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 |
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| Affiliation: | 1. Department of Legal Medicine, Kansai Medical University, 2-5-1 Shin-machi, Hirakata, Osaka 573-1010, Japan;2. Fourth Biological Section, National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan;3. Department of Forensic Medicine, Kyoto University Graduate School of Medicine, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan;1. MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China;2. Institute of Archaeological Science, Fudan University, Shanghai 200433, China;3. Deepreads Biotech, Guangzhou 510663, China;4. Guangzhou Forensic Science Institute, Guangzhou 510030, China;5. Forensic Science Centre of Maoming Public Security Department, Guangdong Province, Maoming 525000, China;6. Criminal Justice College of China University of Political Science and Law, Beijing 100088, China;1. ESR, Private Bag 92021, Auckland 1142, New Zealand;2. University of Auckland, Department of Statistics, Private Bag 92019, Auckland 1142, New Zealand;3. Principal Forensic Services Ltd, United Kingdom;4. Forensic Science South Australia, 21 Divett Place, SA 5000, Australia;5. School of Biological Sciences, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia;1. New York City Office of Chief Medical Examiner, Department of Forensic Biology, 421 East 26th Street, New York, NY 10016, USA;2. NicheVision Forensics, LLC., 526 South Main Street, Akron, OH 44311, USA;3. New York City Public Health Laboratory, Department of Health and Mental Hygiene, 455 East 26th Street, New York, NY 10016, USA;1. Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08102, USA;2. Department of Computer Science, Rutgers University, Camden, NJ 08102, USA;3. Biomedical Forensic Sciences Program, Boston University School of Medicine, Boston, MA 02118, USA;4. Research Laboratory for Electronics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA;5. Department of Plant Biology and Pathology, Rutgers University, New Brunswick, NJ 08901, USA;6. School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA 5095, Australia;1. Department of Forensic Sciences, Oslo University Hospital, Oslo, Norway;2. Instituto de Ciencias Forenses, Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain;3. Institute of Clinical Medicine, University of Oslo, Oslo, Norway |
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| Abstract: | 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. |
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| Keywords: | Forensic DNA typing Short tandem repeat Probabilistic genotyping Continuous model GlobalFiler Developmental validation |
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