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Performance of microarray and liquid based capture methods for target enrichment for massively parallel sequencing
Anna Kiialainen1, Olof Karlberg, Annika Ahlford
1Department of Medical Sciences, Uppsala University, Uppsala, Sweden. anna.kiialainen@medsci.uu.se
Plos One
|February 25, 2011
Summary
Comparing two target enrichment methods for sequencing, Nimblegen sequence capture arrays and SureSelect hybrid capture, revealed Nimblegen yielded more single nucleotide polymorphism (SNP) discoveries. However, SureSelect offered higher on-target read percentages.
Area of Science:
- Genomics
- Molecular Biology
Background:
- Targeted sequencing is crucial for cost-efficient biological research.
- Selecting the appropriate target enrichment method is challenging.
Purpose of the Study:
- To compare Nimblegen sequence capture arrays and SureSelect liquid-based hybrid capture for target enrichment.
- To evaluate their effectiveness in massively parallel sequencing and single nucleotide polymorphism (SNP) discovery.
Main Methods:
- Prepared sequencing libraries from HapMap samples using both Nimblegen and SureSelect methods.
- Sequenced libraries on Illumina Genome Analyzer and mapped reads to the genome.
- Called variants, including SNPs, from the sequenced data.
Main Results:
- SureSelect libraries had higher on-target read percentages (74-75%) compared to Nimblegen (41-67%).
- Nimblegen probes covered a larger target region (0.6 Mb more).
- Nimblegen method identified more SNPs, including novel ones, per sample.
Conclusions:
- Nimblegen method resulted in more SNP discoveries, indicating superior performance for variant detection.
- SureSelect method demonstrated higher efficiency in read mapping to targeted regions.
- The choice between methods involves a trade-off between SNP yield and read-mapping efficiency.
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