Relative quantitation of restriction fragment length polymorphic DNAs via DNA melting analysis provides an effective way to determine allele frequencies

Hyunjoo Yu, Imhoi Koo, Sangkyun Jeong

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

To accurately and precisely estimate the allele frequencies in DNA pools for a cost-effective approach to correlate genetic variations to phenotypic traits, we exploited differential melting kinetics between restriction fragment length polymorphic DNAs. The allele frequencies of two SNPs in a series of DNA mixtures with known allelic compositions of the SNPs were determined by analyzing the meltings of restricted PCR amplicons, yielding a result with a root mean square error (RMSE) of 0.014 relative to the expected values and a standard deviation (SD) of 0.018 from triplicate measurements. This method was then applied in the measurement of genotype frequencies in DNA pools in which varying numbers of genomic DNAs were intermingled while maintaining uniform quantitative contribution. Analyses of 10 SNPs demonstrated the feasibility of this method in an economical and highly accurate manner as the results yielded an RMSE value of 0.027 and a SD of 0.019.

Original languageEnglish (US)
Pages (from-to)355-361
Number of pages7
JournalGenomics
Volume94
Issue number5
DOIs
StatePublished - Nov 1 2009

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Nucleic Acid Denaturation
Gene Frequency
DNA
Single Nucleotide Polymorphism
Freezing
Genotype
Costs and Cost Analysis
Polymerase Chain Reaction

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

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abstract = "To accurately and precisely estimate the allele frequencies in DNA pools for a cost-effective approach to correlate genetic variations to phenotypic traits, we exploited differential melting kinetics between restriction fragment length polymorphic DNAs. The allele frequencies of two SNPs in a series of DNA mixtures with known allelic compositions of the SNPs were determined by analyzing the meltings of restricted PCR amplicons, yielding a result with a root mean square error (RMSE) of 0.014 relative to the expected values and a standard deviation (SD) of 0.018 from triplicate measurements. This method was then applied in the measurement of genotype frequencies in DNA pools in which varying numbers of genomic DNAs were intermingled while maintaining uniform quantitative contribution. Analyses of 10 SNPs demonstrated the feasibility of this method in an economical and highly accurate manner as the results yielded an RMSE value of 0.027 and a SD of 0.019.",
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Relative quantitation of restriction fragment length polymorphic DNAs via DNA melting analysis provides an effective way to determine allele frequencies. / Yu, Hyunjoo; Koo, Imhoi; Jeong, Sangkyun.

In: Genomics, Vol. 94, No. 5, 01.11.2009, p. 355-361.

Research output: Contribution to journalArticle

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