ABSTRACT
Ancestry inference for an individual can only be as good as the reference populations with allele frequency data on the SNPs being used. If the most relevant ancestral population(s) does not have data available for the SNPs studied, then analyses based on DNA evidence may indicate a quite distantly related population, albeit one among the more closely related of the existing reference populations. We have added reference population allele frequencies for 14 additional population samples (with >1100 individuals studied) to the 125 population samples previously published for the Kidd Lab 55 AISNP panel. Allele frequencies are now publicly available for all 55 SNPs in ALFRED and FROG-kb for a total of 139 population samples. This Kidd Lab panel of 55 ancestry informative SNPs has been incorporated in commercial kits by both ThermoFisher Scientific and Illumina for massively parallel sequencing. Researchers employing those kits will find the enhanced set of reference populations useful.
Subject(s)
Ethnicity/genetics , Gene Frequency , Genetics, Population , Polymorphism, Single Nucleotide , Racial Groups/genetics , Databases, Genetic , Genotype , High-Throughput Nucleotide Sequencing , HumansABSTRACT
Neighbourhood risk factors for Campylobacter infection in Danish broilers were evaluated. Campylobacter infection status of a flock was identified by PCR analysis of cloacal swab samples collected as a part of national surveillance program. Included into the study were, in total, 10,876 broiler flocks sent by 226 farms to processing plants from 2007 to 2009. A multivariable logistic regression model with autocorrelation structure was used to model the effect of exposure variables on the probability of being tested positive to Campylobacter. Results showed a significant protective effect with the absence of infected neighbours within a distance of 2 km. The analysis was adjusted for potential confounding factors. Seasonal cyclic patterns of the Campylobacter infection was accounted for by using sine and cosine function. Predicted probability maps showed a heterogeneous spatial and temporal risk of Campylobacter infection in Danish broiler.