RGD Reference Report - New Gene Variants Associated with the Risk of Chronic HBV Infection. - Rat Genome Database

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New Gene Variants Associated with the Risk of Chronic HBV Infection.

Authors: Fan, Mengjie  Wang, Jing  Wang, Sa  Li, Tengyan  Pan, Hong  Liu, Hankui  Xu, Huifang  Zhernakova, Daria V  O'Brien, Stephen J  Feng, Zhenru  Chang, Le  Dai, Erhei  Lu, Jianhua  Xi, Hongli  Yu, Yanyan  Zhang, Jianguo  Wang, Binbin  Zeng, Zheng 
Citation: Fan M, etal., Virol Sin. 2020 Aug;35(4):378-387. doi: 10.1007/s12250-020-00200-x. Epub 2020 Apr 15.
RGD ID: 40903057
Pubmed: PMID:32297155   (View Abstract at PubMed)
PMCID: PMC7462954   (View Article at PubMed Central)
DOI: DOI:10.1007/s12250-020-00200-x   (Journal Full-text)

Some patients with chronic hepatitis B virus (HBV) infection failed to clear HBV, even persistently continue to produce antibodies to HBV. Here we performed a two stage genome wide association study in a cohort of Chinese patients designed to discover single nucleotide variants that associate with HBV infection and clearance of HBV. The first stage involved genome wide exome sequencing of 101 cases (HBsAg plus anti-HBs positive) compared with 102 control patients (anti-HBs positive, HBsAg negative). Over 80% of individual sequences displayed 20 × sequence coverage. Adapters, uncertain bases > 10% or low-quality base calls (> 50%) were filtered and compared to the human reference genome hg19. In the second stage, 579 chronic HBV infected cases and 439 HBV clearance controls were sequenced with selected genes from the first stage. Although there were no significant associated gene variants in the first stage, two significant gene associations were discovered when the two stages were assessed in a combined analysis. One association showed rs506121-"T" allele [within the dedicator of cytokinesis 8 (DOCK8) gene] was higher in chronic HBV infection group than that in clearance group (P = 0.002, OR = 0.77, 95% CI [0.65, 0.91]). The second association involved rs2071676-A allele within the Carbonic anhydrase (CA9) gene that was significantly elevated in chronic HBV infection group compared to the clearance group (P = 0.0003, OR = 1.35, 95% CI [1.15, 1.58]). Upon replication these gene associations would suggest the influence of DOCK8 and CA9 as potential risk genetic factors in the persistence of HBV infection.



RGD Manual Disease Annotations    Click to see Annotation Detail View

  
Object SymbolSpeciesTermQualifierEvidenceWithNotesSourceOriginal Reference(s)
CA9Humanhepatitis B disease_progressionIAGP DNA:SNP::rs2071676(human)RGD 
Car9Rathepatitis B disease_progressionISOCA9 (Homo sapiens)DNA:SNP::rs2071676(human)RGD 
Car9Mousehepatitis B disease_progressionISOCA9 (Homo sapiens)DNA:SNP::rs2071676(human)RGD 
DOCK8Humanhepatitis B disease_progressionIAGP DNA:SNP::rs506121(human)RGD 
Dock8Mousehepatitis B disease_progressionISODOCK8 (Homo sapiens)DNA:SNP::rs506121(human)RGD 
Dock8Rathepatitis B disease_progressionISODOCK8 (Homo sapiens)DNA:SNP::rs506121(human)RGD 

Objects Annotated

Genes (Rattus norvegicus)
Car9  (carbonic anhydrase 9)
Dock8  (dedicator of cytokinesis 8)

Genes (Mus musculus)
Car9  (carbonic anhydrase 9)
Dock8  (dedicator of cytokinesis 8)

Genes (Homo sapiens)
CA9  (carbonic anhydrase 9)
DOCK8  (dedicator of cytokinesis 8)


Additional Information