基于测序的基因分型简介
过去，基于芯片的单核苷酸多态性(SNP)筛查方法是分析许多植物和动物的性状并将其与基因组区域建立关联的首选方法。由于测序成本持续下降，研究人员正在开发利用新一代测序(NGS)技术进行基因分型的新方法。
基于测序的基因分型或新一代基因分型是一种用于发现新的动植物SNP位点并进行基因分型研究的基因筛查方法。对于某些应用（例如基因型筛查及基因定位），基于测序的基因分型为基因变异研究提供了一种比芯片成本更低的替代方法。
基于测序的基因分型的优势
- 可对众多样本的预定基因变异区域测序
- 为某些应用提供较低的单位样本成本
- 与芯片相比，可减少预设位点的偏好性
- 可检测除SNP以外的变异，包括微小插入、缺失以及微卫星变异
- 在参考基因组缺失的情况下，支持样本对比分析
- 支持基因定位、筛查回交线、纯化测试、构建单体型图、关联定位以及用于植物研究的基因组选择。
基于大型基因组(> 5 Mb)测序的基因分型
基于测序的基因分型是一种经济高效的方法，适用于具有复杂基因组或资源有限的群体。使用的技术包括基于扩增子的靶向测序、以杂交为基础的富集测序以及基于序列的限制性酶简化基因分型。
如果要使用此方法获得最佳结果，Illumina建议您具备以下条件：
- 参考基因组
- 多样性丰富的样本
- 多样本之间的微调覆盖
- 变异检出格式(VCF)文件转换器
- 支持杂合子检测和冗余校验中的模糊容忍度，以最大限度减少误报
基于测序的基因分型方法
目前已开发出多种基于测序的基因分型方法。1–4富集方法对植物很有效，因为植物通常包括重复的基因组区域。限制性酶方法适合研究没有基因组先验知识的物种。
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Comprehensive Genotyping by Sequencing Workflow
Illumina sequencing by synthesis (SBS) chemistry is the most widely adopted NGS technology, generating approximately 90% of global sequencing data.*
Illumina offers integrated sequencing workflows that simplify the entire process, from library preparation to data analysis and biological interpretation.
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DesignStudio Software
An easy-to-use online software tool that provides dynamic feedback to optimize probe designs.
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Local Run Manager
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BaseSpace BWA Aligner AppAligns samples (consisting of FASTQ files) to a reference genome.
BaseSpace Whole-Genome Sequencing AppQuickly extracts biological information from whole-genome sequences, using Isaac alignment and variant calling.
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BaseSpace Correlation EngineA growing library of curated genomic data to support researchers in identifying disease mechanisms, drug targets, and biomarkers.
基于小型基因组(≤ 5 Mb)测序的基因分型
对于小型基因组（例如果蝇）或广受关注的研究物种（例如拟南芥），可以使用参考相关的标准全基因组测序或重测序方法完成基因分型和变异筛查。浅度测序可用于进化分析或对比分析。
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References
- Mamanova L, Coffey AJ, Scott CE, et al. Target-enrichment strategies for next-generation sequencing. Nat Methods. 2010;7:111-118.
- Liu S, Yeh CT, Tang HM, Nettleton D, Schnable PS. Gene mapping via bulked segregant RNA-Seq (BSR-Seq). PLoS One. 2012;7:e36406.
- Cronn R, Knaus BJ, Liston A, et al. Targeted enrichment strategies for next generation plant biology. Am J Bot. 2012;99:291-311.
- Andolfatto P, Davison D, Erezyilmaz D, et al. Multiplexed shotgun genotyping for rapid and efficient genetic mapping. Genome Res. 2011;21:610-617.
*Data calculations on file. Illumina, Inc., 2015