TY - JOUR
T1 - Prediction of biogeographical ancestry in admixed individuals
AU - Cheung, Elaine Y.Y.
AU - Gahan, Michelle Elizabeth
AU - McNevin, Dennis
N1 - Publisher Copyright:
© 2018 Elsevier B.V.
PY - 2018/9/1
Y1 - 2018/9/1
N2 - Estimation of ancestral affiliation for human genotypes is now possible for major geographic populations and has been employed for forensic casework. Prediction algorithms, such as the Snipper Bayesian classifier, have the ability to classify non-admixed BGA in African (AFR), European (EUR), East Asian (EAS), and most Amerindian (NAM) individuals, but are not always appropriate for admixed individuals. Artificial admixture was simulated for all possible admixture ratios (1:1, 3:1, 2:1:1, and 1:1:1:1) from four grandparents. The simulated genotypes were used to test the accuracy of various prediction algorithms, most successful of which were the population genetics program, STRUCTURE, and a novel genetic distance algorithm (GDA). STRUCTURE was ideal for admixed individuals with 1:1 and 3:1 ratios from AFR, EUR, EAS, and NAM reference populations. Individuals with 1:1:1:1 BGA proportions were more accurately predicted by GDA. The use of hypothetical root genotypes improved the accuracy of GDA predictions for 1:1 and 3:1 admixtures and STRUCTURE classification of 1:1:1:1 admixture. The GDA requires only allele or genotype frequency values from each reference population, which offers a simpler sampling and input formatting procedure than is required by STRUCTURE. It can also be implemented in a spreadsheet without the need for long run times.
AB - Estimation of ancestral affiliation for human genotypes is now possible for major geographic populations and has been employed for forensic casework. Prediction algorithms, such as the Snipper Bayesian classifier, have the ability to classify non-admixed BGA in African (AFR), European (EUR), East Asian (EAS), and most Amerindian (NAM) individuals, but are not always appropriate for admixed individuals. Artificial admixture was simulated for all possible admixture ratios (1:1, 3:1, 2:1:1, and 1:1:1:1) from four grandparents. The simulated genotypes were used to test the accuracy of various prediction algorithms, most successful of which were the population genetics program, STRUCTURE, and a novel genetic distance algorithm (GDA). STRUCTURE was ideal for admixed individuals with 1:1 and 3:1 ratios from AFR, EUR, EAS, and NAM reference populations. Individuals with 1:1:1:1 BGA proportions were more accurately predicted by GDA. The use of hypothetical root genotypes improved the accuracy of GDA predictions for 1:1 and 3:1 admixtures and STRUCTURE classification of 1:1:1:1 admixture. The GDA requires only allele or genotype frequency values from each reference population, which offers a simpler sampling and input formatting procedure than is required by STRUCTURE. It can also be implemented in a spreadsheet without the need for long run times.
KW - Admixture
KW - Biogeographical ancestry (BGA)
KW - Genetic distance
KW - Single nucleotide polymorphisms (SNPs)
KW - STRUCTURE
KW - Gene Frequency
KW - Humans
KW - Genotype
KW - Continental Population Groups/genetics
KW - DNA/genetics
KW - Algorithms
KW - Pedigree
KW - Polymorphism, Single Nucleotide
KW - Principal Component Analysis
UR - http://www.scopus.com/inward/record.url?scp=85049466952&partnerID=8YFLogxK
U2 - 10.1016/j.fsigen.2018.06.013
DO - 10.1016/j.fsigen.2018.06.013
M3 - Article
C2 - 29986229
AN - SCOPUS:85049466952
SN - 1872-4973
VL - 36
SP - 104
EP - 111
JO - Forensic Science International: Genetics
JF - Forensic Science International: Genetics
ER -