An_evaluation_of_different_strategies_for_large_scale_pooled_sequencing_study_design_-sc-2011-07-06T13:42:44Z-290
An_evaluation_of_different_strategies_for_large_scale_pooled_sequencing_study_design_
Second generation sequencing technology has enabled the design of large-scale sequencing experiments in targeted disease-related regions in thousands of cases and controls. Cost implications dictate a pooled DNA sequencing design, evaluation of allele frequency differences based on the resequenced samples and large-scale targeted follow-up in further samples. To evaluate the feasibility of this approach and to assess different study design strategies, we have carried out a pilot study which tests the feasibility of PCR-based and pull-down DNA pooling for (a) SNP discovery and (b) allele frequency comparison purposes. All samples are from the HapMap. The sample composition of different pools is listed below: Pool 1: 1 HapMap Individual (NA12249) Pool 2: 2 HapMap Individuals (NA12249, NA12156) Pool 3: 10 HapMap Individuals (NA12249, NA12156, NA12004, NA11831, NA12716, NA11832, NA11993, NA12057, NA11995, NA12006) Pool 4: 20 HapMap Individuals (NA12249, NA12156, NA12004, NA11831, NA12716, NA11832, NA11993, NA12057, NA11995, NA12006, NA12144, NA12802, NA12146, NA12005, NA12003, NA07000, NA12043, NA12044, NA11992, NA11881) Some pools were carried out in duplicate to assess reproducibility. We focused on 10 (PD), 7(PCR) chromosomal regions, ~2(PD), ~1.6 (PCR) Mb in total. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
As the field of complex disease genetics enters the sequencing era, there are still uncertainties about large-scale sequencing study design. This pilot study aims to address questions about sequencing strategy when working with pooled DNA and its objective is to inform the planning of further, large-scale disease-specific experiments. We follow both a PCR-based and sequence capture approach to sequencing pools of different sizes for target regions of interest.