ArticleAmerican journal of human genetics1998
A simple method for analyzing microsatellite allele image patterns generated from DNA pools and its application to allelic association studies.
Article in American journal of human genetics, 1998. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Polymorphism analysis of tri- and tetranucleotide repeat microsatellite markers in Hanwoo cattle.Journal of animal science and technology · 2024Article
- Impaired Reorganization of Centrosome Structure Underlies Human Infantile Dilated Cardiomyopathy.Circulation · 2023Article
- Article
- 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
- The discrepancy among single nucleotide variants detected by DNA and RNA high throughput sequencing data.BMC genomics · 2017Article
- Hypoplastic Left Heart Syndrome Sequencing Reveals a Novel NOTCH1 Mutation in a Family with Single Ventricle Defects.Pediatric cardiology · 2017Article
- Kinesin-5 inhibitor resistance is driven by kinesin-12.The Journal of cell biology · 2016Article
- Results of a "GWAS plus:" general cognitive ability is substantially heritable and massively polygenic.PloS one · 2014Article
- An evaluation of allele frequency estimation accuracy using pooled sequencing data.International journal of computational biology and drug design · 2013Article
- Evaluation of allele frequency estimation using pooled sequencing data simulation.TheScientificWorldJournal · 2013Article
- Analysis of phenotypic and microsatellite-based diversity of maize landraces in India, especially from the north east Himalayan region.Genetica · 2010Article
- A new approach to characterize populations of Schistosoma mansoni from humans: development and assessment of microsatellite analysis of pooled miracidia.Tropical medicine & international health : TM & IH · 2009Article
- Association study in the 5q31-32 linkage region for schizophrenia using pooled DNA genotyping.BMC psychiatry · 2008Article
- Applicability of DNA pools on 500 K SNP microarrays for cost-effective initial screens in genomewide association studies.BMC genomics · 2007Article
- Evaluation of DNA pooling for the estimation of microsatellite allele frequencies: a case study using striped bass (Morone saxatilis).Genetics · 2006Article
- Pooled DNA genotyping on Affymetrix SNP genotyping arrays.BMC genomics · 2006Article
- Genotyping DNA pools on microarrays: tackling the QTL problem of large samples and large numbers of SNPs.BMC genomics · 2005Article
- Evaluation of microsatellite markers in association studies: a search for an immune-related susceptibility gene in sarcoidosis.Immunogenetics · 2005Article
- Efficiency of single-nucleotide polymorphism haplotype estimation from pooled DNA.Proceedings of the National Academy of Sciences of the United States of America · 2003Article
- Validation of single nucleotide polymorphism quantification in pooled DNA samples with SNaPIT. A glycosylase-mediated methods for polymorphism detection method.Molecular biotechnology · 2002Article
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Authors and funding
7 authors.
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Abstract
Allelic association studies provide the most powerful method for locating genes of small effect contributing to complex diseases and traits. However, in outbred populations, allelic association is usually maintained only over distances of <=1 cM. Therefore, systematic searches over large regions are costly. Here we present a method involving DNA pooling that can be used as a rapid preliminary screen for allelic association with the most common class of polymorphic markers, single-sequence repeats. Patient and control samples are pooled separately, and markers are typed in the two pools. By use of primers with fluorescent 5' ends, PCR products can be analyzed on an automated sequencing apparatus. Allele image patterns (AIPs) produced for the two groups are overlaid and differences in pattern area between pools computed. From this, a DeltaAIP statistic is calculated from the difference in areas between the two AIPs expressed as a fraction of the total shared and nonshared area. AIPs of a range of different-sized pools were generated by computer simulation for markers with a range of allele sizes and frequencies. DeltaAIPs from pools and chi2 values for individual genotypings were compared, with both simulated and real data from microsatellite markers. The results demonstrated a high correlation between DeltaAIP and chi2 values. DeltaAIP analysis of real microsatellite data indicated the feasibility of using this method in systematic searches for allelic association and generated a small number of false positives but few false negatives. We conclude that DeltaAIP analysis of DNA pools can be used effectively and efficiently as a rapid screen for allelic association in case-control studies.
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