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Background  The global burden of chronic liver disease is rising. Besides environmental, behavioral, viral and metabolic factors, genetic polymorphisms in patatin-like phospholipase-3 ( PNPLA3)  and vitamin D receptor ( VDR ) genes have been related to the development of chronic liver disease and progression towards liver cancer. Although their prevalence differs remarkably among ethnic groups, the frequency of these polymorphisms in South American populations -whose genetic background is highly admixed- has been poorly studied. Hence, the aim of this study was to characterize polymorphisms related to chronic liver disease and their association with the genetic ancestry of South American populations.    Results  DNA samples from 258 healthy unrelated male volunteers were analyzed. The frequencies of G and C alleles of rs738409 polymorphism ( PNPLA3  gene) were 74 % and 26 %, respectively; whereas the bAt (CCA) haplotype ( VDR  gene) was observed in 32.5 % of the samples. The GG genotype of  PNPLA3  rs738409 and the bAt (CCA) haplotype -associated with an increased risk of chronic liver disease and progression towards liver cancer- were significantly more frequent among samples exhibiting maternal and paternal Native American haplogroups (63.7 % and 64.6 %), intermediate among admixed samples (45.1 % and 44.9 %;  p  = 0.03) and the lowest for Non-native American ancestry (30.1 % and 29.6 %;  p  = 0.001 and  p  = 0.0008).    Conclusions  These results suggest that individuals with Native American ancestry might have a high risk of chronic liver disorders and cancer. Furthermore, these data not only support the molecular evaluation of ancestry in multi-ethnic population studies, but also suggest that the characterization of these variants in South American populations may be useful for establishing public health policies aimed at high risk ethnic communities.    Electronic supplementary material  The online version of this article (doi:10.1186/s12863-015-0255-3) contains supplementary material, which is available to authorized users.

Influence of ethnicity on the distribution of genetic polymorphisms associated with risk of chronic liver disease in South American populations