scholarly journals Genome-wide copy number analyses identified novel cancer genes in hepatocellular carcinoma

Hepatology ◽  
2011 ◽  
Vol 54 (4) ◽  
pp. 1227-1236 ◽  
Author(s):  
Deshui Jia ◽  
Lin Wei ◽  
Weijie Guo ◽  
Ruopeng Zha ◽  
Meiyan Bao ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Copy Number ◽  
Cancer Genes ◽  
Genome Wide

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 Multiple-level copy number variations in circulating cell-free DNA for prognostic prediction of hepatocellular carcinoma with radical treatments

2020 ◽  
Author(s):  
Yang Wang ◽  
Xiangxu Wang ◽  
Kaixiang Zhou ◽  
Yang Liu ◽  
Zhenyuan Bian ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Copy Number ◽  
Copy Number Variations ◽  
Prognostic Biomarkers ◽  
Multiple Level ◽  
Circulating Free Dna ◽  
Free Dna ◽  
Kaplan Meier ◽  
Genome Wide ◽  
Low Coverage

Abstract Background Copy number variations (CNVs) in circulating free DNA (cfDNA) are emerging as minimally invasive prognostic biomarkers for various cancers. However, little has been reported on the multiple-level analysis of cfDNA CNVs for hepatocellular carcinoma (HCC) patients with radical treatments. Methods Here, CNVs at genome-wide, chromosomal-arm and bin levels were analyzed in cfDNA from 117 HCC patients receiving radical treatments via low-coverage whole genome sequencing. Then, the relationship between cfDNA CNVs and clinical outcomes was explored. Our results showed that a concordant profile of CNVs was observed between cfDNA and tumor tissue DNA. Three genome-wide CNV indicators including tumor fraction (TFx), prediction score (P-score) and stability score (S-score) were calculated based on genome-wide cfDNA CNVs. Results Kaplan-Meier analysis showed that the patients with high TFx, P-score and S-score exhibited a significantly poorer overall survival (OS) and recurrence free survival (RFS) than those with low TFx, P-score and S-score, respectively (All P < 0.05). Furthermore, a group of high frequency cfDNA CNVs at chromosomal-arm level including loss of 4q, 17p, 19p and the gain of 8q, 1q clearly predicted prognosis of HCC patients. Finally, a bin-level risk score was constructed based on three most relevant prognostic bin regions identified by a LASSO model. Patients with high bin-score had a significantly poorer OS than those with low bin-score (P < 0.001). Conclusion Altogether, our study indicates that the multiple-level cfDNA CNVs are significantly associated with OS and RFS in HCC patients with radical treatments, suggesting that cfDNA CNVs detected by low-coverage WGS may be used as potential prognostic biomarkers of HCC patients.

scholarly journals Plasma DNA tissue mapping by genome-wide methylation sequencing for noninvasive prenatal, cancer, and transplantation assessments

2015 ◽  
Vol 112 (40) ◽  
pp. E5503-E5512 ◽  
Author(s):  
Kun Sun ◽  
Peiyong Jiang ◽  
K. C. Allen Chan ◽  
John Wong ◽  
Yvonne K. Y. Cheng ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Pregnant Women ◽  
Genetic Markers ◽  
Copy Number ◽  
Circulating Dna ◽  
Plasma Dna ◽  
Copy Number Aberrations ◽  
Genome Wide ◽  
Dna Pool ◽  
Different Tissues

Plasma consists of DNA released from multiple tissues within the body. Using genome-wide bisulfite sequencing of plasma DNA and deconvolution of the sequencing data with reference to methylation profiles of different tissues, we developed a general approach for studying the major tissue contributors to the circulating DNA pool. We tested this method in pregnant women, patients with hepatocellular carcinoma, and subjects following bone marrow and liver transplantation. In most subjects, white blood cells were the predominant contributors to the circulating DNA pool. The placental contributions in the plasma of pregnant women correlated with the proportional contributions as revealed by fetal-specific genetic markers. The graft-derived contributions to the plasma in the transplant recipients correlated with those determined using donor-specific genetic markers. Patients with hepatocellular carcinoma showed elevated plasma DNA contributions from the liver, which correlated with measurements made using tumor-associated copy number aberrations. In hepatocellular carcinoma patients and in pregnant women exhibiting copy number aberrations in plasma, comparison of methylation deconvolution results using genomic regions with different copy number status pinpointed the tissue type responsible for the aberrations. In a pregnant woman diagnosed as having follicular lymphoma during pregnancy, methylation deconvolution indicated a grossly elevated contribution from B cells into the plasma DNA pool and localized B cells as the origin of the copy number aberrations observed in plasma. This method may serve as a powerful tool for assessing a wide range of physiological and pathological conditions based on the identification of perturbed proportional contributions of different tissues into plasma.

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 Combination of Genome-Wide Polymorphisms and Copy Number Variations of Pharmacogenes in Koreans

2021 ◽  
Vol 11 (1) ◽  
pp. 33
Author(s):  
Nayoung Han ◽  
Jung Mi Oh ◽  
In-Wha Kim
Keyword(s):  
Copy Number ◽  
Genome Wide Association Study ◽  
Copy Number Gain ◽  
Copy Number Variations ◽  
Gene Gain ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Haplotype Blocks ◽  
Genome Wide ◽  
Control And Prevention

For predicting phenotypes and executing precision medicine, combination analysis of single nucleotide variants (SNVs) genotyping with copy number variations (CNVs) is required. The aim of this study was to discover SNVs or common copy CNVs and examine the combined frequencies of SNVs and CNVs in pharmacogenes using the Korean genome and epidemiology study (KoGES), a consortium project. The genotypes (N = 72,299) and CNV data (N = 1000) were provided by the Korean National Institute of Health, Korea Centers for Disease Control and Prevention. The allele frequencies of SNVs, CNVs, and combined SNVs with CNVs were calculated and haplotype analysis was performed. CYP2D6 rs1065852 (c.100C>T, p.P34S) was the most common variant allele (48.23%). A total of 8454 haplotype blocks in 18 pharmacogenes were estimated. DMD ranked the highest in frequency for gene gain (64.52%), while TPMT ranked the highest in frequency for gene loss (51.80%). Copy number gain of CYP4F2 was observed in 22 subjects; 13 of those subjects were carriers with CYP4F2*3 gain. In the case of TPMT, approximately one-half of the participants (N = 308) had loss of the TPMT*1*1 diplotype. The frequencies of SNVs and CNVs in pharmacogenes were determined using the Korean cohort-based genome-wide association study.

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