Inferring relative proportions of DNA variants from sequencing electropherograms
Inferring relative proportions of DNA variants from sequencing electropherograms
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DOI：
10.1093/bioinformatics/btp583
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发表时间：
2009-12-15
期刊：
影响因子：
5.8
通讯作者：
Bonthron, D. T.
中科院分区：
文献类型：
--
作者：
Carr, I. M.;Robinson, J. I.;Bonthron, D. T.
动机：确定DNA样品中单核苷酸序列变异（SNV）的相对拷贝数是一个常见的实验目标。各种方法可以应用于这个问题，虽然基于杂交的方法往往遭受高设置成本和适应性差，而其他方法（如焦磷酸测序）可能不是所有实验室都可以使用。从标准染料终止剂电泳图中提取相对拷贝数信息的潜力很少被探索，但这种技术便宜且广泛使用。由于几个生物学上重要的基因座有旁系同源的副本，干扰基因分型，也可能显示拷贝数变异（CNV），有许多情况下，其中确定的相对拷贝数的SNVs是可取的。结果：我们已经开发了一个桌面应用程序，QSVanalyzer，它允许高通量定量的DNA序列中含有SNVs的比例。在重建实验中，QSV分析仪准确地估计了已知的SNV的相对比例。通过分析大量的基因组DNA样本，我们证明了该软件不仅能够分析常见的双等位基因SNV，而且能够分析四个基因组旁系同源物之间的基因转换所在的基因座内的SNV，以及另一个受CNV影响的基因座内的SNV。
Motivation: Determination of the relative copy number of single-nucleotide sequence variants (SNVs) within a DNA sample is a frequent experimental goal. Various methods can be applied to this problem, although hybridization-based approaches tend to suffer from high-setup cost and poor adaptability, while others (such as pyrosequencing) may not be accessible to all laboratories. The potential to extract relative copy number information from standard dye-terminator electropherograms has been little explored, yet this technology is cheap and widely accessible. Since several biologically important loci have paralogous copies that interfere with genotyping, and which may also display copy number variation (CNV), there are many situations in which determination of the relative copy number of SNVs is desirable.Results: We have developed a desktop application, QSVanalyzer, which allows high-throughput quantification of the proportions of DNA sequences containing SNVs. In reconstruction experiments, QSVanalyzer accurately estimated the known relative proportions of SNVs. By analyzing a large panel of genomic DNA samples, we demonstrate the ability of the software to analyze not only common biallelic SNVs, but also SNVs within a locus at which gene conversion between four genomic paralogs operates, and within another that is subject to CNV.