Functional relevance of synonymous alleles reflected in allele rareness in the population |
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Authors: | Eu-Hyun Im Yoonsoo Hahn Sun Shim Choi |
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Institution: | 1. Division of Biomedical Convergence, College of Biomedical Science, Institute of Bioscience & Biotechnology, Kangwon National University, Chuncheon 24341, Republic of Korea;2. Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea |
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Abstract: | We provide theoretical evidence supporting the non-neutrality of synonymous alleles by investigating the rareness of synonymous alleles in the population. We find a significantly greater number of synonymous rare alleles than conventional neutral alleles derived from noncoding regions. A permutation experiment shows that the rareness of synonymous alleles is not a byproduct of random statistical noise. We then compare the frequencies of synonymous rare alleles and common alleles in various functional contexts in which synonymous alleles are known to be involved. Subsequently, we perform logistic regression analysis to elucidate the effect size of each independent factor contributing to the rareness of synonymous alleles. Additionally, we show that changes in optimality caused by synonymous mutations resulting in rare SNPs in the population tend to be biased toward optimality loss. We think that our study will contribute to the development of novel strategies for identifying functional synonymous mutations. |
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Keywords: | Synonymous codon usage bias Common SNP Rare SNP Natural selection |
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