A novel application of pattern recognition for accurate SNP and indel discovery from high-throughput data: targeted resequencing of the glucocorticoid receptor co-chaperone FKBP5 in a Caucasian population.
A novel application of pattern recognition for accurate SNP and indel discovery from high-throughput data: targeted resequencing of the glucocorticoid receptor co-chaperone FKBP5 in a Caucasian population.
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DOI：
10.1016/j.ymgme.2011.08.019
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发表时间：
2011-12
影响因子：
3.8
通讯作者：
Rossetti, Sandro
中科院分区：
文献类型：
--
作者：
Pelleymounter, Linda L.;Moon, Irene;Johnson, Julie A.;Laederach, Alain;Halvorsen, Matt;Eckloff, Bruce;Abo, Ryan;Rossetti, Sandro
从高通量数据中精确检测单核苷酸多态性（SNP）和插入/缺失（indels）仍然是一个重大的生物信息学挑战。在下一代测序可以常规用于临床之前，准确的检测是必要的。在研究方面，科学进步受到数据缺口的阻碍，例如罕见变异、非编码区变异和插入缺失的发现代表性不足。假阳性和假阴性的持续存在阻碍了完全自动化，并需要额外的手动验证步骤。我们的方法提出了模式识别和灵敏度分析的应用，以消除假阳性，并帮助从高通量数据中检测SNP/indel基因座和基因型。我们选择FK 506结合蛋白51（FKBP 5）（6p21.31）作为我们的临床靶点，因为它在调节生理和合成糖皮质激素的药理学反应中的作用，也因为基因组区域的复杂性。我们检测到FKBP 5基因在160 kb区域内的遗传变异。共发现613个SNPs和57个indel，其中包括一个3.3kb的缺失。我们使用三个独立的数据集验证了我们的方法，并与桑格测序和Affyssin和Illumina微阵列，实现了99%的一致性。此外，我们能够检测到267个新的罕见变异，并评估连锁不平衡。我们的结果显示98%的灵敏度和特异性，表明真和假变体之间接近完美的分类。该过程可扩展且易于自动化，下游过滤器仅需1.5小时即可同时分析96个个体。我们提供的例子，我们的精度水平如何揭示多个位点的相互作用，其预测的影响mRNA的稳定性，扰动的热休克蛋白90结合位点，和FKBP 5表达的个体差异。最后，我们将展示我们对罕见变异的发现如何改变目前对这一基因座进化的概念。
The detection of single nucleotide polymorphisms (SNPs) and insertion/deletions (indels) with precision from high-throughput data remains a significant bioinformatics challenge. Accurate detection is necessary before next-generation sequencing can routinely be used in the clinic. In research, scientific advances are inhibited by gaps in data, exemplified by the underrepresented discovery of rare variants, variants in non-coding regions and indels. The continued presence of false positives and false negatives prevents full automation and requires additional manual verification steps. Our methodology presents applications of both pattern recognition and sensitivity analysis to eliminate false positives and aid in the detection of SNP/indel loci and genotypes from high-throughput data. We chose FK506-binding protein 51(FKBP5) (6p21.31) for our clinical target because of its role in modulating pharmacological responses to physiological and synthetic glucocorticoids and because of the complexity of the genomic region. We detected genetic variation across a160 kb region encompassing FKBP5. 613 SNPs and 57 indels, including a 3.3 kb deletion were discovered. We validated our method using three independent data sets and, with Sanger sequencing and Affymetrix and Illumina microarrays, achieved 99% concordance. Furthermore we were able to detect 267 novel rare variants and assess linkage disequilibrium. Our results showed both a sensitivity and specificity of 98%, indicating near perfect classification between true and false variants. The process is scalable and amenable to automation, with the downstream filters taking only 1.5 hours to analyze 96 individuals simultaneously. We provide examples of how our level of precision uncovered the interactions of multiple loci, their predicted influences on mRNA stability, perturbations of the hsp90 binding site, and individual variation in FKBP5 expression. Finally we show how our discovery of rare variants may change current conceptions of evolution at this locus.
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影响因子：
64.5
作者：
Hafner M;Landthaler M;Burger L;Khorshid M;Hausser J;Berninger P;Rothballer A;Ascano M Jr;Jungkamp AC;Munschauer M;Ulrich A;Wardle GS;Dewell S;Zavolan M;Tuschl T
通讯作者：
Tuschl T
BAMVIEW：在参考序列的上下文中查看映射的读取对齐数据。
影响因子：
5.8
作者：
Carver, Tim;Bohme, Ulrike;Otto, Thomas D.;Parkhill, Julian;Berriman, Matthew
通讯作者：
Berriman, Matthew
影响因子：
48
作者：
Kidd, Jeffrey M.;Sampas, Nick;Antonacci, Francesca;Graves, Tina;Fulton, Robert;Hayden, Hillary S.;Alkan, Can;Malig, Maika;Ventura, Mario;Giannuzzi, Giuliana;Kallicki, Joelle;Anderson, Paige;Tsalenko, Anya;Yamada, N. Alice;Tsang, Peter;Kaul, Rajinder;Wilson, Richard K.;Bruhn, Laurakay;Eichler, Evan E.
通讯作者：
Eichler, Evan E.
DOI：
10.1016/j.bbapap.2009.02.014
发表时间：
2009-05
期刊：
Biochimica et biophysica acta
影响因子：
--
作者：
Fung KL;Gottesman MM
通讯作者：
Gottesman MM
影响因子：
3.8
作者：
Hubler, TR;Scammell, JG
通讯作者：
Scammell, JG