Genome-wide analysis of copy number variation identifies candidate gene loci associated with the progression of non-alcoholic fatty liver disease.
Between 10 and 25% of individuals with non-alcoholic fatty liver disease (NAFLD) develop hepatic fibrosis leading to cirrhosis and hepatocellular carcinoma (HCC). To investigate the molecular basis of disease progression, we performed a genome-wide analysis of copy number variation (CNV) in a total...
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2014
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oai:doaj.org-article:a543aa02099c4469afb9733498d5a2f02021-11-18T08:22:36ZGenome-wide analysis of copy number variation identifies candidate gene loci associated with the progression of non-alcoholic fatty liver disease.1932-620310.1371/journal.pone.0095604https://doaj.org/article/a543aa02099c4469afb9733498d5a2f02014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24743702/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Between 10 and 25% of individuals with non-alcoholic fatty liver disease (NAFLD) develop hepatic fibrosis leading to cirrhosis and hepatocellular carcinoma (HCC). To investigate the molecular basis of disease progression, we performed a genome-wide analysis of copy number variation (CNV) in a total of 49 patients with NAFLD [10 simple steatosis and 39 non-alcoholic steatohepatitis (NASH)] and 49 matched controls using high-density comparative genomic hybridization (CGH) microarrays. A total of 11 CNVs were found to be unique to individuals with simple steatosis, whilst 22 were common between simple steatosis and NASH, and 224 were unique to NASH. We postulated that these CNVs could be involved in the pathogenesis of NAFLD progression. After stringent filtering, we identified four rare and/or novel CNVs that may influence the pathogenesis of NASH. Two of these CNVs, located at 13q12.11 and 12q13.2 respectively, harbour the exportin 4 (XPO4) and phosphodiesterase 1B (PDE1B) genes which are already known to be involved in the etiology of liver cirrhosis and HCC. Cross-comparison of the genes located at these four CNV loci with genes already known to be associated with NAFLD yielded a set of genes associated with shared biological processes including cell death, the key process involved in 'second hit' hepatic injury. To our knowledge, this pilot study is the first to provide CNV information of potential relevance to the NAFLD spectrum. These data could prove invaluable in predicting patients at risk of developing NAFLD and more importantly, those who will subsequently progress to NASH.Shamsul Mohd ZainRosmawati MohamedDavid N CooperRozaimi RazaliSanjay RampalSanjiv MahadevaWah-Kheong ChanArif AnwarNurul Shielawati Mohamed RosliAnis Shafina MahfudzPhaik-Leng CheahRoma Choudhury BasuZahurin MohamedPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 4, p e95604 (2014) |
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Medicine R Science Q Shamsul Mohd Zain Rosmawati Mohamed David N Cooper Rozaimi Razali Sanjay Rampal Sanjiv Mahadeva Wah-Kheong Chan Arif Anwar Nurul Shielawati Mohamed Rosli Anis Shafina Mahfudz Phaik-Leng Cheah Roma Choudhury Basu Zahurin Mohamed Genome-wide analysis of copy number variation identifies candidate gene loci associated with the progression of non-alcoholic fatty liver disease. |
| description |
Between 10 and 25% of individuals with non-alcoholic fatty liver disease (NAFLD) develop hepatic fibrosis leading to cirrhosis and hepatocellular carcinoma (HCC). To investigate the molecular basis of disease progression, we performed a genome-wide analysis of copy number variation (CNV) in a total of 49 patients with NAFLD [10 simple steatosis and 39 non-alcoholic steatohepatitis (NASH)] and 49 matched controls using high-density comparative genomic hybridization (CGH) microarrays. A total of 11 CNVs were found to be unique to individuals with simple steatosis, whilst 22 were common between simple steatosis and NASH, and 224 were unique to NASH. We postulated that these CNVs could be involved in the pathogenesis of NAFLD progression. After stringent filtering, we identified four rare and/or novel CNVs that may influence the pathogenesis of NASH. Two of these CNVs, located at 13q12.11 and 12q13.2 respectively, harbour the exportin 4 (XPO4) and phosphodiesterase 1B (PDE1B) genes which are already known to be involved in the etiology of liver cirrhosis and HCC. Cross-comparison of the genes located at these four CNV loci with genes already known to be associated with NAFLD yielded a set of genes associated with shared biological processes including cell death, the key process involved in 'second hit' hepatic injury. To our knowledge, this pilot study is the first to provide CNV information of potential relevance to the NAFLD spectrum. These data could prove invaluable in predicting patients at risk of developing NAFLD and more importantly, those who will subsequently progress to NASH. |
| format |
article |
| author |
Shamsul Mohd Zain Rosmawati Mohamed David N Cooper Rozaimi Razali Sanjay Rampal Sanjiv Mahadeva Wah-Kheong Chan Arif Anwar Nurul Shielawati Mohamed Rosli Anis Shafina Mahfudz Phaik-Leng Cheah Roma Choudhury Basu Zahurin Mohamed |
| author_facet |
Shamsul Mohd Zain Rosmawati Mohamed David N Cooper Rozaimi Razali Sanjay Rampal Sanjiv Mahadeva Wah-Kheong Chan Arif Anwar Nurul Shielawati Mohamed Rosli Anis Shafina Mahfudz Phaik-Leng Cheah Roma Choudhury Basu Zahurin Mohamed |
| author_sort |
Shamsul Mohd Zain |
| title |
Genome-wide analysis of copy number variation identifies candidate gene loci associated with the progression of non-alcoholic fatty liver disease. |
| title_short |
Genome-wide analysis of copy number variation identifies candidate gene loci associated with the progression of non-alcoholic fatty liver disease. |
| title_full |
Genome-wide analysis of copy number variation identifies candidate gene loci associated with the progression of non-alcoholic fatty liver disease. |
| title_fullStr |
Genome-wide analysis of copy number variation identifies candidate gene loci associated with the progression of non-alcoholic fatty liver disease. |
| title_full_unstemmed |
Genome-wide analysis of copy number variation identifies candidate gene loci associated with the progression of non-alcoholic fatty liver disease. |
| title_sort |
genome-wide analysis of copy number variation identifies candidate gene loci associated with the progression of non-alcoholic fatty liver disease. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2014 |
| url |
https://doaj.org/article/a543aa02099c4469afb9733498d5a2f0 |
| work_keys_str_mv |
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| _version_ |
1718421878183297024 |