scholarly journals Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing

2021 ◽  
Vol 39 (9) ◽  
pp. 1141-1150 ◽  
Author(s):  
Wenming Xiao ◽  
Luyao Ren ◽  
Zhong Chen ◽  
Li Tai Fang ◽  
Yongmei Zhao ◽  
...  
2019 ◽  
Author(s):  

AbstractClinical applications of precision oncology require accurate tests that can distinguish tumor-specific mutations from errors introduced at each step of next generation sequencing (NGS). For NGS to successfully improve patient lives, discriminating between true mutations and artifacts is crucial.We systematically interrogated somatic mutations in paired tumor-normal cell lines to identify factors affecting detection reproducibility and accuracy. Different types of samples with varying input amount and tumor purity were processed using multiple library construction protocols. Whole-genome and whole-exome sequencing were carried out at six sequencing centers followed by processing with nine bioinformatics pipelines to evaluate their reproducibility. We identified artifacts due to sample and library processing and evaluated the capabilities and limitations of bioinformatics tools for artifact detection and removal.By examining the interaction and effect of various wet lab and computational parameters concomitantly, here we recommend actionable best practices for mutation detection in clinical applications using NGS technologies.


2015 ◽  
Vol 97 ◽  
Author(s):  
EYAL REINSTEIN

SummaryWhole-genome and whole-exome sequencing for clinical applications is now an integral part of medical genetics practice. The term newborn screening refers to public health programs designed to screen newborns for various treatable metabolic conditions, by measuring levels of circulating blood metabolites. The availability and significant decrease in sequencing costs has raised the question of whether metabolic newborn screening should be replaced by whole-genome or whole-exome sequencing. While newborn genome sequencing can potentially increase the number of disorders identified by newborn screening, the generalization of its practice raises a number of important ethical issues. This short article argues that there are medical, psychological, ethical and economic reasons why widespread dissemination of newborn screening is still premature.


2018 ◽  
Vol 20 (11) ◽  
pp. 1328-1333 ◽  
Author(s):  
Ahmed Alfares ◽  
Taghrid Aloraini ◽  
Lamia Al subaie ◽  
Abdulelah Alissa ◽  
Ahmed Al Qudsi ◽  
...  

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