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Modeling the minus two base pair stutter ratio of the D1S1656 locus: A sequence-based mixture distribution model
Shota Inokuchi1, Koji Fujii2, Hiroaki Nakanishi3
1Department of Forensic Medicine, Graduate School of Medicne, Juntendo University, 2-1-1 Hongo, Bunkyo-ku, Tokyo, Japan; National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba, Japan; Forensic Science Laboratory, Tokyo Metropolitan Police Department, 3-35-21 Shakujiidai, Nerima-ku, Tokyo, Japan.
This study introduces a stutter ratio model for the D1S1656 locus in short tandem repeat (STR) typing. The model helps interpret stutter patterns in capillary electrophoresis, improving DNA analysis accuracy.
Area of Science:
- Forensic Genetics
- Molecular Biology
- Population Genetics
Background:
- Short tandem repeat (STR) typing is crucial in forensic genetics.
- Understanding stutter patterns, particularly minus two base pair stutter (-2bpSR), is essential for accurate STR analysis.
- The D1S1656 locus presents unique challenges due to its repetitive structure.
Purpose of the Study:
- To propose and validate a stutter ratio model for the D1S1656 locus.
- To investigate the relationship between allele types, defined by the longest uninterrupted stretch of two base repeat motif (2bpLUS), and -2bpSR.
- To develop a statistical model for estimating the probability of sequence types within repeat numbers.
Main Methods:
- Massively parallel sequencing of DNA from 108 Japanese individuals.
- Analysis of the 2bpLUS value within the flanking region of the D1S1656 locus.
- Collection of -2bpSR data using the GlobalFiler Kit and a 3500xL Genetic Analyzer.
- Modeling -2bpSR using a mixture log-normal distribution based on 2bpLUS classification.
- Estimation of probabilities using logistic regression across five major populations.
Main Results:
- Alleles at the D1S1656 locus were classified into two types based on 2bpLUS values.
- Significant differences in -2bpSR were observed between these two allele types.
- A mixture log-normal distribution model effectively represented the -2bpSR data.
- Population-specific probabilities for sequence types were estimated.
Conclusions:
- The proposed -2bpSR model provides a framework for interpreting stutter at the D1S1656 locus.
- Allele classification based on 2bpLUS is a valuable approach for understanding stutter variations.
- This model is expected to enhance the accuracy and reliability of STR typing in forensic applications.
