Analysis of Trio Half Sibling Testing.

OBJECTIVES: To establish an analytical method for half sibling testing involving common three relatives' participation. METHODS: Based on the half sibling testing scenarios with the known biological mother, grandfather or uncle, and two unidentified controversial half siblings participating, two opposing hypotheses were set. Lineage reconstruction according to Mendel's law of heredity was carried out, and the calculation formula of the half sibling kinship index was derived. Verification of actual cases was carried out and the results were compared with duo half sibling testing. RESULTS: In the scenarios of the known biological mother, grandfather and uncle participating in half sibling testing, the kinship calculation formulae of 54, 91 and 99 genotype combinations for kinship index calculation were deduced respectively. The actual cases showed higher kinship indexes in trio half sibling testing compared with duo half sibling testing. CONCLUSIONS: It is beneficial to obtain more genetic information for family reconstruction and improvement of the strength of genetic evidence for half sibling testing by adding known relatives.

Identification Strategy of Biological Half Sibling Relationship.

OBJECTIVES: To compare the application value of the likelihood ratio (LR) method and identity by state (IBS) method in the identification involving half sibling relationships, and to provide a reference for the setting of relevant standards for identification of half sibling relationship. METHODS: (1) Based on the same genetic marker combinations, the reliability of computer simulation method was verified by comparing the distributions of cumulated identity by state score (CIBS) and combined full sibling index in actual cases with the distributions in simulated cases. (2) In different numbers of three genetic marker combinations, the simulation of full sibling, half sibling and unrelated individual pairs, each 1 million pairs, was obtained; the CIBS, as well as the corresponding types of cumulative LR parameters, were calculated. (3) The application value of LR method was compared with that of IBS method, by comparing the best system efficiency provided by LR method and IBS method when genetic markers in different amounts and of different types and accuracy were applied to distinguish the above three relational individual pairs. (4) According to the existing simulation data, the minimum number of genetic markers required to distinguish half siblings from the other two relationships using different types of genetic markers was estimated by curve fitting. RESULTS: (1) After the rank sum test, under the premise that the real relationship and the genetic marker combination tested were the same, there was no significant difference between the simulation method and the results obtained in the actual case. (2) In most cases, under the same conditions, the system effectiveness obtained by LR method was greater than that by IBS method. (3) According to the existing data, the number of genetic markers required for full-half siblings and half sibling identification could be obtained by curve fitting when the system effectiveness reached 0.95 or 0.99. CONCLUSIONS: When distinguishing half sibling from full sibling pairs or unrelated pairs, it is recommended to give preference to the LR method, and estimate the required number of markers according to the identification types and the population data, to ensure the identification effect.

Application of Microhaplotypes in Sibling Kinship Testing.

OBJECTIVES: To investigate the efficacy of different numbers of microhaplotype (MH) loci and the introduction of different reference samples on the identification of full sibling, half sibling and differentiation between full sibling and half sibling kinships, and to explore the effect of changing mutation rate on sibling testing. METHODS: First, a family map involving three generations was established, and four full sibling identification models, five half sibling identification models and five models distinguishing full and half siblings were constructed for different reference samples introduced. Based on the results of the previous study, two sets of nonbinary SNP-MH containing 34 and 54 loci were selected. Based on the above MH loci, 100 000 pairs of full sibling vs. unrelated individuals, 100 000 pairs of half sibling vs. unrelated individuals and 100 000 pairs of full sibling vs. half sibling were simulated based on the corresponding sibling kinship testing models, and the efficacy of each sibling kinship testing model was analyzed by the likelihood ratio algorithm under different thresholds. The mutant rate of 54 MH loci was changed to analyze the effect of mutation rate on sibling identification. RESULTS: In the same relationship testing model, the systematic efficacy of sibling testing was positively correlated with the number of MH loci detected. With the same number of MH loci, the efficacy of full sibling testing was better than that of uncle or grandfather when the reference sample introduced was a full sibling of A, but there was no significant difference in the identification efficacy of the four reference samples introduced for full sibling and half sibling differentiation testing. In addition, the mutation rate had a slight effect on the efficacy of sibling kinship testing. CONCLUSIONS: Increasing the number of MH loci and introducing reference samples of known relatives can increase the efficacy of full sibling testing, half sibling testing, and differentiation between full and half sibling kinships. The level of mutation rate in sibling testing by likelihood ratio method has a slight but insignificant effect on the efficacy.

Optimization of an amplicon sequencing-based microsatellite panel and protocol for stock identification and kinship inference of lake trout (Salvelinus namaycush).

Kinship-based methods of population assessment such as close-kin mark-recapture require accurate and efficient genotyping methods capable of resolving complex relationships among kin. Inference of such relationships can be difficult using biallelic loci due to the large number of markers required to obtain the necessary power. Sequencing-based microsatellite panels offer an efficient alternative, combining high polymorphism with efficient next-generation methods. Here we construct, optimize, and test one such panel for lake trout (Salvelinus namaycush) using a combination of previously-published loci adapted for sequencing and de novo loci mined from a genome assembly. We performed three rounds of primer optimization, yielding a final panel of 131 loci, followed by testing with two different levels of PCR multiplexing (all primers in one or two groups) and two different reaction volumes (5 and 10 µL). Our results showed that the use of the largest multiplex and smallest reaction volume did not substantially change results, allowing significant cost and time savings. To test panel accuracy, we used both a set of 153 known-origin samples from origins of management interest and a series of hatchery crosses representing nine families with parent-offspring, half-sibling, and largely-unrelated pairs. Our results indicate that sequencing-based microsatellite panels can efficiently and accurately provide the information required for a population genetics analyses including population assignment, calculation of between-population F ST, and kinship-based population estimation techniques. Such techniques are seeing increasing applications for a wide range of taxa; our findings should provide insight and guidance for the development of the necessary molecular resources.

Analysis of Trio Half Sibling Testing / 法医学杂志

OBJECTIVES@#To establish an analytical method for half sibling testing involving common three relatives' participation.@*METHODS@#Based on the half sibling testing scenarios with the known biological mother, grandfather or uncle, and two unidentified controversial half siblings participating, two opposing hypotheses were set. Lineage reconstruction according to Mendel's law of heredity was carried out, and the calculation formula of the half sibling kinship index was derived. Verification of actual cases was carried out and the results were compared with duo half sibling testing.@*RESULTS@#In the scenarios of the known biological mother, grandfather and uncle participating in half sibling testing, the kinship calculation formulae of 54, 91 and 99 genotype combinations for kinship index calculation were deduced respectively. The actual cases showed higher kinship indexes in trio half sibling testing compared with duo half sibling testing.@*CONCLUSIONS@#It is beneficial to obtain more genetic information for family reconstruction and improvement of the strength of genetic evidence for half sibling testing by adding known relatives.

Identification Strategy of Biological Half Sibling Relationship / 法医学杂志

OBJECTIVES@#To compare the application value of the likelihood ratio (LR) method and identity by state (IBS) method in the identification involving half sibling relationships, and to provide a reference for the setting of relevant standards for identification of half sibling relationship.@*METHODS@#(1) Based on the same genetic marker combinations, the reliability of computer simulation method was verified by comparing the distributions of cumulated identity by state score (CIBS) and combined full sibling index in actual cases with the distributions in simulated cases. (2) In different numbers of three genetic marker combinations, the simulation of full sibling, half sibling and unrelated individual pairs, each 1 million pairs, was obtained; the CIBS, as well as the corresponding types of cumulative LR parameters, were calculated. (3) The application value of LR method was compared with that of IBS method, by comparing the best system efficiency provided by LR method and IBS method when genetic markers in different amounts and of different types and accuracy were applied to distinguish the above three relational individual pairs. (4) According to the existing simulation data, the minimum number of genetic markers required to distinguish half siblings from the other two relationships using different types of genetic markers was estimated by curve fitting.@*RESULTS@#(1) After the rank sum test, under the premise that the real relationship and the genetic marker combination tested were the same, there was no significant difference between the simulation method and the results obtained in the actual case. (2) In most cases, under the same conditions, the system effectiveness obtained by LR method was greater than that by IBS method. (3) According to the existing data, the number of genetic markers required for full-half siblings and half sibling identification could be obtained by curve fitting when the system effectiveness reached 0.95 or 0.99.@*CONCLUSIONS@#When distinguishing half sibling from full sibling pairs or unrelated pairs, it is recommended to give preference to the LR method, and estimate the required number of markers according to the identification types and the population data, to ensure the identification effect.

Application of Microhaplotypes in Sibling Kinship Testing / 法医学杂志

OBJECTIVES@#To investigate the efficacy of different numbers of microhaplotype (MH) loci and the introduction of different reference samples on the identification of full sibling, half sibling and differentiation between full sibling and half sibling kinships, and to explore the effect of changing mutation rate on sibling testing.@*METHODS@#First, a family map involving three generations was established, and four full sibling identification models, five half sibling identification models and five models distinguishing full and half siblings were constructed for different reference samples introduced. Based on the results of the previous study, two sets of nonbinary SNP-MH containing 34 and 54 loci were selected. Based on the above MH loci, 100 000 pairs of full sibling vs. unrelated individuals, 100 000 pairs of half sibling vs. unrelated individuals and 100 000 pairs of full sibling vs. half sibling were simulated based on the corresponding sibling kinship testing models, and the efficacy of each sibling kinship testing model was analyzed by the likelihood ratio algorithm under different thresholds. The mutant rate of 54 MH loci was changed to analyze the effect of mutation rate on sibling identification.@*RESULTS@#In the same relationship testing model, the systematic efficacy of sibling testing was positively correlated with the number of MH loci detected. With the same number of MH loci, the efficacy of full sibling testing was better than that of uncle or grandfather when the reference sample introduced was a full sibling of A, but there was no significant difference in the identification efficacy of the four reference samples introduced for full sibling and half sibling differentiation testing. In addition, the mutation rate had a slight effect on the efficacy of sibling kinship testing.@*CONCLUSIONS@#Increasing the number of MH loci and introducing reference samples of known relatives can increase the efficacy of full sibling testing, half sibling testing, and differentiation between full and half sibling kinships. The level of mutation rate in sibling testing by likelihood ratio method has a slight but insignificant effect on the efficacy.

A Semi-Automated SNP-Based Approach for Contaminant Identification in Biparental Polyploid Populations of Tropical Forage Grasses.

Artificial hybridization plays a fundamental role in plant breeding programs since it generates new genotypic combinations that can result in desirable phenotypes. Depending on the species and mode of reproduction, controlled crosses may be challenging, and contaminating individuals can be introduced accidentally. In this context, the identification of such contaminants is important to avoid compromising further selection cycles, as well as genetic and genomic studies. The main objective of this work was to propose an automated multivariate methodology for the detection and classification of putative contaminants, including apomictic clones (ACs), self-fertilized individuals, half-siblings (HSs), and full contaminants (FCs), in biparental polyploid progenies of tropical forage grasses. We established a pipeline to identify contaminants in genotyping-by-sequencing (GBS) data encoded as allele dosages of single nucleotide polymorphism (SNP) markers by integrating principal component analysis (PCA), genotypic analysis (GA) measures based on Mendelian segregation, and clustering analysis (CA). The combination of these methods allowed for the correct identification of all contaminants in all simulated progenies and the detection of putative contaminants in three real progenies of tropical forage grasses, providing an easy and promising methodology for the identification of contaminants in biparental progenies of tetraploid and hexaploid species. The proposed pipeline was made available through the polyCID Shiny app and can be easily coupled with traditional genetic approaches, such as linkage map construction, thereby increasing the efficiency of breeding programs.

Application of ITO Method in Determination of Special Half-Sibling Relationship / 法医学杂志

OBJECTIVES@#To identify whether the relationship between Zhang A, Zhang B, Zhang C and Zhang X is the half-sibling relationship whose mother is sister (hereinafter referred to as the special half-sibling relationship) or the common first cousin relationship and discuss the application of ITO method in discriminating the special kinship.@*METHODS@#DNA was extracted from blood stain of four identified individuals, PowerPlex® 21 System and AGCU 21+1 STR kit were used to detect autosomal STR genetic markers. Investigator® Argus X-12 QS kit was used to detect the X chromosome STR genetic markers, the special half-sibling index (SHSI) and first cousin index (FCI) and their likelihood ratio (LR) were calculated by ITO method.@*RESULTS@#The LR results of SHSI to FCI, which were calculated based on autosomal STR genotyping and the analysis of X-STR genotyping results suggested that the relationship between Zhang A, Zhang B, Zhang C and Zhang X was inclined to be a special half-sibling relationship.@*CONCLUSIONS@#For the identification of special kinship, it is necessary to comprehensively apply various genetic markers according to the case. After the conclusion that shared alleles cannot be excluded from the analysis, ITO method can be further used to establish discriminant assumptions according to the specific case to obtain objective and reliable identification opinions.

Application of ITO Method in Determination of Special Half-Sibling Relationship.

OBJECTIVES: To identify whether the relationship between Zhang A, Zhang B, Zhang C and Zhang X is the half-sibling relationship whose mother is sister (hereinafter referred to as the special half-sibling relationship) or the common first cousin relationship and discuss the application of ITO method in discriminating the special kinship. METHODS: DNA was extracted from blood stain of four identified individuals, PowerPlex® 21 System and AGCU 21+1 STR kit were used to detect autosomal STR genetic markers. Investigator® Argus X-12 QS kit was used to detect the X chromosome STR genetic markers, the special half-sibling index (SHSI) and first cousin index (FCI) and their likelihood ratio (LR) were calculated by ITO method. RESULTS: The LR results of SHSI to FCI, which were calculated based on autosomal STR genotyping and the analysis of X-STR genotyping results suggested that the relationship between Zhang A, Zhang B, Zhang C and Zhang X was inclined to be a special half-sibling relationship. CONCLUSIONS: For the identification of special kinship, it is necessary to comprehensively apply various genetic markers according to the case. After the conclusion that shared alleles cannot be excluded from the analysis, ITO method can be further used to establish discriminant assumptions according to the specific case to obtain objective and reliable identification opinions.

Calculation of Likelihood Ratio for Identifying Half Sibling Relationship When Both Biological Mothers Participate.

ABSTRACT: Objective To derive the formulae for likelihood ratio （LR） calculation of half sibling relationships when both mothers participate. Methods Based on the fact that both biological mothers participate in the identification of half sibling relationship between the two individuals, test hypothesis for the identification of half sibling relationship was established. Conditional probability ratios of genetic evidence under null hypothesis and alternative hypothesis conditions were simplified, and then applied to a real case of half sibling relationship identification. At the same time, the LR of half sibling relationships under the assumption that only a single biological mother or none of the biological mothers participate were respectively calculated. Results In the cases of identification of half sibling relationship from same fathers, with no biological father involved, after the same genetic indicator test analysis, when both biological mothers participate in the identification, the accumulated LR value was higher than that of accumulated LR with only a single biological mother or no parents participating. Conclusion When the autosome STR test is used for the identification and analysis of half sibling relationship between two individuals, the calculation of LR is more simple, intuitive and operable with both mothers participating. The biological mothers should participate in the test as much as possible, otherwise the number of STR loci would need to be increased for a more specific conclusion.

Calculation of Likelihood Ratio for Identifying Half Sibling Relationship When Both Biological Mothers Participate / 法医学杂志

Objective To derive the formulae for likelihood ratio （LR） calculation of half sibling relationships when both mothers participate. Methods Based on the fact that both biological mothers participate in the identification of half sibling relationship between the two individuals, test hypothesis for the identification of half sibling relationship was established. Conditional probability ratios of genetic evidence under null hypothesis and alternative hypothesis conditions were simplified, and then applied to a real case of half sibling relationship identification. At the same time, the LR of half sibling relationships under the assumption that only a single biological mother or none of the biological mothers participate were respectively calculated. Results In the cases of identification of half sibling relationship from same fathers, with no biological father involved, after the same genetic indicator test analysis, when both biological mothers participate in the identification, the accumulated LR value was higher than that of accumulated LR with only a single biological mother or no parents participating. Conclusion When the autosome STR test is used for the identification and analysis of half sibling relationship between two individuals, the calculation of LR is more simple, intuitive and operable with both mothers participating. The biological mothers should participate in the test as much as possible, otherwise the number of STR loci would need to be increased for a more specific conclusion.

IPED2X: a robust pedigree reconstruction algorithm for complicated pedigrees.

Reconstruction of family trees, or pedigree reconstruction, for a group of individuals is a fundamental problem in genetics. Some recent methods have been developed to reconstruct pedigrees using genotype data only. These methods are accurate and efficient for simple pedigrees which contain only siblings, where two individuals share the same pair of parents. A most recent method IPED2 is able to handle complicated pedigrees with half-sibling relationships, where two individuals share only one parent. However, the method is shown to miss many true positive half-sibling relationships as it removes all suspicious half-sibling relationships during the parent construction process. In this work, we propose a novel method IPED2X, which deploys a more robust algorithm for parent construction in the pedigrees by considering more possible operations rather than simple deletion. We convert the parent construction problem into a graph labeling problem and propose a more effective labeling algorithm. We show in our experiments that IPED2X is more powerful on capturing the true half-sibling relationships, which further leads to better reconstruction accuracy.

Analysis and Countermeasure for Complex Cases in Adoption Paternity Testing / 中山大学学报(医学科学版)

[Objective] To explore how to deal with the paternity test of complex adoption cases. [Method] Samples from 13 families, in which adoptive parents were suspected related to biological parents, were genotyped using "Identifder + Sinofder + Powerplex 16" combined system (D8S1179, D21S11, D7S820, CSFIPO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, VWA, TPOX, D18S51, D5S818, FGA, D6S1043, D12S391, PentaD, PentaE) followed by further statistical analysis. [Result] Among all 13 cases, 2 were completely accordance with the Mendel law, PI > 10 000. There found more than 3 inconsistent loci in 8 cases. And found 1～2 inconsistent loci in 3 cases, needed to test more STR loci until PI≥10 000. The half sibling index (HSI) was also calculated with ITO method. The adoptive parents of 2 cases were not excluded from a full sibling with biological parents. In addition, Y-STR loci were tested for 4 cases (father/son). Two adoptive fathers of them were not excluded from the paternal relationship with biological fathers. [Conclusion] The most (76.9%) of all (13) complex adoptive cases of paternity test could be drawn a definite conclusion with combined system of "Identifder + Sinefiler + Powerplexl6". Minority (23.1%) of them was not definite yet and needed testing more STIR loci. Meanwhile, we suggested adding Y-STR tests and providing HSI for reference.