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Open Access Highly Accessed Research article

Frequencies of single nucleotide polymorphisms in genes regulating inflammatory responses in a community-based population

Han-Yao Huang1*, Lucy Thuita2, Paul Strickland3, Sandra C Hoffman1, George W Comstock1 and Kathy J Helzlsouer14

Author Affiliations

1 Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA

2 Department of Biostatistics & Epidemiology/Wb4, Cleveland Clinic Foundation, Cleveland, Ohio, USA

3 Department of Environmental Health Sciences, Johns Hopkins School of Public Health, Baltimore, Maryland, USA

4 Prevention and Research Center, Women's Center for Health & Medicine, Mercy Medical Center, Baltimore, Maryland, USA

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BMC Genetics 2007, 8:7  doi:10.1186/1471-2156-8-7

Published: 14 March 2007

Abstract

Background

Allele frequencies reported from public databases or articles are mostly based on small sample sizes. Differences in genotype frequencies by age, race and sex have implications for studies designed to examine genetic susceptibility to disease.

In a community-based cohort of 9,960 individuals, we compared the allele frequencies of 49 single nucleotide polymorphisms (SNPs) of genes involved in inflammatory pathways to the frequencies reported on public databases, and examined the genotypes frequencies by age and sex. The genes in which SNPs were analyzed include CCR2, CCR5, COX1, COX2, CRP, CSF1, CSF2, IFNG, IL1A, IL1B, IL2, IL4, IL6, IL8, IL10, IL13, IL18, LTA, MPO, NOS2A, NOS3, PPARD, PPARG, PPARGC1 and TNF.

Results

Mean(SD) age was 53.2(15.5); 98% were Caucasians and 62% were women. Only 1 out of 33 SNPs differed from the SNP500Cancer database in allele frequency by >10% in Caucasians (n = 9,831), whereas 12 SNPs differed by >10% (up to 50%) in African Americans (n = 105). Two out of 15 SNPs differed from the dbSNP database in allele frequencies by >10% in Caucasians, and 5 out of 15 SNPs differed by >10% in African Americans. Age was similar across most genotype groups. Genotype frequencies did not differ by sex except for TNF(rs1799724), IL2(rs2069762), IL10(rs1800890), PPARG(rs1801282), and CRP(rs1800947) with differences of less than 4%.

Conclusion

When estimating the size of samples needed for a study, particularly if a reference sample is used, one should take into consideration the size and ethnicity of the reference sample. Larger sample size is needed for public databases that report allele frequencies in non-Caucasian populations.