The y-axis represents different chromosome region markers. Z scored log2 ratio are shown from -2 to 2. Red indicates chromosome gain and blue indicates chromosome loss.
Fig 5.
The differential Log2 ratios between HCC and CCA in candidate regions.
The graph of log2 ratio of chromosome region 2q12.3 (A), 10q21.3(B), 19p13.2(C), 5q32 (D), 7q21.13 (E) and 21q21.3 (F) in HCC and CCA.
Fig 6.
HCC and CCA cases were validated using the FISH technique.
(A) HCC case showed a negative result for 1p36 loss or gain with normal nuclei containing two orange and two green signals. (B) HCC case displayed a gain of 1p36 indicated by three orange and two green signals. (C) CCA case exhibited a loss of 1p36 characterized by one orange signal and two green signals. (D-F) Proliferative hepatocytes cases with normal nuclei. (G-I) Cholangitis cases with normal nuclei.