Application of variant-calling algorithms for Mendelian disorders: lessons from whole-exome sequencing in Charcot-Marie-Tooth disease

2013 ◽  
Vol 86 (3) ◽  
pp. 298-299
Author(s):  
Y.B. Hong ◽  
J. Jung ◽  
S.-C. Jung ◽  
K.W. Chung ◽  
B.-O. Choi
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Variant Calling ◽  
Charcot Marie Tooth ◽  
Charcot Marie Tooth Disease ◽  
Mendelian Disorders ◽  
Whole Exome ◽  
Tooth Disease

Whole exome sequencing identifies three recessive FIG4-mutations in an apparently dominant pedigree with Charcot-Marie-Tooth disease

2015 ◽  
Vol 25 (4) ◽  
pp. 359-360 ◽  
Author(s):  
Wladimir Bocca Vieira de Rezende Pinto ◽  
Acary Souza Bulle Oliveira ◽  
Paulo Victor Sgobbi de Souza
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Charcot Marie Tooth ◽  
Charcot Marie Tooth Disease ◽  
Whole Exome ◽  
Tooth Disease

Whole exome sequencing reveals a broader variant spectrum of Charcot-Marie-Tooth disease type 2

Neurogenetics ◽  
2019 ◽  
Vol 21 (2) ◽  
pp. 79-86
Author(s):  
Shan Lin ◽  
Liu-Qing Xu ◽  
Guo-Rong Xu ◽  
Ling-Ling Guo ◽  
Bi-Juan Lin ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Disease Type ◽  
Charcot Marie Tooth ◽  
Charcot Marie Tooth Disease ◽  
Whole Exome ◽  
Tooth Disease

scholarly journals Whole exome sequencing identifies three recessive FIG4 mutations in an apparently dominant pedigree with Charcot–Marie–Tooth disease

2014 ◽  
Vol 24 (8) ◽  
pp. 666-670 ◽  
Author(s):  
Manoj P. Menezes ◽  
Leigh Waddell ◽  
Guy M. Lenk ◽  
Simranpreet Kaur ◽  
Daniel G. MacArthur ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Charcot Marie Tooth ◽  
Charcot Marie Tooth Disease ◽  
Whole Exome ◽  
Tooth Disease

scholarly journals Multiple Variant Calling Pipelines in Wheat Whole Exome Sequencing

2021 ◽  
Vol 22 (19) ◽  
pp. 10400
Author(s):  
H. Busra Cagirici ◽  
Bala Ani Akpinar ◽  
Taner Z. Sen ◽  
Hikmet Budak
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Variant Calling ◽  
High Sensitivity ◽  
Whole Exome ◽  
The Impact ◽  
Multiple Reference ◽  
Reference Genomes ◽  
Selection Of ◽  
Variant Identification

The highly challenging hexaploid wheat (Triticum aestivum) genome is becoming ever more accessible due to the continued development of multiple reference genomes, a factor which aids in the plight to better understand variation in important traits. Although the process of variant calling is relatively straightforward, selection of the best combination of the computational tools for read alignment and variant calling stages of the analysis and efficient filtering of the false variant calls are not always easy tasks. Previous studies have analyzed the impact of methods on the quality metrics in diploid organisms. Given that variant identification in wheat largely relies on accurate mining of exome data, there is a critical need to better understand how different methods affect the analysis of whole exome sequencing (WES) data in polyploid species. This study aims to address this by performing whole exome sequencing of 48 wheat cultivars and assessing the performance of various variant calling pipelines at their suggested settings. The results show that all the pipelines require filtering to eliminate false-positive calls. The high consensus among the reference SNPs called by the best-performing pipelines suggests that filtering provides accurate and reproducible results. This study also provides detailed comparisons for high sensitivity and precision at individual and population levels for the raw and filtered SNP calls.

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