Efficient discovery of single-nucleotide polymorphisms in coding regions of human genes

被引：13
作者：
Hu G. [1 ,3 ,4 ]
Modrek B. [1 ,3 ,4 ]
Riise Stensland H.M.F. [2 ]
Saarela J. [2 ]
Pajukanta P. [2 ]
Kustanovich V. [2 ]
Peltonen L. [2 ]
Nelson S.F. [2 ]
Lee C. [1 ,3 ,4 ]
机构：
[1] Department of Chemistry and Biochemistry, University of California, Los Angeles, CA
[2] Department of Human Genetics, University of California, Los Angeles, CA
[3] UCLADOE Laboratory for Structural Biology and Molecular Medicine, University of California, Los Angeles, CA
[4] Molecular Biology Institute, University of California, CA
来源：
The Pharmacogenomics Journal | 2002年 / 2卷 / 4期
基金：
美国国家卫生研究院; 美国国家科学基金会;
关键词：
Bioinformatics; cSNP; Data mining; EST; Functional genomics; Polymorphism;
D O I：
10.1038/sj.tpj.6500109
中图分类号：
学科分类号：
摘要：
Single nucleotide polymorphisms in protein coding regions (cSNPs) are of great interest for their effects on phenotype and potential for mapping disease genes. We have identified 5400 novel exonic SNPs from alignments of public EST data to the draft human genome sequence, and approximately 12 000 more novel exonic SNPs from EST cluster alignments. We found 82% of the genomic-aligned SNPs and 63% of the EST-only SNPs to be detectably polymorphic in 20 Finnish DNA samples. 37% of the SNPs mapped to known protein coding regions, yielding 6500 distinct, novel cSNPs from the two datasets. These data reveal selection against mutations that alter protein structure, and distinct classes of genes under strongly positive vs. negative pressure from natural selection for amino acid replacement (detected by KAKratio). We have searched these cSNPs for compatibility with the amino acid profile at each site and structural impact on protein core stability.
引用
收藏
页码：236 / 242
页数：6
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