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一个单核酸变体的比较研究要求个人非高加索血统测序样本

HyeonSeul Park¹, JungSoo Gim^2,3,4

¹BK21 FOUR, Department of Integrative Biological Sciences, Chosun University, Gwangju, Republic of Korea.

Genes & genomics

|August 31, 2023

概括

有效的全基因组测序 (WGS) 变异调用对不同种族至关重要. 具有GRCh38引用的Novoalign-GATK4管道,省略了PCR无数据的标记重复步骤,提供最佳性能.

科学领域:

基因组学就是基因组学.
生物信息学是一种生物信息学.
人口遗传学人口遗传学

背景情况:

全基因组测序 (WGS) 的成本正在下降,其临床用途正在增加.
从个人WGS数据进行高效的变量调用是必要的.
目前的管道使用GRCh38和NA12878,其种族代表性有限.

研究的目的:

评估不同族裔个人WGS数据的变量调用管道效率.
为了确定参考基因组和WGS数据之间的种族匹配是否会影响结果.
为了确定特定于种族的最佳变量调用工作流程.

主要方法:

来自韩国受试者的生成WGS数据,DNA阵列和桑格验证的变体.
使用GRCh38和KOREF (韩国参考基因组) 应用8个变异调用管道到WGS数据.
来自不同种族起源的WGS数据与参考基因组对齐.

主要成果:

不管是种族匹配/不匹配,Novoalign-GATK4显示出最有效的性能.
一般来说,GRCh38的整体表现更好,尽管召回有很大的差异.
删除"标记重复"步骤降低了计算成本,而不会影响PCR无WGS数据的性能.

结论:

建议Novoalign+GATK4与GRCh38用于个人无PCRWGS变异调用.
这种工作流是有效的,不管测序的个体的种族.
建议在没有PCR的WGS数据中省略"标记复制"步骤,以减少计算负担.

关键词:

替代基因组参考替代基因组参考在MHC变异调用中,MHC变异调用.标记复制的复制不属于高加索地区的非白人.个人变体调用个人变体调用.变体调用管道的变体

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