Multiplexed array-based and in-solution genomic enrichment for flexible and cost-effective targeted next-generation sequencing

M. Harakalova, M. Mokry, B. Hrdlickova, I. Renkens, K.J. Duran, H. van Roekel, N. Lansu, M. van Roosmalen, E. de Bruijn, I.J. Nijman, W.P. Kloosterman, E. Cuppen

Onderzoeksoutput: Bijdrage aan wetenschappelijk tijdschrift/periodieke uitgaveArtikelWetenschappelijkpeer review

Samenvatting

The unprecedented increase in the throughput of DNA sequencing driven by next-generation technologies now allows efficient analysis of the complete protein-coding regions of genomes (exomes) for multiple samples in a single sequencing run. However, sample preparation and targeted enrichment of multiple samples has become a rate-limiting and costly step in high-throughput genetic analysis. Here we present an efficient protocol for parallel library preparation and targeted enrichment of pooled multiplexed bar-coded samples. The procedure is compatible with microarray-based and solution-based capture approaches. The high flexibility of this method allows multiplexing of 3-5 samples for whole-exome experiments, 20 samples for targeted footprints of 5 Mb and 96 samples for targeted footprints of 0.4 Mb. From library preparation to post-enrichment amplification, including hybridization time, the protocol takes 5-6 d for array-based enrichment and 3-4 d for solution-based enrichment. Our method provides a cost-effective approach for a broad range of applications, including targeted resequencing of large sample collections (e.g., follow-up genome-wide association studies), and whole-exome or custom mini-genome sequencing projects. This protocol gives details for a single-tube procedure, but scaling to a manual or automated 96-well plate format is possible and discussed.
Originele taal-2Engels
Pagina's (van-tot)1870-1886
TijdschriftNature Protocols
Volume6
Nummer van het tijdschrift12
DOI's
StatusGepubliceerd - 2011

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