ArticleGenome research2009
Overlapping pools for high-throughput targeted resequencing.
Article in Genome research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
40 citing papers in PubMed.
- A vision of how low-coverage sequence data should contribute to genetic evaluation in the future.Journal of animal science · 2025Article
- Use of overlapping DNA pools to discern genetic differences despite pooling error.Journal of animal science · 2023Article
- A joint use of pooling and imputation for genotyping SNPs.BMC bioinformatics · 2022Article
- A novel nonlinear dimension reduction approach to infer population structure for low-coverage sequencing data.BMC bioinformatics · 2021Article
- Efficient high-throughput SARS-CoV-2 testing to detect asymptomatic carriers.Science advances · 2020Article
- s-dePooler: determination of polymorphism carriers from overlapping DNA pools.BMC bioinformatics · 2019Article
- Assessing risk for Mendelian disorders in a Bronx population.Molecular genetics & genomic medicine · 2017Article
- An accurate clone-based haplotyping method by overlapping pool sequencing.Nucleic acids research · 2016Article
- Use of a targeted, combinatorial next-generation sequencing approach for the study of bicuspid aortic valve.BMC medical genomics · 2014Article
- Quantitative group testing-based overlapping pool sequencing to identify rare variant carriers.BMC bioinformatics · 2014Article
- Large-scale mapping of transposable element insertion sites using digital encoding of sample identity.Genetics · 2014Article
- eALPS: estimating abundance levels in pooled sequencing using available genotyping data.Journal of computational biology : a journal of computational molecular cell biology · 2013Article
- Estimating population size via line graph reconstruction.Algorithms for molecular biology : AMB · 2013Article
- Combinatorial pooling enables selective sequencing of the barley gene space.PLoS computational biology · 2013Article
- Rare variant discovery and calling by sequencing pooled samples with overlaps.Bioinformatics (Oxford, England) · 2013Article
- Analysis and optimal design for association studies using next-generation sequencing with case-control pools.Genetic epidemiology · 2012Article
- Construction of a rationally designed antibody platform for sequencing-assisted selection.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Accurate variant detection across non-amplified and whole genome amplified DNA using targeted next generation sequencing.BMC genomics · 2012Article
- Improving mapping and SNP-calling performance in multiplexed targeted next-generation sequencing.BMC genomics · 2012Article
- Weighted pooling--practical and cost-effective techniques for pooled high-throughput sequencing.Bioinformatics (Oxford, England) · 2012Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Resequencing genomic DNA from pools of individuals is an effective strategy to detect new variants in targeted regions and compare them between cases and controls. There are numerous ways to assign individuals to the pools on which they are to be sequenced. The naïve, disjoint pooling scheme (many individuals to one pool) in predominant use today offers insight into allele frequencies, but does not offer the identity of an allele carrier. We present a framework for overlapping pool design, where each individual sample is resequenced in several pools (many individuals to many pools). Upon discovering a variant, the set of pools where this variant is observed reveals the identity of its carrier. We formalize the mathematical framework for such pool designs and list the requirements from such designs. We specifically address three practical concerns for pooled resequencing designs: (1) false-positives due to errors introduced during amplification and sequencing; (2) false-negatives due to undersampling particular alleles aggravated by nonuniform coverage; and consequently, (3) ambiguous identification of individual carriers in the presence of errors. We build on theory of error-correcting codes to design pools that overcome these pitfalls. We show that in practical parameters of resequencing studies, our designs guarantee high probability of unambiguous singleton carrier identification while maintaining the features of naïve pools in terms of sensitivity, specificity, and the ability to estimate allele frequencies. We demonstrate the ability of our designs in extracting rare variations using short read data from the 1000 Genomes Pilot 3 project.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.