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Updated: May 25, 2026
09:34
Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
Published on: April 4, 2018
An integrative variant analysis suite for whole exome next-generation sequencing data
Danny Challis1, Jin Yu, Uday S Evani
1The Human Genome Sequencing Center, Baylor College of Medicine, Houston, USA.
BMC Bioinformatics
|January 14, 2012
Summary
The Atlas2 Suite offers a new tool for analyzing whole exome sequencing data, improving variant calling accuracy and accessibility for researchers. This pipeline enhances the discovery of genetic variations from next-generation sequencing data.
Area of Science:
- Genomics
- Bioinformatics
Background:
- Whole exome capture sequencing is a routine method for analyzing coding regions of the genome.
- Existing tools lack specialization for variant calling in whole exome sequencing data.
Purpose of the Study:
- To develop and implement an integrative variant analysis pipeline optimized for whole exome sequencing data.
- To provide a user-friendly tool for variant discovery and analysis across multiple next-generation sequencing platforms.
Main Methods:
- Utilized statistical models trained on validated whole-exome capture sequencing data.
- Developed the Atlas2 Suite, an integrative variant analysis pipeline.
- Employed logistic regression models with user-adjustable cutoffs for variant calling.
Main Results:
- The Atlas2 Suite achieves high sensitivity (96.7%) in separating true SNPs and INDELs from sequencing errors.
- The pipeline is optimized for SOLiD, Illumina, and Roche 454 sequencing platforms.
- Applied the Atlas2 Suite to 92 whole exome samples from the 1000 Genomes Project.
Conclusions:
- The Atlas2 Suite is available for download and has been integrated into the Genboree Workbench.
- Provides a web interface for variant calling, viewing, and analysis, accessible to scientists with minimal informatics expertise.
- Streamlines the process from variant discovery to functional genomics analysis for the broader scientific community.
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