Article
Genetics & Heredity
Athina Vidaki, Benjamin Planterose Jimenez, Brando Poggiali, Vivian Kalamara, Kristiaan J. van der Gaag, Silvana C. E. Maas, Mohsen BIOS Consortium, Mohsen Ghanbari, Titia Sijen, Manfred Kayser
Summary: Tobacco smoking is a widespread habit with significant health risks and mortality. This study aims to predict smoking habits using blood DNA methylation. The results show high reproducibility of methylation measurements and accurate prediction of smoking habits using corrected data.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2023)
Article
Genetics & Heredity
Ruiyang Tao, Qiannan Xu, Shouyu Wang, Ruocheng Xia, Qi Yang, Anqi Chen, Yiling Qu, Yehui Lv, Suhua Zhang, Chengtao Li
Summary: With the development of massively parallel sequencing (MPS), the kinship analysis has become more convenient. In this study, 243 Chinese Han individuals from 17 families were sequenced using the ForenSeq Signature Kit, and the analysis was conducted using likelihood ratio and identical by state methods. The results showed that the kit was effective in analyzing parent-child, full sibling, and most second-degree kinships.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2022)
Review
Genetics & Heredity
Cordula Haas, Jacqueline Neubauer, Andrea Patrizia Salzmann, Erin Hanson, Jack Ballantyne
Summary: Transcriptome analyses have seen significant growth in forensic genetics in recent years, with applications such as body fluid and tissue identification, determining stain and donor age, estimating post-mortem interval, and conducting post mortem death investigations. The introduction of Massively Parallel Sequencing (MPS) has opened up new possibilities for this field, allowing for high-resolution analyses and whole transcriptome sequencing of forensically relevant materials.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2021)
Article
Genetics & Heredity
Koji Fujii, Yusuke Mita, Haruhiko Watahiki, Takashi Fukagawa, Tetsushi Kitayama, Natsuko Mizuno, Hiroaki Nakahara, Kazumasa Sekiguchi
Summary: This study reports the identification of off-target haplotypes in mitochondrial DNA sequencing, which are likely caused by polymorphic nuclear mitochondrial DNA sequences (NumtS). The off-target haplotypes showed perfect matches to polymorphic NumtS and other related sequences, indicating a distant genetic relationship to modern human mtDNA.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2022)
Article
Genetics & Heredity
Lucinda Davenport, Laurence Devesse, Denise Syndercombe Court, David Ballard
Summary: The study focuses on the analysis of SNPs for identity or kinship applications in forensic genetics. It shows that including flanking region variation in the analysis can significantly reduce the match probability between different populations, improving the accuracy and reliability of identification.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2023)
Article
Medicine, Legal
Jennifer M. Young, D. Power, P. Kanokwongnuwut, A. Linacre
Summary: This study presents the first application of direct PCR coupled with MPS to generate forensic intelligence SNP data from latent DNA. By analysing results from 60 touched samples, the study demonstrated the ability of this approach to obtain informative genetic data from trace amounts of DNA.
INTERNATIONAL JOURNAL OF LEGAL MEDICINE
(2021)
Article
Multidisciplinary Sciences
Ye-Lim Kwon, Bo Min Kim, Eun Young Lee, Kyoung-Jin Shin
Summary: This study utilized MPS technology to analyze 25 STRs from 350 samples of four populations, revealing that the sequence-based MPS method showed a higher number of alleles and unique alleles in SE33 compared to the length-based CE method.
SCIENTIFIC REPORTS
(2021)
Article
Medicine, Legal
Theresa E. Gross, Jan Fleckhaus, Peter M. Schneider
Summary: The survey conducted among forensic practitioners in Europe showed a high interest in using massively parallel sequencing (MPS) platforms for forensic DNA analysis and DNA phenotyping. Most participants either already own an MPS platform or plan to acquire one in the near future, demonstrating a strong desire to explore MPS applications in forensic genetics. The results of the survey will be valuable for organizing training workshops on various aspects of MPS-based DNA phenotyping for the forensic genetics scientific community.
INTERNATIONAL JOURNAL OF LEGAL MEDICINE
(2021)
Article
Chemistry, Multidisciplinary
Yu-An Kuo, Cheulhee Jung, Yu-An Chen, Hung-Che Kuo, Oliver S. Zhao, Trung D. Nguyen, James R. Rybarski, Soonwoo Hong, Yuan- Chen, Dennis C. Wylie, John A. Hawkins, Jada N. Walker, Samuel W. J. Shields, Jennifer S. Brodbelt, Jeffrey T. Petty, Ilya J. Finkelstein, Hsin-Chih Yeh
Summary: The study revealed that the nucleobases at positions 7-12 of the 18-nucleotide-long activator are critical to creating bright NCBs, while positions 4-6 and 2-4 are hotspots to generate yellow-orange and red POTs.
ADVANCED MATERIALS
(2022)
Article
Medicine, Legal
Elaine J. Lewis, Erin Weaver, Audrey Hoyle, Robert Lagace, Fabio Oldoni, Daniele Podini
Summary: Genotype profiling is crucial in forensics, with advancements in technology necessitating re-analysis of DNA data from the 1990s to overcome potential confounding factors like paralogous genes.
INTERNATIONAL JOURNAL OF LEGAL MEDICINE
(2022)
Article
Ethics
Marcus Smith, Seumas Miller
Summary: This article discusses the implications of using massively parallel sequencing (MPS) in forensic genomics and highlights the ethical concerns associated with it. The authors argue that individuals have a collective moral responsibility to submit their DNA to law enforcement agencies for the greater good of society, but also emphasize the need for legislation to regulate the use of this technology and ensure the protection of individuals' moral rights.
JOURNAL OF BIOETHICAL INQUIRY
(2023)
Article
Genetics & Heredity
J. M. Young, A. Linacre
Summary: MPS technology has revolutionized genomics and human DNA profiling, allowing for advanced studies on biodiversity in high biomass environmental samples. However, its translation to forensic science is still in its infancy due to challenges in merging traditional forensic practices with unfamiliar DNA technologies and complex datasets. Further research is needed to fully integrate eDNA into forensic casework and overcome current limitations.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2021)
Article
Biochemical Research Methods
James Gooch, Sireethorn Tungsirisurp, Hayley Costanzo, Richard Napier, Nunzianda Frascione
Summary: The study selected ssDNA aptamers against human sperm cells using Cell-SELEX and massively parallel sequencing technologies, revealing promising aptamer candidates that selectively bind sperm cells. These aptamers have the potential to increase the efficiency of sexual offence investigations by facilitating sperm detection.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Chengliang Yang, Meiyun He, Changhui Liu, Xueyuan Liu, Miaoqiang Lun, Qin Su, Xiaolong Han, Hong Liu, Mengge Wang, Ling Chen, Chao Liu
Summary: A custom MPS InDel panel containing 114 InDels was developed and validated, demonstrating its robustness and application value in forensic studies.
Article
Genetics & Heredity
Jing Liu, Yonglin Su, Yufeng Wen, Lirong Jiang, Suyu Li, Mengyao Zhao, Xiacan Chen, Zheng Wang
Summary: In this study, the genotype data of 74 microhaplotypes (MHs) in three Chinese populations were analyzed using Ion Torrent semiconductor sequencing. Results showed that the Ion AmpliSeq MH-74 Plex Microhaplotype Research Panel is highly polymorphic and can be used as an effective tool for human forensics.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2023)
Article
Genetics & Heredity
Frank R. Wendt, Anna-Liina Rahikainen, Jonathan L. King, Antti Sajantila, Bruce Budowle
PHARMACOGENOMICS JOURNAL
(2020)
Article
Biochemical Research Methods
Brian Young, Michael Marciano, Karin Crenshaw, George Duncan, Luigi Armogida, Bruce McCord
Summary: The first autosomal sequence-based allele frequency database for forensic massively parallel sequencing has been published, eliminating one of the barriers to implementing MPS in casework. A procedure has been described to address match probabilities when casework samples are generated using an MPS kit with different trim sites, providing a framework for comparison of different kits or databases and accommodating comparison of MPS and CE profiles.
Article
Multidisciplinary Sciences
Evelyn K. Guevara, Jukka U. Palo, Sanni Oversti, Jonathan L. King, Maria Seidel, Monika Stoljarova, Frank R. Wendt, Magdalena M. Bus, Anna Guengerich, Warren B. Church, Sonia Guillen, Lutz Roewer, Bruce Budowle, Antti Sajantila
Article
Genetics & Heredity
Utpal Smart, Jennifer Churchill Cihlar, Sammed N. Mandape, Melissa Muenzler, Jonathan L. King, Bruce Budowle, August E. Woerner
Summary: Despite the challenges of resolving mitotypes from mixtures occurring in certain ratios, a bioinformatic mixture deconvolution method centered on population-based phasing was developed and validated in this study. By leveraging external reference panels and simulations, the accuracy of deconvolution was confirmed when haplotypes in the mixture were similar to those in the reference panel and the mixture ratios were appropriate. The proposed framework automates the reconstruction of complete individual mitotypes from mixtures, even in ratios that have traditionally been considered problematic.
Article
Genetics & Heredity
August E. Woerner, Sammed Mandape, Jonathan L. King, Melissa Muenzler, Benjamin Crysup, Bruce Budowle
Summary: Unique molecular identifiers (UMIs) are a promising approach to track and correct errors in PCR and sequencing, particularly for interpreting short tandem repeats (STRs). The bioinformatics pipeline strumi offers an alignment-free machine learning algorithm that clusters reads into UMI families and infers consensus super-reads with high accuracy. UMIs have the potential to simplify probabilistic genotyping systems and reduce uncertainty.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2021)
Article
Genetics & Heredity
Benjamin Crysup, August E. Woerner, Jonathan L. King, Bruce Budowle
Summary: Genetic methods are expanding, transitioning from forensic genetic assays limited to tens of loci to forensic genomic approaches that can assess thousands to millions of loci. Subtle distinctions between genetic assays and their genomic counterparts can impact forensic match statistics. A graph algorithm is described in the study to assess forensic match statistics on mitochondrial DNA mixtures in a way that is invariant to variant calling conventions and alignment parameters.
Article
Genetics & Heredity
Evelyn K. Guevara, Jukka U. Palo, Jonathan L. King, Magdalena M. Bus, Sonia Guillen, Bruce Budowle, Antti Sajantila
Summary: This study genetically characterized five populations from the Northeastern Peruvian Andes and provided autosomal short tandem repeat and identity informative single nucleotide polymorphism data. The results showed deviations from Hardy-Weinberg equilibrium in certain loci and increased allele numbers due to sequence variation. The new data aid in filling gaps in the genetic landscape of South America and offer valuable information for forensic genetic studies in Peru.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2021)
Article
Genetics & Heredity
Jonathan L. King, August E. Woerner, Sammed N. Mandape, Kapema Bupe Kapema, Rodrigo Soares Moura-Neto, Rosane Silva, Bruce Budowle
Summary: Since 2013, STRait Razor has provided a software solution for analyzing MPS data, including primary and secondary analysis. The software, accessible through browsers or as a standalone application, enables quick processing of data and report generation. A preliminary triaging system has been implemented to assist users in interpreting loci suspected of heterozygote imbalance.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2021)
Article
Biochemical Research Methods
Magdalena M. Bus, Erik A. C. de Jong, Jonathan L. King, Walter van der Vliet, Joop Theelen, Bruce Budowle
Summary: The single-step PCR library preparation method utilizes RC probes, universal tails, Illumina indexes, and adapters. RC-PCR is advantageous in amplifying degraded DNA, reducing steps and contamination risk, and successfully targeting SNPs. The developed 85 SNP-plex panel of RC-PCR provides higher discrimination power than the previous 27-plex for challenging DNA sample analyses.
Article
Genetics & Heredity
Rodrigo Moura-Neto, Jonathan L. King, Isadora Mello, Victor Dias, Benjamin Crysup, August E. Woerner, Bruce Budowle, Rosane Silva
Summary: Forensic DNA typing using MPS provides additional information on STR variation, enabling faster analysis and reduced sample usage. The PowerSeq (TM) Auto/Y System is a multiplex forensic kit for MPS, analyzing autosomal and Y-STR markers for forensic genetic applications.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2021)
Article
Medicine, Legal
Jianye Ge, Jonathan King, Sammed Mandape, Bruce Budowle
Summary: The deconvolution of mixture samples is a challenging task for DNA forensic laboratories, but recent research has shown promise in this area by developing novel forensic markers like macrohaplotypes to improve interpretative capabilities.
INTERNATIONAL JOURNAL OF LEGAL MEDICINE
(2021)
Article
Genetics & Heredity
Sammed N. Mandape, Utpal Smart, Jonathan L. King, Melissa Muenzler, Kapema Bupe Kapema, Bruce Budowle, August E. Woerner
Summary: Short tandem repeats of the nuclear genome have typically been used to analyze forensic DNA mixtures, but when nuclear DNA is degraded or limited, mitochondrial DNA markers are a powerful alternative. Limited software tools are available for interpreting mtDNA mixtures, but the Mitochondrial Mixture Deconvolution and Interpretation Tool (MMDIT) can automate this process. MMDIT can deconvolve mtDNA mixtures into donor haplotypes and estimate match probabilities, making it a valuable tool for forensic DNA analysis.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2021)
Article
Genetics & Heredity
Brian Young, Tom Faris, Luigi Armogida
Summary: This study discusses how accuracy and precision in DNA sequencing can be expressed using Levenshtein distance, and how this method can be compared with alternative measures.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2021)
Article
Genetics & Heredity
Jianye Ge, Jonathan L. King, Amy Smuts, Bruce Budowle
Summary: This study attempts to develop a systematic method for interpreting single-cell profiles from mixtures in forensic genetics, providing a new paradigm for forensic genetic casework interpretation.
Article
Biology
C. G. M. Santos, N. G. Rolim-Filho, C. A. Domingues, M. Dornelas-Ribeiro, J. L. King, B. Budowle, R. S. Moura-Neto, R. Silva
Summary: The study found that physical performance of Brazilian elite military personnel is associated with mitochondrial polymorphic loci, particularly the G11914A position in the NADPH gene component of the electron transport chain. mtDNA of the NF group was more similar to genomes from African countries, while the frequency of the G allele was higher in group F individuals. The results suggest that high performance of military personnel may be influenced by genomic traits.
BRAZILIAN JOURNAL OF MEDICAL AND BIOLOGICAL RESEARCH
(2021)