ArticlePloS one2011
Efficient and cost effective population resequencing by pooling and in-solution hybridization.
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 29 papers.
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Who cites it
29 citing papers in PubMed.
- A simplified hybrid capture approach retains high specificity and enables PCR-free workflow.BMC genomics · 2025Article
- Competitive Growth Assay of MutagenizedFrontiers in plant science · 2020Article
- Identification of polymorphisms in the bovine collagenous lectins and their association with infectious diseases in cattle.Immunogenetics · 2018Article
- Effective discovery of rare variants by pooled target capture sequencing: A comparative analysis with individually indexed target capture sequencing.Mutation research · 2018Article
- Spectrum of mutations in monogenic diabetes genes identified from high-throughput DNA sequencing of 6888 individuals.BMC medicine · 2017Article
- Whole-genome resequencing of 100 healthy individuals using DNA pooling.Experimental and therapeutic medicine · 2016Article
- Next Generation Sequencing of Pooled Samples: Guideline for Variants' Filtering.Scientific reports · 2016Article
- Genetic landscape of APOE in human longevity revealed by high-throughput sequencing.Mechanisms of ageing and development · 2016Article
- Quantitative high resolution melting: two methods to determine SNP allele frequencies from pooled samples.BMC genetics · 2015Article
- Fast individual ancestry inference from DNA sequence data leveraging allele frequencies for multiple populations.BMC bioinformatics · 2015Article
- Article
- Evidence for the role of EPHX2 gene variants in anorexia nervosa.Molecular psychiatry · 2014Article
- Allele frequencies of variants in ultra conserved elements identify selective pressure on transcription factor binding.PloS one · 2014Article
- Design of DNA pooling to allow incorporation of covariates in rare variants analysis.PloS one · 2014Article
- A two-dimensional pooling strategy for rare variant detection on next-generation sequencing platforms.PloS one · 2014Article
- Accurate detection of subclonal single nucleotide variants in whole genome amplified and pooled cancer samples using HaloPlex target enrichment.BMC genomics · 2013Article
- Investigating the genetics of Bti resistance using mRNA tag sequencing: application on laboratory strains and natural populations of the dengue vector Aedes aegypti.Evolutionary applications · 2013Article
- Article
- Article
- Population-based rare variant detection via pooled exome or custom hybridization capture with or without individual indexing.BMC genomics · 2012Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
High-throughput sequencing of targeted genomic loci in large populations is an effective approach for evaluating the contribution of rare variants to disease risk. We evaluated the feasibility of using in-solution hybridization-based target capture on pooled DNA samples to enable cost-efficient population sequencing studies. For this, we performed pooled sequencing of 100 HapMap samples across ∼ 600 kb of DNA sequence using the Illumina GAIIx. Using our accurate variant calling method for pooled sequence data, we were able to not only identify single nucleotide variants with a low false discovery rate (<1%) but also accurately detect short insertion/deletion variants. In addition, with sufficient coverage per individual in each pool (30-fold) we detected 97.2% of the total variants and 93.6% of variants below 5% in frequency. Finally, allele frequencies for single nucleotide variants (SNVs) estimated from the pooled data and the HapMap genotype data were tightly correlated (correlation coefficient > = 0.995).
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Registered trials
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