GEO DataSets

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome variation profiling by SNP array

4 related Platforms

315 Samples

Download data

(Submitter supplied) Introduction: According to the clonal model of tumor evolution, trunk alterations arise at early stages and are ubiquitous. Through the characterization of early stages of hepatocarcinogenesis, we aimed to identify trunk alterations in HCC and study their intra- and inter-tumor distribution in more advanced lesions. Methods: 151 samples representing the multi-step process of hepatocarcinogenesis were analyzed by targeted-sequencing and SNP array. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL18281

59 Samples

Download data: TXT

(Submitter supplied) Introduction: According to the clonal model of tumor evolution, trunk alterations arise at early stages and are ubiquitous. Through the characterization of early stages of hepatocarcinogenesis, we aimed to identify trunk alterations in HCC and study their intra- and inter-tumor distribution in more advanced lesions. Methods: 151 samples representing the multi-step process of hepatocarcinogenesis were analyzed by targeted-sequencing and SNP array. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL18281

69 Samples

Download data: TXT

(Submitter supplied) Introduction: According to the clonal model of tumor evolution, trunk alterations arise at early stages and are ubiquitous. Through the characterization of early stages of hepatocarcinogenesis, we aimed to identify trunk alterations in HCC and study their intra- and inter-tumor distribution in more advanced lesions. Methods: 151 samples representing the multi-step process of hepatocarcinogenesis were analyzed by targeted-sequencing and SNP array. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL22678

82 Samples

Download data: TXT

(Submitter supplied) Introduction: According to the clonal model of tumor evolution, trunk alterations arise at early stages and are ubiquitous. Through the characterization of early stages of hepatocarcinogenesis, we aimed to identify trunk alterations in HCC and study their intra- and inter-tumor distribution in more advanced lesions. Methods: 151 samples representing the multi-step process of hepatocarcinogenesis were analyzed by targeted-sequencing and SNP array. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL18900

56 Samples

Download data: TXT

(Submitter supplied) Introduction: According to the clonal model of tumor evolution, trunk alterations arise at early stages and are ubiquitous. Through the characterization of early stages of hepatocarcinogenesis, we aimed to identify trunk alterations in HCC and study their intra- and inter-tumor distribution in more advanced lesions. Methods: 151 samples representing the multi-step process of hepatocarcinogenesis were analyzed by targeted-sequencing and SNP array. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL14951

49 Samples

Download data: TXT

(Submitter supplied) We analyzed 801 primary HCC developed in 720 patients. Samples were collected from 1992 to 2016 in three French tertiary liver centers in patients treated by liver resection, liver transplantation (surgical samples) and in patients treated by radiofrequency ablation and with advanced HCC treated by non-curative therapies (tumor biopsies). All samples obtained from surgical samples or tumor biopsy were immediately frozen in liquid nitrogen and stored at -80°C prior extraction. more...

Organism:

Homo sapiens

Type:

Expression profiling by RT-PCR

Platform:

GPL26393

687 Samples

Download data: TXT

(Submitter supplied) Whole exome sequencing and copy number analysis was performed on 231 hepatocellular carcinomas (72% with hepatitis B viral infection) that were classified as early-stage hepatocellular carcinomas, candidates for surgical resection. Recurrent mutations were validated by Sanger sequencing. Unsupervised genomic analyses identified an association between specific genetic aberrations and postoperative clinical outcomes. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL16131

462 Samples

Download data: CEL, CYCHP

(Submitter supplied) SNP array data from 125 hepatocellular carcinomas were used to detect recurrent copy number alterations.

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platforms:

GPL6986 GPL13135

237 Samples

Download data: TXT

(Submitter supplied) Multiple carcinogenesis is one of the major characteristics of human hepatocellular carcinoma (HCC). The history of multiple tumors, i.e., whether they are derived from a common precancerous or cancerous ancestor or individually from hepatocytes, is a major issue. Multiple HCC is clinically classified into intratumor metastasis (IM) and multicentric carcinogenesis (MC). Molecular markers differentiating IM and MC are of interest to clinical practitioners because clinical diagnosis of IM and MC often leads to different therapies. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by array

Platform:

GPL5477

20 Samples

Download data: TXT

(Submitter supplied) Genome-wide DNA methylation profiling of cirrhosis and dysplastic liver samples. The Illumina Infinium 450k Human DNA methylation BeadChip was used to obtain DNA methylation profiles across approximately 485,577 CpGs sites. Samples included 130 cirrhosis and 8 exhibiting dysplasia. The manuscript includes an integrative analysis of these samples along with samples from normal liver and HCC already deposited under GSE63898.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

138 Samples

Download data: TXT

(Submitter supplied) We profiled the mutations and gene expressions of early and advanced hepatocellular carcinoma (HCC) related with Hepatitis B-viral infection. Integrative analysis was performed with whole-exome sequencing and gene expression profiles of the 12 cases of early and advanced HCCs and paired non-tumoral adjacent liver tissues.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

12 Samples

Download data: TXT

(Submitter supplied) We have generated an immune classifier able to identify patients belonging to the immune subclass of HCC. Characteristics of the immune subclass resemble those of patients who most respond to immunotherapy. We performed microarray expression of the tumors of two patients before starting treatment with nivolumab to verify if the immune classifier generated was able to predict response to immunotherapy.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL15207

2 Samples

Download data: CEL

(Submitter supplied) Hepatocellular carcinoma (HCC) is ranked second in cancer-associated deaths worldwide. Most cases of HCC are secondary to either a viral hepatitis infection (hepatitis B or C) or cirrhosis (alcoholism being the most common cause of hepatic cirrhosis). It is a complex and heterogeneous tumor due to activation of multiple cellular pathways and molecular alterations.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

91 Samples

Download data: CEL

(Submitter supplied) Mouse models of hepatocellular carcinoma (HCC) simulate specific subgroups of human HCC. We investigated hepatocarcinogenesis in Mdr2-KO mice, a model of inflammation-associated HCC, using gene expression profiling and immunohistochemical analyses. Gene expression profiling demonstrated that although Mdr2-KO mice differ from other published murine HCC models, they share several important deregulated pathways and many coordinately differentially expressed genes with human HCC datasets. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL339

15 Samples

Download data: CEL

(Submitter supplied) Hepatocellular carcinoma (HCC) is one of the most common malignancies worldwide. Understanding of the intratumoral heterogeneity of HCC is instructive for developing personalized therapy and molecular biomarkers. We applied whole exome sequencing to a total of 63 samples from 11 patients to resolve the genetic architecture and subclonal diversification. Notably, spatial genomic diversity was found in all 11 HCC cases, with 33% of the driver mutations being heterogeneous. more...

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

26 Samples

Download data: IDAT, TXT

(Submitter supplied) We performed whole exome sequencing and copy number analysis for 15 triplets, each comprising normal colorectal tissue, primary colorectal carcinoma, and its synchronous matched liver metastasis. We analyzed the similarities and differences between primary colorectal carcinoma and matched liver metastases in regards to somatic mutations and somatic copy number alterationss (SCNAs). The genomic profiling demonstrated mutations in APC(73%), KRAS (33%), ARID1A and PIK3CA (6.7%) genes between primary colorectal and metastatic liver tumors. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; Genome variation profiling by genome tiling array

Platform:

GPL16131

45 Samples

Download data: CEL, CYCHP, TXT

(Submitter supplied) Hepatocellular carcinoma (HCC) is a prevalent human cancer with rising incidence worldwide. Human HCC is frequently associated with chronic liver inflammation and cirrhosis, pathophysiological processes that are a consequence of chronic viral infection, disturbances in metabolism, or exposure to chemical toxicants. To better characterize the pathogenesis of HCC, we used a human disease-relevant mouse model of fibrosis-associated hepatocarcinogenesis. more...

Organism:

Mus musculus

Type:

Genome variation profiling by genome tiling array

Platform:

GPL10449

36 Samples

Download data: TXT

(Submitter supplied) To characterize the genetic alterations that instigate hepatitis C virus-induced hepatocellular carcinoma (HCC), we conducted an integrative genomic analysis of 103 HCCs. Most tumors harbored 1q gain, 8q gain or 8p loss, with occasional alterations in 13 additional chromosome arms. In addition to amplifications at 11q13 in 6 tumors, 4 tumors harbored focal gains at 6p21 incorporating VEGFA, which were confirmed in 4 of 113 HCC in an independent validation set. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array; SNP genotyping by SNP array

Platform:

GPL3720

197 Samples

Download data: CEL, TXT

(Submitter supplied) To characterize the genetic alterations that instigate hepatitis C virus-induced hepatocellular carcinoma (HCC), we conducted an integrative genomic analysis of 103 HCCs. Most tumors harbored 1q gain, 8q gain or 8p loss, with occasional alterations in 13 additional chromosome arms. In addition to amplifications at 11q13 in 6 tumors, 4 tumors harbored focal gains at 6p21 incorporating VEGFA, which were confirmed in 4 of 113 HCC in an independent validation set. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

91 Samples

Download data: CEL, TXT