From next-generation sequencing alignments to accurate comparison and validation of single-nucleotide variants: the pibase software.
From next-generation sequencing alignments to accurate comparison and validation of single-nucleotide variants: the pibase software.
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DOI：
10.1093/nar/gks836
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发表时间：
2013-01-07
影响因子：
14.9
通讯作者：
Franke A
中科院分区：
文献类型：
--
作者：
Forster M;Forster P;Elsharawy A;Hemmrich G;Kreck B;Wittig M;Thomsen I;Stade B;Barann M;Ellinghaus D;Petersen BS;May S;Melum E;Schilhabel MB;Keller A;Schreiber S;Rosenstiel P;Franke A
研究单核苷酸变异（SNV）的科学家，通过下一代测序软件推断，通常需要关于真实变异，伪影和序列覆盖缺口的进一步信息。在临床诊断中，例如，SNV通常必须通过目视检查或几个独立的SNV调用器来验证。我们在这里证明，0.5-60%的相关SNV可能由于覆盖缺口而未被检测到，或者可能被错误识别。即使是很低的错误率也可能掩盖真实的生物信号，特别是在临床诊断、比较健康细胞与受影响细胞的研究、古基因年代测定或法医学中。出于这些原因，我们开发了一个名为pibase的软件包，它适用于二倍体和单倍体基因组、外显子组或靶向富集数据。PIBase从用户指定坐标处的比对文件中提取关于核苷酸的细节，并鉴定可再现的基因型（如果存在的话）。在测试案例中，pibase以99.98%的特异性识别基因型，比其他工具好10倍。pibase还使用核苷酸信号提供健康细胞和受影响细胞之间的成对比较（比基于基因型的方法准确10倍，正如我们在单卵双胞胎的案例研究中所展示的那样）。该比较工具还解决了检测拷贝数变异基因座中或异质肿瘤序列中的杂合SNV内的等位基因不平衡的问题。
Scientists working with single-nucleotide variants (SNVs), inferred by next-generation sequencing software, often need further information regarding true variants, artifacts and sequence coverage gaps. In clinical diagnostics, e.g. SNVs must usually be validated by visual inspection or several independent SNV-callers. We here demonstrate that 0.5–60% of relevant SNVs might not be detected due to coverage gaps, or might be misidentified. Even low error rates can overwhelm the true biological signal, especially in clinical diagnostics, in research comparing healthy with affected cells, in archaeogenetic dating or in forensics. For these reasons, we have developed a package called pibase, which is applicable to diploid and haploid genome, exome or targeted enrichment data. pibase extracts details on nucleotides from alignment files at user-specified coordinates and identifies reproducible genotypes, if present. In test cases pibase identifies genotypes at 99.98% specificity, 10-fold better than other tools. pibase also provides pair-wise comparisons between healthy and affected cells using nucleotide signals (10-fold more accurately than a genotype-based approach, as we show in our case study of monozygotic twins). This comparison tool also solves the problem of detecting allelic imbalance within heterozygous SNVs in copy number variation loci, or in heterogeneous tumor sequences.
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影响因子：
14.9
作者：
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通讯作者：
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影响因子：
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作者：
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影响因子：
30.8
作者：
Girard, Simon L.;Gauthier, Julie;Rouleau, Guy A.
通讯作者：
Rouleau, Guy A.