Effective screening of informative single nucleotide polymorphisms using the novel method of restriction fragment mass polymorphism.

ABSTRACT

Restriction fragment mass polymorphism (RFMP) was applied to pooled DNA for selecting informative single nucleotide polymorphisms (SNPs). A total of 225 coding non-synonymous SNPs (cnSNPs) from immunomodulating genes known to be involved in the pathogenesis of asthma were selected from the National Center for Biotechnology Information's (NCBI) SNP database (dbSNP). DNA samples from 200 healthy Koreans were pooled, amplified by polymerase chain reaction, digested with restriction enzymes and the fragments analysed by mass spectrometry. Only 30 of the 225 cnSNPs (13.3%) were informative, i.e.had a minor allele frequency>10%. The percentage of informative cnSNPs varied according to the validation status of the dbSNP, being 42.3% (22/52) when validated by multiple submissions and frequency data, 8.7% (2/23) when validated by multiple submissions alone and 9.1% (3/33) when validated by frequency data alone. Most of the 112 unvalidated cnSNPs were not informative. In conclusion, the RFMP method using pooled DNA is useful in selecting informative SNPs, as also is validation status in the dbSNP.