Rapid SNP allele frequency determination in genomic DNA pools by pyrosequencing.
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TLDR
This work has developed an accurate and reproducible protocol for allele frequency determination using Pyrosequencing technology in large genomic DNA pools (374 individuals), which allows the rapid determination of allelefrequency differences in case/control groups for association studies and susceptibility gene discovery in complex diseases.Abstract:
Individual genotyping of single nucleotide polymorphisms (SNPs) remains expensive, especially for linkage disequilibrium mapping strategies involving high-throughput SNP genotyping On one hand, current methods may suit scientific and laboratory needs in regard to accuracy, reproducibility/robustness, and large-scale application On the other hand, a cheaper and less time-consuming alternative to individual genotyping is the use of SNP allele frequencies determined in DNA pools We have developed an accurate and reproducible protocol for allele frequency determination using PyrosequencingTM technology in large genomic DNA pools (374 individuals) The measured correlation (R2) in large DNA pools was 0980 In the context of disease-associated SNPs studies, we compared the allele frequencies between the disease (eg, type 2 diabetes and obesity) and control groups detected by either individual genotyping or Pyrosequencing of DNA pools In large pools, the variation between the two methods was 15 ± 09% Iread more
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References
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A genome-wide scan for human obesity genes reveals a major susceptibility locus on chromosome 10.
Jörg Hager,Jörg Hager,Christian Dina,Stephan Francke,Séverine Dubois,Mouna Houari,Vincent Vatin,Emmanuel Vaillant,Nathalie Lorentz,Arnaud Basdevant,Karine Clément,Karine Clément,Bernard Guy-Grand,Philippe Froguel +13 more
TL;DR: A genome-wide scan in affected sibpairs to identify chromosomal regions linked to obesity in a collection of French families suggests that there is a major gene on chromosome 10p implicated in the development of human obesity and the existence of two further loci influencing leptin levels.
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High-Throughput Methods for Detection of Genetic Variation
TL;DR: The most frequently used techniques and instrumental settings applied in different combinations are described, and other methods that are less broadly used but have interesting potentials are discussed.
Journal ArticleDOI
Determining SNP allele frequencies in DNA pools.
TL;DR: Both radiation-based methods for the determination of SNP allele frequencies gave accurate and reproducible results, suggesting they are suitable for use in DNA pooling experiments.