Ontology highlight
ABSTRACT:
PROVIDER: PRJEB58644 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Sun_3snp.vcf.csi | Other | |||
| Sun_3snp.vcf.gz | Vcf |
Items per page: 5 1 - 2 of 2 |
Similar Datasets
Project description:Sequencing information of rs970797, rs3132682, rs3094165 of 637 liver cancer patients
2023-01-03 | PRJEB58644 | EVA
Project description:A large panel of 81 liver cancer cell models, designated as LIver cancer MOdel REpository (LIMORE) was constructed. These cell lines include 31 public cell lines and 50 new cell models establishend from Chinese liver cancer patients. Whole genome sequencing (WGS), exome sequencing (WES) and RNA sequencing (RNAseq) were performed to obtain the genetic information for these cell lines. These cell lines and associated data provide new models and also a rich resource for liver cancer.
2019-06-17 | GSE97098 | GEO
Project description:Despite the large amounts of transcriptome data generated for many non-model organisms, there has been a much lesser uptake of individual genomic sequencing for detecting SNPs and determining haplotypes in these species. Transcriptome data represents a source of variant information, specifically for coding DNA, however there is little information on the accuracy, coverage and limitations of using transcriptomic data for the identification of single nucleotide polymorphisms (SNPs) in non-model organisms. To investigate this, we generated the first whole exome design for bovine using the Roche Nimblegen Developer system (Roche, USA) and used it to sequence and call SNPs from a lactating dairy cow model with genetically divergent fertility phenotypes (Fert+, n=8; Fert-, n=8). We compared these results to SNPs called from liver and muscle transcriptomes from the same animals. Our exome demonstrated 99.1% coverage of the target design of 56.7MB, whereas the transcriptomes only covered 60 and 54.5% of 44.2 and 42.8MB in liver and muscle respectively. We found that specificity of SNP detection in the transcriptome data is ~75% following basic hard-filtering, but could be increased marginally to ~80% by increasing the minimum threshold of reads covering a SNP, and number of samples in which it was found. Functional annotation of non-synonymous SNPs specific to both the high and low fertility phenotype identified immune response-related genes, supporting previous work that identified this process as key to the phenotype.
2015-10-08 | GSE62160 | GEO
Project description:Nine specimens from three colorectal cancer (CRC) patients including adjacent normal tissue, primary tumor, and lever metastasis tissue, and three specimens from 3 CRC patients without liver metastasis were collected for RNA sequencing analysis.
2018-12-25 | GSE92914 | GEO
Project description:Purpose: Chronic Hepatitis B virus (HBV) infection leads to liver fibrosis which is a major risk factor in Hepatocellular carcinoma (HCC) and an independent risk factor of recurrence after HCC tumor resection. HBV genome can be inserted into human genome, and chronic inflammation may trigger somatic mutations. Several studies characterized HBV integration sites in HCC patients with regard to frequently occurring hotspots. However, how HBV integration and other genomic changes contribute to the risk of tumor recurrence with regard to different degree of liver fibrosis is not clearly understood. In this study, we aim to find potential molecular mechanisms underlying tumor recurrence of HBV-associated HCC (HBV-HCC) with different degree of liver fibrosis. Methods: We performed RNA sequencing of 21 pairs of tumor and non-neoplastic liver tissues of HBV-HCC patients and performed comprehensive genomic analysis of our RNAseq data and public available sequencing data related to HBV-HCC. We developed a robust pipeline for sensitively identifying HBV integration sites based on sequencing data. Simulations with sequencing data showed that our method outperformed existing methods. We also compared SNPs of each sample with SNPs in cancer census database and inferred patient’s pathogenic SNP loads in tumor and non-neoplastic liver tissues. Conclusions: The HBV-integration and pathogenic SNP load patterns for HCC recurrence risk vary depending on liver fibrosis stage, suggesting potentially different tumorigenesis mechanisms for low and high liver fibrosis patients.
2018-03-01 | GSE94660 | GEO
Project description:Proteomic sequencing of A. sapidissima liver tissue from three different culture temperatures was performed to identify information on key regulated proteins.
2024-02-27 | PXD050168 |
Project description:With the whole genome SNPs array information, we could evaluate the copy number variation of samples so as to find out specific DNA aberrations in non-Hodgkin lymphma comparing with reactive hyperplasia patients.
2016-05-24 | GSE47357 | GEO
Project description:We adapted the DiR barcode-based parallel reporter assay systems strategy to systematically identify the breast cancer related SNPs that affect gene expression by modulating activities of regulatory elements. Among 293 SNPs linked with GWAS-identified breast cancer-risk SNPs, we found seven functional regulatory SNPs in MCF7 cells. Further mechanism study indicates that one SNP regulates gene expression in breast cancer malignancy. The DiR system has great potential to advance the functional study of risk SNPs that have associations with polygenic diseases. Our findings hold great promise in benefiting breast cancer patients with prognostic prediction.
2021-06-16 | GSE178198 | GEO
Project description:We adapted the DiR barcode-based parallel reporter assay systems strategy to systematically identify the SNPs that affect gene expression by modulating activities of regulatory elements. Among 293 SNPs linked with GWAS-identified prostate cancer-risk SNPs, we found 32, 9, and 11 regulatory SNPs in 22Rv1, PC-3, and LNCaP cells. Further mechanism study indicates that one SNP regulates gene expression in prostate cancer malignancy. The DiR system has great potential to advance the functional study of risk SNPs that have associations with polygenic diseases. Our findings hold great promise in benefiting prostate cancer patients with prognostic prediction.
2021-01-30 | GSE165765 | GEO
Project description:Genetic variations play an important role in tumor development and metastasis. Hepatocellular carcinoma (HCC) is one of leading cause of cancer-related death. Despite improvements in surveillance and clinical treatment strategies, the prognosis of HCC remains dismal. Affymetrix SNP 6.0 array were used to evaluate the genetic characteristics of tumor DNA in 30 HBV-related HCC patients who were underwent liver transplantation. Recurrence related SNPs were selected and validated.
2012-10-26 | GSE29667 | GEO