Characterizing the genetic basis of bacterial phenotypes using genome-wide association studies: a new direction for bacteriology.
Characterizing the genetic basis of bacterial phenotypes using genome-wide association studies: a new direction for bacteriology.
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DOI：
10.1186/s13073-014-0109-z
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发表时间：
2014
期刊：
影响因子：
12.3
通讯作者：
Massey RC
中科院分区：
文献类型：
--
作者：
Read TD;Massey RC
全基因组关联研究（GWAS）已成为真核遗传学家越来越重要的方法，有助于识别数百种遗传性疾病的遗传多态性。尽管细菌基因组相对简单，但GWAS用于鉴定重要细菌表型的多态性的应用直到最近才通过基因组测序技术的进步而成为可能。细菌GWAS现在即将成熟，这要归功于大量数据集的可用性，以及通过改进验证策略提供的连接基因组学和传统遗传方法的潜力。在过去的两年中，已经发表了少量开创性的细菌GWAS，检查了75到3,000多个菌株。实验设计多种多样，利用细菌中不同的过程产生变异。在某种程度上，可以使用为真核系统开发的软件来分析细菌GWAS的数据，但必须考虑基因组进化的重要差异。细菌GWASs的最大实验优势是进行下游因果关系验证和机制剖析的潜力。我们回顾了这一领域的最新进展和面临的挑战，并提出了改进细菌GWASs验证的策略。
Genome-wide association studies (GWASs) have become an increasingly important approach for eukaryotic geneticists, facilitating the identification of hundreds of genetic polymorphisms that are responsible for inherited diseases. Despite the relative simplicity of bacterial genomes, the application of GWASs to identify polymorphisms responsible for important bacterial phenotypes has only recently been made possible through advances in genome sequencing technologies. Bacterial GWASs are now about to come of age thanks to the availability of massive datasets, and because of the potential to bridge genomics and traditional genetic approaches that is provided by improving validation strategies. A small number of pioneering GWASs in bacteria have been published in the past 2 years, examining from 75 to more than 3,000 strains. The experimental designs have been diverse, taking advantage of different processes in bacteria for generating variation. Analysis of data from bacterial GWASs can, to some extent, be performed using software developed for eukaryotic systems, but there are important differences in genome evolution that must be considered. The greatest experimental advantage of bacterial GWASs is the potential to perform downstream validation of causality and dissection of mechanism. We review the recent advances and remaining challenges in this field and propose strategies to improve the validation of bacterial GWASs.
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影响因子：
56.3
作者：
Grad, Yonatan H.;Kirkcaldy, Robert D.;Trees, David;Dordel, Janina;Harris, Simon R.;Goldstein, Edward;Weinstock, Hillard;Parkhill, Julian;Hanage, William P.;Bentley, Stephen;Lipsitch, Marc
通讯作者：
Lipsitch, Marc
影响因子：
4.5
作者：
Chewapreecha C;Marttinen P;Croucher NJ;Salter SJ;Harris SR;Mather AE;Hanage WP;Goldblatt D;Nosten FH;Turner C;Turner P;Bentley SD;Parkhill J
通讯作者：
Parkhill J
影响因子：
10.7
作者：
Bertels F;Silander OK;Pachkov M;Rainey PB;van Nimwegen E
通讯作者：
van Nimwegen E
影响因子：
9.4
作者：
Gordon NC;Price JR;Cole K;Everitt R;Morgan M;Finney J;Kearns AM;Pichon B;Young B;Wilson DJ;Llewelyn MJ;Paul J;Peto TE;Crook DW;Walker AS;Golubchik T
通讯作者：
Golubchik T
DOI：
10.1007/s004380051001
发表时间：
1999-04-01
期刊：
MOLECULAR AND GENERAL GENETICS
影响因子：
--
作者：
Gertz, S;Engelmann, S;Hecker, M
通讯作者：
Hecker, M