title: IBC CARe microarray allelic population prevalences in an American Indian population.
abstract: BACKGROUND
  The prevalence of variant alleles among single nucleotide polymorphisms (SNPs) is not well known for many minority populations. These population allele frequencies (PAFs) are necessary to guide genetic epidemiology studies and to understand the population specific contribution of these variants to disease risk. Large differences in PAF among certain functional groups of genes could also indicate possible selection pressure or founder effects of interest. The 50K SNP, custom genotyping microarray (CARe) was developed, focusing on about 2,000 candidate genes and pathways with demonstrated pathophysiologic influence on cardiovascular disease (CVD).
  
  
  METHODS
  The CARe microarray was used to genotype 216 unaffected controls in a study of pre-eclampsia among a Northern Plains, American Indian tribe. The allelic prevalences of 34,240 SNPs suitable for analysis, were determined and compared with corresponding HapMap prevalences for the Caucasian population. Further analysis was conducted to compare the frequency of statistically different prevalences among functionally related SNPs, as determined by the DAVID Bioinformatics Resource.
  
  
  RESULTS
  Of the SNPs with PAFs in both datasets, 9.8%,37.2% and 47.1% showed allele frequencies among the American Indian population greater than, less than and either greater or less than (respectively) the HapMap Caucasian population. The 2,547 genes were divided into 53 functional groups using the highest stringency criteria. While none of these groups reached the Bonferroni corrected p value of 0.00094, there were 7 of these 53 groups with significantly more or less differing PAFs, each with a probability of less than 0.05 and an overall probability of 0.0046.
  
  
  CONCLUSIONS
  In comparison to the HapMap Caucasian population, there are substantial differences in the prevalence among an American Indian community of SNPs related to CVD. Certain functional groups of genes and related SNPs show possible evidence of selection pressure or founder effects.
authors.affiliation: Science Department, Turtle Mountain Community College, Belcourt, North Dakota, United States of America ; School of Medicine and Health Sciences, University of North Dakota, Grand Forks, North Dakota, United States of America.
authors.forename: Lyle G
authors.initials: LG
authors.lastname: Best
authors.forename: Cindy M
authors.initials: CM
authors.lastname: Anderson
authors.forename: Richa
authors.initials: R
authors.lastname: Saxena
authors.forename: Berta
authors.initials: B
authors.lastname: Almoguera
authors.forename: Hareesh
authors.initials: H
authors.lastname: Chandrupatla
authors.forename: Candelaria
authors.initials: C
authors.lastname: Martin
authors.forename: Gilbert
authors.initials: G
authors.lastname: Falcon
authors.forename: Kylie
authors.initials: K
authors.lastname: Keplin
authors.forename: Nichole
authors.initials: N
authors.lastname: Pearson
authors.forename: Brendan J
authors.initials: BJ
authors.lastname: Keating
mesh_terms: D000328:Adult; D000483:Alleles; D002318:Cardiovascular Diseases / Q000235:genetics*; D002874:Chromosome Mapping; D005260:Female; D018703:Founder Effect; D005787:Gene Frequency; D005838:Genotype; D006801:Humans; D007198:Indians, North American / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide; D015995:Prevalence; D014481:United States; D044465:White People; D055815:Young Adult
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