Validation of bcbio-nextgen Pipeline Based on NextSeq500 Exome Sequencing

Abstract

We evaluated the performance of bcbio-nextgen pipeline for clinical whole exome sequencing (WES) using Genome in a Bottle (GIAB) NA12878 reference sample with Agilent Clinical Research Exome (CRE) v2 panel and Agilent SureSelect XT2 library preparation kit. The current literature on NA12878 reference materials predominantly describes the performance of WES-based pipelines for Illumina HiSeqX. Here, we evaluated the analytical performance of the bcbio-nextgen pipeline for WES for Illumina NextSeq500. We compared the performance of the bcbio-nextgen pipeline with the performance of other WES-based pipelines reported in literature. Our comparative analyses showed that the sensitivity and precision of our study compared favourably with the performance of other bioinformatics pipelines. Notably, our results demonstrate that analytical sensitivity of WES deteriorates outside of capture regions and suggests that any variants identified outside of capture regions are more likely to be lower confidence variants and therefore require confirmatory testing. Careful consideration of intersect between genomic regions of interest (ROI) and capture regions is required to achieve optimal performance of WES for clinical applications.