Quantitative technologies for allele frequency estimation of SNPs in DNA pools

Sagiv Shifman, Anne Pisanté-Shalom, Benjamin Yakir, Ariel Darvasi*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

49 Scopus citations


We have compared several genotyping methods to assess their applicability to single nucleotide polymorphism (SNP) allele frequency estimation in DNA pools. The accuracy of these methods (restriction fragment length polymorphism, real-time pyrophosphate DNA sequencing, single base extension with fluorescently labeled ddNTPs, homogeneous 5′-nuclease assay, and MALDI-TOF mass spectrometry) was tested by calculating the standard deviation among heterozygous individuals (which are natural DNA pools with 50% representation of each allele) and by estimating allele frequency in artificial pools. We show that although the methods differ in their accuracy, they can all serve for quantification of allele frequency in DNA pools with reasonable accuracy. We found that the influence of the error variance attributed to pool construction on quantification accuracy is insignificant and is SNP dependent.

Original languageAmerican English
Pages (from-to)429-434
Number of pages6
JournalMolecular and Cellular Probes
Issue number6
StatePublished - Dec 2002

Bibliographical note

Funding Information:
We wish to thank Naomi Zak for her helpful comments. This work was supported by the FIRST foundation of the Israel Academy of Sciences.


  • Allele frequency
  • Association
  • DNA pooling
  • SNPs


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