Open Access Research article

Mammalian NPC1 genes may undergo positive selection and human polymorphisms associate with type 2 diabetes

Nasser M Al-Daghri123*, Rachele Cagliani4, Diego Forni4, Majed S Alokail123, Uberto Pozzoli4, Khalid M Alkharfy1235, Shaun Sabico123, Mario Clerici67 and Manuela Sironi4

Author Affiliations

1 Biomarkers Research Program, Biochemistry Department, College of Science, King Saud University, King Abdullah road, Riyadh 11451, Kingdom of Saudi Arabia

2 Prince Mutaib Chair for Biomarkers of Osteoporosis Research, King Saud University, King Abdullah road, Riyadh 11451, Kingdom of Saudi Arabia

3 Center of Excellence in Biotechnology, King Saud University, King Abdullah road, Riyadh 11451, Kingdom of Saudi Arabia

4 Bioinformatics, Scientific Institute IRCCS E.MEDEA, Via Don L. Monza 20, Bosisio Parini 23842, Italy

5 Clinical Pharmacy Department, College of Pharmacy, King Saud University, King Abdullah road, Riyadh 11451, Kingdom of Saudi Arabia

6 Department of Molecular Medicine, Don Gnocchi Foundation IRCCS, ONLUS, Piazetta Morandi, Milano 20100, Italy

7 Department of Pathophysiology and Transplantation, Milano University Medical School, Via Fratelli Cervi, Milano 20090, Italy

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BMC Medicine 2012, 10:140  doi:10.1186/1741-7015-10-140

Published: 15 November 2012

Additional files

Additional file 1:

Table S1: Likelihood ratio test statistics for models of variable selective pressure among sites. The table reports results of the likelihood ratio tests (M7 versus M8 and M8a versus M8) using the F3X4 codon frequency model. Figure S1: Multiple protein alignment of NPC1 mammalian genes. The figure shows the NPC1 multiple species alignment (41 species, Clustal format); positively selected sites and human nonsynonymous polymorphisms are highlighted. Figure S2: Branch-site random effects likelihood (branch-site REL) analysis of NPC1 genes. The figure shows a branch-site REL analysis of NPC1 with the width and color of each branch indicating the strength of selection. Figure S3: Sliding-window analysis of nucleotide diversity along NPC1 using the 1000 Genomes Project data. The figure shows θW and π calculated for Yoruba, Europeans and Asians in sliding windows of 5 kb moving along the NPC1 gene region. Figure S4: Sliding-window analysis of FST along NPC1 using the 1000 Genomes Project data. The figure shows FST (YRI/CEU/CHB-JPT) calculated in 5 kb windows moving along the NPC1 gene region.

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