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

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：

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

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

 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

Coverage depth calculation

默认理想情况下，碱基覆盖度的深浅代表插入或缺失

 

 gatk提供了碱基覆盖度的计算，参数如下：

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

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：Bölükbaşı, Esra Yıldız, 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.

 

转载于:https://www.cnblogs.com/chenwenyan/p/8073436.html