Dataset Information

WTCCC3 case-control study for Primary Biliary Cirrhosis

ABSTRACT: Genome-wide association scan was performed in 1,840 cases of primary biliary cirrhosis and 5,163 controls. Replication of new associations was tested in an independent set of 620 cases and 2,514 controls.

PROVIDER: EGAS00000000039 | EGA |

REPOSITORIES: EGA

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Genome-wide association study identifies 12 new susceptibility loci for primary biliary cirrhosis.

Mells George F GF Floyd James A B JA Morley Katherine I KI Cordell Heather J HJ Franklin Christopher S CS Shin So-Youn SY Heneghan Michael A MA Neuberger James M JM Donaldson Peter T PT Day Darren B DB Ducker Samantha J SJ Muriithi Agnes W AW Wheater Elizabeth F EF Hammond Christopher J CJ Dawwas Muhammad F MF Jones David E DE Peltonen Leena L Alexander Graeme J GJ Sandford Richard N RN Anderson Carl A CA

Nature genetics 20110313 4

In addition to the HLA locus, six genetic risk factors for primary biliary cirrhosis (PBC) have been identified in recent genome-wide association studies (GWAS). To identify additional loci, we carried out a GWAS using 1,840 cases from the UK PBC Consortium and 5,163 UK population controls as part of the Wellcome Trust Case Control Consortium 3 (WTCCC3). We followed up 28 loci in an additional UK cohort of 620 PBC cases and 2,514 population controls. We identified 12 new susceptibility loci (at ...[more]

PMID: 21399635

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Project description:BACKGROUND & AIMS: The effectiveness of surveillance for hepatocellular carcinoma (HCC) in patients with cirrhosis is limited, due to inadequate risk stratification and suboptimal performance of current screening modalities.METHODS: We developed a multicenter prospective cohort of patients with cirrhosis undergoing surveillance with MRI and applied global untargeted metabolomics to 612 longitudinal serum samples from 203 patients. Among them, 37 developed HCC during follow-up.RESULTS: We identified 150 metabolites with significant abundance changes in samples collected prior to HCC (Cases) compared to samples from patients who did not develop HCC (Controls). Tauro-conjugated bile acids and gamma-glutamyl amino acids were increased, while acyl-cholines and deoxycholate derivatives were decreased. Seven amino acids including serine and alanine had strong associations with HCC risk, while strong protective effects were observed for N-acetylglycine and glycerophosphorylcholine. Machine learning using the 150 metabolites, age, gender, and PNPLA3 and TMS6SF2 single nucleotide polymorphisms, identified 15 variables giving optimal performance. Among them, N-acetylglycine had the highest AUC in discriminating Cases and Controls. When restricting Cases to samples collected within 1 year prior to HCC (Cases-12M), additional metabolites including microbiota-derived metabolites were identified. The combination of the top six variables identified by machine learning (alpha-fetoprotein, 6-bromotryptophan, N-acetylglycine, salicyluric glucuronide, testosterone sulfate and age) had good performance in discriminating Cases-12M from Controls (AUC 0.88, 95% CI 0.83-0.93). Finally, 23 metabolites distinguished Cases with LI-RADS-3 lesions from Controls with LI-RADS-3 lesions, with reduced abundance of acyl-cholines and glycerophosphorylcholine-related lysophospholipids in Cases.CONCLUSIONS: This study identified N-acetylglycine, amino acids, bile acids and choline-derived metabolites as biomarkers of HCC risk, and microbiota-derived metabolites as contributors to HCC development.

Dataset Information

WTCCC3 case-control study for Primary Biliary Cirrhosis

Publications

Genome-wide association study identifies 12 new susceptibility loci for primary biliary cirrhosis.

Similar Datasets

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