Detection of base substitution-type somatic mosaicism of the NLRP3 gene with >99.9% statistical confidence by massively parallel sequencing.
Detection of base substitution-type somatic mosaicism of the NLRP3 gene with >99.9% statistical confidence by massively parallel sequencing.
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DOI：
10.1093/dnares/dsr047
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发表时间：
2012-04
期刊：
影响因子：
--
通讯作者：
Ohara O
中科院分区：
文献类型：
--
作者：
Izawa K;Hijikata A;Tanaka N;Kawai T;Saito MK;Goldbach-Mansky R;Aksentijevich I;Yasumi T;Nakahata T;Heike T;Nishikomori R;Ohara O
慢性婴儿神经性皮肤和关节综合征（CINCA），也称为脑源性多系统炎性疾病（NOMID），是一种显性遗传性全身性自身炎性疾病，由NLRP 3基因中的杂合子生殖系功能获得性突变引起。最近，我们发现了一个高发病率的NLRP 3体细胞镶嵌在明显突变阴性的CINCA/NOMID患者使用亚克隆和随后的毛细管DNA测序。重要的是快速诊断体细胞NLRP 3嵌合体，以确保适当的治疗。然而，这种方法需要大量的时间、成本和劳动力的投资，这妨碍了低水平体细胞NLRP 3嵌合体的常规遗传诊断。我们开发了一种常规的管道，使用大规模并行DNA测序检测具有统计学显著性的NLRP 3的低水平等位基因。为了解决从测序错误中区分低水平等位基因的关键问题，我们首先构建了14个聚合酶链反应产物的错误率图，这些聚合酶链反应产物覆盖了Roche 454 GS-FLX测序仪上50个无嵌合现象的对照样品的整个编码NLRP 3外显子。基于这些结果，我们制定了每条链中每个序列变异的统计置信度值，以区分测序错误和真实的遗传变异，即使在低水平等位基因中，从而以99.9%或更高的置信度检测等位基因频率低至1%的碱基置换。
Chronic infantile neurological cutaneous and articular syndrome (CINCA), also known as neonatal-onset multisystem inflammatory disease (NOMID), is a dominantly inherited systemic autoinflammatory disease and is caused by a heterozygous germline gain-of-function mutation in the NLRP3 gene. We recently found a high incidence of NLRP3 somatic mosaicism in apparently mutation-negative CINCA/NOMID patients using subcloning and subsequent capillary DNA sequencing. It is important to rapidly diagnose somatic NLRP3 mosaicism to ensure proper treatment. However, this approach requires large investments of time, cost, and labour that prevent routine genetic diagnosis of low-level somatic NLRP3 mosaicism. We developed a routine pipeline to detect even a low-level allele of NLRP3 with statistical significance using massively parallel DNA sequencing. To address the critical concern of discriminating a low-level allele from sequencing errors, we first constructed error rate maps of 14 polymerase chain reaction products covering the entire coding NLRP3 exons on a Roche 454 GS-FLX sequencer from 50 control samples without mosaicism. Based on these results, we formulated a statistical confidence value for each sequence variation in each strand to discriminate sequencing errors from real genetic variation even in a low-level allele, and thereby detected base substitutions at an allele frequency as low as 1% with 99.9% or higher confidence.
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使用下一代靶向重新取样对稀有突变的超敏感检测。
影响因子：
14.9
作者：
Flaherty P;Natsoulis G;Muralidharan O;Winters M;Buenrostro J;Bell J;Brown S;Holodniy M;Zhang N;Ji HP
通讯作者：
Ji HP
慢性婴儿神经系统，皮肤，关节综合征的患者NLRP3体细胞镶嵌的发病率很高：国际多中心协作研究的结果。
影响因子：
--
作者：
Tanaka, Naoko;Izawa, Kazushi;Saito, Megumu K.;Sakuma, Mio;Oshima, Koichi;Ohara, Osamu;Nishikomori, Ryuta;Morimoto, Takeshi;Kambe, Naotomo;Goldbach-Mansky, Raphaela;Aksentijevich, Ivona;de Saint Basile, Genevieve;Neven, Benedicte;van Gijn, Marielle;Frenkel, Joost;Arostegui, Juan I.;Yaguee, Jordi;Merino, Rosa;Ibanez, Mercedes;Pontillo, Alessandra;Takada, Hidetoshi;Imagawa, Tomoyuki;Kawai, Tomoki;Yasumi, Takahiro;Nakahata, Tatsutoshi;Heike, Toshio
通讯作者：
Heike, Toshio
影响因子：
64.8
作者：
通讯作者：
--
影响因子：
3.9
作者：
Milhavet, Florian;Cuisset, Laurence;Touitou, Isabelle
通讯作者：
Touitou, Isabelle
DOI：
10.1073/pnas.0801523105
发表时间：
2008-09-02
影响因子：
11.1
作者：
Campbell, Peter J.;Pleasance, Erin D.;Stratton, Michael R.
通讯作者：
Stratton, Michael R.