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Methods for follow-up research of exome analysis:外显子后续分析研究思路总结

时间:2017-12-20 15:00:21      阅读:227      评论:0      收藏:0      [点我收藏+]

标签:lis   频率   预测   express   var   lin   can   cti   mod   

外显子后续分析研究思路一般有以下几种(Methods for follow-up research of exome analysis):

1、对突变频率、突变类型、突变方式进行统计分析

Mutations statistical analysis

具体见下图:

技术分享图片

参考文献:Di, Jiabo, et al. "Whole exome sequencing reveals intertumor heterogeneity and distinct genetic origins of sporadic synchronous colorectal cancer." International journal of cancer(2017).

2、对变异的保守性进行评估

Conservation score calculation

技术分享图片

一般用Genomic Evolutionary Rate Profiling这个网站进行保守性得分评估(网址:https://personal.broadinstitute.org/mgarber/GERP/documentation.pdf)

参考文献:Wang, Binbin, et al. "Sequence variants of KHDRBS1 as high penetrance susceptibility risks for primary ovarian insufficiency by mis-regulating mRNA alternative splicing." Human Reproduction 32.10 (2017): 2138-2146.

3、目标基因在不同组织上表达度比较

Gene expression in different tissue

技术分享图片

 The Human Protein Atlas database 数据库提供了基因在不同组织表达度比较的信息(网站地址:http://www.proteinatlas.org/)

参考文献:Wang, Binbin, et al. "Sequence variants of KHDRBS1 as high penetrance susceptibility risks for primary ovarian insufficiency by mis-regulating mRNA alternative splicing." Human Reproduction 32.10 (2017): 2138-2146.

4、碱基覆盖深度比较

默认理想情况下,碱基覆盖度的深浅代表插入或缺失

Coverage depth calculation

技术分享图片

 

 gatk提供了碱基覆盖度的计算,参数如下:

技术分享图片

gatk碱基覆盖度计算网址:

https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_coverage_DepthOfCoverage.php

参考文献:Fedida, Joel, et al. "Contribution of exome sequencing for genetic diagnostic in arrhythmogenic right ventricular cardiomyopathy/dysplasia." PloS one 12.8 (2017): e0181840.

5、结构和功能分析

Structural and functional analysis in mutation

技术分享图片

swissmodel网站提供了变异氨基酸导致结构变化的可视化界面(网站地址:https://swissmodel.expasy.org/)

使用方法详见:蛋白质结构模型和功能预测:Swiss-model工具的使用

参考文献:Bölükba??, Esra Y?ld?z, et al. "Homozygous mutation in CEP19, a gene mutated in morbid obesity, in Bardet-Biedl syndrome with predominant postaxial polydactyly." Journal of medical genetics (2017): jmedgenet-2017.

 

Methods for follow-up research of exome analysis:外显子后续分析研究思路总结

标签:lis   频率   预测   express   var   lin   can   cti   mod   

原文地址:http://www.cnblogs.com/chenwenyan/p/8073436.html

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