Review of Current Methods, Applications, and Data Management for the Bioinformatics Analysis of Whole Exome Sequencing

Abstract

The advent of next-generation sequencing technologies has greatly promoted advances in the study of human diseases at the genomic, transcriptomic, and epigenetic levels. Exome sequencing, where the coding region of the genome is captured and sequenced at a deep level, has proven to be a cost-effective method to detect disease-causing variants and discover gene targets. In this review, we outline the general framework of whole exome sequence data analysis. We focus on established bioinformatics tools and applications that support five analytical steps: raw data quality assessment, pre-processing, alignment, post-processing, and variant analysis (detection, annotation, and prioritization). We evaluate the performance of open-source alignment programs and variant calling tools using simulated and benchmark datasets, and highlight the challenges posed by the lack of concordance among variant detection tools. Based on these results, we recommend adopting multiple tools and resources to reduce false positives and increase the sensitivity of variant calling. In addition, we briefly discuss the current status and solutions for big data management, analysis, and summarization in the field of bioinformatics.

Exploring the landscape of pathogenic genetic variation in the ExAC population database: insights of relevance to variant classification

“…Additionally, these databases are utilized in next-generation sequencing pipelines to exclude common variants that are less likely to be pathogenic. 3,4 If the frequency threshold is set too low or if the data set used to ascertain frequency contains affected individuals, then potentially disease-causing variants may be filtered out in the early stages of the pipeline. Therefore, the utility of large frequency databases to support classification and analysis of variants is rapidly gaining momentum.…”

Clinical exome sequencing in neurologic disease

“…The process, however, becomes much more extensive for exome sequencing because of the larger dataset being evaluated and is complicated by technical issues of quality, data processing, genomic alignment, and variant analysis that can vary among laboratories. 32 Because most laboratories performing exome sequencing utilize different methods for variant assessment, they may potentially interpret identical variants in different ways as a result (e.g., pathogenic, likely pathogenic, or benign vs uncertain significance, discussed further below). These differences in analytic method, when made transparent, can be assessed by the ordering clinician and utilized in the final clinical interpretation.…”

Single Nucleotide Variants in A Family of Monozygotic Twins Discordant for the Phenotype Congenital Megaureter: A Genomic Analysis

“…Array capture was used to isolate relevant human genes [Roche/NimblegenSeqCap EZ Human Exome Library v2.0]. These genes were sequenced on the Illumina HiSeq2000 platform [19].…”