Massively parallel sequencing of forensic STRs: Considerations of the DNA commission of the International Society for Forensic Genetics (ISFG) on minimal nomenclature requirements
Massively parallel sequencing of forensic STRs: Considerations of the DNA commission of the International Society for Forensic Genetics (ISFG) on minimal nomenclature requirements
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DOI：
10.1016/j.fsigen.2016.01.009
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发表时间：
2016-05-01
影响因子：
3.1
通讯作者：
Phillips, Christopher
中科院分区：
文献类型：
--
作者：
Parson, Walther;Ballard, David;Phillips, Christopher
国际法医遗传学学会（ISFG）的DNA委员会正在审查法医界采用大规模平行测序（MPS）技术进行短串联重复序列（STR）基因分型之前需要考虑的因素。MPS产生的序列数据提供了STR标记的重复等位基因结构和可能存在于重复区侧翼区域的变体的精确描述。当STR包含重复基序的复杂排列时，序列数据揭示的遗传多态性水平可以显著增加。由于重复结构可能是复杂的，并且包括多个核苷酸基序的取代、插入、缺失、可变串联重复排列和侧翼区域SNP，因此建立的毛细管电泳（CE）等位基因描述必须由STR等位基因命名的新系统补充，它保留了与CE数据的向后兼容性，CE数据目前填充了国家DNA数据库，并将继续为未来产生。年因此，迫切需要产生用于描述复杂序列的标准化框架，其能够与目前使用的源自常规CE系统的重复等位基因命名法进行比较。重要的是要按层次顺序辨别三个层次的信息：（i）序列，（ii）比对，和（iii）STR序列数据的命名。我们提出了一个序列（文本）字符串格式的数据存储的最低要求，实验室应遵循时，采用MPS的STR。我们进一步讨论了保持现有和未来数据之间的兼容性所需的变异注释和序列比较框架。该系统必须易于使用和解释的DNA专家，基于一个普遍可访问的基因组组装，并在一般法医界开始大规模生成序列数据的MPS摄取之前到位。虽然基于CE的STR分析的既定命名法在未来将保持不变，但基于序列的STR基因型的命名法将需要遵循更新的规则，并由翻译MPS序列以匹配CE惯例的专家系统生成，以保证不同代STR数据之间的兼容性。(C)2016爱思唯尔爱尔兰有限公司版权所有。
The DNA Commission of the International Society for Forensic Genetics (ISFG) is reviewing factors that need to be considered ahead of the adoption by the forensic community of short tandem repeat (STR) genotyping by massively parallel sequencing (MPS) technologies. MPS produces sequence data that provide a precise description of the repeat allele structure of a STR marker and variants that may reside in the flanking areas of the repeat region. When a STR contains a complex arrangement of repeat motifs, the level of genetic polymorphism revealed by the sequence data can increase substantially. As repeat structures can be complex and include substitutions, insertions, deletions, variable tandem repeat arrangements of multiple nucleotide motifs, and flanking region SNPs, established capillary electrophoresis (CE) allele descriptions must be supplemented by a new system of STR allele nomenclature, which retains backward compatibility with the CE data that currently populate national DNA databases and that will continue to be produced for the coming years. Thus, there is a pressing need to produce a standardized framework for describing complex sequences that enable comparison with currently used repeat allele nomenclature derived from conventional CE systems. It is important to discern three levels of information in hierarchical order (i) the sequence, (ii) the alignment, and (iii) the nomenclature of STR sequence data. We propose a sequence (text) string format the minimal requirement of data storage that laboratories should follow when adopting MPS of STRs. We further discuss the variant annotation and sequence comparison framework necessary to maintain compatibility among established and future data. This system must be easy to use and interpret by the DNA specialist, based on a universally accessible genome assembly, and in place before the uptake of MPS by the general forensic community starts to generate sequence data on a large scale. While the established nomenclature for CE-based STR analysis will remain unchanged in the future, the nomenclature of sequence-based STR genotypes will need to follow updated rules and be generated by expert systems that translate MPS sequences to match CE conventions in order to guarantee compatibility between the different generations of STR data. (C) 2016 Elsevier Ireland Ltd. All rights reserved.