Modeling the minus two base pair stutter ratio of the D1S1656 locus: A sequence-based mixture distribution model

Effect existence of aging on stutter ratio evaluated via Bayesian inference

The stochastic behavior of the stutter ratio (SR) in capillary electrophoresis-based DNA typing is currently described and predicted using statistical models in forensic genetics. Clarifying this behavior can help obtain more objective and robust evidence to the court in terms of mixture interpretation. This study aimed to investigate the effect existence of aging on SR via a Bayesian framework. Nail scrapings and clippings were collected from 68 healthy individuals with informed consent. Samples were classified by age-class: young group (0-16 years; n = 36) and older-adult group (>61 years; n = 32). Then, they were compared in terms of their SRs for each simple repeat locus included in GlobalFiler Kit. Bayesian modeling was performed with lognormal distribution model, which implemented multiple linear regression, allele and age-class as explanatory variables. For all simple repeat loci, the median of the posterior distribution of the age-class parameter was a positive value. For CSF1PO and D7S820, the 95% credible interval of the posterior distribution did not include 0. Our data suggested that aging slightly increases the SR. These findings might help elucidate the stochastic behavior of SR.

Development and validation of Kongoh ver. 3.0.1: Open-source software for DNA mixture interpretation in the GlobalFiler system based on a quantitative continuous model

Probabilistic genotyping software based on continuous models is effective for interpreting DNA profiles derived from DNA mixtures and small DNA samples. In this study, we updated our previously developed Kongoh software (to ver. 3.0.1) to interpret DNA profiles typed using the GlobalFiler™ PCR Amplification Kit. Recently, highly sensitive typing systems such as the GlobalFiler system have facilitated the detection of forward, double-back, and minus 2-nt stutters; therefore, we implemented statistical models for these stutters in Kongoh. In addition, we validated the new version of Kongoh using 2-4-person mixtures and DNA profiles with degradation in the GlobalFiler system. The likelihood ratios (LRs) for true contributors and non-contributors were well separated as the information increased (i.e., larger peak height and fewer contributors), and these LRs tended to neutrality as the information decreased. These trends were observed even in profiles with DNA degradation. The LR values were highly reproducible, and the accuracy of the calculation was also confirmed. Therefore, Kongoh ver. 3.0.1 is useful for interpreting DNA mixtures and degraded DNA samples in the GlobalFiler system.

Evaluation of probability distribution models for stutter ratios in the typing system of GlobalFiler and 3500xL Genetic Analyzer

As DNA typing systems have become increasingly sensitive in recent years, probability distribution models for back, forward, double-back, and minus 2-nt stutter ratios have been desired to be considered in DNA evidence interpretation using specific software programs. However, experimental investigations have been insufficient, especially for forward, double-back, and minus 2-nt stutters. In this study, we experimentally reevaluated the probability distribution models for each stutter ratio in the typing systems of GlobalFiler™ PCR Amplification Kit and 3500xL Genetic Analyzer from Thermo Fisher Scientific. In addition, to enhance the reliability of longest uninterrupted stretch (LUS) values and corrected allele numbers used in previously developed models for stutter ratios using sequence information (i.e., LUS model and multi-seq model), we propose the weighted average of LUS values and corrected allele numbers based on the number of observations in sequence-based population data. Back stutter ratios demonstrated a positive correlation with allele numbers (allele model) in eight loci, LUS values (LUS model) in eight loci, and corrected allele numbers (multi-seq model) in five loci. The forward stutter ratios (FSRs) of D22S1045 followed the LUS model. FSRs other than D22S1045 and double-back stutter ratios followed the LUS model by considering multiple loci together. Minus 2-nt stutter ratios observed in SE33 and D1S1656 did not increase with the increase in the allele numbers. The adopted models for each stutter ratio can be implemented in software programs for DNA evidence interpretation and enable a reliable interpretation of crime stain profiles in forensic caseworks.