IS-seq: a novel high throughput survey of in vivo IS6110 transposition in multiple Mycobacterium tuberculosis genomes.
IS-seq: a novel high throughput survey of in vivo IS6110 transposition in multiple Mycobacterium tuberculosis genomes.
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DOI：
10.1186/1471-2164-13-249
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发表时间：
2012-06-15
期刊：
影响因子：
4.4
通讯作者：
Del Portillo P
中科院分区：
文献类型：
--
作者：
Reyes A;Sandoval A;Cubillos-Ruiz A;Varley KE;Hernández-Neuta I;Samper S;Martín C;García MJ;Ritacco V;López L;Robledo J;Zambrano MM;Mitra RD;Del Portillo P
插入元件IS6110是结核分枝杆菌基因组变异的主要来源之一，结核杆菌是人类结核病的病原体。虽然IS 6110已被广泛用作流行病学标记，但精确的染色体插入位点的鉴定受到技术挑战的限制。在这里，我们提出了IS-SEQ，一种新的方法，它结合了使用Illumina技术的高通量测序和高效的组合样本多路复用来同时探测519株临床分离株，在一次实验中几乎识别了该元件的所有侧翼区域。我们在不同的分离株上共鉴定出6976个IS6110侧翼区域。当用参考菌株验证时，该方法具有100%的特异性和98%的阳性预测值。这些插入既映射到编码区，也映射到非编码区，在某些情况下中断了被认为对毒力或体外生长至关重要的基因。根据插入位点将菌株划分为家族，并观察到与以前的研究高度一致。这种高通量IS-SEQ方法也可用于绘制其他生物体的插入图谱，扩展了以前对体内中断位点的调查，并为探索结核分枝杆菌菌株中断的后果提供了基线。
The insertion element IS6110 is one of the main sources of genomic variability in Mycobacterium tuberculosis, the etiological agent of human tuberculosis. Although IS 6110 has been used extensively as an epidemiological marker, the identification of the precise chromosomal insertion sites has been limited by technical challenges. Here, we present IS-seq, a novel method that combines high-throughput sequencing using Illumina technology with efficient combinatorial sample multiplexing to simultaneously probe 519 clinical isolates, identifying almost all the flanking regions of the element in a single experiment. We identified a total of 6,976 IS6110 flanking regions on the different isolates. When validated using reference strains, the method had 100% specificity and 98% positive predictive value. The insertions mapped to both coding and non-coding regions, and in some cases interrupted genes thought to be essential for virulence or in vitro growth. Strains were classified into families using insertion sites, and high agreement with previous studies was observed. This high-throughput IS-seq method, which can also be used to map insertions in other organisms, extends previous surveys of in vivo interrupted loci and provides a baseline for probing the consequences of disruptions in M. tuberculosis strains.
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影响因子：
3.2
作者：
McEvoy, Christopher R. E.;Warren, Robin M.;Gey van Pittius, Nicolaas C.
通讯作者：
Gey van Pittius, Nicolaas C.
影响因子：
9.4
作者：
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通讯作者：
Rastogi, N
影响因子：
3.1
作者：
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通讯作者：
Bishai, WR
影响因子：
9.4
作者：
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通讯作者：
vanEmbden, J
影响因子：
3.7
作者：
Comas I;Homolka S;Niemann S;Gagneux S
通讯作者：
Gagneux S