Gene-centric characteristics of genome-wide association studies
文献类型：期刊论文
| 作者 | Dong, Changzheng1,2,3; Qian, Ziliang2,3; Jia, Peilin2,3; Wang, Ying1; Huang, Wei1,4; Li, Yixue2,5 |
| 刊名 | Plos one
 |
| 出版日期 | 2007-12-05 |
| 卷号 | 2期号:12页码:8 |
| ISSN号 | 1932-6203 |
| DOI | 10.1371/journal.pone.0001262 |
| 通讯作者 | Huang, wei(huangwei@chgc.sh.cn) |
| 英文摘要 | Background. the high-throughput genotyping chips have contributed greatly to genome-wide association (gwa) studies to identify novel disease susceptibility single nucleotide polymorphisms ( snps). the high-density chips are designed using two different snp selection approaches, the direct gene-centric approach, and the indirect quasi-random snps or linkage disequilibrium (ld)-based tagsnps approaches. although all these approaches can provide high genome coverage and ascertain variants in genes, it is not clear to which extent these approaches could capture the common genic variants. it is also important to characterize and compare the differences between these approaches. methodology/principal findings. in our study, by using both the phase ii hapmap data and the disease variants extracted from omim, a gene-centric evaluation was first performed to evaluate the ability of the approaches in capturing the disease variants in caucasian population. then the distribution patterns of snps were also characterized in genic regions, evolutionarily conserved introns and nongenic regions, ontologies and pathways. the results show that, no mater which snp selection approach is used, the current high-density snp chips provide very high coverage in genic regions and can capture most of known common disease variants under hapmap frame. the results also show that the differences between the direct and the indirect approaches are relatively small. both have similar snp distribution patterns in these gene-centric characteristics. conclusions/significance. this study suggests that the indirect approaches not only have the advantage of high coverage but also are useful for studies focusing on various functional snps either in genes or in the conserved regions that the direct approach supports. the study and the annotation of characteristics will be helpful for designing and analyzing gwa studies that aim to identify genetic risk factors involved in common diseases, especially variants in genes and conserved regions. |
| WOS研究方向 | Science & Technology - Other Topics |
| WOS类目 | Multidisciplinary Sciences |
| 语种 | 英语 |
| WOS记录号 | WOS:000207459400011 |
| 出版者 | PUBLIC LIBRARY SCIENCE |
| URI标识 | http://www.irgrid.ac.cn/handle/1471x/2381417 |
| 专题 | 中国科学院大学 |
| 通讯作者 | Huang, Wei |
| 作者单位 | 1.Chinese Natl Human Genome Ctr Shanghai, Shanghai, Peoples R China 2.Chinese Acad Sci, Shanghai Inst Biol Sci, Key Lab Syst Biol, Bioinformat Ctr, Shanghai, Peoples R China 3.Chinese Acad Sci, Grad Sch, Beijing, Peoples R China 4.Shanghai Jiao Tong Univ, Sch Med, Rui Jin Hosp, Shanghai 200030, Peoples R China 5.Shanghai Ctr Bioinformat Technol, Shanghai, Peoples R China |
| 推荐引用方式 GB/T 7714 | Dong, Changzheng,Qian, Ziliang,Jia, Peilin,et al. Gene-centric characteristics of genome-wide association studies[J]. Plos one,2007,2(12):8. |
| APA | Dong, Changzheng,Qian, Ziliang,Jia, Peilin,Wang, Ying,Huang, Wei,&Li, Yixue.(2007).Gene-centric characteristics of genome-wide association studies.Plos one,2(12),8. |
| MLA | Dong, Changzheng,et al."Gene-centric characteristics of genome-wide association studies".Plos one 2.12(2007):8. |
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来源：中国科学院大学
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