ArticlePloS one2011
Performance of microarray and liquid based capture methods for target enrichment for massively parallel sequencing and SNP discovery.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 32 citations in OpenAlex.
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- Limitations in next-generation sequencing-based genotyping of breast cancer polygenic risk score loci.European journal of human genetics : EJHG · 2024Article
- A rare CHD5 haplotype and its interactions with environmental factors predicting hepatocellular carcinoma risk.BMC cancer · 2018Article
- Efficient genome-wide genotyping strategies and data integration in crop plants.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2018Review
- A highly robust and optimized sequence-based approach for genetic polymorphism discovery and genotyping in large plant populations.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2016Article
- Estimating the Ages of Selection Signals from Different Epochs in Human History.Molecular biology and evolution · 2016Article
- Targeted enrichment of the black cottonwood (Populus trichocarpa) gene space using sequence capture.BMC genomics · 2012Article
- Mitochondrial disease genetic diagnostics: optimized whole-exome analysis for all MitoCarta nuclear genes and the mitochondrial genome.Discovery medicine · 2012Article
- A direct comparison of next generation sequencing enrichment methods using an aortopathy gene panel- clinical diagnostics perspective.BMC medical genomics · 2012Article
- Solution-based targeted genomic enrichment for precious DNA samples.BMC biotechnology · 2012Article
- High-throughput detection of actionable genomic alterations in clinical tumor samples by targeted, massively parallel sequencing.Cancer discovery · 2012Article
- Next-generation sequencing technologies and applications for human genetic history and forensics.Investigative genetics · 2011Article
- Comparison of solution-based exome capture methods for next generation sequencing.Genome biology · 2011Article
- Genome-wide genetic marker discovery and genotyping using next-generation sequencing.Nature reviews. Genetics · 2011Review
- Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA.Scientific reports · 2011Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Targeted sequencing is a cost-efficient way to obtain answers to biological questions in many projects, but the choice of the enrichment method to use can be difficult. In this study we compared two hybridization methods for target enrichment for massively parallel sequencing and single nucleotide polymorphism (SNP) discovery, namely Nimblegen sequence capture arrays and the SureSelect liquid-based hybrid capture system. We prepared sequencing libraries from three HapMap samples using both methods, sequenced the libraries on the Illumina Genome Analyzer, mapped the sequencing reads back to the genome, and called variants in the sequences. 74-75% of the sequence reads originated from the targeted region in the SureSelect libraries and 41-67% in the Nimblegen libraries. We could sequence up to 99.9% and 99.5% of the regions targeted by capture probes from the SureSelect libraries and from the Nimblegen libraries, respectively. The Nimblegen probes covered 0.6 Mb more of the original 3.1 Mb target region than the SureSelect probes. In each sample, we called more SNPs and detected more novel SNPs from the libraries that were prepared using the Nimblegen method. Thus the Nimblegen method gave better results when judged by the number of SNPs called, but this came at the cost of more over-sampling.
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