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      Human profiling from STR and SNP analysis of tropical bed bug, Cimex hemipterus, for forensic science

      research-article
      1 , 1 , 2 ,
      Scientific Reports
      Nature Publishing Group UK
      Biotechnology, Genetics

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          Abstract

          Tropical bed bugs, Cimex hemipterus, which commonly feeds on human blood, may be useful in forensic applications. However, unlike the common bed bug, Cimex lectularius, there is no information regarding tropical bed bug, C. hemipterus, being studied for its applications in forensics. Thus, in this study, lab-reared post-feeding tropical bed bugs were subjected to Short Tandem Repeat (STR) and Single Nucleotide Polymorphism (SNP) analyses to establish the usage of tropical bed bugs in forensics. Several post-feeding times (0, 5, 14, 30, and 45 days) were tested to determine when a complete human DNA profile could still be obtained after the bugs had taken the blood meal. The results showed that complete STR and SNP profiles could only be obtained from the D0 sample. The profile completeness decreased over time, and partial STR and SNP profiles could be obtained up to 45 days post-blood meal. The generated SNP profiles, complete or partial, were also viable for HIrisPlex-S phenotype prediction. In addition, field-collected bed bugs were also used to examine the viability of the tested STR markers, and the STR markers detected mixed profiles. The findings of this study established that the post-blood meal of tropical bed bugs is a suitable source of human DNA for forensic STR and SNP profiling. Human DNA recovered from bed bugs can be used to identify spatial and temporal relations of events.

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          Primer3—new capabilities and interfaces

          Polymerase chain reaction (PCR) is a basic molecular biology technique with a multiplicity of uses, including deoxyribonucleic acid cloning and sequencing, functional analysis of genes, diagnosis of diseases, genotyping and discovery of genetic variants. Reliable primer design is crucial for successful PCR, and for over a decade, the open-source Primer3 software has been widely used for primer design, often in high-throughput genomics applications. It has also been incorporated into numerous publicly available software packages and web services. During this period, we have greatly expanded Primer3’s functionality. In this article, we describe Primer3’s current capabilities, emphasizing recent improvements. The most notable enhancements incorporate more accurate thermodynamic models in the primer design process, both to improve melting temperature prediction and to reduce the likelihood that primers will form hairpins or dimers. Additional enhancements include more precise control of primer placement—a change motivated partly by opportunities to use whole-genome sequences to improve primer specificity. We also added features to increase ease of use, including the ability to save and re-use parameter settings and the ability to require that individual primers not be used in more than one primer pair. We have made the core code more modular and provided cleaner programming interfaces to further ease integration with other software. These improvements position Primer3 for continued use with genome-scale data in the decade ahead.
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            The HIrisPlex system for simultaneous prediction of hair and eye colour from DNA.

            Recently, the field of predicting phenotypes of externally visible characteristics (EVCs) from DNA genotypes with the final aim of concentrating police investigations to find persons completely unknown to investigating authorities, also referred to as Forensic DNA Phenotyping (FDP), has started to become established in forensic biology. We previously developed and forensically validated the IrisPlex system for accurate prediction of blue and brown eye colour from DNA, and recently showed that all major hair colour categories are predictable from carefully selected DNA markers. Here, we introduce the newly developed HIrisPlex system, which is capable of simultaneously predicting both hair and eye colour from DNA. HIrisPlex consists of a single multiplex assay targeting 24 eye and hair colour predictive DNA variants including all 6 IrisPlex SNPs, as well as two prediction models, a newly developed model for hair colour categories and shade, and the previously developed IrisPlex model for eye colour. The HIrisPlex assay was designed to cope with low amounts of template DNA, as well as degraded DNA, and preliminary sensitivity testing revealed full DNA profiles down to 63pg input DNA. The power of the HIrisPlex system to predict hair colour was assessed in 1551 individuals from three different parts of Europe showing different hair colour frequencies. Using a 20% subset of individuals, while 80% were used for model building, the individual-based prediction accuracies employing a prediction-guided approach were 69.5% for blond, 78.5% for brown, 80% for red and 87.5% for black hair colour on average. Results from HIrisPlex analysis on worldwide DNA samples imply that HIrisPlex hair colour prediction is reliable independent of bio-geographic ancestry (similar to previous IrisPlex findings for eye colour). We furthermore demonstrate that it is possible to infer with a prediction accuracy of >86% if a brown-eyed, black-haired individual is of non-European (excluding regions nearby Europe) versus European (including nearby regions) bio-geographic origin solely from the strength of HIrisPlex eye and hair colour probabilities, which can provide extra intelligence for future forensic applications. The HIrisPlex system introduced here, including a single multiplex test assay, an interactive tool and prediction guide, and recommendations for reporting final outcomes, represents the first tool for simultaneously establishing categorical eye and hair colour of a person from DNA. The practical forensic application of the HIrisPlex system is expected to benefit cases where other avenues of investigation, including STR profiling, provide no leads on who the unknown crime scene sample donor or the unknown missing person might be. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.
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              The HIrisPlex-S system for eye, hair and skin colour prediction from DNA: Introduction and forensic developmental validation

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                Author and article information

                Contributors
                abdhafiz@usm.my
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                27 January 2023
                27 January 2023
                2023
                : 13
                : 1506
                Affiliations
                [1 ]GRID grid.11875.3a, ISNI 0000 0001 2294 3534, Household and Structural Urban Entomology Laboratory, Vector Control Research Unit, School of Biological Sciences, , Universiti Sains Malaysia, ; 11800 Penang, Minden, Malaysia
                [2 ]GRID grid.412113.4, ISNI 0000 0004 1937 1557, Centre for Insect Systematics, , Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), ; Selangor, Malaysia
                Article
                28774
                10.1038/s41598-023-28774-y
                9883228
                36707655
                97439cf1-e097-4075-a5ed-c49786945da9
                © The Author(s) 2023

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 13 June 2022
                : 24 January 2023
                Funding
                Funded by: Fundamental Research Grant (FRGS), 203/PBIOLOGI/6711681
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                © The Author(s) 2023

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                biotechnology,genetics
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                biotechnology, genetics

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