Whole-exome sequencing of hepatocellular carcinoma biopsies (proteogenomic study)

We performed a proteogenomic analysis of hepatocellular carcinomas (HCCs) across clinical stages and etiologies to define the deregulated pathways and heterogeneity among HCCs. We identified pathways that are differentially regulated on the genomic, transcriptomic, proteomic and phosphoproteomic levels. Integrative clustering identified HCC subgroups that show distinct regulation of biological processes, metabolic reprogramming and kinase activation.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 4 Publications

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001008182	All 122 HCC biopsies and 115 non-tumoral tissues from 114 patients were subjected to whole-exome sequencing. Whole-exome capture was performed using the SureSelectXT Clinical Research Exome (Agilent Technologies) or SureSelect Human All Exon V6+COSMIC (Agilent Technologies) platforms according to the manufacturer’s guidelines. Sequencing was performed on an Illumina HiSeq 2500 at the Genomics Facility Basel according to the manufacturer’s guidelines. Paired-end 101-bp reads were generated.	Illumina HiSeq 2500	237

Publications	Citations
Supervised learning based on tumor imaging and biopsy transcriptomics predicts response of hepatocellular carcinoma to transarterial chemoembolization. Boldanova T, Fucile G, Vosshenrich J, Suslov A, Ercan C, Coto-Llerena M, Terracciano LM, Zech CJ, Boll DT, Wieland S, Heim MH. Cell Rep Med 2: 2021 100444	2
Integrative proteogenomic characterization of hepatocellular carcinoma across etiologies and stages. Ng CKY, Dazert E, Boldanova T, Coto-Llerena M, Nuciforo S, Ercan C, Suslov A, Meier MA, Bock T, Schmidt A, Ketterer S, Wang X, Wieland S, Matter MS, Colombi M, Piscuoglio S, Terracciano LM, Hall MN, Heim MH. Nat Commun 13: 2022 2436	44
Multi-omics subtyping of hepatocellular carcinoma patients using a Bayesian network mixture model. Suter P, Dazert E, Kuipers J, Ng CKY, Boldanova T, Hall MN, Heim MH, Beerenwinkel N. PLoS Comput Biol 18: 2022 e1009767	3
Arginine reprograms metabolism in liver cancer via RBM39. Mossmann D, Müller C, Park S, Ryback B, Colombi M, Ritter N, Weißenberger D, Dazert E, Coto-Llerena M, Nuciforo S, Blukacz L, Ercan C, Jimenez V, Piscuoglio S, Bosch F, Terracciano LM, Sauer U, Heim MH, Hall MN. Cell 186: 2023 5068-5083.e23	21