FunGeST - Functional Genomics from cancer research to personalized medicine

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This DAC controls 26 datasets

Dataset ID	Description	Technology	Samples
EGAD00001000131	Genetic landscape of hepatocellular carcinoma	Illumina HiSeq 2000	48
EGAD00001000737	Whole exome sequencing data from 30 donors (46 tumors and 30 non-tumoral whole exome sequencing, paired-end, HiSeq 2000, Illumina) collected by the Inserm U674, PI Jessica Zucman-Rossi - Institut National du Cancer (INCa), PI Fabien Calvo, France.	Illumina HiSeq 2000	76
EGAD00001000749	None	Illumina HiSeq 2000	12
EGAD00001001096	None	Illumina HiSeq 2000	419
EGAD00001001423	None	Illumina HiSeq 2000	7
EGAD00001001645	None	Illumina Genome Analyzer II Illumina HiSeq 2000	28
EGAD00001003092	Using sequencing and gene expression analyses, we identified a subgroup of HCA characterized by fusion of the INHBE and GLI1 genes and activation of sonic hedgehog pathway. Molecular subtypes of HCAs associated with different patients’ risk factors for HCA, disease progression, and pathology features of tumors. This classification system might be used to select treatment strategies for patients with HCA. Related Publication: Molecular Classification of Hepatocellular Adenoma Associates With Risk Factors, Bleeding, and Malignant Transformation Nault, Jean-CharlesLaurent, Christophe et al. Gastroenterology , Volume 152 , Issue 4 , 880 - 894.e6 http://dx.doi.org/10.1053/j.gastro.2016.11.042	Illumina HiSeq 2000	21
EGAD00001003281	Genomic alterations driving tumorigenesis result from the interaction of environmental exposures and endogeneous cellular processes. With a diversity of risk factors including viral infection, carcinogenic exposures and metabolic diseases, liver cancer is an ideal model to study these interactions. Whole genome sequencing of liver tumors identified 10 mutational signatures showing distinct relationships with environmental exposures, replication and transcription. Transcription-coupled damage was specifically associated with the liver-specific signature 16 and alcohol intake. Flood of indels were identified in very highly expressed hepato-specific genes, likely resulting from replication-transcription collisions. Reconstruction of sub-clonal architecture revealed mutational signature evolution during tumor development exemplified by the vanishing of aflatoxin-B1 signature in African migrants. These findings shed new light on the natural history of liver cancers.	Illumina HiSeq 2000	52
EGAD00001003993	The present series corresponds to 161 RNA-seq samples from tumors with matched WES or WGS. Hepatocellular carcinoma (HCC) accounts for more than 90% of liver cancers, and is a major health problem. It is the 3rd cause of cancer-related mortality. Advances in genomic analyses have formed a comprehensive understanding of different underlying pathobiological layers resulting in hepatocarcinogenesis. Thus, the development of next-generation sequencing technologies has made it possible to generate more comprehensive catalogues of somatic alteration events (single nucleotide substitutions, structural variations, and epigenetic changes) in liver cancer genome than ever before.	Illumina HiSeq 2000	161
EGAD00001003994	The present series corresponds to 24 whole genome sequencing (12 Tumoral/Non-tumoral pairs). Hepatocellular carcinoma (HCC) accounts for more than 90% of liver cancers, and is a major health problem. It is the 3rd cause of cancer-related mortality. Advances in genomic analyses have formed a comprehensive understanding of different underlying pathobiological layers resulting in hepatocarcinogenesis. Thus, the development of next-generation sequencing technologies has made it possible to generate more comprehensive catalogues of somatic alteration events (single nucleotide substitutions, structural variations, and epigenetic changes) in liver cancer genome than ever before.	Illumina HiSeq 2000	28
EGAD00001004141	This study contain the WGS and RNA-seq aligned bam files for this particular inflammatory hepatocellular adenoma sample.	Illumina HiSeq 2000 Illumina HiSeq 4000	2
EGAD00001004180	The French ICGC project on liver tumors is coordinated by Pr Jessica Zucman-Rossi and funded by Inca (French Institute for Cancer). The aim of the present project is to identify the catalog of somatic and germline mutations in liver tumors using whole genome (WGS) and whole exome sequencing (WGS), integrated with DNA methylation and RNA sequencing (RNA-seq) data. The present series corresponds to 60 whole exome tumor/normal pairs with matched RNA-seq.	Illumina HiSeq 2000 Illumina HiSeq 4000	120
EGAD00001004484	Adeno-associated virus (AAV) is a defective mono-stranded DNA virus, endemic in human population (35-80%). Recurrent clonal AAV2 insertions are associated with the pathogenesis of rare human hepatocellular carcinoma (HCC) developed on normal liver. This study aimed to characterize the natural history of AAV infection in the liver and its consequence in tumor development. In silico analyses using viral capture data explored viral variants and new clonal insertions. Clonal AAV insertions were positive selected during HCC development on non-cirrhotic liver challenging the notion of AAV as a non-pathogenic virus.	Illumina HiSeq 2000	20
EGAD00001004555	The aim of our project is to decipher the genomic of advanced hepatocellular carcinoma using whole exome sequencing. To this purpose, we aim to compare genetic landscape of advanced hepatocellular carcinoma with early tumor in order to understand the mechanisms of tumor progression. This work will also help to identify new therapeutic targets potentially useful to treat patients at advanced stage. This dataset contain whole exome sequencing aligned reads for 41 tumor with matched normal samples	Illumina HiSeq 2000 Illumina HiSeq 4000	39
EGAD00001004938	Hepatocellular carcinoma (HCC) is a heterogeneous aggressive malignancy with low efficacy of current therapies at advanced stages. We integrated molecular and pharmacological profiling of a large panel of liver cancer cell lines (LCCL) to assess their clinical relevance as HCC preclinical models and identify new effective therapies and biomarkers of response. Here, we performed multi-omic analysis including whole-exome, RNA and microRNA sequencing in a series 34 LCCL. Molecular profiles of LCCL and primary HCC were compared and we searched for molecular features associated with drug response. Our panel of LCCL faithfully recapitulated the most aggressive molecular “proliferation class” of HCC.	Illumina HiSeq 2000 Illumina HiSeq 4000	34
EGAD00001005283	None	Illumina HiSeq 2000 Illumina HiSeq 4000	30
EGAD00001005284	None	Illumina HiSeq 2000 Illumina HiSeq 4000	22
EGAD00001005308	None	Illumina HiSeq 2000 Illumina HiSeq 4000	112
EGAD00001006426	This study contain the WGS and WEX aligned bam files and RNA-seq fastq files for human liver tumors.	HiSeq X Five Illumina HiSeq 2000 Illumina HiSeq 4000 Illumina NovaSeq 6000	183
EGAD00001007762	None	Illumina HiSeq 4000 Illumina MiSeq	82
EGAD00001007858	None	HiSeq X Five Illumina HiSeq 4000 Illumina NovaSeq 6000	234
EGAD00001009669	None	HiSeq X Five Illumina HiSeq 4000 Illumina NovaSeq 6000	18
EGAD00001009743	None	Illumina NovaSeq 6000	1
EGAD00001009745	None	HiSeq X Five Illumina HiSeq 4000 Illumina NovaSeq 6000	1
EGAD00001010049	None	Illumina NovaSeq 6000	8
EGAD00001011097	Additional datasets linked to EGAS00001006692	Illumina NovaSeq 6000	1