Performance comparison of bench-top next generation sequencers using microdroplet PCR-based enrichment for targeted sequencing in patients with autism spectrum disorder.
Performance comparison of bench-top next generation sequencers using microdroplet PCR-based enrichment for targeted sequencing in patients with autism spectrum disorder.
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DOI：
10.1371/journal.pone.0074167
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Matsumoto N
中科院分区：
文献类型：
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作者：
Koshimizu E;Miyatake S;Okamoto N;Nakashima M;Tsurusaki Y;Miyake N;Saitsu H;Matsumoto N
下一代测序（NGS）结合靶基因的富集使得能够高效且低成本地测序用于遗传疾病的多个基因。本研究的目的是验证我们的方法在自闭症谱系障碍（ASD）的综合突变检测的准确性和灵敏度。我们评估了台式Ion Torrent PGM和Illumina MiSeq平台作为突变检测优化解决方案的性能，使用基于微滴PCR的62个ASD相关基因富集。使用NGS对10名已知突变的患者进行测序，以验证我们方法的灵敏度。MiSeq的整体读取质量更好，主要是因为与PGM相关的indel相关错误增加。两种平台的SNV检测灵敏度相似，表明它们都适用于人类基因组中的SNV检测。接下来，我们使用这些方法分析了28名ASD患者，并在与ASD相关的基因中发现了22种新的变异，其中一种突变仅由MiSeq检测到。因此，我们的结果支持靶基因富集和NGS的结合作为研究ASD罕见变异的有价值的分子方法。
Next-generation sequencing (NGS) combined with enrichment of target genes enables highly efficient and low-cost sequencing of multiple genes for genetic diseases. The aim of this study was to validate the accuracy and sensitivity of our method for comprehensive mutation detection in autism spectrum disorder (ASD). We assessed the performance of the bench-top Ion Torrent PGM and Illumina MiSeq platforms as optimized solutions for mutation detection, using microdroplet PCR-based enrichment of 62 ASD associated genes. Ten patients with known mutations were sequenced using NGS to validate the sensitivity of our method. The overall read quality was better with MiSeq, largely because of the increased indel-related error associated with PGM. The sensitivity of SNV detection was similar between the two platforms, suggesting they are both suitable for SNV detection in the human genome. Next, we used these methods to analyze 28 patients with ASD, and identified 22 novel variants in genes associated with ASD, with one mutation detected by MiSeq only. Thus, our results support the combination of target gene enrichment and NGS as a valuable molecular method for investigating rare variants in ASD.
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影响因子：
16.2
作者：
Iossifov I;Ronemus M;Levy D;Wang Z;Hakker I;Rosenbaum J;Yamrom B;Lee YH;Narzisi G;Leotta A;Kendall J;Grabowska E;Ma B;Marks S;Rodgers L;Stepansky A;Troge J;Andrews P;Bekritsky M;Pradhan K;Ghiban E;Kramer M;Parla J;Demeter R;Fulton LL;Fulton RS;Magrini VJ;Ye K;Darnell JC;Darnell RB;Mardis ER;Wilson RK;Schatz MC;McCombie WR;Wigler M
通讯作者：
Wigler M
DOI：
10.1073/pnas.0501432102
发表时间：
2005-08-09
影响因子：
11.1
作者：
Prasad, HC;Zhu, CB;Blakely, RD
通讯作者：
Blakely, RD
影响因子：
6.9
作者：
BAILEY, A;LECOUTEUR, A;RUTTER, M
通讯作者：
RUTTER, M
影响因子：
46.9
作者：
Loman, Nicholas J.;Misra, Raju V.;Pallen, Mark J.
通讯作者：
Pallen, Mark J.
使用下一代 DNA 测序数据进行变异发现和基因分型的框架。
影响因子：
30.8
作者：
通讯作者：
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