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Caputo M, Sala A, Corach D. Reference population database for 24 STR loci of selected provinces of Argentina. Mol Biol Rep 2023:10.1007/s11033-023-08497-z. [PMID: 37219673 DOI: 10.1007/s11033-023-08497-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/28/2023] [Indexed: 05/24/2023]
Abstract
BACKGROUND Argentinean population is the result of admixture between South Amerindians, Europeans and to a lesser degree, Africans. Since the advent of forensic molecular genetics, the construction of local reference databases became mandatory. Aiming to further extend the technical quality reference database of Argentina, we present herein the allele frequencies for 24 autosomal STRs, including D22S1045, and SE33 (not previously reported for Argentina in STRidER). CONCLUSIONS Genotypes of 6454 unrelated individuals (3761 males and 2694 females) from 13 out of 23 provinces were analysed. Forensic parameters were calculated for each marker. The observed heterozygosity ranged from 0.661 (TPOX) to 0.941 (SE33). The locus SE33 was revealed to be the most informative marker showing the highest values for PIC (0.955), GD (0.952), TPI (8.455) and PE (0.879). On the other hand, TPOX turned out to be the least informative marker: PIC (0.618), GD (0.669), and PE (0.371). The high number of analyzed individuals allowed detecting low frequency alleles and microvariants in CSF1PO; D16S539 and D21S11 D18S51; PENTA D; PENTA E and at locus D6S1043. METHODS AND RESULTS This study is the most extensive for Argentina and complements the already reported information concerning the autosomal STRs commonly used in forensic identification. The results were submitted passing STRidER quality control standards (QC), receiving the reference number STR000327 v.2.
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Affiliation(s)
- Mariela Caputo
- Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Biotecnología, Inmunología y Genética. Catedra de Genética Forense, Centro de Referencia en Identificación Humana y Servicio de Huellas Digitales Genéticas (SHDG), Universidad de Buenos Aires, CABA, Argentina.
- CONICET. Consejo Nacional de Investigaciones Científicas y Técnicas, CABA, Argentina.
| | - Andrea Sala
- Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Biotecnología, Inmunología y Genética. Catedra de Genética Forense, Centro de Referencia en Identificación Humana y Servicio de Huellas Digitales Genéticas (SHDG), Universidad de Buenos Aires, CABA, Argentina
- CONICET. Consejo Nacional de Investigaciones Científicas y Técnicas, CABA, Argentina
| | - Daniel Corach
- Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Biotecnología, Inmunología y Genética. Catedra de Genética Forense, Centro de Referencia en Identificación Humana y Servicio de Huellas Digitales Genéticas (SHDG), Universidad de Buenos Aires, CABA, Argentina
- CONICET. Consejo Nacional de Investigaciones Científicas y Técnicas, CABA, Argentina
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Bonilla C, Mejia-Lancheros C. The Skin We Live in: Pigmentation Traits and Tanning Behaviour in British Young Adults, an Observational and Genetically-Informed Study. Genes (Basel) 2022; 13:896. [PMID: 35627282 PMCID: PMC9140533 DOI: 10.3390/genes13050896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 02/04/2023] Open
Abstract
Skin cancer incidence has been increasing worldwide, representing a particularly high burden for populations of European ancestry. Outdoor and indoor tanning using ultraviolet (UV) radiation devices are major risk factors for skin cancer. While tanning behaviours can be modified by targeted interventions to reduce skin cancer rates, there is insufficient evidence on the motivations for tanning preferences and their relationship with pigmentation phenotypes. The present observational and genetically-informed study investigates motives for tanning and the role that pigmentation phenotypes play on outdoor and indoor tanning behaviour in British young adults. This study included 3722 participants from the Avon Longitudinal Study of Parents and Children in South West England, with data on pigmentation features, tanning ability and preferences, and SNP genotypes. Liking to tan and outdoor tanning were strongly influenced by pigmentary traits and tanning ability. However, the association of these phenotypes with UV indoor tanning was weaker. Our results provide evidence to support the implementation of skin cancer preventative interventions that consider individual biological characteristics and motives for undergoing outdoor and indoor tanning.
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Affiliation(s)
- Carolina Bonilla
- Departamento de Medicina Preventiva, Faculdade de Medicina, Universidade de São Paulo, São Paulo CEP 01246-903, Brazil
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
| | - Cilia Mejia-Lancheros
- MAP Centre for Urban Health Solutions, Li Ka Shing Knowledge Institute, St. Michael’s Hospital, Unity Health Toronto, Toronto, ON M5B 1W8, Canada;
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Carratto TMT, Marcorin L, do Valle-Silva G, de Oliveira MLG, Donadi EA, Simões AL, Castelli EC, Mendes-Junior CT. Prediction of eye and hair pigmentation phenotypes using the HIrisPlex system in a Brazilian admixed population sample. Int J Legal Med 2021; 135:1329-1339. [PMID: 33884487 DOI: 10.1007/s00414-021-02554-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 02/26/2021] [Indexed: 01/23/2023]
Abstract
Human pigmentation is a complex trait, probably involving more than 100 genes. Predicting phenotypes using SNPs present in those genes is important for forensic purpose. For this, the HIrisPlex tool was developed for eye and hair color prediction, with both models achieving high accuracy among Europeans. Its evaluation in admixed populations is important, since they present a higher frequency of intermediate phenotypes, and HIrisPlex has demonstrated limitations in such predictions; therefore, the performance of this tool may be impaired in such populations. Here, we evaluate the set of 24 markers from the HIrisPlex system in 328 individuals from Ribeirão Preto (SP) region, predicting eye and hair color and comparing the predictions with their real phenotypes. We used the HaloPlex Target Enrichment System and MiSeq Personal Sequencer platform for massively parallel sequencing. The prediction of eye and hair color was accomplished by the HIrisPlex online tool, using the default prediction settings. Ancestry was estimated using the SNPforID 34-plex to observe if and how an individual's ancestry background would affect predictions in this admixed sample. Our sample presented major European ancestry (70.5%), followed by African (21.1%) and Native American/East Asian (8.4%). HIrisPlex presented an overall sensitivity of 0.691 for hair color prediction, with sensitivities ranging from 0.547 to 0.782. The lowest sensitivity was observed for individuals with black hair, who present a reduced European contribution (48.4%). For eye color prediction, the overall sensitivity was 0.741, with sensitivities higher than 0.85 for blue and brown eyes, although it failed in predicting intermediate eye color. Such struggle in predicting this phenotype category is in accordance with what has been seen in previous studies involving HIrisPlex. Individuals with brown eye color are more admixed, with European ancestry decreasing to 62.6%; notwithstanding that, sensitivity for brown eyes was almost 100%. Overall sensitivity increases to 0.791 when a 0.7 threshold is set, though 12.5% of the individuals become undefined. When combining eye and hair prediction, hit rates between 51.3 and 68.9% were achieved. Despite the difficulties with intermediate phenotypes, we have shown that HIrisPlex results can be very helpful when interpreted with caution.
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Affiliation(s)
- Thássia Mayra Telles Carratto
- Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes, 3900, SP, 14040-901, Ribeirão Preto, Brazil
| | - Letícia Marcorin
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, 14049-900, Brazil
| | - Guilherme do Valle-Silva
- Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes, 3900, SP, 14040-901, Ribeirão Preto, Brazil
| | | | - Eduardo Antônio Donadi
- Divisão de Imunologia Clínica, Departamento de Clínica Médica, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, 14048-900, Brazil
| | - Aguinaldo Luiz Simões
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, 14049-900, Brazil
| | - Erick C Castelli
- Departamento de Patologia, Faculdade de Medicina de Botucatu, Unesp - Universidade Estadual Paulista, Botucatu, SP, 18618-970, Brazil
| | - Celso Teixeira Mendes-Junior
- Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes, 3900, SP, 14040-901, Ribeirão Preto, Brazil.
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Zheng J, Huo D, Wen H, Shang Q, Sun W, Xu Z. Corneal-Smart Phone: A novel method to intelligently estimate postmortem interval. J Forensic Sci 2020; 66:356-364. [PMID: 33112427 DOI: 10.1111/1556-4029.14611] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 11/29/2022]
Abstract
The changes of postmortem corneal opacity are often used to roughly estimate the postmortem interval (PMI) in forensic practice. The difficulty associated with this time estimate is the lack of objective means to rapidly quantify postmortem corneal changes in crime scenes. This study constructed a data analysis model of PMI estimation and implemented an intelligent analysis system for examining the sequential changes of postmortem corneal digital images, named Corneal-Smart Phone, which can be used to quickly estimate PMI. The smart phone was used in combination with an attachment device that provided a darkroom environment and a steady light source to capture postmortem corneal images. By segmenting the corneal pupil region images, six color features, Red (R), Green (G), Blue (B), Hue (H), Saturation (S), Brightness (V) and four texture features Contrast (CON), Correlation (COR), Angular Second Moment (ASM), and Homogeneity (HOM), were extracted and correlated with PMI model. The results indicated that CON had the highest correlation with PMI (R2 = 0.983). No intra/intersubject variation in CON values were observed (p > 0.05). With the increase in ambient temperature or the decrease in humidity, the CON values were increased. PMI prediction error was <3 h within 36 h postmortem and extended to about 6-8 h after 36 h postmortem. The correct classification rate of the blind test samples was 82%. Our study provides a method that combines postmortem corneal image acquisition and digital image analysis to enable users to quickly obtain PMI estimation.
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Affiliation(s)
- JiLong Zheng
- Department of Forensic Medicine, Criminal Investigation Police University of China, Shenyang, China
| | - DeMin Huo
- Criminal Investigation Division of Jiading District Bureau of Shanghai Public Security Bureau, Shanghai, China
| | - HongYang Wen
- Center of Software Research and Development, Criminal Investigation Police University of China, Shenyang, China
| | - QingFa Shang
- Department of Forensic Medicine, Criminal Investigation Police University of China, Shenyang, China
| | - WenKai Sun
- Department of Forensic Medicine, Criminal Investigation Police University of China, Shenyang, China
| | - ZiTong Xu
- Department of Forensic Medicine, Criminal Investigation Police University of China, Shenyang, China
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Evaluation of HIrisplex-S system markers for eye, skin and hair color prediction in an admixed Brazilian population. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Zheng J, Huo D, Wang J, Zhao K, Teng Y, Ma Y. [Temporal pattern of postmortem color changes in the pupil region of the cornea in rabbits]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2018; 38:1266-1269. [PMID: 30377122 DOI: 10.3969/j.issn.1673-4254.2018.10.19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
OBJECTIVE To explore the temporal pattern of postmortem color changes in the pupil region of the cornea for noninvasive estimation of the postmortem interval (PMI). METHODS Two rabbit models of air embolism and drowning were established in a dark room at a temperature of 20 ℃ with a relative humidity of 30%. The corneal images of the rabbits were acquired using a digital camera at two-hour intervals within 72 h after death. The pupil region on the corneal images was segmented using computer image processing technique (MATLAB), and the parameters of 6 image color features (RGBHSV) were extracted. Regression analysis was used to analyze the relationship between these parameters and the PMI, and the effects of different death causes on the changes of the corneal color features were also assessed. RESULTS Within 72 h after death from different causes, the R, G and B values of the pupil region on the corneal images all tended to increase with the PMI, showing a good fitting with the PMI (P < 0.01). No significant correlation was found between the values of H, S and V and the PMI (P>0.05). The R, G and B values in the pupil region on the corneal images showed consistent variation trends after death from the two causes, and their correlations with PMI were also similar. The measured values of R, G and B in air embolism group were greater than those in the drowning group. CONCLUSIONS The postmortem color changes of the pupil region on corneal images follow an identifiable temporal pattern and can vary across different causes of death. The regression equations established in this study provide references for non-invasive and objective estimation of the PMI.
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Affiliation(s)
- Jilong Zheng
- Department of Forensic Medicine, Criminal Investigation Police University of China, Shenyang 110035, China
| | - Demin Huo
- Department of Forensic Medicine, Criminal Investigation Police University of China, Shenyang 110035, China
| | - Jiulin Wang
- Criminal Investigation Brigade of Nanchang Public Security Bureau, Nanchang 330000, China
| | - Kaifang Zhao
- Department of Forensic Medicine, Criminal Investigation Police University of China, Shenyang 110035, China
| | - Yue Teng
- Department of Forensic Medicine, Criminal Investigation Police University of China, Shenyang 110035, China
| | - Yu Ma
- Department of Forensic Medicine, Criminal Investigation Police University of China, Shenyang 110035, China
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