Developing A Novel Panel Of Genome-wide Ancestry Informative Markers For Bio-geographical Ancestry Estimates

Object: To screen and select a panel of ancestry informative markersand develop a multiplexed assay for description of genetic components ofAsian, European and African populations and individual ancestry inference.Comparing with the genetic markers such as STR, SNP analysis has severaladvantages over the standard practice, including short amplicons, lowmutation rates and associating with plentiful genetic information, allowingthe amplification of degraded DNA samples. With the association analysesbetween SNPs and the phenotypes, more information can be obtained aboutthe DNA samples, which is particularly attractive for forensic identificationapplying to the practical caseworks.Methods: Based on the previous publications and the information fromthe international database, a set of SNPs are selected using for ancestryoriginal inference with the better results of the parameter of populationgenetics. SNP typing is performed using12-plex GenomelabTMSNPstream genotyping system based on the principles of the single baseextension. Population and casework samples are collected for validation tests of the system. Based on the genotyping data of1096samples of11populations from the HapMap database,35AIMs were finally selectedfrom432SNPs screened from52phenotypic correlation genes.Multiplexed assay was developed based on the micro sequencing-generalchip technologies and population allele frequency database was set up.1096samples from HapMap were analyzed by this panel of AIMs to testifythe efficacy, then,357unrelated DNA samples from10populations wererecruited for assay validation. Finally, population genetic components andindividual genetic composition were generated by STRUCTURE, andindividual ancestry inference could be made together with the results of therandom matching probabilities.Results: The35-AIMs assay is well balanced for Hardy-Weinbergequilibrium (p>0.001) and there is no linkage disequilibrium （r2<0.1）.Thirty-five SNPs that displayed highly contrasting allele frequenciesamong the populations involved in this study. All35SNPs were arrangedinto three PCR pools and the amplicon sizes ranged from90bp to154bp.The lowest concentration that produced a complete SNP profile was0.0625ng/μl, and the lowest need of DNA sample is0.375ng. This panel of AIMswas configured with remarkable and balanced discriminatory power amongAfrican, European, and East Asian ancestries. The allele frequencydistribution of each SNP varies greatly between these three ancestry groups.There are11East Asian AIMs (large δ values of African/East Asian and European/East Asian) with a median Fst of0.549(0.356-0.648),12European AIMs (large δ values of African/European and European/EastAsian) with a median Fst of0.536(0.401-0.963), and12African AIMs(large δ values of African/European and African/East Asian) with a medianFst of0.579(0.414-0.645). The population structure and the individualstructure are described with the pie chart. With the results of the randommatching probabilities, ancestry component analyses for1096samplesfrom HapMap and357recruited samples are consistent with the knownorigin, and the original ancestry inference can be obtained accurately.Conclusion: The established panel filtrated and developed by the35AIMs can be applied to analyze the genetic components of Asian, Europeanand African populations and individual genetic composition, which will beefficient for error-control caused by population stratification in geneticassociation analyses and for individual ancestry inference in forensic DNAtest.