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.
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