Calculation of the Paternity Index for STR with tri-allelic patterns in paternity testing

The calculation of the paternity index (PI) value of common bi-allelic genotypes at STR loci has been standardized in paternity cases. However, for tri-allelic patterns, a rare category of genotyping aberration in forensic practice, the statistical analysis in paternity testing remains disputed. The Type 1 tri-allelic pattern generally results from somatic mutation in the early stage of individual development. The Type 2 tri-allelic pattern is commonly generated by segmental duplication in the genome. In this study, practical and theoretical aspects of the evaluation of evidence concerning the Type 1 and Type 2 tri-allelic patterns in healthy individuals are discussed based on the likelihood ratio (LR) in different categories of kinship cases. The calculation of the PI value concerning tri-allelic genotypes is formulated according to the generation and genetic transmission of tri-allelic patterns. Meanwhile, a package tool named TriPI is developed to assist the calculation of the PI value in paternity testing concerning tri-allelic subjects, which could benefit the evaluation of the weight of evidence in the interpretation of tri-allelic pattern in forensic practice.

An unbalanced tri-allelic pattern at the D10S1248 locus: Characteristics, genetic basis and transmission

To address issues related to unbalanced tri-allelic patterns, an example at the D10S1248 locus characterized by the sum of heights of alleles 13 and 15 approximately equal to allele 14 was intensively investigated. The coexistence of these three alleles was confirmed by profiling the rs2246512-D10S1248 marker using fluorescently labelled primers and allelic sequencing. Multi-tissue genotyping revealed that this pattern had chimeric characteristics, and pedigree analysis found that allele 13 or allele 14 were inherited to offspring independently of the other two alleles. These evidences suggest that the pattern should stem from a somatic mutation in early embryonic development and that peak height ratio is not an accurate indicator of mutation time point and direction. The rs2246538-D10S1248-rs2246512 marker was subsequently used to determine the mutation from allele 15 to allele 13. Notably, allele 13 with the lowest peak height was misidentified as a stutter peak when genotyped using next generation sequencing.

Characterization of the extra copy of TPOX locus with tri-allelic pattern

BACKGROUND

An STR locus with tri-allelic pattern is occasionally observed in routine forensic casework. The extra copy of TPOX locus with tri-allelic pattern in populations has been assumed to be inserted into an X chromosome, which took place forth before the Bantu expansion in Africa. Nonetheless, the exact location of the duplication and the form of rearrangement in the human genome has not been clarified yet.

RESULTS

In this study, we investigated the extra copy of type 2 tri-allelic pattern at TPOX in various populations. While allele 10 is the major third allele in Africa, allele 11 appears more frequent in America and overwhelming in Chinese and Korean populations, which might attribute to the population substructures. Results from the investigation of family cases showed that the transmission of the extra allele had a similar genetic pattern of autosomal genes. Furthermore, a whole-genome sequencing followed by bioinformatics analysis revealed that the intact form of chromosomal duplication and rearrangement occurred ~ 407 kb away from the authentic TPOX locus on chromosome 2 in two cases. The breakpoints of the insertion were further validated in most other tri-allelic subjects, which can imply the identical origin from the ancestral extra copy. Nevertheless, de novo chromosomal duplication and rearrangement at thyroid peroxidase gene occur in populations.

CONCLUSIONS

Instead of the extra allele 10 in African populations, the main third allele at TPOX with tri-allelic pattern is allele 11 in Chinese and Korean populations. The insertion of the extra copy into chromosome 2 occurs in most subjects with tri-allelic pattern at TPOX and demonstrates the transmission of the third allele from parents to offspring. The breakpoints of the ancestral extra copy are defined, which shows evidence of its inheritance from African populations. In addition, the simple validation method would help improve tri-allelic pattern calling, distinguish de novo chromosomal rearrangements, and also count the frequencies among different geographic regions. Therefore, the statistical interpretation of tri-allelic pattern at TPOX could be enhanced during forensic practice.