Evidence map›Paper›PMID 32393195›Full record

ArticleBMC cancer2020

Knowledge-based analyses reveal new candidate genes associated with risk of hepatitis B virus related hepatocellular carcinoma.

Deke Jiang, Jiaen Deng, Changzheng Dong, Xiaopin Ma, Qianyi Xiao, Bin Zhou, Chou Yang, Lin Wei, Carly Conran, S Lilly Zheng and 9 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC cancer, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
10citing papers in PubMed, 1 pooled it
1.0field-weighted citation impact, top 23% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

10 citing papers in PubMed, 1 synthesis or guideline pooled it, 11 citations in OpenAlex.

  1. Pooled it
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

19 authors at 9 institutions in 3 countries.

Deke JiangState Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Institutes of Liver Diseases Research of Guangdong Province, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China.
Jiaen DengDepartment of Psychiatry, the University of Hong Kong, Pokfulam, Hong Kong.
Changzheng DongNingbo University School of Medicine, Ningbo, China.
Xiaopin MaState Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.
Qianyi XiaoCenter for Genomic Translational Medicine and Prevention, School of Public Health, Fudan University, Shanghai, China.
Bin ZhouState Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Institutes of Liver Diseases Research of Guangdong Province, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China.
Chou YangState Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Institutes of Liver Diseases Research of Guangdong Province, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China.
Lin WeiProgram of Computational Genomics & Medicine, NorthShore University HealthSystem, Evanston, IL, USA.
Carly ConranProgram for Personalized Cancer Care, NorthShore University HealthSystem, Pritzker School of Medicine, University of Chicago, Evanston, IL, USA.
S Lilly ZhengProgram of Computational Genomics & Medicine, NorthShore University HealthSystem, Evanston, IL, USA.
Irene Oi-Lin NgDepartment of Pathology, the University of Hong Kong, Pokfulam, Hong Kong.
Long YuState Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.
Jianfeng XuProgram of Computational Genomics & Medicine, NorthShore University HealthSystem, Evanston, IL, USA.
Pak C ShamThe Centre for Genomic Sciences, the University of Hong Kong, Pokfulam, Hong Kong.
Xiaolong QiState Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Institutes of Liver Diseases Research of Guangdong Province, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China.
Jinlin HouState Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Institutes of Liver Diseases Research of Guangdong Province, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China.
Yuan JiDepartment of Public Health Sciences, University of Chicago, Chicago, IL, USA.
Guangwen CaoDepartment of Epidemiology, Second Military Medical University, Shanghai, China. gcao@smmu.edu.cn.
Miaoxin LiDepartment of Psychiatry, the University of Hong Kong, Pokfulam, Hong Kong. limiaoxin@mail.sysu.edu.cn.
University of Hong Kong · HKFudan University · CNNanfang Hospital · CNNorthShore University HealthSystem · USSouthern Medical University · CNChicago Department of Public Health · USNingbo University · CNSecond Military Medical University · CNUniversity of Chicago · US

Funding

Hong Kong Health and the Medical Research Fund 01121436the Innovative Research Team Project of Guangxi Province 2017GXNSFGA198002the Key-Area Research and Development Program of Guangdong Province (CN) 2019B020227004the Local Innovative and Research Teams Project of Guangdong Pearl River Talents Program No. 2017BT01S131the National Natural Science Foundation of China 31100895the National Natural Science Foundation of China 31771401the National Natural Science Foundation of China 81402297the National Natural Science Foundation of China 81472618the National Natural Science Foundation of China 81670535the National Science and Technology Major Projec No. 2017ZX10202202the National Science and Technology Major Project 2018ZX10301202the Outstanding Youths Development Scheme of Nanfang Hospital, Southern Medical University No. 2017J001
6 · The paper itself

Abstract

backgroundRecent genome-wide association studies (GWASs) have suggested several susceptibility loci of hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) by statistical analysis at individual single-nucleotide polymorphisms (SNPs). However, these loci only explain a small fraction of HBV-related HCC heritability. In the present study, we aimed to identify additional susceptibility loci of HBV-related HCC using advanced knowledge-based analysis.

methodsWe performed knowledge-based analysis (including gene- and gene-set-based association tests) on variant-level association p-values from two existing GWASs of HBV-related HCC. Five different types of gene-sets were collected for the association analysis. A number of SNPs within the gene prioritized by the knowledge-based association tests were selected to replicate genetic associations in an independent sample of 965 cases and 923 controls.

resultsThe gene-based association analysis detected four genes significantly or suggestively associated with HBV-related HCC risk: SLC39A8, GOLGA8M, SMIM31, and WHAMMP2. The gene-set-based association analysis prioritized two promising gene sets for HCC, cell cycle G1/S transition and NOTCH1 intracellular domain regulates transcription. Within the gene sets, three promising candidate genes (CDC45, NCOR1 and KAT2A) were further prioritized for HCC. Among genes of liver-specific expression, multiple genes previously implicated in HCC were also highlighted. However, probably due to small sample size, none of the genes prioritized by the knowledge-based association analyses were successfully replicated by variant-level association test in the independent sample.

conclusionsThis comprehensive knowledge-based association mining study suggested several promising genes and gene-sets associated with HBV-related HCC risks, which would facilitate follow-up functional studies on the pathogenic mechanism of HCC.

Indexed as

Genetic Predisposition to DiseasePolymorphism, Single NucleotideBiomarkers, TumorCarcinoma, HepatocellularCase-Control StudiesFemaleFollow-Up StudiesGenome-Wide Association StudyHepatitis BHepatitis B virusHumansKnowledge BasesLiver NeoplasmsMaleMiddle AgedPrognosisBiomarkers, TumorHepatitis B virusHepatocellular carcinomaKnowledge-based genetic associationSusceptibility

Identifiers

PMID32393195
PMCPMC7216662
OpenAlexW3021298681

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.