Performance comparison of four exome capture systems for deep sequencing

BackgroundRecent developments in deep (next-generation) sequencing technologies are significantly impacting medical research. The global analysis of protein coding regions in genomes of interest by whole exome sequencing is a widely used application. Many technologies for exome capture are commercially available; here we compare the performance of four of them: NimbleGen’s SeqCap EZ v3.0, Agilent’s SureSelect v4.0, Illumina’s TruSeq Exome, and Illumina’s Nextera Exome, all applied to the same human tumor DNA sample.ResultsEach capture technology was evaluated for its coverage of different exome databases, target coverage efficiency, GC bias, sensitivity in single nucleotide variant detection, sensitivity in small indel detection, and technical reproducibility. In general, all technologies performed well; however, our data demonstrated small, but consistent differences between the four capture technologies. Illumina technologies cover more bases in coding and untranslated regions. Furthermore, whereas most of the technologies provide reduced coverage in regions with low or high GC content, the Nextera technology tends to bias towards target regions with high GC content.ConclusionsWe show key differences in performance between the four technologies. Our data should help researchers who are planning exome sequencing to select appropriate exome capture technology for their particular application.

[1]  T. Fennell,et al.  Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries , 2011, Genome Biology.

[2]  C. Fairhead,et al.  Insertion site preference of Mu, Tn5, and Tn7 transposons , 2012, Mobile DNA.

[3]  Shawn W. Polson,et al.  Evaluation of a Transposase Protocol for Rapid Generation of Shotgun High-Throughput Sequencing Libraries from Nanogram Quantities of DNA , 2011, Applied and Environmental Microbiology.

[4]  S. Mundlos,et al.  Whole exome sequencing identified a novel zinc-finger gene ZNF141 associated with autosomal recessive postaxial polydactyly type A , 2012, Journal of Medical Genetics.

[5]  J. Kitzman,et al.  which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Whole exome capture in solution with 3Gbp of data , 2010 .

[6]  Gautier Koscielny,et al.  Ensembl 2012 , 2011, Nucleic Acids Res..

[7]  Tatiana Tatusova,et al.  NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins , 2004, Nucleic Acids Res..

[8]  R. Friedl,et al.  Whole Exome Sequencing Reveals Uncommon Mutations in the Recently Identified Fanconi Anemia Gene SLX4/FANCP , 2013, Human mutation.

[9]  Jan Freudenberg,et al.  Single nucleotide variation analysis in 65 candidate genes for CNS disorders in a representative sample of the European population. , 2003, Genome research.

[10]  M. Spector,et al.  A comparative analysis of exome capture , 2011, Genome Biology.

[11]  P. Taberlet,et al.  The power and promise of population genomics: from genotyping to genome typing , 2003, Nature Reviews Genetics.

[12]  Hugo Y. K. Lam,et al.  Performance comparison of exome DNA sequencing technologies , 2011, Nature Biotechnology.

[13]  Hui Jiang,et al.  Comprehensive comparison of three commercial human whole-exome capture platforms , 2011, Genome Biology.

[14]  Carsten Schwarz,et al.  Genomewide comparison of DNA sequences between humans and chimpanzees. , 2002, American journal of human genetics.

[15]  G. Weinstock,et al.  Direct selection of human genomic loci by microarray hybridization , 2007, Nature Methods.

[16]  Z. Xuan,et al.  Genome-wide in situ exon capture for selective resequencing , 2007, Nature Genetics.

[17]  J. Maguire,et al.  Solution Hybrid Selection with Ultra-long Oligonucleotides for Massively Parallel Targeted Sequencing , 2009, Nature Biotechnology.

[18]  Heikki Joensuu,et al.  Comparison of solution-based exome capture methods for next generation sequencing , 2011, Genome Biology.

[19]  K. Nakayama,et al.  Exome sequencing identifies a novel TTN mutation in a family with hereditary myopathy with early respiratory failure , 2013, Journal of Human Genetics.

[20]  Eric M. Morrow,et al.  Using Whole-Exome Sequencing to Identify Inherited Causes of Autism , 2013, Neuron.

[21]  Jiasen Lu,et al.  Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays. , 2000, Nucleic acids research.

[22]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[23]  Jonathan M. Mudge,et al.  The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. , 2009, Genome research.