基于测序的基因分型方法

在某些应用中,使用NGS研究基因变异的成本比芯片低

基于测序的基因分型

动植物测序

无论用于从头测序、转录组分析、基于测序的基因分型还是宏基因组学,NGS技术都可促进动植物农业研究的发展。了解动植物测序的更多信息

NGS技术可促进农业研究发展

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。

  • 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。
基于测序的基因分型的优势

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

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。

基于测序的基因分型方法
Genotyping by Sequencing in Agriculture

AgResearch uses genotyping by sequencing to overcome cost and resource hurdles associated with genomic selection of minor livestock species, such as the Meredith Dairy goat herd.

Read Interview
Genotyping by Sequencing in Agriculture

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.

Click on the below to view products for each workflow step.

DesignStudio Software

An easy-to-use online software tool that provides dynamic feedback to optimize probe designs.

AmpliSeq for Illumina Custom Panels

Create custom targeted sequencing panels optimized for content of interest.

Nextera XT DNA Library Prep Kit

Library preparation for small genomes (bacteria, archaea, viruses), amplicons, and plasmids in less than 90 minutes.

Library Prep Kit Selector

Determine the best kit for your needs based on project type, starting material, and method or application.

MiSeq Series

Speed and simplicity for targeted and small genome sequencing.

NextSeq Series

Flexible power for whole-genome, transcriptome, and targeted resequencing.

HiSeq Series
Power and efficiency for large-scale genomics.
NovaSeq 6000 System

Scalable throughput and flexibility for virtually any genome, sequencing method, and scale of project.

Platform Comparison Tool

Compare sequencing platforms and identify the best system for your lab and applications.

Sequencing Reagents

Find kits that include sequencing reagents, flow cells, and/or buffers tailored to each Illumina sequencing system.

Local Run Manager

An on-premises software solution for creating sequencing runs, monitoring run status, and analyzing data.

BaseSpace BWA Aligner App

Aligns samples (consisting of FASTQ files) to a reference genome.

BaseSpace Whole-Genome Sequencing App

Quickly extracts biological information from whole-genome sequences, using Isaac alignment and variant calling.

BaseSpace Sequence Hub

The Illumina genomics computing environment for NGS data analysis and management.

BaseSpace Correlation Engine

A growing library of curated genomic data to support researchers in identifying disease mechanisms, drug targets, and biomarkers.

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。

了解详情
构建单体型图谱
Plant and Animal Sequencing
Plant and Animal Sequencing

NGS technology can benefit agricultural studies of plants and animals, whether it is used for de novo sequencing, transcriptome analysis, genotyping by sequencing, or metagenomics. Learn more about plant and animal sequencing.

Commercial Agriculture
Commercial Agriculture and Genomics

The application of genomics in commercial agriculture is helping breeders and researchers perform trait screening, parentage testing, and more. Learn more about commercial agriculture and genomics.

Interested in receiving newsletters, case studies, and information on genomic analysis techniques? Enter your email address.
Genotyping by Sequencing in Agrigenomics
Genotyping by Sequencing in Agrigenomics

This application spotlight describes the advantages and considerations of several sequence-based genotyping research methods.

Access PDF
Revitalizing Fish Populations With NGS
Revitalizing Fish Populations With NGS

Scientists developed Genotyping-in-Thousands by Sequencing (GT-Seq) to genotype thousands of fish simultaneously.

Access PDF
Amplicon Sequencing
Amplicon Sequencing

Amplicon sequencing is a highly targeted approach that researchers can use to genotype large genomes.

Learn More
References
  1. Mamanova L, Coffey AJ, Scott CE, et al. Target-enrichment strategies for next-generation sequencing. Nat Methods. 2010;7:111-118.
  2. Liu S, Yeh CT, Tang HM, Nettleton D, Schnable PS. Gene mapping via bulked segregant RNA-Seq (BSR-Seq). PLoS One. 2012;7:e36406.
  3. Cronn R, Knaus BJ, Liston A, et al. Targeted enrichment strategies for next generation plant biology. Am J Bot. 2012;99:291-311.
  4. 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