ArticleProceedings of the National Academy of Sciences of the United States of America2003
Efficiency of single-nucleotide polymorphism haplotype estimation from pooled DNA.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 64 citations in OpenAlex.
- CSHAP: efficient haplotype frequency estimation based on sparse representation.Bioinformatics (Oxford, England) · 2019Article
- Maximum-parsimony haplotype frequencies inference based on a joint constrained sparse representation of pooled DNA.BMC bioinformatics · 2013Article
- Maximum likelihood estimation of frequencies of known haplotypes from pooled sequence data.Molecular biology and evolution · 2013Article
- Fast and accurate haplotype frequency estimation for large haplotype vectors from pooled DNA data.BMC genetics · 2012Article
- A linear-time algorithm for reconstructing zero-recombinant haplotype configuration on a pedigree.BMC bioinformatics · 2012Article
- Cardiac signaling genes exhibit unexpected sequence diversity in sporadic cardiomyopathy, revealing HSPB7 polymorphisms associated with disease.The Journal of clinical investigation · 2010Article
- Optimal DNA pooling-based two-stage designs in case-control association studies.Human heredity · 2009Article
- Testing linkage disequilibrium from pooled DNA: a contingency table perspective.Statistics in medicine · 2008Article
- Molecular genetics of addiction and related heritable phenotypes: genome-wide association approaches identify "connectivity constellation" and drug target genes with pleiotropic effects.Annals of the New York Academy of Sciences · 2008Review
- MPDA: microarray pooled DNA analyzer.BMC bioinformatics · 2008Article
- A survey on haplotyping algorithms for tightly linked markers.Journal of bioinformatics and computational biology · 2008Article
- Evaluation of DNA pooling for the estimation of microsatellite allele frequencies: a case study using striped bass (Morone saxatilis).Genetics · 2006Article
- PDA: Pooled DNA analyzer.BMC bioinformatics · 2006Article
- Constructing the parental linkage phase and the genetic map over distances <1 cM using pooled haploid DNA.Genetics · 2006Article
- Using DNA pools for genotyping trios.Nucleic acids research · 2006Article
- Integrated analysis of genetic data with R.Human genomics · 2006Review
- Selecting additional tag SNPs for tolerating missing data in genotyping.BMC bioinformatics · 2005Article
- A comprehensive literature review of haplotyping software and methods for use with unrelated individuals.Human genomics · 2005Review
- Linkage disequilibrium and association studies in higher plants: present status and future prospects.Plant molecular biology · 2005Review
- A survey of current software for haplotype phase inference.Human genomics · 2004Article
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
The efficiency of single-nucleotide polymorphism haplotype analysis may be increased by DNA pooling, which can dramatically reduce the number of genotyping assays. We develop a method for obtaining maximum likelihood estimates of haplotype frequencies for different pool sizes, assess the accuracy of these estimates, and show that pooling DNA samples is efficient in estimating haplotype frequencies. Although pooling K individuals increases ambiguities, at least for small pool size K and small numbers of loci, the uncertainty of estimation increases <K times that of unpooled DNA. We also develop the asymptotic variance-covariance of maximum likelihood estimates and evaluate the accuracy of variance estimates by Monte Carlo methods. When the sample size of pools is moderately large, the asymptotic variance estimates are rather accurate. Completely or partially missing genotyping information is allowed for in our analysis. Finally, our methods are applied to single-nucleotide polymorphisms in the angiotensinogen gene.
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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.