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Abstract
The use of phylogenetic analysis to predict positive selection specific to human genes is complicated by the very close evolutionary relationship with our nearest extant primate relatives, chimpanzees. To assess the power and limitations inherent in use of maximum-likelihood (ML) analysis of codon substitution patterns in such recently diverged species, a series of simulations was performed to assess the impact of several parameters of the evolutionary model on prediction of human-specific positive selection, including branch length and d(N)/d(S) ratio. Parameters were varied across a range of values observed in alignments of 175 transcription factor (TF) genes that were sequenced in 12 primate species. The ML method largely lacks the power to detect positive selection that has occurred since the most recent common ancestor between humans and chimpanzees. An alternative null model was developed on the basis of gene-specific evaluation of the empirical distribution of ML results, using simulated neutrally evolving sequences. This empirical test provides greater sensitivity to detect lineage-specific positive selection in the context of recent evolutionary divergence.
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Moritani M, Togawa K, Yaguchi H, Fujita Y, Yamaguchi Y, Inoue H, Kamatani N, Itakura M. Identification of diabetes susceptibility loci in db mice by combined quantitative trait loci analysis and haplotype mapping. Genomics 2006; 88:719-730. [PMID: 16919419 DOI: 10.1016/j.ygeno.2006.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2006] [Revised: 07/06/2006] [Accepted: 07/06/2006] [Indexed: 11/16/2022]
Abstract
To identify the disease-susceptibility genes of type 2 diabetes, we performed quantitative trait loci (QTL) analysis in F(2) populations generated from a BKS.Cg-m+/+Lepr(db) and C3H/HeJ intercross, taking advantage of genetically determined obesity and diabetes traits associated with the db gene. A genome-wide scan in the F(2) populations divided by sex and db genotypes identified 14 QTLs in total and 3 major QTLs on chromosome (Chr) 3 (LOD 5.78) for fat pad weight, Chr 15 (LOD 6.64) for body weight, and Chr 16 (LOD 8.15) for blood glucose concentrations. A linear-model-based genome scan using interactive covariates allowed us to consider sex- or sex-by db-specific effects of each locus. For the most significant QTL on Chr 16, the high-resolution haplotype comparison between BKS and C3H strains reduced the critical QTL interval from 20 to 4.6 Mb by excluding shared haplotype regions and identified 11 nonsynonymous single-nucleotide polymorphisms in six candidate genes.
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Affiliation(s)
- Maki Moritani
- Division of Genetic Information, Institute for Genome Research, The University of Tokushima, Tokushima 770-8503, Japan
| | - Katsuhiko Togawa
- Division of Genetic Information, Institute for Genome Research, The University of Tokushima, Tokushima 770-8503, Japan; First Institute of New Drug Discovery, Otsuka Pharmaceutical, Inc., Tokushima 771-0192, Japan
| | - Hiroshi Yaguchi
- Division of Pharmacology, Drug Safety and Metabolism, Otsuka Pharmaceutical Factory, Inc., Naruto 772-8601, Japan
| | - Yuka Fujita
- Division of Genetic Information, Institute for Genome Research, The University of Tokushima, Tokushima 770-8503, Japan
| | - Yuka Yamaguchi
- Division of Genetic Information, Institute for Genome Research, The University of Tokushima, Tokushima 770-8503, Japan
| | - Hiroshi Inoue
- Division of Genetic Information, Institute for Genome Research, The University of Tokushima, Tokushima 770-8503, Japan
| | - Naoyuki Kamatani
- Division of Statistical Genetics, Department of Advanced Biomedical Engineering and Science, Tokyo Women's Medical University, Tokyo, Japan
| | - Mitsuo Itakura
- Division of Genetic Information, Institute for Genome Research, The University of Tokushima, Tokushima 770-8503, Japan.
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