Jakupciak John P
Cipher Systems, 2661 Riva Road, Annapolis, MD 21401, USA.
J Biomark. 2013;2013:861823. doi: 10.1155/2013/861823. Epub 2013 Dec 8.
Sequencing is accepted as the "gold" standard for genetic analysis and continues to be used as a validation and reference tool. The idea of using sequence analysis directly for sample characterization has been met with skepticism. However, herein, utility of direct use of sequencing to identify multiple genomes present in samples is presented and reviewed. All samples and "pure" isolates are populations of genomes. Population-Sequencing is the use of probabilistic matching tools in combination with large volumes of sequence information to identify genomes present, based on DNA analysis across entire genomes to determine genome assignments, to calculate confidence scores of major and minor genome content. Accurate genome identification from mixtures without culture purification steps can achieve phylogenetic classification by direct analysis of millions of DNA fragments. Genome sequencing data of mixtures can function as biomarkers for use to interrogate genetic content of samples and to establish a sample profile, inclusive of major and minor genome components, drill down to identify rare SNP and mutation events, compare relatedness of genetic content between samples, profile-to-profile, and provide a probabilistic or statistical scoring confidence for sample characterization and attribution. The application of Population-Sequencing will facilitate sample characterization and genome identification strategies.
测序被公认为基因分析的“金”标准，并继续用作验证和参考工具。直接使用序列分析进行样本表征的想法一直受到质疑。然而，本文介绍并探讨了直接使用测序来识别样本中存在的多个基因组的实用性。所有样本和“纯”分离株都是基因组群体。群体测序是将概率匹配工具与大量序列信息相结合，基于对整个基因组的DNA分析来确定基因组归属，计算主要和次要基因组含量的置信度得分，从而识别存在的基因组。无需培养纯化步骤即可从混合物中准确识别基因组，通过直接分析数百万个DNA片段实现系统发育分类。混合物的基因组测序数据可作为生物标志物，用于探究样本的遗传内容并建立样本概况，包括主要和次要基因组成分，深入识别罕见的单核苷酸多态性（SNP）和突变事件，比较样本之间遗传内容的相关性、样本概况之间的相关性，并为样本表征和归属提供概率或统计评分置信度。群体测序的应用将促进样本表征和基因组识别策略。
