The Effectiveness Evaluations And Kinship Predictions Of The SNPs For Kinship Analyses Of Han Nationality Under Multiple Strategies

Background:Kinship testing is used to prove whether there is a specific kinship between individuals according to the law of heredity by genotyping various genetic markers,which has the critical roles in criminal investigations,missing person searches,and identifying disaster victims.With the progress of DNA sequencing technology,the widespread use of various DNA genetic markers and the practical needs in criminal,civil or administrative affairs,the scope of kinship testing has expanded from the conventional paternity testing to the complex kinship testing such as full sibling,half sibling,first cousin and other distant kinships in the forensic practice.The identifications of different kinships are one of the major tasks of forensic genetic researches and practice,and can provide the strong scientific evidence for criminal proceedings,civil affairs,administrative affairs,and the identification of the victims at the scene of disasters.The applications of forensic genealogy to search for distant relatives can broaden the scope of the search for unknown individuals in existing databases and exert the tracing function of DNA evidence to a greater extent,which has the important scientific value and practical significance.Methods and contents:(1)Based on the MGISEQ-2000 sequencing platform,genetic profiles of 1993 SNP loci of unrelated individuals from Chinese Han population were obtained.Allele frequencies and various forensic parameters of 1993 SNP loci were calculated to evaluate their genetic polymorphisms in Chinese Han population residing in different regions.The population genetic structure of the Chinese Han population as well as its genetic associations and differences with other reference populations were evaluated based on 1993 SNP loci by calculating the genetic distances and pairwise fixation index,phylogenetic trees,principal component analyses and ADMIXTURE analyses between Chinese Han and reference populations,which provided the basic genetic data for the subsequent evaluations of the system efficiency in kinship identifications.(2)DNA samples from 119 Chinese Han individuals from eight families were sequenced on MGISEQ-2000 sequencing platform.Totally six different kinds of kinships including parent-child pairs,full siblings,half siblings,grandparent-grandchild,uncle-nephew/niece,aunt-nephew/niece and first cousin pairs were involved in our study.In order to apply the panel for complex kinship analyses in Chinese Han population,system powers of this panel for kinship identifications were also evaluated based on both the LR and IBS methods.Besides,the SNP loci were randomly reduced to simulate the SNP profiles of degraded DNA samples,and further evaluated their effectiveness for kinship identifications.Finally,the prediction efficiencies of the 1993 SNP loci for first-degree,second-degree,first-cousin kinships and unrelated individuals were investigated by calculating the kinship coefficient values.(3)Asian Screening Array chip was used to detect high-density SNP loci in unrelated individuals and pedigree samples of Chinese Han population.After SNP filtering,haplotype phasing and IBD analyses,the numbers and lengths of shared IBD segments for all pairs of individuals were calculated,and the distributions of IBD fragments in different kinships were investigated.Based on the IBD data,the prediction accuracy and efficiencies of high-density SNP loci on different kinships and unrelated individuals was evaluated using different algorithms.Results and conclusions:(1)Genetic polymorphism assessments indicated that most of the SNP loci were in the state of HWE and linkage equilibrium after Bonferroni adjusting.Although there were varied degrees of genetic polymorphisms among the 1993 SNP loci in Han Chinese,more than 70%of the SNP loci had high genetic polymorphisms.The combined power of discrimination and probability of exclusion of all SNP loci could meet the requirements of individual identifications and paternity testing in Chinese Han population.Population genetic analyses showed that the ancestry compositions of Chinese Han population were the same as those of the CHB and CHS in 1000 Genome Project.Chinese Han population had the smallest the genetic distance with CHB and CHS.Besides,there was no significant population genetic divergence within Chinese Han populations.(2)Kinship analyses indicated that MGIEasy 1993 SNP loci could be used as an effective tool to kinship identifications including paternity testing,full sibling testing,second-degree kinships and first-cousin kinship analyses.Firstly,based on the LR method,this panel could distinguish firstdegree and second-degree pairs from unrelated individuals when LR threshold was set to 10000.LR>1000 and LR<0.001 are recommended as the thresholds of identifying the first-cousin kinship and the unrelated individuals,respectively,and the system power of such thresholds is 0.9470.Secondly,based on the distributions of CIBS values,we found that the first-degree and second-degree kinships could distinguish from unrelated individuals.However,there were overlaps between the CIBS distributions of the second-degree and first-cousin kinships as well as the first-cousin kinships and unrelated individuals.These results indicated that CIBS method could be a supplementary tool in the identifications of first-degree and second-degree kinships.A large scale of kinship pairs from different families are still needed to validate CIBS thresholds.Thirdly,this panel performed an effective kinship inference power for the predictions of first-degree,second-degree kinships and unrelated individual pairs while a low sensitivity in the prediction of first-cousin kinships.Besides,system effectiveness for different SNP loci in kinship identifications were evaluated,and the results indicated that the increase in the numbers of SNP loci could improve the effectiveness for the identification of distant kinships.When the thresholds of LR were set to 10000,3000 SNP loci with an expected heterozygosity greater than 0.4 and exclusion probability greater than 0.1 could distinguish the first-cousin kinship from unrelated individuals,with a system efficiency of more than 95%.Finally,the recommended LR and IBS thresholds for kinship identifications and the corresponding system effectiveness were constructed under the premise of accuracy of 99%,which could provide the guidance for the application of forensic kinship identifications.(3)The ASA microarray chip was used to conduct high density SNP genotyping for DNA samples of Chinese Han population.In this section,we initially explored the IBD distributions among different kinships in Chinese Han population.The distribution of IBD segments of first-degree to fourth-degree kinship in Chinese Han population were generally consistent with the data in the "shared cM project" database,but the upper and lower limits of the distribution were different with the data in the database.Based on the shared IBD segments,multiple algorithms were used to predict the kinships between different individuals.The results showed that the prediction accuracies were relatively higher for the close kinships,while the prediction accuracies for the fourthdegree kinship or more distant kinship were limited.