Common contaminants in next-generation sequencing that hinder discovery of low-abundance microbes.
Common contaminants in next-generation sequencing that hinder discovery of low-abundance microbes.
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DOI：
10.1371/journal.pone.0097876
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发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Brash DE
中科院分区：
文献类型：
--
作者：
Laurence M;Hatzis C;Brash DE
全宏基因组鸟枪DNA文库的无偏高通量测序是一种有前途的新方法，用于鉴定临床标本中的微生物，与其他技术不同，它不限于已知序列。与大多数测序应用不同，它对实验室污染物高度敏感，因为这些污染物似乎来自临床标本。为了评估序列污染物的程度和多样性，我们将来自六个中心的57个“1000基因组计划”测序运行与四个最大的NCBI BLAST数据库进行比对，在所有运行中检测不同污染物物种的读段，并在NCBI基因组数据库的组装基因组中鉴定最常见的这些污染物属（慢生根瘤菌）。这些微生物中的许多已被报道为超纯水系统的污染物。旨在识别临床标本中新型微生物的研究不仅将大大受益于预防措施，如对水进行广泛的紫外线照射和使用独立技术进行交叉验证，而且还将共同努力对常见污染物的完整基因组进行测序，以便通过计算减去它们。
Unbiased high-throughput sequencing of whole metagenome shotgun DNA libraries is a promising new approach to identifying microbes in clinical specimens, which, unlike other techniques, is not limited to known sequences. Unlike most sequencing applications, it is highly sensitive to laboratory contaminants as these will appear to originate from the clinical specimens. To assess the extent and diversity of sequence contaminants, we aligned 57 “1000 Genomes Project” sequencing runs from six centers against the four largest NCBI BLAST databases, detecting reads of diverse contaminant species in all runs and identifying the most common of these contaminant genera (Bradyrhizobium) in assembled genomes from the NCBI Genome database. Many of these microorganisms have been reported as contaminants of ultrapure water systems. Studies aiming to identify novel microbes in clinical specimens will greatly benefit from not only preventive measures such as extensive UV irradiation of water and cross-validation using independent techniques, but also a concerted effort to sequence the complete genomes of common contaminants so that they may be subtracted computationally.
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影响因子：
64.8
作者：
通讯作者：
--
DOI：
10.1056/nejmoa1211115
发表时间：
2013-08-08
期刊：
The New England journal of medicine
影响因子：
--
作者：
Bhatt AS;Freeman SS;Herrera AF;Pedamallu CS;Gevers D;Duke F;Jung J;Michaud M;Walker BJ;Young S;Earl AM;Kostic AD;Ojesina AI;Hasserjian R;Ballen KK;Chen YB;Hobbs G;Antin JH;Soiffer RJ;Baden LR;Garrett WS;Hornick JL;Marty FM;Meyerson M
通讯作者：
Meyerson M
影响因子：
2.7
作者：
Duncan, Christopher G.;Leary, Rebecca J.;Yan, Hai
通讯作者：
Yan, Hai
影响因子：
3.7
作者：
Schmieder R;Edwards R
通讯作者：
Edwards R
影响因子：
2.8
作者：
Sutcliffe, Siobhan;De Marzo, Angelo M.;Sfanos, Karen S.;Laurence, Martin
通讯作者：
Laurence, Martin