Performance comparison of exome DNA sequencing technologies

Abstract

Whole exome sequencing by high-throughput sequencing of target-enriched genomic DNA (exome-seq) has become common in basic and translational research as a means of interrogating the interpretable part of the human genome at relatively low cost. Presented here is a comparison of three major commercial exome sequencing platforms from Agilent, Illumina and Nimblegen applied to the same human blood sample. The Nimblegen platform, which is the only one to use high-density overlapping baits, provides increased efficiency of enrichment and sensitivity for detecting variants but covers fewer genomic regions than the other platforms. As a result, Nimblegen requires the least amount of sequencing to sensitively detect small variants, but Agilent and Illumina are able to detect a greater total number of variants with additional sequencing. Illumina in particular captures the untranslated regions, which are missing from the Nimblegen and Agilent platforms. Exome sequencing and whole genome sequencing (WGS) of the same sample were also compared, demonstrating that exome-seq allows for the detection of additional small variants missed by WGS. These data suggest that WGS experiments benefit from being supplemented with targeted exome-seq data. This study serves to assist the community in selecting the optimal exome-seq platform for their experiments, as well as proving that exome-seq is capable of identifying important coding variations that are missed by a typical WGS experiment.

Next-generation sequencing in the clinic: Promises and challenges

“…Consequently, both sample DNA quantity and cost per assay for target enrichment are substantially reduced. Currently, three major commercial products including Agilent's Sure-Select (array-based and solution-based), Nimblegen's SeqCap (array-based and solution-based) and Illumina's TruSeq (solution-based) in conjunction with NGS platforms have been proven highly effective in exome sequencing [50,51]. Thus far, a number of studies have reported the identification of causal mutations by exome sequencing for many genetic diseases [52,53] and cancers [54][55][56][57][58][59][60][61][62][63] (Table 2).…”

Clinical application of massively parallel sequencing in the molecular diagnosis of glycogen storage diseases of genetically heterogeneous origin

“…In comparison with the most commonly used multiplex PCR enrichment method for MPS sequencing, 31 the custom-designed in-solution capture is better suited for clinical diagnostics because it can be easily scaled up and automated with robotic liquid handling. For a clinical test, all novel variants with possible clinical significance must be verified.…”

Lessons learned from gene identification studies in Mendelian epilepsy disorders

“…Differences in variant callings due to capturing, sequencing technology, and mapping algorithms have been extensively reported. [26][27][28] To handle and analyze the generated data most labs have also developed custom pipelines over the years. If such pipeline is not available, we recommend the user-friendly and web-based tool Galaxy and Broad's Genome Analysis Toolkit (GATK) variant caller to compile, annotate, and analyze data.…”