外显子组测序解决了明显的偶发发现，并揭示了导致遗传性运动感觉神经病的 SH3TC2 变异等位基因的进一步复杂性。
Exome sequencing resolves apparent incidental findings and reveals further complexity of SH3TC2 variant alleles causing Charcot-Marie-Tooth neuropathy.
机构信息
Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA ; Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
出版信息
Genome Med. 2013 Jun 27;5(6):57. doi: 10.1186/gm461. eCollection 2013.
BACKGROUND
The debate regarding the relative merits of whole genome sequencing (WGS) versus exome sequencing (ES) centers around comparative cost, average depth of coverage for each interrogated base, and their relative efficiency in the identification of medically actionable variants from the myriad of variants identified by each approach. Nevertheless, few genomes have been subjected to both WGS and ES, using multiple next generation sequencing platforms. In addition, no personal genome has been so extensively analyzed using DNA derived from peripheral blood as opposed to DNA from transformed cell lines that may either accumulate mutations during propagation or clonally expand mosaic variants during cell transformation and propagation.
METHODS
We investigated a genome that was studied previously by SOLiD chemistry using both ES and WGS, and now perform six independent ES assays (Illumina GAII (x2), Illumina HiSeq (x2), Life Technologies' Personal Genome Machine (PGM) and Proton), and one additional WGS (Illumina HiSeq).
RESULTS
We compared the variants identified by the different methods and provide insights into the differences among variants identified between ES runs in the same technology platform and among different sequencing technologies. We resolved the true genotypes of medically actionable variants identified in the proband through orthogonal experimental approaches. Furthermore, ES identified an additional SH3TC2 variant (p.M1?) that likely contributes to the phenotype in the proband.
CONCLUSIONS
ES identified additional medically actionable variant calls and helped resolve ambiguous single nucleotide variants (SNV) documenting the power of increased depth of coverage of the captured targeted regions. Comparative analyses of WGS and ES reveal that pseudogenes and segmental duplications may explain some instances of apparent disease mutations in unaffected individuals.
背景
全基因组测序（WGS）与外显子组测序（ES）的相对优势的争论集中在比较成本、每个被检测碱基的平均覆盖深度，以及它们在识别每种方法所识别的众多变异体中的医学可操作变异体方面的相对效率。然而，很少有基因组同时使用多种下一代测序平台进行 WGS 和 ES 检测。此外，还没有一个基因组使用源自外周血的 DNA 进行如此广泛的分析，而不是使用可能在增殖过程中积累突变或在细胞转化和增殖过程中克隆性扩展嵌合体变异体的转化细胞系中的 DNA。
方法
我们研究了一个先前使用 SOLiD 化学技术通过 ES 和 WGS 进行研究的基因组，现在进行了六个独立的 ES 分析（Illumina GAII（x2）、Illumina HiSeq（x2）、Life Technologies 的个人基因组机器（PGM）和 Proton），以及一个额外的 WGS（Illumina HiSeq）。
结果
我们比较了不同方法识别的变体，并深入了解了在同一技术平台的 ES 运行之间以及不同测序技术之间识别的变体之间的差异。我们通过正交实验方法确定了在先证者中识别出的医学可操作变体的真实基因型。此外，ES 还鉴定出了另一个 SH3TC2 变体（p.M1?），该变体可能导致先证者的表型。
结论
ES 鉴定出了更多的医学可操作变体，并通过增加捕获的靶向区域的覆盖深度来帮助解决有疑问的单核苷酸变体（SNV），从而证明了其强大功能。WGS 和 ES 的比较分析表明，假基因和片段重复可能解释了一些未受影响个体中明显疾病突变的原因。
Zotero 插件