Comprehensive comparison of three commercial human whole-exome capture platforms

Abstract

BackgroundExome sequencing, which allows the global analysis of protein coding sequences in the human genome, has become an effective and affordable approach to detecting causative genetic mutations in diseases. Currently, there are several commercial human exome capture platforms; however, the relative performances of these have not been characterized sufficiently to know which is best for a particular study.ResultsWe comprehensively compared three platforms: NimbleGen's Sequence Capture Array and SeqCap EZ, and Agilent's SureSelect. We assessed their performance in a variety of ways, including number of genes covered and capture efficacy. Differences that may impact on the choice of platform were that Agilent SureSelect covered approximately 1,100 more genes, while NimbleGen provided better flanking sequence capture. Although all three platforms achieved similar capture specificity of targeted regions, the NimbleGen platforms showed better uniformity of coverage and greater genotype sensitivity at 30- to 100-fold sequencing depth. All three platforms showed similar power in exome SNP calling, including medically relevant SNPs. Compared with genotyping and whole-genome sequencing data, the three platforms achieved a similar accuracy of genotype assignment and SNP detection. Importantly, all three platforms showed similar levels of reproducibility, GC bias and reference allele bias.ConclusionsWe demonstrate key differences between the three platforms, particularly advantages of solutions over array capture and the importance of a large gene target set.

Whole exome sequencing for cancer – is there evidence of clinical utility?

“…[13][14][15][16] However, overall coverage rates varied between studies and platforms, ranging from .80% in two studies 15,16 to 59% (for Agilent SureSelect [Agilent Technologies]) in one study. 13 In addition, where available, enrichment efficiency also varied among studies, ranging from 56.4%-89.6% for the Agilent SureSelect (Agilent Technologies) platform. 13,15,16 This variation may be explained by the different depths of coverage used by each study.…”

“…Table 1 presents comparisons between the different exome enrichment platforms, some that are currently being used by commercial laboratories in the US. Two studies were conducted in individuals of Asian descent, 13,14 and two studies were of white individuals. 15,16 For all studies, a high genotype concordance (.98%) was estimated.…”

Gene discovery in familial cancer syndromes by exome sequencing: prospects for the elucidation of familial colorectal cancer type X

“…The development of commercial whole-exome enrichment kits by Agilent, Illumina, and Nimblegen has been largely responsible for making exome sequencing feasible in practical terms for the ordinary laboratory. [1][2][3][4] During the enrichment steps, the genomic regions of interest (ie, all exons) are captured, whereas the unwanted DNA sequences (ie, the non-coding regions) are removed before sequencing, leading to a significant reduction in the proportion of the genome that needs to be sequenced. As a consequence, a greater sequencing depth (ie, a larger number of sequence reads covering a given region) of the targeted regions can be achieved.…”

“…[1][2][3][4] The advent of exome sequencing has already contributed significantly toward the identification of new causal mutations (and genes) for a number of previously unresolved Mendelian disorders such as Kabuki syndrome, Miller syndrome, Sensenbrenner syndrome, and Fowler syndrome to name just a few. Further, exome sequencing has proven to be an effective tool to interrogate the genetic basis of Mendelian disorders in samples derived from both families and unrelated individuals.…”

The Role of New Sequencing Technology in Identifying Rare Mutations in New Susceptibility Genes for Cancer

“…The so-called next-generation sequencing technologies have become affordable to a large number of laboratories with increasingly diverse applications. Although cost still limits inspiration and aspiration in some settings, commercial competition has rapidly made significant advances such as whole human exome sequencing, via high-throughput exome-enrichment kits [1,2], affordable for studies of considerable scope [3,4 • , 5 • , 6, 7 •• ]. Constant increases in the amounts of sequencing data that can be generated from single instrument runs now place whole genome sequencing close to parity with whole exome sequencing from several perspectives [8].…”