Population screening of single-nucleotide polymorphisms exemplified by analysis of 8000 alleles.
The authors describe a method in which the population frequency of single-nucleotide polymorphisms (SNPs) can be efficiently detected and their allele frequencies accurately measured. Selected SNPs in TNFbeta, IL-4, and CTLA-4 were used to demonstrate the method. Blood from 4000 individuals was pooled, DNA was extracted, and target sequences were PCR amplified and analyzed by denaturant capillary electrophoresis. Alleles were separated into peaks based on melting properties of the double DNA helix. Frequencies of the different alleles were determined by calculating the area under the peaks. Allele frequencies and Hardy-Weinberg equilibrium estimated from the pooled data were verified by analyzing 7.5% of the samples randomly selected from the blood donor series. The method herein is equally suitable for single-samples and/or pooled-samples analysis of SNPs, in which sample treatment is kept to a minimum. The potential throughput of the method is beyond obtainable numbers of samples.
Department of Surgical Oncology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo, Norway.
Per Olaf
PO
Ekstrøm
Jens
J
Bjørheim
Gustav
G
Gaudernack
Karl-Erik
KE
Giercksky
D000483:Alleles; D015703:Antigens, CD; D000943:Antigens, Differentiation / Q000235:genetics; D001483:Base Sequence; D015982:Bias; D060908:CTLA-4 Antigen; D019075:Electrophoresis, Capillary / Q000379:methods*; D005820:Genetic Testing / Q000379:methods*; D005828:Genetics, Population; D006579:Heterozygote; D006801:Humans; D015847:Interleukin-4 / Q000235:genetics; D008233:Lymphotoxin-alpha / Q000235:genetics; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction / Q000379:methods; D020641:Polymorphism, Single Nucleotide
D015703:Antigens, CD; D000943:Antigens, Differentiation; D060908:CTLA-4 Antigen; C556706:CTLA4 protein, human; D008233:Lymphotoxin-alpha; D015847:Interleukin-4