ArticleNucleic acids research2005
PPC: an algorithm for accurate estimation of SNP allele frequencies in small equimolar pools of DNA using data from high density microarrays.
Article in Nucleic acids research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Screening of cerebral infarction-related genetic markers using a Cox regression analysis between onset age and heterozygosity at randomly selected short tandem repeat loci.Journal of thrombosis and thrombolysis · 2012Trial
- Deciphering the Genetic Diversity of Landraces With High-Throughput SNP Genotyping of DNA Bulks: Methodology and Application to the Maize 50k Array.Frontiers in plant science · 2020Article
- Single nucleotide polymorphisms to discriminate different classes of hybrid between wild Atlantic salmon and aquaculture escapees.Evolutionary applications · 2016Article
- Machine learning approach for pooled DNA sample calibration.BMC bioinformatics · 2015Article
- Comparison of genotyping using pooled DNA samples (allelotyping) and individual genotyping using the affymetrix genome-wide human SNP array 6.0.BMC genomics · 2013Article
- Efficient association analysis between colorectal cancer and allelic polymorphisms of HLA-DQB1 by comparison of age of onset.Oncology letters · 2012Article
- Genome-wide association study identifies PERLD1 as asthma candidate gene.BMC medical genetics · 2011Article
- Article
- Combining DNA pooling with selective recombinant genotyping for increased efficiency in fine mapping.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2010Article
- A genome-wide association study of social and non-social autistic-like traits in the general population using pooled DNA, 500 K SNP microarrays and both community and diagnosed autism replication samples.Behavior genetics · 2010Article
- Validation of pooled genotyping on the Affymetrix 500 k and SNP6.0 genotyping platforms using the polynomial-based probe-specific correction.BMC genetics · 2009Article
- Microarray-based estimation of SNP allele-frequency in pooled DNA using the Langmuir kinetic model.BMC genomics · 2008Article
- The nature of nurture: a genomewide association scan for family chaos.Behavior genetics · 2008Article
- Genome-wide quantitative trait locus association scan of general cognitive ability using pooled DNA and 500K single nucleotide polymorphism microarrays.Genes, brain, and behavior · 2008Article
- MPDA: microarray pooled DNA analyzer.BMC bioinformatics · 2008Article
- Highly cost-efficient genome-wide association studies using DNA pools and dense SNP arrays.Nucleic acids research · 2008Article
- Fractioned DNA pooling: a new cost-effective strategy for fine mapping of quantitative trait loci.Genetics · 2007Article
- Applicability of DNA pools on 500 K SNP microarrays for cost-effective initial screens in genomewide association studies.BMC genomics · 2007Article
- Allelotyping of pooled DNA with 250 K SNP microarrays.BMC genomics · 2007Article
- Identification of the genetic basis for complex disorders by use of pooling-based genomewide single-nucleotide-polymorphism association studies.American journal of human genetics · 2007Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Robust estimation of allele frequencies in pools of DNA has the potential to reduce genotyping costs and/or increase the number of individuals contributing to a study where hundreds of thousands of genetic markers need to be genotyped in very large populations sample sets, such as genome wide association studies. In order to make accurate allele frequency estimations from pooled samples a correction for unequal allele representation must be applied. We have developed the polynomial based probe specific correction (PPC) which is a novel correction algorithm for accurate estimation of allele frequencies in data from high-density microarrays. This algorithm was validated through comparison of allele frequencies from a set of 10 individually genotyped DNA's and frequencies estimated from pools of these 10 DNAs using GeneChip 10K Mapping Xba 131 arrays. Our results demonstrate that when using the PPC to correct for allelic biases the accuracy of the allele frequency estimates increases dramatically.
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