scholarly journals Forensic DNA Phenotyping: starting point to prediction model in Pernambuco population, Brazil

2021 ◽  
Vol 10 (13) ◽  
pp. e262101320955
Author(s):  
Juliana Maria de Souza ◽  
Michael Lopes Bastos ◽  
Bárbara de Oliveira Silva ◽  
Karla Giselle Gomes de Lima ◽  
Giwellington Silva de Albuquerque ◽  
...  
Keyword(s):  
Skin Color ◽  
Prediction Models ◽  
Nucleotide Polymorphisms ◽  
Forensic Dna ◽  
Single Nucleotide ◽  
New Information ◽  
Starting Point ◽  
Color Data ◽  
The One ◽  
Few Data

The study of Externally Visible Characteristics (EVC) of pigmentation associated with SNPs (Single Nucleotide Polymorphisms) has become a target in the forensic field due to the possibility of phenotypically characterizing an individual. In Brazil, there are few data that shows the evaluation of some these markers, so further studies are necessary to understand better the pigmentation process related to genetic markers. The aim of this study was to test the association between 8 SNPs  present in HIrisplex tool and EVC to provide a starting point for the development of prediction models for heterogeneous populations like the one in Pernambuco. Were evaluated 176 individuals by associations between self-reported eye, hair and skin color data and polymorphisms. Artificial intelligence tools were used for the prediction models. Significant associations were found between rs1800404 (OCA2), rs6058017 (ASIP), rs16891982 (SLC45A2) and rs1426654 (SLC24A5) with (EVC). The prediction models evaluated showed satisfactory prediction rates, rates above 60% for skin color and above 70% for eyes and hair. The associations found in our data show the importance of SNPs evaluation used in DNA Phenotyping, because of its ability to provide new information in the context of criminal investigations. Our data indicate that is possible to use molecular information to predict phenotypes in miscigenated populations, like the Brazilian population. These polymorphisms could be possible phenotypic predictors for the Pernambuco population.

scholarly journals Evaluation of the VISAGE Basic Tool for Appearance and Ancestry Prediction Using PowerSeq Chemistry on the MiSeq FGx System

Genes ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 708 ◽  
Author(s):  
Leire Palencia-Madrid ◽  
Catarina Xavier ◽  
María de la Puente ◽  
Carsten Hohoff ◽  
Christopher Phillips ◽  
...  
Keyword(s):  
Skin Color ◽  
Massively Parallel Sequencing ◽  
Forensic Genetics ◽  
Nucleotide Polymorphisms ◽  
Forensic Dna ◽  
Basic Tool ◽  
Single Nucleotide ◽  
Technical Developments ◽  
Biogeographical Ancestry ◽  
Forensic Dna Phenotyping

The study of DNA to predict externally visible characteristics (EVCs) and the biogeographical ancestry (BGA) from unknown samples is gaining relevance in forensic genetics. Technical developments in Massively Parallel Sequencing (MPS) enable the simultaneous analysis of hundreds of DNA markers, which improves successful Forensic DNA Phenotyping (FDP). The EU-funded VISAGE (VISible Attributes through GEnomics) Consortium has developed various targeted MPS-based lab tools to apply FDP in routine forensic analyses. Here, we present an evaluation of the VISAGE Basic tool for appearance and ancestry prediction based on PowerSeq chemistry (Promega) on a MiSeq FGx System (Illumina). The panel consists of 153 single nucleotide polymorphisms (SNPs) that provide information about EVCs (41 SNPs for eye, hair and skin color from HIrisPlex-S) and continental BGA (115 SNPs; three overlap with the EVCs SNP set). The assay was evaluated for sensitivity, repeatability and genotyping concordance, as well as its performance with casework-type samples. This targeted MPS assay provided complete genotypes at all 153 SNPs down to 125 pg of input DNA and 99.67% correct genotypes at 50 pg. It was robust in terms of repeatability and concordance and provided useful results with casework-type samples. The results suggest that this MPS assay is a useful tool for basic appearance and ancestry prediction in forensic genetics for users interested in applying PowerSeq chemistry and MiSeq for this purpose.

scholarly journals Associations of hypertension Diabetes Smoking History and SNPs with Responses to Aflibercept Treatment for tAMD and PCV

2019 ◽  
pp. 170-177
Author(s):  
Tanaka K ◽  
Furuya K ◽  
Mori R ◽  
Kawamura A ◽  
Yuzawa M ◽  
...  
Keyword(s):  
Diabetes Mellitus ◽  
Initial Treatment ◽  
Smoking History ◽  
Diabetic Patients ◽  
Therapeutic Effects ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
History Of ◽  
One Year ◽  
The One

Purpose: To determine the correlation between therapeutic effects of IVA treatment on typical AMD (tAMD), and polypoidal choroidal vasculopathy (PCV) and the history of hypertension, diabetes mellitus, smoking history and single nucleotide polymorphisms (SNPs).Methods: Prospective, interventional study. Subjects were assigned to 125 untreated patients with exudative AMD (tAMD: 58 patients, PCV: 67 patients, male: 91:34, mean age 73.4 years). Among the tAMD patients, there were 28 bimonthly injections 30 who received pro re nata (PRN) injections after three monthly injections. Among the PCV patients, 33 were treated with bimonthly injections and 34 received PRN injections after three monthly injections. Therapeutic effects were evaluated by best-corrected visual acuity (BCVA), central retinal thickness (CRT), subfoveal choroidal thickness (CCT), and exudative change after 3 months and 1 year from initial treatment, and also the history of hypertension, diabetes mellitus, smoking and five SNPs (rs10490924, rs800292, rs699947, rs1061170, rs13278062).Results: Improvements of BCVA, CRT were observed in all groups at 1 year after initial treatment. The one-yearchange in CRT showed significant improvement in nonsmokers than smokers in tAMD. The one-year change in CRT indicated a significant improvement in non-diabetic patients in PCV. There was more exudation at both 3 months and 1 year who had smoking history in tAMD. With respect to the rs1061170 mutation of tAMD, in the case with TT type, significant residual exudation was noted at both 3 and 12 months.Conclusions: The history of smoking and diabetes could be influence to IVA treatment for AMD.

scholarly journals Prediction of Early Childhood Caries Based on Single Nucleotide Polymorphisms Using Neural Networks

Genes ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 462
Author(s):  
Katarzyna Zaorska ◽  
Tomasz Szczapa ◽  
Maria Borysewicz-Lewicka ◽  
Michał Nowicki ◽  
Karolina Gerreth
Keyword(s):  
Neural Network ◽  
Early Childhood ◽  
Logistic Regression ◽  
Single Nucleotide Polymorphisms ◽  
Early Childhood Caries ◽  
Prediction Models ◽  
Oral Epithelium ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Childhood Caries

Background: Several genes and single nucleotide polymorphisms (SNPs) have been associated with early childhood caries. However, they are highly age- and population-dependent and the majority of existing caries prediction models are based on environmental and behavioral factors only and are scarce in infants. Methods: We examined 6 novel and previously analyzed 22 SNPs in the cohort of 95 Polish children (48 caries, 47 caries-free) aged 2–3 years. All polymorphisms were genotyped from DNA extracted from oral epithelium samples. We used Fisher’s exact test, receiver operator characteristic (ROC) curve and uni-/multi-variable logistic regression to test the association of SNPs with the disease, followed by the neural network (NN) analysis. Results: The logistic regression (LogReg) model showed 90% sensitivity and 96% specificity, overall accuracy of 93% (p < 0.0001), and the area under the curve (AUC) was 0.970 (95%CI: 0.912–0.994; p < 0.0001). We found 90.9–98.4% and 73.6–87.2% prediction accuracy in the test and validation predictions, respectively. The strongest predictors were: AMELX_rs17878486 and TUFT1_rs2337360 (in both LogReg and NN), MMP16_rs1042937 (in NN) and ENAM_rs12640848 (in LogReg). Conclusions: Neural network prediction model might be a substantial tool for screening/early preventive treatment of patients at high risk of caries development in the early childhood. The knowledge of potential risk status could allow early targeted training in oral hygiene and modifications of eating habits.

scholarly journals Development and Implementation of Polygenic Risk Score in Vietnamese Population

2019 ◽  
Vol 2019 (2) ◽  
pp. 75-83
Author(s):  
Nguyễn Trần Thế Hùng ◽  
Lê Đức Hậu
Keyword(s):  
Risk Score ◽  
Prediction Models ◽  
European Ancestry ◽  
Polygenic Risk Score ◽  
Clinical Settings ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Polygenic Risk ◽  
Vietnamese Population ◽  
Artery Disease

Recent technological advancements and availability of genetic databases have facilitated the integration of genetic factors into risk prediction models. A Polygenic Risk Score (PRS) combines the effect of many Single Nucleotide Polymorphisms (SNP) into a single score. This score has lately been shown to have a clinically predictive value in various common diseases. Some clinical interpretations of PRS are summarized in this review for coronary artery disease, breast cancer, prostate cancer, diabetes mellitus, and Alzheimer’s disease. While these findings gave support to the implementation of PRS in clinical settings, the populations of interest were derived mainly from European ancestry. Therefore, applying these findings to non-European ancestry (Vietnamese in this context) requires many efforts and cautions. This review aims to articulate the evidence supporting the clinical use of PRS, the concepts behind the validity of PRS, approach to implement PRS in Vietnamese population, and cautions in selecting methods and thresholds to develop an appropriate PRS.

scholarly journals Developing a high resolution melting method for genotyping and predicting association of SNP rs353291 with breast cancer in the Vietnamese population

2017 ◽  
Vol 4 (12) ◽  
pp. 1812 ◽  
Author(s):  
Luan Huu Huynh ◽  
Phuong Thi-Kim Bui ◽  
Thanh Thi-Ngoc Nguyen ◽  
Hue Thi Nguyen
Keyword(s):  
Breast Cancer ◽  
High Resolution ◽  
High Resolution Melting ◽  
Risk Allele ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
P Values ◽  
Potential Biomarker ◽  
Vietnamese Population ◽  
The One

Introduction: Breast cancer is the one of the most common types of cancer as well as the second leading cause of cancer death in women in the world. In recent studies, microRNAs (miRNAs) have been demonstrated to play a crucial role as a new potential biomarker in the association with breast cancer. Single Nucleotide Polymorphisms (SNPs) located on specific miRNA may result in breast cancer. Among the SNPs, SNP rs353291 has shown to be associated with breast cancer in individuals of Caucasian background. Furthermore, this SNP is observed in a high percentage of mutant alleles in the Vietnamese population. Thus, SNP rs353291 was selected as a candidate SNP for investigation in this study. The frequency of SNP rs353291 was evaluated by High Resolution Melting (HRM) method, which is a highly powerful method to detect variants in DNA sequence, especially for SNP genotyping. Methods: In this study, the association between this SNP and risk of breast cancer in the Vietnamese population was evaluated in 90 cases and 96 healthy controls via genotyping using an optimized HRM protocol. Result: The genotyping results revealed that SNP rs353291 is a polymorphism in the Vietnamese population. We have successfully identified frequencies of AA, AG and GG to be 40%, 42.2% and 17.8%, respectively. In particular, the calculated frequencies of allele G was 61.1% while risk allele A was 38.9%. The association between this SNP and breast cancer in Vietnam revealed that there is an obvious decreased risk of breast cancer among Vietnamese population when comparing G allele to A allele (G vs A: OR=0.92, 95% CI: 0.62-1.36, p= 0.677); the results also showed that heterozygote model had a reduced risk of breast cancer compared to dominant model (GA+GG vs AA: OR=0.94, 95% CI: 0.52-1.70, p=0.839). Conclusion: However, since the p-values were >0.05, our results only show a correlation rather than a significant association between SNP rs353291 and breast cancer risk in the Vietnamese population.

scholarly journals The Plateau Method for Forensic DNA SNP Mixture Deconvolution

2017 ◽  
Author(s):  
Darrell O. Ricke ◽  
Joe Isaacson ◽  
James Watkins ◽  
Philip Fremont-Smith ◽  
Tara Boettcher ◽  
...  
Keyword(s):  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
High Throughput Sequencing ◽  
Nucleotide Polymorphisms ◽  
Forensic Dna ◽  
Dna Mixtures ◽  
Single Nucleotide ◽  
Mixture Deconvolution ◽  
Dna Mixture ◽  
Short Tandem

AbstractIdentification of individuals in complex DNA mixtures remains a challenge for forensic analysts. Recent advances in high throughput sequencing (HTS) are enabling analysis of DNA mixtures with expanded panels of Short Tandem Repeats (STRs) and/or Single Nucleotide Polymorphisms (SNPs). We present the plateau method for direct SNP DNA mixture deconvolution into sub-profiles based on differences in contributors’ DNA concentrations in the mixtures in the absence of matching reference profiles. The Plateau method can detect profiles of individuals whose contribution is as low as 1/200 in a DNA mixture (patent pending)1.

scholarly journals THE ASSOCIATION OF ERAP2 GENE POLYMORPHISMS WITH SERONEGATIVE SPONDYLOARTHROPATHIES IN HLA-B27 NEGATIVE ROMANIANS

2016 ◽  
Vol 25 (2) ◽  
pp. 78-87
Author(s):  
Laura Ioana Cherciu ◽  
◽  
Marius Cherciu ◽  
Luis Ovidiu Popa ◽  
Mihai Bojinca ◽  
...  
Keyword(s):  
Gene Polymorphisms ◽  
Minor Allele ◽  
Nucleotide Polymorphisms ◽  
Hla B27 ◽  
Single Nucleotide ◽  
Seronegative Spondyloarthropathies ◽  
Polymerase Chain ◽  
The One ◽  
Negative Controls ◽  
Control Study

Objective. Our aim was to investigate whether two ERAP2 single nucleotide polymorphisms (rs2910686 and rs2248374) influence spondyloarthritis (SpA) susceptibility in Romanians. Methods. The case control study included 139 controls and 192 SpA patients. The two polymorphisms were genotyped by real time polymerase chain reaction (RT-PCR). The association tests for allele, genotype and haplotype frequencies for each polymorphism were performed with PLINK 1.9. Results. The genotypes and allele frequencies of the two SNPs in general SpA group vs. controls showed no association except for a possible marginal one for the minor allele A of rs2248374 (p = 0.08). In HLA-B27 negative SpA cohort the minor allele (A) frequency (55.4%) of SNP rs2248374 was significantly higher than the one in HLA-B27 controls (44.5%) (p = 0.012). HLA-B27 negative carriers of minor allele A present a higher risk of developing SpA (p = 0.015). Also for the second ERAP2 gene variant investigated (rs2910686) the minor allele T frequency was significantly higher (46.5%) in HLA-B27 negative SPA patients when compared with HLA-B27 negative controls (36%) (p = 0.02). The haplotype of the minor alleles (AC) is a risk factor for HLA-B27 negative SpA (p = 0.019), while the haplotype of the major alleles (GT) is a protective one against the disease in HLA-B27 negative cohorts (p = 0.009). Conclusions. Both ERAP2 gene polymorphisms investigated, especially rs2248374, influence SpA susceptibility, but this influence is limited only to the HLA-B27 negative individuals.

scholarly journals TranslucentID: Detecting Individuals with High Confidence in Saturated DNA SNP Mixtures

2018 ◽  
Author(s):  
Darrell O. Ricke ◽  
James Watkins ◽  
Philip Fremont-Smith ◽  
Tara Boettcher ◽  
Eric Schwoebel
Keyword(s):  
High Throughput Sequencing ◽  
Nucleotide Polymorphisms ◽  
Forensic Dna ◽  
Mixture Analysis ◽  
High Confidence ◽  
Dna Mixtures ◽  
Single Nucleotide ◽  
Minor Alleles ◽  
Dna Mixture ◽  
Mixture Samples

AbstractHigh throughput sequencing (HTS) of complex DNA mixtures with single nucleotide polymorphisms (SNPs) panels can identify multiple individuals in forensic DNA mixture samples. SNP mixture analysis relies upon the exclusion of non-contributing individuals with the subset of SNP loci with no detected minor alleles in the mixture. Few, if any, individuals are anticipated to be detectable in saturated mixtures by this mixture analysis approach because of the increased probability of matching random individuals. Being able to identify a subset of the contributors in saturated HTS SNP mixtures is valuable for forensic investigations. A desaturated mixture can be created by treating a set of SNPs with the lowest minor allele ratios as having no minor alleles. Leveraging differences in DNA contributor concentrations in saturated mixtures, we introduce TranslucentID for the identification of a subset of individuals with high confidence who contributed DNA to saturated mixtures by desaturating the mixtures.

scholarly journals The face as folded object: Race and the problems with ‘progress’ in forensic DNA phenotyping

2021 ◽  
pp. 030631272110355
Author(s):  
Roos Hopman
Keyword(s):  
Twentieth Century ◽  
Skin Color ◽  
Scientific Progress ◽  
Scientific Practices ◽  
Forensic Dna ◽  
Facial Shape ◽  
The Face ◽  
Color Data ◽  
Collection Practices ◽  
Forensic Dna Phenotyping

Forensic DNA phenotyping (FDP) encompasses a set of technologies aimed at predicting phenotypic characteristics from genotypes. Advocates of FDP present it as the future of forensics, with an ultimate goal of producing complete, individualised facial composites based on DNA. With a focus on individuals and promised advances in technology comes the assumption that modern methods are steadily moving away from racial science. Yet in the quantification of physical differences, FDP builds upon some nineteenth- and twentieth-century scientific practices that measured and categorised human variation in terms of race. In this article I complicate the linear temporal approach to scientific progress by building on the notion of the folded object. Drawing on ethnographic fieldwork conducted in various genetic laboratories, I show how nineteenth- and early twentieth-century anthropological measuring and data-collection practices and statistical averaging techniques are folded into the ordering of measurements of skin color data taken with a spectrophotometer, the analysis of facial shape based on computational landmarks and the collection of iris photographs. Attending to the historicity of FDP facial renderings, I bring into focus how race comes about as a consequence of temporal folds.

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