scholarly journals Clinical implication of recurrent copy number alterations in hepatocellular carcinoma and putative oncogenes in recurrent gains on 1q

2008 ◽  
Vol 123 (12) ◽  
pp. 2808-2815 ◽  
Author(s):  
Tae-Min Kim ◽  
Seon-Hee Yim ◽  
Seung-Hun Shin ◽  
Hai-Dong Xu ◽  
Yu-Chae Jung ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Clinical Implication ◽  
Copy Number ◽  
Copy Number Alterations

Sex-dependent differences in DNA copy number alterations in hepatocellular carcinoma

2012 ◽  
Vol 32 (1) ◽  
pp. 5-9 ◽  
Author(s):  
Bing-ji WEN ◽  
Wen-ming CONG ◽  
Ai-zhong WANG ◽  
Song-qin HE ◽  
Hong-mei JIANG ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Copy Number ◽  
Copy Number Alterations ◽  
Dna Copy Number ◽  
Dna Copy Number Alterations

scholarly journals Convergent Evolution of Copy Number Alterations in Multi-Centric Hepatocellular Carcinoma

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Carolin Lackner ◽  
Luca Quagliata ◽  
William Cross ◽  
Sebastian Ribi ◽  
Karl Heinimann ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Copy Number ◽  
Convergent Evolution ◽  
Copy Number Alterations

scholarly journals Correlating Genomic Copy Number Alterations with Clinicopathologic Findings in A Case Series of Hepatocellular Carcinoma

2020 ◽  
Author(s):  
Gang Peng ◽  
Hongyan Chai ◽  
Weizhen Ji ◽  
Yufei Lu ◽  
Shengming Wu ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Copy Number ◽  
Case Series ◽  
Oligonucleotide Array ◽  
Good Survival ◽  
Survival Outcomes ◽  
Copy Number Alterations ◽  
Acgh Analysis ◽  
Clinicopathologic Findings ◽  
Grade Iii

Abstract Background: Oligonucleotide array comparative genomic hybridization (aCGH) analysis has been used for detecting somatic copy number alterations (CNAs) in various types of tumors. This study aimed to assess the clinical utility of aCGH for a case series of hepatocellular carcinoma (HCC) and to evaluate the correlation between CNAs and clinicopathologic findings.Methods: Survival outcomes from this case series were analyzed based on Barcelona-Clinic Liver Cancer Stage (BCLC), Edmondson-Steiner grade (E-S), and recurrence status. aCGH was performed on 75 HCC cases with paired DNA samples from tumor and adjacent nontumor tissues. Correlation of CNAs with clinicopathologic findings was analyzed by Wilcoxon rank test and clustering vs. K means. Results: The survival outcomes indicated that BCLC stages and recurrence status could be predictors and E-S grades could be a modifier for HCC. The most common CNAs involved gains of 1q and 8q and a loss of 16q (50%), losses of 4q and 17p and a gain of 5p (40%), and losses of 8p and 13q (30%). Correlation and clustering analyses noted that losses of 4q13.2q35.2 and 10q22.3q26.13 seen in cases of stage A, grade III and nonrecurrence were likely associated with good survival, while loss of 1p36.31p22.1 and gains of 2q11.2q21.2 and 20p13p11.1 seen in cases of stage C, grade III and recurrence were possibly associated with worst prognosis. Conclusions: These results indicated that aCGH analysis could be used to detect recurrent CNAs and involved key genes and pathways in patients with HCC. Further analysis on a large case series to validate the association of CNAs with clinicopathologic findings of HCC could provide information to interpret CNAs and predict prognosis.

Overlapping high-resolution copy number alterations in cancer genomes identified putative cancer genes in hepatocellular carcinoma

Hepatology ◽  
2010 ◽  
Vol 52 (5) ◽  
pp. 1690-1701 ◽  
Author(s):  
Chian-Feng Chen ◽  
En-Chi Hsu ◽  
Kuen-Tyng Lin ◽  
Pang-Hsien Tu ◽  
Hung-Wei Chang ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
High Resolution ◽  
Copy Number ◽  
Cancer Genes ◽  
Copy Number Alterations ◽  
Cancer Genomes

scholarly journals Correlating genomic copy number alterations with clinicopathologic findings in 75 cases of hepatocellular carcinoma

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Gang Peng ◽  
Hongyan Chai ◽  
Weizhen Ji ◽  
Yufei Lu ◽  
Shengming Wu ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Copy Number ◽  
Oligonucleotide Array ◽  
Good Survival ◽  
Survival Outcomes ◽  
Comparative Genomic ◽  
Copy Number Alterations ◽  
Acgh Analysis ◽  
Clinicopathologic Findings ◽  
Grade Iii

Abstract Background Oligonucleotide array comparative genomic hybridization (aCGH) analysis has been used for detecting somatic copy number alterations (CNAs) in various types of tumors. This study aimed to assess the clinical utility of aCGH for cases of hepatocellular carcinoma (HCC) and to evaluate the correlation between CNAs and clinicopathologic findings. Methods aCGH was performed on 75 HCC cases with paired DNA samples from tumor and adjacent nontumor tissues. Survival outcomes from these cases were analyzed based on Barcelona-Clinic Liver Cancer Stage (BCLC), Edmondson-Steiner grade (E-S), and recurrence status. Correlation of CNAs with clinicopathologic findings was analyzed by Wilcoxon rank test and clustering vs. K means. Results The survival outcomes indicated that BCLC stages and recurrence status could be predictors and E-S grades could be a modifier for HCC. The most common CNAs involved gains of 1q and 8q and a loss of 16q (50%), losses of 4q and 17p and a gain of 5p (40%), and losses of 8p and 13q (30%). Analyses of genomic profiles and clusters identified that losses of 4q13.2q35.2 and 10q22.3q26.13 seen in cases of stage A, grade III and nonrecurrence were likely correlated with good survival, while loss of 1p36.31p22.1 and gains of 2q11.2q21.2 and 20p13p11.1 seen in cases of stage C, grade III and recurrence were possibly correlated with worst prognosis. Conclusions These results indicated that aCGH analysis could be used to detect recurrent CNAs and involved key genes and pathways in patients with HCC. Further analysis on a large case series to validate the correlation of CNAs with clinicopathologic findings of HCC could provide information to interpret CNAs and predict prognosis.

Identification of prognostic biomarkers of hepatocellular carcinoma via long noncoding RNA expression and copy number alterations

Epigenomics ◽  
2020 ◽  
Vol 12 (15) ◽  
pp. 1303-1315
Author(s):  
Weibo Du ◽  
Wenbiao Chen ◽  
Zheyue Shu ◽  
Dairong Xiang ◽  
Kefan Bi ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Copy Number ◽  
Noncoding Rna ◽  
Noncoding Rnas ◽  
The Cancer Genome Atlas ◽  
Differentially Expressed ◽  
Prognostic Biomarkers ◽  
Copy Number Alterations ◽  
Sequencing Data ◽  
Cancer Genome Atlas

Aim: This study aimed to identify long noncoding RNAs (lncRNAs) with potential to be prognostic biomarkers of hepatocellular carcinoma (HCC) by analyzing copy number alterations (CNAs). Methods: RNA Sequencing data of 369 HCC patients was downloaded from The Cancer Genome Atlas database and analyzed with a series of systematic bioinformatics methods. Results: LncRNA-CNA association analysis revealed that many lncRNAs were located in sites frequently amplified or deleted. Three upregulated lncRNAs (LINC00689, SNHG20 and MAFG-AS1) with copy amplification and one downregulated lncRNA TMEM220-AS1 with copy deletion were associated with poor prognosis of HCC. Conclusion: This study reveals that differentially expressed lncRNAs correlate with CNAs in HCC. Moreover, the differentially expressed lncRNAs and their copy amplification/deletions could be promising prognostic biomarkers of HCC.

scholarly journals Correlating genomic copy number alterations with clinicopathologic findings in a case series of hepatocellular carcinoma

2020 ◽  
Author(s):  
Gang Peng ◽  
Hongyan Chai ◽  
Weizhen Ji ◽  
Yufei Lu ◽  
Shengming Wu ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Copy Number ◽  
Case Series ◽  
Oligonucleotide Array ◽  
Good Survival ◽  
Survival Outcomes ◽  
Copy Number Alterations ◽  
Acgh Analysis ◽  
Clinicopathologic Findings ◽  
Grade Iii

Abstract Background: Oligonucleotide array comparative genomic hybridization (aCGH) analysis has been used for detecting somatic copy number alterations (CNAs) in various types of tumors. This study aimed to assess the clinical utility of aCGH for a case series of hepatocellular carcinoma (HCC) and to evaluate the correlation between CNAs and clinicopathologic findings.Methods: Survival outcomes from this case series were analyzed based on Barcelona-Clinic Liver Cancer Stage (BCLC), Edmondson-Steiner grade (E-S), and recurrence status. aCGH was performed on 75 HCC cases with paired DNA samples from tumor and adjacent nontumor tissues. Correlation of CNAs with clinicopathologic findings was analyzed by Wilcoxon rank test and clustering vs. K means.Results: The survival outcomes indicated that BCLC stages and recurrence status could be predictors and E-S grades could be a modifier for HCC. The most common CNAs involved gains of 1q and 8q and a loss of 16q (50%), losses of 4q and 17p and a gain of 5p (40%), and losses of 8p and 13q (30%). Analyses of genomic profiles and clusters identified that losses of 4q13.2q35.2 and 10q22.3q26.13 seen in cases of stage A, grade III and nonrecurrence were likely correlated with good survival, while loss of 1p36.31p22.1 and gains of 2q11.2q21.2 and 20p13p11.1 seen in cases of stage C, grade III and recurrence were possibly correlated with worst prognosis. Conclusions: These results indicated that aCGH analysis could be used to detect recurrent CNAs and involved key genes and pathways in patients with HCC. Further analysis on a large case series to validate the correlation of CNAs with clinicopathologic findings of HCC could provide information to interpret CNAs and predict prognosis.

scholarly journals Characterization of copy number alterations in a mouse model of fibrosis‐associated hepatocellular carcinoma reveals concordance with human disease

2016 ◽  
Vol 5 (3) ◽  
pp. 574-585 ◽  
Author(s):  
Grace Chappell ◽  
Grace O. Silva ◽  
Takeki Uehara ◽  
Igor P. Pogribny ◽  
Ivan Rusyn
Keyword(s):  
Hepatocellular Carcinoma ◽  
Mouse Model ◽  
Human Disease ◽  
Copy Number ◽  
Copy Number Alterations
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