ArticleBioinformatics (Oxford, England)2008
Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies.
Article in Bioinformatics (Oxford, England), 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 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
8 citing papers in PubMed.
- Visual analysis of the quantitative composition of metagenomic communities: the AmphoraVizu webserver.Microbial ecology · 2015Article
- Combinatorial pooling enables selective sequencing of the barley gene space.PLoS computational biology · 2013Article
- Improving mapping and SNP-calling performance in multiplexed targeted next-generation sequencing.BMC genomics · 2012Article
- Empirical validation of pooled whole genome population re-sequencing in Drosophila melanogaster.PloS one · 2012Article
- LDx: estimation of linkage disequilibrium from high-throughput pooled resequencing data.PloS one · 2012Article
- A computer simulator for assessing different challenges and strategies of de novo sequence assembly.Genes · 2010Article
- A statistical method for the detection of variants from next-generation resequencing of DNA pools.Bioinformatics (Oxford, England) · 2010Article
- Overlapping pools for high-throughput targeted resequencing.Genome research · 2009Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
New generation sequencing technologies offer unique opportunities and challenges for re-sequencing studies. In this article, we focus on re-sequencing experiments using the Solexa technology, based on bacterial artificial chromosome (BAC) clones, and address an experimental design problem. In these specific experiments, approximate coordinates of the BACs on a reference genome are known, and fine-scale differences between the BAC sequences and the reference are of interest. The high-throughput characteristics of the sequencing technology makes it possible to multiplex BAC sequencing experiments by pooling BACs for a cost-effective operation. However, the way BACs are pooled in such re-sequencing experiments has an effect on the downstream analysis of the generated data, mostly due to subsequences common to multiple BACs. The experimental design strategy we develop in this article offers combinatorial solutions based on approximation algorithms for the well-known max n-cut problem and the related max n-section problem on hypergraphs. Our algorithms, when applied to a number of sample cases give more than a 2-fold performance improvement over random partitioning.
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Registered trials
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