ArticleNucleic acids research2010
Identification of rare alleles and their carriers using compressed se(que)nsing.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 16 papers.
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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
16 citing papers in PubMed.
- Genome wide association studies in yam reveal the challenge of high heterozygosity.Scientific reports · 2025Article
- Combining whole genome sequencing and non-adaptive group testing for large-scale ethnicity screens.BMC bioinformatics · 2025Article
- Best Practices in Designing, Sequencing, and Identifying Random DNA Barcodes.Journal of molecular evolution · 2023Review
- Use of compressed sensing to expedite high-throughput diagnostic testing for COVID-19 and beyond.PLoS computational biology · 2022Article
- Efficient high-throughput SARS-CoV-2 testing to detect asymptomatic carriers.Science advances · 2020Article
- An accurate clone-based haplotyping method by overlapping pool sequencing.Nucleic acids research · 2016Article
- iPipet: sample handling using a tablet.Nature methods · 2014Article
- Quantitative group testing-based overlapping pool sequencing to identify rare variant carriers.BMC bioinformatics · 2014Article
- Combinatorial pooling enables selective sequencing of the barley gene space.PLoS computational biology · 2013Article
- Analysis and optimal design for association studies using next-generation sequencing with case-control pools.Genetic epidemiology · 2012Article
- Weighted pooling--practical and cost-effective techniques for pooled high-throughput sequencing.Bioinformatics (Oxford, England) · 2012Article
- Sequencing of high-complexity DNA pools for identification of nucleotide and structural variants in regions associated with complex traits.European journal of human genetics : EJHG · 2012Article
- A novel approach for the simultaneous analysis of common and rare variants in complex traits.Bioinformatics and biology insights · 2012Article
- Statistical mutation calling from sequenced overlapping DNA pools in TILLING experiments.BMC bioinformatics · 2011Article
- Genotyping common and rare variation using overlapping pool sequencing.BMC bioinformatics · 2011Article
- Compressed Genotyping.IEEE transactions on information theory · 2010Article
Corrections and comments
- Erratum issued
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Identification of rare variants by resequencing is important both for detecting novel variations and for screening individuals for known disease alleles. New technologies enable low-cost resequencing of target regions, although it is still prohibitive to test more than a few individuals. We propose a novel pooling design that enables the recovery of novel or known rare alleles and their carriers in groups of individuals. The method is based on a Compressed Sensing (CS) approach, which is general, simple and efficient. CS allows the use of generic algorithmic tools for simultaneous identification of multiple variants and their carriers. We model the experimental procedure and show via computer simulations that it enables the recovery of rare alleles and their carriers in larger groups than were possible before. Our approach can also be combined with barcoding techniques to provide a feasible solution based on current resequencing costs. For example, when targeting a small enough genomic region (∼100 bp) and using only ∼10 sequencing lanes and ∼10 distinct barcodes per lane, one recovers the identity of 4 rare allele carriers out of a population of over 4000 individuals. We demonstrate the performance of our approach over several publicly available experimental data sets.
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