The Development Of A Novel Ancestry Inference DIP System For Degraded Samples And Its Application In Population Genetics And Forensics

Objects:Forensic ancestry inference assisted in case investigation and litigation activities by inferring the biogeographic origin of samples.DIPs were widely distributed in the genome.In most instances,DIPs were expressed stably and had low mutation rates.The frequencies of some DIPs were quite different among different populations,which made them useful in forensic ancestry inference.The fragment lengths of DIPs were short,and the electrophoresis profile of DIPs had no stutter peaks,which made them promising in forensic applications and suitable for degraded sample detection.DIPs were genetic markers of length polymorphs that can be examined by nextgeneration sequencing platforms(NGS)or capillary electrophoresis platforms(CE).The NGS had not yet been routinely used in forensic applications.The present study adopted the PCR-CE platform due to its high accuracy and low cost.China was located in East Asia and has many ethnic groups.The groups from southern EAS(S-EAS)and northern EAS(N-EAS)had differences in genetic structures.In the present study,we hope to establish a PCR-based ancestry inference DIP panel that could distinguish groups from five continental,S-EAS,and N-EAS and apply the panel to analyze the genetic structure of the Ningxia Han group,the Hunan Han group,and the Yugur group.Methods:Firstly,autosomal biallelic DIPs suitable for ancestry inference were selected from the dbSNP database;secondly,the population data from 1000 Genomes Project Phase 3 were used to evaluate the forensic applications efficiencies of the loci;thirdly,a multiplex PCR system including the 56 A-DIPs,3 Y-DIPs,and the Amelogenin was developed.The validation studies were conducted according to the validation guidelines recommended by the Scientific Working Group on DNA Analysis Methods(SWGDAM);Finally,the newly constructed system was used to type samples of Hunan Han,Ningxia Han,and Gansu Yugur.The genotype data were analyzed by STRAF,Snipper v2.5,STRUCTURE v2.3.4,Mega 7,TreeMix,and TBtools.A random forest model was built by R software.Results:A forensic ancestry inference system including 56 A-DIPs,3 Y-DIPs,and the Amelogenin was established with amplicon sizes limited to 200bp.The high sensitivity and human specificity made it suitable for degraded sample analysis.The panel could differentiate groups from five continental and could differentiate groups from the north of East Asia(N-EAS)and the south of East Asia(S-EAS).By analyzing the genetic characteristic of Ningxia Han,Hunan Han,and Gansu Yugur,the results showed that Ningxia Han had a typical N-EAS genetic structure,and the Hunan Han had more characteristics of S-EAS.The Yugur also showed N-EAS characteristics.By calculating the forensic parameters,the panel met the standard for forensic personal identification.By applying the random forest model,93.71%of Ningxia Han were inferred from N-EAS,88.63%of Hunan Han were inferred from belonged to S-EAS,and 96.90%of Yugur were inferred from N-EAS.The results showed that the 56 ADIPs had high efficiency in forensic ancestry inference.