Whole genome sequencing and its applications in medical genetics

doi:10.1007/s40484-016-0067-0

Quant. Biol.

2016, Vol. 4

Issue (2) : 115-128 https://doi.org/10.1007/s40484-016-0067-0

REVIEW

Whole genome sequencing and its applications in medical genetics

Jiaxin Wu, Mengmeng Wu, Ting Chen, Rui Jiang(

)

MOE Key Laboratory of Bioinformatics, Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST; Department of Automation, Tsinghua University, Beijing 100084, China

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Abstract

Fundamental improvement was made for genome sequencing since the next-generation sequencing (NGS) came out in the 2000s. The newer technologies make use of the power of massively-parallel short-read DNA sequencing, genome alignment and assembly methods to digitally and rapidly search the genomes on a revolutionary scale, which enable large-scale whole genome sequencing (WGS) accessible and practical for researchers. Nowadays, whole genome sequencing is more and more prevalent in detecting the genetics of diseases, studying causative relations with cancers, making genome-level comparative analysis, reconstruction of human population history, and giving clinical implications and instructions. In this review, we first give a typical pipeline of whole genome sequencing, including the lab template preparation, sequencing, genome assembling and quality control, variants calling and annotations. We compare the difference between whole genome and whole exome sequencing (WES), and explore a wide range of applications of whole genome sequencing for both mendelian diseases and complex diseases in medical genetics. We highlight the impact of whole genome sequencing in cancer studies, regulatory variant analysis, predictive medicine and precision medicine, as well as discuss the challenges of the whole genome sequencing.

Author Summary

Whole genome sequencing is prevalent in detecting the genetics of diseases, studying causative relations with cancers, making genome-level comparative analysis, and giving clinical implications and instructions. In this review, we give a typical pipeline of whole genome sequencing, compare the difference between whole genome and whole exome sequencing, and explore a wide range of applications of whole genome sequencing in medical genetics. We highlight the impact of whole genome sequencing in cancer studies, regulatory variant analysis, predictive medicine and precision medicine, and discuss the challenges of the whole genome sequencing.

Keywords whole genome sequencing whole exome sequencing next-generation sequencing non-coding regulatory variant

Corresponding Author(s): Rui Jiang

About author:

Tongcan Cui and Yizhe Hou contributed equally to this work.

Just Accepted Date: 21 March 2016 Online First Date: 11 May 2016 Issue Date: 26 May 2016

Cite this article:

Jiaxin Wu,Mengmeng Wu,Ting Chen, et al. Whole genome sequencing and its applications in medical genetics[J]. Quant. Biol., 2016, 4(2): 115-128.

URL:

https://academic.hep.com.cn/qb/EN/10.1007/s40484-016-0067-0
https://academic.hep.com.cn/qb/EN/Y2016/V4/I2/115

Fig.1 A typical pipeline of whole genome sequencing.

Tab.1 Comparison of whole genome sequencing platforms.

Tab.2 Alignment and genome assembling tools.

Tab.3 Quality assessment tools before the assembling.

Tab.4 Quality assessment tools for genome assemblers.

Tab.5 Variants calling tools for detect SNVs, CNVs or SVs.

Tab.6 Comparison between whole genome and whole exome sequencing.

Tab.7 Various types of QTLs.

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