title: Comparison and evaluation of two exome capture kits and sequencing platforms for variant calling.
abstract: BACKGROUND
  To promote the clinical application of next-generation sequencing, it is important to obtain accurate and consistent variants of target genomic regions at low cost. Ion Proton, the latest updated semiconductor-based sequencing instrument from Life Technologies, is designed to provide investigators with an inexpensive platform for human whole exome sequencing that achieves a rapid turnaround time. However, few studies have comprehensively compared and evaluated the accuracy of variant calling between Ion Proton and Illumina sequencing platforms such as HiSeq 2000, which is the most popular sequencing platform for the human genome. The Ion Proton sequencer combined with the Ion TargetSeq Exome Enrichment Kit together make up TargetSeq-Proton, whereas SureSelect-Hiseq is based on the Agilent SureSelect Human All Exon v4 Kit and the HiSeq 2000 sequencer.
  
  
  RESULTS
  Here, we sequenced exonic DNA from four human blood samples using both TargetSeq-Proton and SureSelect-HiSeq. We then called variants in the exonic regions that overlapped between the two exome capture kits (33.6 Mb). The rates of shared variant loci called by two sequencing platforms were from 68.0 to 75.3% in four samples, whereas the concordance of co-detected variant loci reached 99%. Sanger sequencing validation revealed that the validated rate of concordant single nucleotide polymorphisms (SNPs) (91.5%) was higher than the SNPs specific to TargetSeq-Proton (60.0%) or specific to SureSelect-HiSeq (88.3%). With regard to 1-bp small insertions and deletions (InDels), the Sanger sequencing validated rates of concordant variants (100.0%) and SureSelect-HiSeq-specific (89.6%) were higher than those of TargetSeq-Proton-specific (15.8%).
  
  
  CONCLUSIONS
  In the sequencing of exonic regions, a combination of using of two sequencing strategies (SureSelect-HiSeq and TargetSeq-Proton) increased the variant calling specificity for concordant variant loci and the sensitivity for variant loci called by any one platform. However, for the sequencing of platform-specific variants, the accuracy of variant calling by HiSeq 2000 was higher than that of Ion Proton, specifically for the InDel detection. Moreover, the variant calling software also influences the detection of SNPs and, specifically, InDels in Ion Proton exome sequencing.
authors.affiliation: Core Genomic Facility and CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China. zhanggq@big.ac.cn.
authors.forename: Guoqiang
authors.initials: G
authors.lastname: Zhang
authors.affiliation: Core Genomic Facility and CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China. wangjf@big.ac.cn.
authors.forename: Jianfeng
authors.initials: J
authors.lastname: Wang
authors.affiliation: Core Genomic Facility and CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China. yangjin@big.ac.cn.
authors.forename: Jin
authors.initials: J
authors.lastname: Yang
authors.affiliation: Core Genomic Facility and CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China. wjli@big.ac.cn.
authors.forename: Wenjie
authors.initials: W
authors.lastname: Li
authors.affiliation: Core Genomic Facility and CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China. dengyt@big.ac.cn.
authors.forename: Yutian
authors.initials: Y
authors.lastname: Deng
authors.affiliation: Core Genomic Facility and CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China. lijing@big.ac.cn.
authors.forename: Jing
authors.initials: J
authors.lastname: Li
authors.affiliation: Core Genomic Facility and CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China. huangjun@big.ac.cn.
authors.forename: Jun
authors.initials: J
authors.lastname: Huang
authors.affiliation: Core Genomic Facility and CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China. husn@big.ac.cn.
authors.forename: Songnian
authors.initials: S
authors.lastname: Hu
authors.affiliation: Core Genomic Facility and CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China. zhangbing@big.ac.cn.
authors.forename: Bing
authors.initials: B
authors.lastname: Zhang
mesh_terms: D059472:Exome; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing / Q000191:economics / Q000295:instrumentation* / Q000379:methods; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000191:economics / Q000295:instrumentation* / Q000379:methods