Case Control Study
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World J Hepatol. Jun 27, 2014; 6(6): 435-442
Published online Jun 27, 2014. doi: 10.4254/wjh.v6.i6.435
Pooled genetic analysis in ultrasound measured non-alcoholic fatty liver disease in Indian subjects: A pilot study
Vishnubhotla Venkata Ravi Kanth, Mitnala Sasikala, Padaki Nagaraja Rao, Urmila Steffie Avanthi, Kalashikam Rajender Rao, Duvvuru Nageshwar Reddy
Vishnubhotla Venkata Ravi Kanth, Mitnala Sasikala, Urmila Steffie Avanthi, Asian Healthcare Foundation, Hyderabad 500082, India
Padaki Nagaraja Rao, Duvvuru Nageshwar Reddy, Asian Institute of Gastroenterology, Hyderabad 500082, India
Kalashikam Rajender Rao, Division of Endocrinology and Metabolism, National Institute of Nutrition, Tarnaka, Hyderabad 500082, India
Author contributions: Ravi Kanth VV, Sasikala M and Rao PN designed the research; Rao PN and Nageshwar Reddy D recruited patients; Ravi Kanth VV and Steffie Avanthi U performed the research; Rao RK contributed reagents/analytic tools; Ravi Kanth VV analyzed the data; Ravi Kanth VV and Sasikala M wrote the paper.
Correspondence to: Padaki Nagaraja Rao, Chief of Hepatology and Nutrition, Asian Institute of Gastroenterology, 6-3-661, Somajiguda, Hyderabad 500082, India.
Telephone: +91-40-23378888 Fax: +91-40-23324255
Received: January 9, 2014
Revised: March 1, 2014
Accepted: May 16, 2014
Published online: June 27, 2014

AIM: To investigate genetic susceptibility in Indian subjects with non-alcoholic fatty liver disease (NAFLD) by performing a pooled genetic study.

METHODS: Study subjects (n = 306) were recruited and categorized into NAFLD and control groups based on ultrasound findings of fatty infiltration. Of the 306 individuals, 156 individuals had fatty infiltration and thus comprised the NAFLD group. One hundred and fifty (n = 150) individuals were normal, without fatty infiltration of the liver, comprising the control group. Blood samples, demographic and anthropometric data from the individuals were collected after obtaining informed consent. Anthropometric data, blood glucose, lipids and liver function tests were estimated using standard methods. Genome wide association studies done to date on NAFLD were identified, 19 single nucleotide polymorphisms (SNPs) were selected from these studies that were reported to be significantly associated with NAFLD and genotyping was performed on the Sequenom platform. Student’s t test for continuous variables and χ2 test was applied to variant carriers from both groups. Required corrections were applied as multiple testing was done.

RESULTS The mean age of the control group was 39.78 ± 10.83 and the NAFLD group was 36.63 ± 8.20 years. The waist circumference of males and females in the control and NAFLD groups were 80.13 ± 10.35; 81.77 ± 13.65 and 94.09 ± 10.53; 92.53 ± 8.27 cms respectively. The mean triglyceride and alanine transaminase (ALT) levels in the control and NAFLD groups were 135.18 ± 7.77 mg/dL; 25.39 ± 14.73 IU/L and 184.40 ± 84.31 mg/dL; 110.20 ± 67.05 IU/L respectively. When χ2 test was applied to the number of individuals carrying the variant risk alleles between the control and NAFLD group, a significant association was seen between rs738409 of the patatin-like phospholipase domain containing 3 (PNPLA3) gene (P = 0.001), rs2073080 of the PARVB gene (P = 0.02), rs2143571 of SAMM50 gene (P = 0.05) and rs6487679 of the pregnancy zone protein (PZP) gene (P = 0.01) with the disease. Variant single nucleotide polymorphisms (SNPs) in NCAN and PNPLA3 gene were associated with higher levels of ALT, whereas variant SNPs in APOC3, PNPLA3, EFCAB4B and COL13A1 were associated with high triglyceride levels. Apart from the above associations, rs2073080, rs343062 and rs6591182 were significantly associated with high BMI; rs2854117 and rs738409 with high triglyceride levels; and rs2073080, rs2143571, rs2228603, rs6487679 and rs738409 with high ALT levels.

CONCLUSION: Pooled genetic analysis revealed an association of SNPs in PNPLA3, PARVB, SAMM50 and PZP genes with NAFLD. SNPs in NCAN and PNPLA3 gene were associated with higher levels of ALT, whereas variant SNPs in APOC3, PNPLA3, EFCAB4B and COL13A1 were associated with high triglyceride levels.

Keywords: Non-alcoholic fatty liver disease, Genome wide association studies, Genetic association, Hepatic steatosis, Genotyping, Single nucleotide polymorphisms, Susceptibility

Core tip: Non-alcoholic fatty liver disease (NAFLD) describes a range of conditions caused by build-up of fat within liver cells in the absence of alcohol consumption. Although obesity, diabetes, age, hypertension and hypertriglyceridemia contribute to the disease, genetics also has an important role to play. Furthermore, in 26%-35% of patients, genetic component is believed to contribute to NAFLD. By identifying significant single nucleotide polymorphisms from genome wide association studies reported from different ethnic populations for NAFLD and performing a pooled genetic association study, this study has identified important genetic risks that could help in identifying individuals with susceptibility at an early stage, thus aiding in better management of the disease.