Academic literature on the topic 'Ancestry prediction'
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Journal articles on the topic "Ancestry prediction"
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Oldoni, Fabio, Rebecca Hart, Kelly Long, Kathrina Maddela, Selena Cisana, Moses Schanfield, Sharon Wootton, et al. "Microhaplotypes for ancestry prediction." Forensic Science International: Genetics Supplement Series 6 (December 2017): e513-e515. http://dx.doi.org/10.1016/j.fsigss.2017.09.209.
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C, Omuruka T., Osunwoke Osunwoke, E. A, Edibamode Edibamode, and E. I. "Palmar Creases and Ancestry Prediction." Scholars International Journal of Anatomy and Physiology 5, no. 2 (February 16, 2022): 41–49. http://dx.doi.org/10.36348/sijap.2022.v05i02.003.
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Background: The importance and usefulness of dermatoglyphics in crime investigation, anthropology and disease prediction have been stressed wide published. However, there is dearth of information on the use of palmar creases as an adjunct tool in the prediction of tribe/ethnicity and ancestral relationship among populations. Hence, this study was aimed at predicting ancestry and tribal/ethnic relationship and genetic link among the Urhobo, Isoko and Ogoni ethnic groups using palmar creases. Materials and Methods: In this cross-sectional, observational and analytical study, 360 subjects- 180, 105 and 75 Urhobo, Ogoni and Isoko subjects were sampled via a multi-stage sampling technique to ensure randomization. Palm print was obtained using Oghenemavwe and Osaat (2015) dermatoglyphic capture method. Statistical analysis was performed using Statistical Package for the Social (SPSS IBM version 23.0). Results and Discussions: Using the Ogoni as a reference tribe, the study (Table 1) showed Pearson's Chi-square Analysis for tribe-associated differences in the distribution of pattern based on type/pattern of head of origin of the major palmar creases on the right and left palms, and this was not statistically significant on both palms. But in Table 2a (tribe-associated differences in the distribution of the general shape/appearance of palmar creases on the right and left palms) was observed to be statistically significant (X2 = 73.283, P = 0.001 for right; X2 = 47.786, P = 0.001 for left) and Table 3a showed that tribe-associated differences in the distribution of Middle longitudinal crease on the right and left palms was statistically significant (X2 = 18.135, P = 0.001 for right; X2 = 36.401, P = 0.001 for left). Conclusion: Middle longitudinal crease in particular and general shape/appearance of palmar creases are discriminatory in distribution amongst the tribe studied and thus suggest a tribal/ethnic relationship and genetic link and common ancestry between the Isoko and Urhobo tribes.
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Moshkov, Nikita, Aleksandr Smetanin, and Tatiana V. Tatarinova. "Local ancestry prediction with PyLAE." PeerJ 9 (December 14, 2021): e12502. http://dx.doi.org/10.7717/peerj.12502.
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Summary We developed PyLAE, a new tool for determining local ancestry along a genome using whole-genome sequencing data or high-density genotyping experiments. PyLAE can process an arbitrarily large number of ancestral populations (with or without an informative prior). Since PyLAE does not involve estimating many parameters, it can process thousands of genomes within a day. PyLAE can run on phased or unphased genomic data. We have shown how PyLAE can be applied to the identification of differentially enriched pathways between populations. The local ancestry approach results in higher enrichment scores compared to whole-genome approaches. We benchmarked PyLAE using the 1000 Genomes dataset, comparing the aggregated predictions with the global admixture results and the current gold standard program RFMix. Computational efficiency, minimal requirements for data pre-processing, straightforward presentation of results, and ease of installation make PyLAE a valuable tool to study admixed populations. Availability and implementation The source code and installation manual are available at https://github.com/smetam/pylae.
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Lippert, Christoph, Riccardo Sabatini, M. Cyrus Maher, Eun Yong Kang, Seunghak Lee, Okan Arikan, Alena Harley, et al. "Identification of individuals by trait prediction using whole-genome sequencing data." Proceedings of the National Academy of Sciences 114, no. 38 (September 5, 2017): 10166–71. http://dx.doi.org/10.1073/pnas.1711125114.
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Prediction of human physical traits and demographic information from genomic data challenges privacy and data deidentification in personalized medicine. To explore the current capabilities of phenotype-based genomic identification, we applied whole-genome sequencing, detailed phenotyping, and statistical modeling to predict biometric traits in a cohort of 1,061 participants of diverse ancestry. Individually, for a large fraction of the traits, their predictive accuracy beyond ancestry and demographic information is limited. However, we have developed a maximum entropy algorithm that integrates multiple predictions to determine which genomic samples and phenotype measurements originate from the same person. Using this algorithm, we have reidentified an average of >8 of 10 held-out individuals in an ethnically mixed cohort and an average of 5 of either 10 African Americans or 10 Europeans. This work challenges current conceptions of personal privacy and may have far-reaching ethical and legal implications.
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Bitarello, Bárbara D., and Iain Mathieson. "Polygenic Scores for Height in Admixed Populations." G3: Genes|Genomes|Genetics 10, no. 11 (September 2, 2020): 4027–36. http://dx.doi.org/10.1534/g3.120.401658.
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Polygenic risk scores (PRS) use the results of genome-wide association studies (GWAS) to predict quantitative phenotypes or disease risk at an individual level, and provide a potential route to the use of genetic data in personalized medical care. However, a major barrier to the use of PRS is that the majority of GWAS come from cohorts of European ancestry. The predictive power of PRS constructed from these studies is substantially lower in non-European ancestry cohorts, although the reasons for this are unclear. To address this question, we investigate the performance of PRS for height in cohorts with admixed African and European ancestry, allowing us to evaluate ancestry-related differences in PRS predictive accuracy while controlling for environment and cohort differences. We first show that the predictive accuracy of height PRS increases linearly with European ancestry and is partially explained by European ancestry segments of the admixed genomes. We show that recombination rate, differences in allele frequencies, and differences in marginal effect sizes across ancestries all contribute to the decrease in predictive power, but none of these effects explain the decrease on its own. Finally, we demonstrate that prediction for admixed individuals can be improved by using a linear combination of PRS that includes ancestry-specific effect sizes, although this approach is at present limited by the small size of non-European ancestry discovery cohorts.
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Cheung, Elaine Y. Y., Michelle Elizabeth Gahan, and Dennis McNevin. "Prediction of biogeographical ancestry in admixed individuals." Forensic Science International: Genetics 36 (September 2018): 104–11. http://dx.doi.org/10.1016/j.fsigen.2018.06.013.
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Jin, Xiao-Ye, Yu-Xin Guo, Chong Chen, Wei Cui, Yan-Fang Liu, Yun-Chun Tai, and Bo-Feng Zhu. "Ancestry Prediction Comparisons of Different AISNPs for Five Continental Populations and Population Structure Dissection of the Xinjiang Hui Group via a Self-Developed Panel." Genes 11, no. 5 (May 4, 2020): 505. http://dx.doi.org/10.3390/genes11050505.
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Ancestry informative markers are genetic markers that show distinct genetic divergences among different populations. These markers can be utilized to discern population substructures and estimate the ancestral origins of unknown individuals. Previously, we developed a multiplex system of 30 ancestry informative single nucleotide polymorphism (AISNP) loci to facilitate ancestral inferences in different continental populations. In the current study, we first compared the ancestry resolutions of the 30 AISNPs and the other previously reported AISNP panels for African, European, East Asian, South Asian and American populations. Next, the genetic components of the Xinjiang Hui group were further explored in comparison to these continental populations based on the 30 AISNPs. Genetic divergence analyses of the 30 AISNPs in these five continental populations revealed that most of the AISNPs showed high genetic differentiations between these populations. Ancestry analysis comparisons of the 30 AISNPs and other published AISNPs revealed that these 30 AISNPs had comparable efficiency to other AISNP panels. Genetic relationship analyses among the studied Hui group and other continental populations demonstrated that the Hui group had close genetic affinities with East Asian populations and might share the genetic ancestries with East Asian populations. Overall, the 30 AISNPs can be used to predict the bio-geographical origins of different continental populations. Moreover, the obtained genetic data of 30 AISNPs in the Hui group can further enrich the extant reference data, which can be used as reference data for ancestry analyses of the Hui group.
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Szeniczey, Tamás. "A nazomaláris szög és szimotikus húr alkalmazása metrikus alapú taxonómiai osztályozási feladatokban." Anthropologiai Közlemények 61 (2020): 53–62. http://dx.doi.org/10.20330/anthropkozl.2020.61.53.
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Ancestry can be estimated in a probabilistic framework using facial morphological signatures of the different population histories. While the assessment of qualitative traits requires more experience, the measurement of the most distinctive quantitative characters usually demands anthropological tools seldom available. However, some of the facial measurements related to ancestry can be easily recorded with a caliper. The study aims to present the efficiency of simotic chord (SC) and nasomalar angle (M77) in ancestry estimation by applying supervised and unsupervised algorithms to classify skulls with European and Asian ancestry. Linear discriminant analysis and Gaussian Mixture models were applied to a subset of the Howells’ craniometric dataset comprised of individuals with European and Asian ancestry. Prediction of ancestry was carried out on a set of craniometric traits describing height, length and width parameters of the crania and then repeated on this set supplemented with M77 and SC measurements. An increased percentage of true positive prediction of ancestry was achieved by involving the M77 and SC measurements.
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Butler, Katherine, Michelle Peck, Jessica Hart, Moses Schanfield, and Daniele Podini. "Molecular “eyewitness”: Forensic prediction of phenotype and ancestry." Forensic Science International: Genetics Supplement Series 3, no. 1 (December 2011): e498-e499. http://dx.doi.org/10.1016/j.fsigss.2011.09.109.
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Mukadam, Naaheed, Olga Giannakopoulou, Nick Bass, Karoline Kuchenbaecker, and Andrew McQuillin. "Genetic risk scores and dementia risk across different ethnic groups in UK Biobank." PLOS ONE 17, no. 12 (December 7, 2022): e0277378. http://dx.doi.org/10.1371/journal.pone.0277378.
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Background Genetic Risk Scores (GRS) for predicting dementia risk have mostly been used in people of European ancestry with limited testing in other ancestry groups. Methods We conducted a logistic regression with all-cause dementia as the outcome and z-standardised GRS as the exposure across diverse ethnic groups. Findings There was variation in frequency of APOE alleles across ethnic groups. Per standard deviation (SD) increase in z-GRS including APOE, the odds ratio (OR) for dementia was 1.73 (95%CI 1.69–1.77). Z-GRS excluding APOE also increased dementia risk (OR 1.21 per SD increase, 95% CI 1.18–1.24) and there was no evidence that ethnicity modified this association. Prediction of secondary outcomes was less robust in those not of European ancestry when APOE was excluded from the GRS. Interpretation z-GRS derived from studies in people of European ancestry can be used to quantify genetic risk in people from more diverse ancestry groups. Urgent work is needed to include people from diverse ancestries in future genetic risk studies to make this field more inclusive.
Dissertations / Theses on the topic "Ancestry prediction"
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Allocco, Dominic. "Use of machine learning techniques for SNP based prediction of ancestry." Thesis, Massachusetts Institute of Technology, 2006. http://hdl.handle.net/1721.1/35550.
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Thesis (S.M.)--Harvard-MIT Division of Health Sciences and Technology, 2006.Includes bibliographical references (leaves 29-30).
Some have argued that the genetic differences between continentally defined groups are relatively small and unlikely to have biomedical significance. In this study, the extent of variation between continentally defined groups was evaluated. Small numbers of randomly selected single nucleotide polymorphisms from the International HapMap Project were used to train classifiers for prediction of ancestral continent of origin. Predictive accuracy was then tested on independent data sets. A high degree of genetic similarity implies that groups will be difficult to distinguish, especially when only a limited amount of genetic information is used. It is shown that the genetic differences between continentally defined groups are sufficiently large that one can accurately predict ancestral continent of origin using only a minute, randomly selected fraction of the genetic variation present in the human genome. Genotype data from only 50 random single nucleotide polymorphisms can be used to predict ancestral continent of origin in the primary test data set with an average accuracy of 95%.
(cont.) Single nucleotide polymorphisms were also characterized as being in introns, coding exons, regulatory regions and regions coding for untranslated mRNA and classifiers constructed using only single nucleotide polymorphisms from a specific category. Predictive accuracy was similar across all of the classifiers created in this manner. Single nucleotide polymorphisms useful for prediction of ancestral continent of origin are common and distributed relatively evenly throughout the genome. These findings demonstrate the extent of variation between continentally defined groups and argue strongly against the contention that genetic differences between groups are too small to have biomedical significance.
by Dominic J. Allocco.
S.M.
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James, Kyle. "DNA-MAP, a knowledge-based decision support system for Australian Defence Force forensic ancestry prediction." Thesis, Queensland University of Technology, 2021. https://eprints.qut.edu.au/213211/1/Kyle_James_Thesis.pdf.
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Development of a Knowledge-Based Decision Support System to predict ancestry of the remains of missing World War Two soldiers in South-East Asia. By utilizing biological and historical information provided by the user, ancestry is assigned based on complex statistical analyses searching for distinctive patterns in the DNA that distinguish between the Australian and Japanese populations. Important features taken into consideration are the detection of a rare event, the effect of sample size and the impact of natural variation.
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Ghaiyed, Andrew Peter. "A genomic ancestry panel for Australian and Japanese WWII military remains recovered in the Asia-Pacific." Thesis, Queensland University of Technology, 2021. https://eprints.qut.edu.au/211296/1/Andrew_Ghaiyed_Thesis.pdf.
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The Ghaiyed population-specific panel (GPSP) is an ancestry prediction strategy comprised of ancestry-informative DNA markers that was developed to assist Unrecovered War Casualties-Army (UWC-A) in the accounting of historical military remains. The GPSP was able to significantly increase the proportion of individuals that could be assigned ancestry compared to conventional methods used by the Forensic Science community and previous UWC-A methodology. The GPSP is supported by the novel application of admixture simulation tools and a modified Chi-square Automatic Interaction Detector/Probability Decision Tree (CHAID/PDT) method for ancestry classification, to more reliably account for the remains of those fallen in previous conflicts.
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Josey, Michelle. "Molecular-Genetic Methods for Predicting Bio-Geographical Ancestry From Bone Specimens to Aid in Forensic Identification." Honors in the Major Thesis, University of Central Florida, 2007. http://digital.library.ucf.edu/cdm/ref/collection/ETH/id/1036.
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This item is only available in print in the UCF Libraries. If this is your Honors Thesis, you can help us make it available online for use by researchers around the world by following the instructions on the distribution consent form at http://library.ucf.edu/Systems/DigitalInitiatives/DigitalCollections/InternetDistributionConsentAgreementForm.pdf You may also contact the project coordinator, Kerri Bottorff, at kerri.bottorff@ucf.edu for more information.Bachelors
Sciences
Forensic Science
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Alkindy, Bassam. "Combining approaches for predicting genomic evolution." Thesis, Besançon, 2015. http://www.theses.fr/2015BESA2012/document.
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En bio-informatique, comprendre comment les molécules d’ADN ont évolué au cours du temps reste un problème ouvert etcomplexe. Des algorithmes ont été proposés pour résoudre ce problème, mais ils se limitent soit à l’évolution d’un caractèredonné (par exemple, un nucléotide précis), ou se focalisent a contrario sur de gros génomes nucléaires (plusieurs milliardsde paires de base), ces derniers ayant connus de multiples événements de recombinaison – le problème étant NP completquand on considère l’ensemble de toutes les opérations possibles sur ces séquences, aucune solution n’existe à l’heureactuelle. Dans cette thèse, nous nous attaquons au problème de reconstruction des séquences ADN ancestrales en nousfocalisant sur des chaînes nucléotidiques de taille intermédiaire, et ayant connu assez peu de recombinaison au coursdu temps : les génomes de chloroplastes. Nous montrons qu’à cette échelle le problème de la reconstruction d’ancêtrespeut être résolu, même quand on considère l’ensemble de tous les génomes chloroplastiques complets actuellementdisponibles. Nous nous concentrons plus précisément sur l’ordre et le contenu ancestral en gènes, ainsi que sur lesproblèmes techniques que cette reconstruction soulève dans le cas des chloroplastes. Nous montrons comment obtenirune prédiction des séquences codantes d’une qualité telle qu’elle permette ladite reconstruction, puis comment obtenir unarbre phylogénétique en accord avec le plus grand nombre possible de gènes, sur lesquels nous pouvons ensuite appuyernotre remontée dans le temps – cette dernière étant en cours de finalisation. Ces méthodes, combinant l’utilisation d’outilsdéjà disponibles (dont la qualité a été évaluée) à du calcul haute performance, de l’intelligence artificielle et de la biostatistique,ont été appliquées à une collection de plus de 450 génomes chloroplastiquesIn Bioinformatics, understanding how DNA molecules have evolved over time remains an open and complex problem.Algorithms have been proposed to solve this problem, but they are limited either to the evolution of a given character (forexample, a specific nucleotide), or conversely focus on large nuclear genomes (several billion base pairs ), the latter havingknown multiple recombination events - the problem is NP complete when you consider the set of all possible operationson these sequences, no solution exists at present. In this thesis, we tackle the problem of reconstruction of ancestral DNAsequences by focusing on the nucleotide chains of intermediate size, and have experienced relatively little recombinationover time: chloroplast genomes. We show that at this level the problem of the reconstruction of ancestors can be resolved,even when you consider the set of all complete chloroplast genomes currently available. We focus specifically on the orderand ancestral gene content, as well as the technical problems this raises reconstruction in the case of chloroplasts. Weshow how to obtain a prediction of the coding sequences of a quality such as to allow said reconstruction and how toobtain a phylogenetic tree in agreement with the largest number of genes, on which we can then support our back in time- the latter being finalized. These methods, combining the use of tools already available (the quality of which has beenassessed) in high performance computing, artificial intelligence and bio-statistics were applied to a collection of more than450 chloroplast genomes
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Leneuve, Dorilas Malika. "Les facteurs de risque de la naissance prématurée en Guyane Française Rosk factors for premature birth in French Guiana: the importance of reducing health inegalities Predictive factors of preterms delivery in French Guiana for singleton pregnancies: definition and validation of a predictive score Risk Factors for Very Preterm Births in French Guiana : The Burden of Induced Preterm Birth African ancestry and the threshold defining preterm delivery: in French Guiana black babies born at 36 weeks are as vulnerable as white babies." Thesis, Guyane, 2019. http://www.theses.fr/2019YANE0003.
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Contexte et objectif : La Guyane Française, département-région d’outre-mer, compte près de 8 000 naissances par année.Depuis 1992, la proportion de naissances prématurées y est importante aux alentours de 13,5% ; soit presque le double de celle de la France (7%). Contrairement à la plupart des pays où une augmentation de la prématurité est observée, en Guyane, son taux est stable. Certes, on pourrait se satisfaire de cette non-augmentation, cependant, les décès liés à la périnatalité restent l’une des principales causes de mortalité prématurée dans ce département. Si en Guyane, le taux de prématurité n’augmente pas, il ne régresse pas non plus. Devant cette absence de régression, il semble important de comprendre les facteurs qui font qu’en Guyane, la prématurité reste si fréquente et si difficile à endiguer. Méthodologie : Ce travail de recherche se décline en quatre axes d'investigations : Une étude rétrospective descriptive, à partir des données du RIGI (Registre d’Issue de Grossesses Informatisé) 2013-2014 de 12 983 naissances viables du département. L’élaboration d’un score prédictif de prématurité à partir du RIGI 2013-2014, confronté aux données du RIGI 2015 de 6 914 naissances viables. Une étude étiologique cas-témoins de la grande prématurité, monocentrique, de Février 2016 à Janvier 2017 dans l’unique établissement de santé de type III de la Région. Enfin, l’analyse du terme moyen à la naissance et de la morbi-mortalité à partir du RIG (Registre d’Issue de Grossesses) 2002-2007 de 35 648 naissances viables et du RIGI 2013-2014. Résultats :Sur la période d’étude, la proportion de naissances prématurées était de 13,5% (1 755/12 983). La proportion de prématurité spontanée et induite était respectivement de 51,3% et 48,7% selon le RIGI 2013-2014.Plus de la moitié (57,2%) de la population d’étude bénéficiait de la sécurité sociale, néanmoins 9,3% (1 211/12 983) n’avait aucune couverture sociale. L’absence de couverture sociale représentait un facteur de risque de prématurité avec un OR ajusté de 1,9 IC à 95% [1,6-2,3] p=0,0001. De même, l’absence d’entretien prénatal tout comme celui de préparation à la naissance multiplieraient par deux le risque de naissance prématurée. D’autre part, le syndrome pré-éclamptique était la principale dysgravidie associée au risque de prématurité (OR ajusté de 6,7 [IC 95% =5,6-8,1] p=0,001). Enfin, l’hypothèse assez répandue, suggérant qu’une partie du taux de prématurité élevée serait liée du fait que les bébés « noirs » seraient plus matures et que les mères « noires » d’ascendance afro-caraibéenne accoucheraient physiologiquement plus tôt, ne ressortait pas dans nos analyses. En effet, il n’y avait pas de différence statistiquement significative de morbi-mortalité pour les nouveau-nés de mères d’origine afro-caribéennes et ceux de femmes caucasiennes.Conclusion : Les travaux réalisés ont retrouvé nombre de facteurs associés à la prématurité, pour certains déjà décrits par ailleurs. Bien qu’à l’échelle individuelle, il était impossible de prédire qui accoucherait prématurément, le poids des facteurs sociaux et du mauvais suivi de grossesse, suggéraient qu’une approche populationnelle pourrait être pertinente. Ainsi les femmes les plus vulnérables résidaient souvent dans des zones bien identifiées qui pourraient faire l’objet d’actions ciblées pour améliorer le suivi et dépister les complications. Cette problématique d’inégalités sociales de santé va bien au-delà de la prématurité et se retrouve pour presque toutes les pathologies, ce qui suggère qu’il y a des synergies à rechercher et que l’échelle populationnelle est sans doute stratégique. Le poids du syndrome pré-éclamptique comme facteur de risque de prématurité induite en Guyane pose question, il semble nettement plus important qu’ailleurs pour des raisons qui restent à éluciderContext and objective: French Guiana, an overseas department and region, has nearly 8,000 births per year.Since 1992, the proportion of premature births, although stable, has remained high at around 13.5%, almost double that of France (7%) (data from the Pregnancy Outcome Register and national perinatal survey). While in most countries we see an increase in prematurity, we could, wrongly, be satisfied with a non-increase in the prematurity rate that would reflect progress. However, deaths from perinatal causes remain one of the main causes of premature mortality in French Guiana and partly explain the gap with France in terms of life expectancy at birth.Given this lack of improvement in the prematurity rate, it seems important to better understand the factors that make prematurity so frequent and so difficult to control in French Guiana. The thesis focused on identifying the predictive factors of prematurity with the ultimate aim of contributing to improving the care of pregnant women and curbing the curve of the prematurity rate. Methodology: This research work is divided into 4 areas of investigation:- A descriptive retrospective study, based on data from the RIGI (Register of Computerized Pregnancy Outcomes) 2013-2014 of 12,983 viable births in the department,- The development of a predictive prematurity score from the 2013-2014 RIGI, compared to the 2015 RIGI data of 6,914 viable births,- A case-control etiological study of extreme prematurity, monocentric, from February 2016 to January 2017 in the only type III health-care institution in the French Guiana Region,- Analysis of the average term at birth and morbidity and mortality from the RIG (Register of Pregnancy Outcomes) 2002-2007 of 35,648 viable births and the RIGI 2013-2014.Results:Over the study period, the proportion of preterm births was 13.5% (1,755/12,983). The proportion of spontaneous prematurity was 51.3% , compared to 48.7% of induced prematurity. More than half (57.2% or 7 421/12 983) of the study population had social security, but 9.3% had no social security coverage. The lack of social security coverage was a risk factor for prematurity with an adjusted OR of 1.9 CI at 95% [1.6-2.3] p=0.0001. Similarly, with regard to pregnancy management, the absence of prenatal care as well as that of birth preparation would double the risk of premature birth. For pathologies associated with pregnancy, pre-eclampsia syndrome was the main dysgravidia associated with the risk of prematurity (OR adjusted by 6.7[95% CI =5.6-8.1] p=0.0001). Finally, the fairly common hypothesis that part of the high prematurity rate is related to the fact that black babies are more mature and black mothers give birth physiologically a little earlier did not emerge in our analyses. Indeed, there was no statistically significant difference in morbidity and mortality for infants born to Afro-Caribbean mothers and Caucasian women. Conclusion: The work carried out has identified many factors associated with prematurity, factors already described elsewhere. Although at the individual level it was impossible to predict who would give birth prematurely, the weight of social factors and poor follow-up suggested that a population-based approach might be appropriate. Thus, the most vulnerable women often reside in well-identified areas that could be the subject of targeted actions to improve follow-up and identify complications. This problem of social inequalities in health goes well beyond prematurity and is found for almost all pathologies, suggesting that there are synergies to be sought and that the population scale is undoubtedly strategic. The weight of preeclampsia as a risk factor for induced prematurity in French Guiana raises questions: indeed, it seems much more important than elsewhere for reasons that remain to be clarified
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Bardan, Felicia. "New forensic DNA profiling techniques for human identification." Thesis, 2019. http://hdl.handle.net/2440/120161.
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Highly degraded biological samples are commonly encountered in missing persons cases, historical human remains, war graves, mass disasters and various forensic casework. As biological tissue degrades, DNA becomes progressively fragmented and chemical modifications can occur, complicating successful standard short tandem repeat typing. Alternative genotyping strategies such as single nucleotide polymorphism typing and the emergence of massively parallel sequencing to examine ancestry and phenotype SNPs have ushered in a new era of forensic intelligence testing for problematic samples. Despite showing promise, a number of technical concerns still exist for the use of these strategies in forensic investigation. The research presented in this thesis explores, develops and assesses alternative techniques using both traditional and new technologies for the retrieval of forensic intelligence data from highly degraded samples. I develop new techniques for the screening and genotyping of highly degraded DNA and generate a new dataset of ancestry data from an Australian population for use in analysing historical samples. Issues relating to the implementation of these technologies are discussed, including laboratory workflow, data analysis and interpretation, ethics, and the need for standard guidelines for forensic laboratories to adopt in their methodology. Specifically, in this thesis I use: • A SNP typing strategy based on conventional techniques and equipment to develop a screening tool that estimates sample degradation and presumptive broad biological profile for the triage of forensic samples – Chapter 2 • Emerging target enrichment and massively parallel sequencing technologies for the generation of ancestry and phenotype data for forensic investigation – Chapter 3 • Techniques developed and assessed in Chapter 2 and 3 to analyse a set of degraded DNA and forensic casework samples, demonstrating the utility of the methods to genotype and provide forensic intelligence data for challenging samples – Chapter 4 • mtDNA and autosomal SNP analysis to construct the first Australian reference population database for ancestry testing of historical human remains – Chapter 5. In essence, my research aimed to explore techniques to improve the genetic assessment of highly degraded and compromised forensic samples, and to build on current knowledge concerning the implementation of such techniques in forensic investigations.Thesis (Ph.D.) -- University of Adelaide, School of Biological Sciences, 2019
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Austin, Ayda Aukahi. "Native Hawaiian risky behavior the role of individual, social, and cultural factors in predicting substance use and violence /." Thesis, 2004. http://proquest.umi.com/pqdweb?index=0&did=775179201&SrchMode=2&sid=3&Fmt=2&VInst=PROD&VType=PQD&RQT=309&VName=PQD&TS=1233348956&clientId=23440.
Full textBooks on the topic "Ancestry prediction"
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Frudakis, Tony Nick. Molecular photofitting: Predicting ancestry and phenotype using DNA. Amsterdam: Elsevier/Academic Press, 2008.
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Frudakis, Tony Nick. Molecular photofitting: Predicting ancestry and phenotype using DNA. Amsterdam: Elsevier/Academic Press, 2008.
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Molecular Photofitting: Predicting Ancestry and Phenotype Using DNA. Academic Press, 2007.
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Frudakis, Tony. Molecular Photofitting: Predicting Ancestry and Phenotype Using DNA. Elsevier Science & Technology Books, 2010.
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Forces, With Ancestral, and Rebecca Rogerson. Language of the Heart: Ancestral Presences, Teachings and Predictions. Independently Published, 2022.
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Kay, Chris, Emily Fisher, and Michael R. Hayden. Epidemiology. Oxford University Press, 2014. http://dx.doi.org/10.1093/med/9780199929146.003.0007.
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The prevalence and persistence of Huntington’s disease (HD) is crucially informed by the causative mutation. Diagnostic and predictive testing has enabled a new era of epidemiologic study of HD, whereby only those who carry an expanded CAG repeat are included in such measures. In Western populations, estimated prevalence of the disease is higher following the introduction of genetic testing, and prevalence may also be increasing in absolute terms. There are worldwide differences in the prevalence of HD by ethnicity and population, which may be accounted for in part by genetic diversity of the CAG repeat and the surrounding haplotype. HD is endemic to all populations, but is most common in populations of European ancestry in which specific disease haplotypes are found. New mutations maintain HD in a population, and genetic differences by population may contribute to differences in the de novo mutation rate.
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Varella, Marco A. C., Jaroslava Varella Valentova, and Ana María Fernández. Evolution of Artistic and Aesthetic Propensities through Female Competitive Ornamentation. Edited by Maryanne L. Fisher. Oxford University Press, 2015. http://dx.doi.org/10.1093/oxfordhb/9780199376377.013.46.
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This chapter highlights and discusses the role of women’s competitive ornamentation as one of the relevant, and so far overlooked, ancestral selective pressures in the evolution of artistic propensities. The authors critically discuss how and why sex differences and sexual selection processes acting on women have been disregarded for more than a decade. The authors review available convergent evidence about sex differences in aesthetics and artistic propensities showing that, overall, women outnumber men. Then the authors propose and show evidence that higher women’s inclination toward artistic domains, including ornamentation of body, behavior, and objects/places, can serve as a social arena for attracting/maintaining mates and dealing with rivals, primarily through self-promotion via competitive ornamentation. The chapter concludes by developing connections with related theories that broaden the scope of the field and highlight predictions for future research.
Book chapters on the topic "Ancestry prediction"
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Ouangraoua, Aïda, Frédéric Boyer, Andrew McPherson, Éric Tannier, and Cedric Chauve. "Prediction of Contiguous Regions in the Amniote Ancestral Genome." In Bioinformatics Research and Applications, 173–85. Berlin, Heidelberg: Springer Berlin Heidelberg, 2009. http://dx.doi.org/10.1007/978-3-642-01551-9_18.
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Ross, Connie M., Gabriel Foley, Mikael Boden, and Elizabeth M. J. Gillam. "Using the Evolutionary History of Proteins to Engineer Insertion-Deletion Mutants from Robust, Ancestral Templates Using Graphical Representation of Ancestral Sequence Predictions (GRASP)." In Methods in Molecular Biology, 85–110. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1826-4_6.
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Weiner, J. S., and Chris Stringer. "A Darwinian Prediction." In The Piltdown Forgery. Oxford University Press, 2003. http://dx.doi.org/10.1093/oso/9780198607809.003.0007.
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On 18 December 1912 Arthur Smith Woodward and Charles Dawson announced to a great and expectant scientific audience the epoch-making discovery of a remote ancestral form of man—The Dawn Man of Piltdown. The news had been made public by the Manchester Guardian about three weeks before, and the lecture room of the Geological Society at Burlington House was crowded as it has never been before or since. There was great excitement and enthusiasm which is still remembered by those who were there; for, in Piltdown man, here in England, was at last tangible, well-nigh incontrovertible proof of Man’s ape-like ancestry; here was evidence, in a form long predicted, of a creature which could be regarded as a veritable confirmation of evolutionary theory. Twenty years had elapsed since Dubois had found the fragmentary remains of the Java ape-man, but by now in 1912 its exact evolutionary significance had come to be invested with some uncertainty and the recent attempt to find more material by the expensive and elaborate expedition under Mme. Selenka had proved entirely unsuccessful. Piltdown man provided a far more complete and certain story. The man from Java, whose geological age was unclear, was represented by a skull cap, two teeth, and a disputed femur. Anatomically there was a good deal of the Piltdown skull and, though the face was missing, there was most of one side of the lower jaw. The stratigraphical evidence was quite sufficient to attest the antiquity of the remains; and to support this antiquity there were the animals which had lived in the remote time of Piltdown man; there was even evidence of the tool-making abilities of Piltdown man. In every way Piltdown man provided a fuller picture of the stage of ancestry which man had reached perhaps some 500,000 years ago. Dawson began by explaining how it came about that he had lighted on the existence of the extremely ancient gravels of the Sussex Ouse: . . . ‘I was walking along a farm-road close to Piltdown Common, Fletching (Sussex), when I noticed that the road had been mended with some peculiar brown flints not usual in the district. . . .
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"On Predicting Hominid Group Sizes." In The Archaeology of Human Ancestry, 222–44. Routledge, 2005. http://dx.doi.org/10.4324/9780203974131-22.
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Cutter, Asher D. "Genealogy in evolution." In A Primer of Molecular Population Genetics, 85–112. Oxford University Press, 2019. http://dx.doi.org/10.1093/oso/9780198838944.003.0005.
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Chapter 5, “Genealogy in evolution,” introduces branching tree diagrams as an intuitive way to visualize the evolutionary relationships between alleles, haplotypes, individuals, and species. It describes the nomenclature of gene tree topologies, the stochasticity in tree shape across genes, and the notion of a most recent common ancestor. This chapter also covers reverse-time genealogical thinking with coalescent theory and how it integrates with predictions about nucleotide polymorphism and the site frequency spectrum. An overview of how phylogenies show between-species genealogical relationships is used to highlight the concepts of orthology and homoplasy, how to calculate and interpret different metrics of DNA sequence divergence, the role of ancestral polymorphism in creating distinct gene trees, the multiple mutational hits problem, and factors that influence calculations of the time to the most recent common ancestor for species trees versus gene trees. This chapter surveys how to think of evolution in terms of genealogies that relate gene copies within a species or among species, and how to connect ideas about gene trees to other ideas in molecular population genetics.
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Murray, Elisabeth A., Steven P. Wise, Mary K. L. Baldwin, and Kim S. Graham. "Beastly brains." In The Evolutionary Road to Human Memory, 38–53. Oxford University Press, 2019. http://dx.doi.org/10.1093/oso/9780198828051.003.0003.
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In this chapter, a brainless cockroach has a shocking experience; a giant anemone eats a lawyer; and a drunken sailor considers the danger of dead bees. But mainly we consider the kinds of memories that evolved in early animals. Some of these ancestors didn’t have a brain, but they could still learn about their world. They could, for example, remember that a particular sensation predicted something beneficial or harmful in the near future. After the brain evolved, memories empowered animals to make similar predictions based on what they chose to do, such as where they went for food or safe haven. These predictions enabled early animals to prepare, in advance, for what was about to happen to them and to make choices attuned to their current needs.
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Gerard, Philip. "Glory Bound." In The Last Battleground, 29–33. University of North Carolina Press, 2019. http://dx.doi.org/10.5149/northcarolina/9781469649566.003.0006.
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Capt. William Henry Asbury Speer marches off to war from his beloved Yadkin River Valley a reluctant soldier who blames the Secessionists for the war. He is captured in battle, then exchanged, and rejoins the 28th regiment. Even as he fights bravely at Fredericksburg and is wounded at Chancellorsville, he campaigns hardest to keep his younger brother out of the war. He survives Pickett’s Charge at Gettysburg and ten more major engagements, rising to command the regiment. He pens a dark poem predicting his on death and near Petersburg is blasted by shrapnel from an artillery shell. Friends cart his body home in a wagon for burial among his Ulster Scots and Quaker ancestors.
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Whitehouse, Harvey. "Imagistic Ritual, Fusion, and Self-Sacrifice." In The Ritual Animal, 82–105. Oxford University Press, 2021. http://dx.doi.org/10.1093/oso/9780199646364.003.0004.
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Efforts to investigate the imagistic mode of religiosity initially focused on the effects of emotionally intense rituals on meaning making. But the discovery of a new psychological construct—identity fusion—made it possible to extend the study of imagistic processes to include increasingly precise measures of the pathways to group bonding. Fusion theory has helped clarify the role of feelings of shared essence, both biological and experiential, in fusing together personal and group identities. And it has allowed researchers to test a host of predictions about the causes and consequences of this for ingroup cooperation and intergroup conflict. This chapter considers how the evolution of the imagistic mode may have benefited ancestral groups, and the individuals belonging to them, but in modern times, it has helped to fuel some of the deadliest forms of violence the world has ever seen.
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Cutter, Asher D. "Molecular deviants." In A Primer of Molecular Population Genetics, 159–94. Oxford University Press, 2019. http://dx.doi.org/10.1093/oso/9780198838944.003.0008.
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Chapter 8, “Molecular deviants: sequence signatures of selection and demography,” dives into the logic and mechanics of some of the most common tests of neutrality to show how and why data can reveal differences from the predictions of the standard neutral model. It introduces approaches based on skewed patterns of polymorphism alone, including Tajima’s D test, and on differentiation or divergence alone, like the Lewontin-Krakauer, Population Branch Statistic (PBS), and K A / K S relative-rates tests. Chapter 8 also covers tests of neutrality that integrate information from both within and between species, including the HKA-test and McDonald-Kreitman (MK) test. The logic for other tests of neutrality also is introduced, including ABBA-BABA, Composite Likelihood Ratio (CLR), Extended Haplotype Homozygosity (EHH), and other approaches. Practical implications of ancestral polymorphism and slightly deleterious polymorphisms are discussed, for example, in calculating and interpreting the neutrality index and fraction of positively selected sites (α). The goal of this chapter is to explain the logic of methods applied to molecular population genetic data to read the story of evolutionary history from the genome.
Conference papers on the topic "Ancestry prediction"
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Jolley, Clarissa R., Hannah J. Lee, Kristen A. Lucas, and William P. McDevitt. "Short Tandem Repeat Analysis as a Novel Method for Biogeographic Ancestry Prediction." In 2022 Systems and Information Engineering Design Symposium (SIEDS). IEEE, 2022. http://dx.doi.org/10.1109/sieds55548.2022.9799365.
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Fejerman, Laura. "Abstract IA12: Variation in genetic ancestry proportions among Latinos and its impact on cancer risk, prediction, and outcomes." In Abstracts: Ninth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; September 25-28, 2016; Fort Lauderdale, FL. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/1538-7755.disp16-ia12.
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Wang, S., F. Qian, Y. Zheng, T. Ogundiran, O. Ojengbede, W. Zheng, W. Blot, et al. "Abstract P5-09-02: Breast cancer risk prediction using a polygenic risk score in women of African ancestry: Findings from GWAS in breast cancer in the African diaspora." In Abstracts: 2016 San Antonio Breast Cancer Symposium; December 6-10, 2016; San Antonio, Texas. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/1538-7445.sabcs16-p5-09-02.
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Toma, Tanjin, Tayo Olufemi-Ajayi, Jeremy Dawson, and Donald Adjeroh. "Random Subspace Projection for Predicting Biogeographical Ancestry." In 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2018. http://dx.doi.org/10.1109/bibm.2018.8621222.
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Baun, Ward O. "Method for the Early Development of a Bayesian Prior Time-to-Failure Distribution for an Evolutionary Product Design." In ASME 2007 International Mechanical Engineering Congress and Exposition. ASMEDC, 2007. http://dx.doi.org/10.1115/imece2007-41022.
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This paper describes a method for the development of a Bayesian prior time-to-failure distribution used as an early estimate of the reliability of a new product which is an evolution of a previous ancestor design. In new product development, it is desirable to estimate the reliability of that new product as early as possible in the development program, in order to quantify future financial risks as a result of service costs, and to facilitate risk-based decision-making. It is difficult to make these reliability estimates sufficiently early in the development cycle to be of use in decision-making because of a lack of information. However, this “lack of information” is often a perception only, particularly when a new design is an evolution of a previous design. Making use of the reliability-related knowledge from an ancestor design can improve the accuracy of reliability predictions of the evolutionary design before testing of that design even commences. The method proposed is as follows. First, develop the list of failure mechanisms for the new product. Second, develop the time-to-failure distribution parameters for each of those mechanisms from ancestor product data, including the uncertainty inherent in each of those parameters. Third, develop a list of all changes being made in the new product design which will affect the reliability of the new design for a particular failure mechanism. Fourth, quantify the impact of each design change as an improvement factor distribution. Fifth, combine the ancestor product time-to-failure distribution parameters and the improvement rate factors using propagation of uncertainty rules to produce an estimate of the time-to-failure distribution parameters for the evolutionary product for each mechanism. Lastly, use Bayes’ rule to incorporate new information as the design process progresses. This method will allow estimates of new product reliability to be made earlier in the product development cycle. In making these estimates, this method will formally use pertinent reliability-related information from the previous generations of a product, and information on the impact of proposed design improvements. The method is architected in a manner that facilitates a structured approach to capturing and managing changes in the state of knowledge regarding the reliability of the new product which occur as the design process progresses. As new information arrives during the design process, in the form of either new field reliability information from the ancestor design, or on the demonstrated effectiveness of design improvements, that information can be formally entered into the model, and the reliability predictions for the product of interest can be updated to reflect that new state of knowledge.
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Yang, Kuan, and Joao C. Setubal. "Homology prediction refinement and reconstruction of gene content and order of ancestral bacterial genomes." In the First ACM International Conference. New York, New York, USA: ACM Press, 2010. http://dx.doi.org/10.1145/1854776.1854810.
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Hasanova, Aytakin. "PREDICTIVE GENETIC SCREENING." In The First International Scientific-Practical Conference- “Modern Tendencies of Dialogue in Multidenominational Society: philosophical, religious, legal view”. IRETC MTÜ, 2020. http://dx.doi.org/10.36962/mtdms202029.
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Human, as a species, is very variable, and his variability is at the basis of his social organization. This variability is maintained, in part, by the chance effects of gene assortment and the variation in these genes is the result of mutations in the past. If our remote ancestors had not mutated we would not he here; further, since no species is likely to he able to reduce its mutation rate substantially by the sort of selection to which it is exposed, we may regard mutations of recent origin as part of the price of having evolved. We are here: all of us have some imperfections we would wish not to have, and many of us are seriously incommoded by poor sight, hearing or thinking. Others among us suffer from some malformation due to faulty development. A few are formed lacking some essential substance necessary to metabolize a normal diet, to clot the blood, or to darken the back of the eye. We will all die and our deaths will normally be related to some variation in our immu-nological defences, in our ability to maintain our arteries free from occlusion, or in some other physiological aptitude. This massive variation, which is the consequence both of chance in the distribution of alleles and variety in the alleles themselves, imposes severe disabilities and handicaps on a substantial proportion of our population. The prospects of reducing this burden by artificial selection from counsel¬ling or selective feticide will be considered and some numerical estimates made of its efficiency and efficacy. Screening is a procedure by which populations are separated into groups, and is widely used for administrative and other purposes. At birth all babies are sexed and divided into two groups. Later the educable majority is selected from the ineducable minority; later still screening continues for both administrative and medical purposes. Any procedure by which populations are sifted into distinct groups is a form of screening, the word being derived from the coarse filter used to separate earth and stones. In medicine its essential features are that the population to be screen¬ed is not knowingly in need of medical attention and the action is taken on behalf of this population for its essential good. A simple example is provided by cervical smear examination, the necessary rationale for which must be the haimless and reliable detection of precancerous changes which can be prevented from becoming irreversible. Any rational decision on the development of such a service must be based on a balance of good and harm and any question of priorities in relation to other services must be based on costing. The balance of good and harm is a value judgement of some complexity. In the example of cervical smears anxiety and the consequences of the occasional removal of a healthy uterus must be weighed against the benefits of the complete removal of a cancerous one, and such matters cannot be costed in monetary terms. In fact, even such an apparently simple procedure as cervical screening is full of unknowns and many of these unknowns can only be resolved by extensive and properly designed studies. In genetic screening the matter is even more complicated, since the screening is often vicarious; that is, one person is screened in order to make a prediction on what may happen to someone else, usually their children, who may be un¬conceived or unborn. Further, the action of such screening may not be designed to ameliorate disease, but to eliminate a fetus which has a high chance of an affliction, or to prevent a marriage in which there is a mutual predisposition to producing abnormal children. These considerations impose very considerable dif¬ferences, since the relative values placed on marriage, on having children within marriage, and on inducing abortion, vary widely between individuals and between societies.
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Ozturk, Utkudeniz, Jose Maria Cabrera, and Jessica Calvo. "A Physically Based Model for High Temperature Deformation of Inconel 718Plus™." In ASME Turbo Expo 2017: Turbomachinery Technical Conference and Exposition. American Society of Mechanical Engineers, 2017. http://dx.doi.org/10.1115/gt2017-64043.
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The microstructural evolution of Inconel 718Plus during hot forming operations is modeled through a physically based model which includes the effects of precipitating particles. Inconel 718Plus has been a successful alloy since its introduction in 2003 owing to its moderate cost, good formability and weldability, and its higher maximum service temperature compared to its ancestor, Inconel 718. It is well known that the service performance and hot-flow characteristics of this alloy are strongly dependent on the microstructure, particularly the grain size. Thus, comprehension of the microstructural evolution and its modeling is an important task. In precipitation hardening superalloys and microalloyed steels, it is particularly more challenging to model the microstructural evolution in the processing windows where material softening and precipitation processes take place concurrently. The model presented in this work is based on dislocation density evolution which is considered as a result of the competition between dislocation generation and dynamic recovery at the early stages of deformation. In the hardening region, recovery through climb is described by the diffusion of vacancies and glide is assumed to be proportional to the strain rate in accordance with the models proposed by Bergstrom. Since the deformation is assumed to be controlled by glide and climb, the peak stress is modeled based on a modified hyperbolic-sine model which takes into account the temperature dependence of self-diffusion of Nickel and elastic modulus. It is known that under high temperature deformation conditions Inconel 718Plus may undergo dynamic precipitation. Second-phase particles in the material may impede the grain boundary motion and contribute to an increase in flow-stress due to Orowan looping. To account for the dynamic precipitation, the present model combines previously obtained experimental results and precipitation models to predict volume fraction and particle radius. For the peak stress modeling, the effect of precipitation is expressed as an extra stress term. The flow stress is calculated for the deformed and the recrystallized material separately and the total flow stress for the material is calculated using a law of mixtures considering the fraction of recrystallized material, while recrystallization is described as a nucleation-growth process via Avrami formalism. Cylindrical compression tests were employed to observe the hot flow behavior and validate the model. The predictions are compared with the experimental findings and good agreement is observed.