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Journal articles on the topic 'Ancestry prediction'

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Author: Grafiati
Published: 10 December 2022
Last updated: 28 January 2023

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1

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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2

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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3

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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4

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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5

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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6

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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7

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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8

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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9

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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10

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.
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11

Zhang, Daiwei, Rounak Dey, and Seunggeun Lee. "Fast and robust ancestry prediction using principal component analysis." Bioinformatics 36, no. 11 (March 20, 2020): 3439–46. http://dx.doi.org/10.1093/bioinformatics/btaa152.

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Abstract Motivation Population stratification (PS) is a major confounder in genome-wide association studies (GWAS) and can lead to false-positive associations. To adjust for PS, principal component analysis (PCA)-based ancestry prediction has been widely used. Simple projection (SP) based on principal component loadings and the recently developed data augmentation, decomposition and Procrustes (ADP) transformation, such as LASER and TRACE, are popular methods for predicting PC scores. However, the predicted PC scores from SP can be biased toward NULL. On the other hand, ADP has a high computation cost because it requires running PCA separately for each study sample on the augmented dataset. Results We develop and propose two alternative approaches: bias-adjusted projection (AP) and online ADP (OADP). Using random matrix theory, AP asymptotically estimates and adjusts for the bias of SP. OADP uses a computationally efficient online singular value decomposition algorithm, which can greatly reduce the computation cost of ADP. We carried out extensive simulation studies to show that these alternative approaches are unbiased and the computation speed can be 16–16 000 times faster than ADP. We applied our approaches to the UK Biobank data of 488 366 study samples with 2492 samples from the 1000 Genomes data as the reference. AP and OADP required 0.82 and 21 CPU hours, respectively, while the projected computation time of ADP was 1628 CPU hours. Furthermore, when inferring sub-European ancestry, SP clearly showed bias, unlike the proposed approaches. Availability and implementation The OADP and AP methods, as well as SP and ADP, have been implemented in the open-source Python software FRAPOSA, available at github.com/daviddaiweizhang/fraposa. Contact leeshawn@umich.edu Supplementary information Supplementary data are available at Bioinformatics online.
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12

Chawla, Reeti, Sylvia E. Badon, Janani Rangarajan, Anna C. Reisetter, Loren L. Armstrong, Lynn P. Lowe, Margrit Urbanek, et al. "Genetic Risk Score for Prediction of Newborn Adiposity and Large-for-Gestational-Age Birth." Journal of Clinical Endocrinology & Metabolism 99, no. 11 (November 1, 2014): E2377—E2386. http://dx.doi.org/10.1210/jc.2013-4221.

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Context: Macrosomic infants are at increased risk for adverse metabolic outcomes. Improving prediction of large-for-gestational-age (LGA) birth may help prevent these outcomes. Objective: This study sought to determine whether genes associated with obesity-related traits in adults are associated with newborn size, and whether a genetic risk score (GRS) predicts LGA birth. Setting and Design: Single nucleotide polymorphisms (SNPs) in 40 regions associated with adult obesity-related traits were tested for association with newborn size. GRS's for birth weight and sum of skinfolds (SSF) specific to ancestry were calculated using the most highly associated SNP for each ancestry in genomic regions with one or more SNPs associated with birth weight and/or SSF in at least one ancestry group or meta-analyses. Participants: Newborns from the Hyperglycemia Adverse Pregnancy Outcomes Study were studied (942 Afro-Caribbean, 1294 Northern European, 573 Mexican-American, and 1182 Thai). Outcome Measures: Birth weight >90th percentile (LGA) and newborn SSF >90th percentile were primary outcomes. Results: After adjustment for ancestry, sex, gestational age at delivery, parity, maternal genotype, maternal smoking/alcohol intake, age, body mass index, height, blood pressure and glucose, 25 and 23 SNPs were associated (P < .001) with birth weight and newborn SSF, respectively. The GRS was highly associated with both phenotypes as continuous variables across all ancestries (P ≤ 1.6 × 10−19) and improved prediction of birth weight and SSF >90th percentile when added to a baseline model incorporating the covariates listed above. Conclusions: A GRS comprised of SNPs associated with adult obesity-related traits may provide an approach for predicting LGA birth and newborn adiposity beyond established risk factors.
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13

Schubert, Ryan, Angela Andaleon, and Heather E. Wheeler. "Comparing local ancestry inference models in populations of two- and three-way admixture." PeerJ 8 (October 2, 2020): e10090. http://dx.doi.org/10.7717/peerj.10090.

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Local ancestry estimation infers the regional ancestral origin of chromosomal segments in admixed populations using reference populations and a variety of statistical models. Integrating local ancestry into complex trait genetics has the potential to increase detection of genetic associations and improve genetic prediction models in understudied admixed populations, including African Americans and Hispanics. Five methods for local ancestry estimation that have been used in human complex trait genetics are LAMP-LD (2012), RFMix (2013), ELAI (2014), Loter (2018), and MOSAIC (2019). As users rather than developers, we sought to perform direct comparisons of accuracy, runtime, memory usage, and usability of these software tools to determine which is best for incorporation into association study pipelines. We find that in the majority of cases RFMix has the highest median accuracy with the ranking of the remaining software dependent on the ancestral architecture of the population tested. Additionally, we estimate the O(n) of both memory and runtime for each software and find that for both time and memory most software increase linearly with respect to sample size. The only exception is RFMix, which increases quadratically with respect to runtime and linearly with respect to memory. Effective local ancestry estimation tools are necessary to increase diversity and prevent population disparities in human genetics studies. RFMix performs the best across methods, however, depending on application, other methods perform just as well with the benefit of shorter runtimes. Scripts used to format data, run software, and estimate accuracy can be found at https://github.com/WheelerLab/LAI_benchmarking.
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14

Mogensen, Helle S., Torben Tvedebrink, Claus Børsting, Vania Pereira, and Niels Morling. "Ancestry prediction efficiency of the software GenoGeographer using a z-score method and the ancestry informative markers in the Precision ID Ancestry Panel." Forensic Science International: Genetics 44 (January 2020): 102154. http://dx.doi.org/10.1016/j.fsigen.2019.102154.

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15

Docherty, Anna R., Arden Moscati, Danielle Dick, Jeanne E. Savage, Jessica E. Salvatore, Megan Cooke, Fazil Aliev, et al. "Polygenic prediction of the phenome, across ancestry, in emerging adulthood." Psychological Medicine 48, no. 11 (November 27, 2017): 1814–23. http://dx.doi.org/10.1017/s0033291717003312.

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AbstractBackgroundIdentifying genetic relationships between complex traits in emerging adulthood can provide useful etiological insights into risk for psychopathology. College-age individuals are under-represented in genomic analyses thus far, and the majority of work has focused on the clinical disorder or cognitive abilities rather than normal-range behavioral outcomes.MethodsThis study examined a sample of emerging adults 18–22 years of age (N = 5947) to construct an atlas of polygenic risk for 33 traits predicting relevant phenotypic outcomes. Twenty-eight hypotheses were tested based on the previous literature on samples of European ancestry, and the availability of rich assessment data allowed for polygenic predictions across 55 psychological and medical phenotypes.ResultsPolygenic risk for schizophrenia (SZ) in emerging adults predicted anxiety, depression, nicotine use, trauma, and family history of psychological disorders. Polygenic risk for neuroticism predicted anxiety, depression, phobia, panic, neuroticism, and was correlated with polygenic risk for cardiovascular disease.ConclusionsThese results demonstrate the extensive impact of genetic risk for SZ, neuroticism, and major depression on a range of health outcomes in early adulthood. Minimal cross-ancestry replication of these phenomic patterns of polygenic influence underscores the need for more genome-wide association studies of non-European populations.
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Houston-Ludlam, Alexandra N., Julia D. Grant, Kathleen K. Bucholz, Pamela A. F. Madden, and Andrew C. Heath. "2266 Big data approaches in translational science: The influence of psychiatric and trauma history in predicting smoking during pregnancy in a cohort of female like-sex twin pairs." Journal of Clinical and Translational Science 2, S1 (June 2018): 38. http://dx.doi.org/10.1017/cts.2018.156.

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OBJECTIVES/SPECIFIC AIMS: Smoking during pregnancy (SDP) is associated with negative health outcomes, both proximal (e.g., preterm labor, cardiovascular changes, low birth weight) and distal (e.g., increased child externalizing behaviors and attention deficit/hyperactivity disorder (ADHD) symptoms, increased risk of child smoking). As pregnancy provides a unique, strong incentive to quit smoking, investigating SDP allows analysis of individual predictive factors of recalcitrant smoking behaviors. Utilizing a female twin-pair cohort provides a model system for characterizing genotype×environment interactions using statistical approaches. METHODS/STUDY POPULATION: Using women from the Missouri Adolescent Female Twin Study, parental report of twin ADHD inattentive and hyperactive symptoms at twin median age 15, and twin report of DSM-IV lifetime diagnosis of major depressive disorder, trauma exposure (physical assault and childhood sexual abuse), collected at median age 22, were merged with Missouri birth record data for enrolled twins, leading to 1553 individuals of European ancestry and 163 individuals of African-American ancestry included in final analyses. A SDP propensity score was calculated from sociodemographic variables (maternal age, marital status, educational attainment, first born child) and used as a 6-level ordinal covariate in subsequent logistic regressions. RESULTS/ANTICIPATED RESULTS: For European ancestry individuals, parental report of hyperactive ADHD symptoms and exposure to childhood sexual abuse were predictive of SDP, while a lifetime diagnosis of major depressive disorder, parental report of inattentive ADHD symptoms, and exposure to assaultive trauma were all not significantly predictive of future SDP. For African-American individuals, none of these variables were significant in predicting future SDP. DISCUSSION/SIGNIFICANCE OF IMPACT: Understanding this relationship of risk-mechanisms is important for clinical understanding of early predictors of SDP and tailoring interventions to at risk individuals. Ultimately, the focus of this research is to mitigate risk to pregnant smokers and their children. Additionally, the cohort-ecological approach informs how well research and administrative (vital record) data agree. This allows for evaluation of whether administrative data improve prediction in research cohorts, and conversely if research data improve prediction over standard sociodemographic variables available in administrative data.
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17

Cheung, Elaine Y. Y., Michelle Elizabeth Gahan, and Dennis McNevin. "Prediction of biogeographical ancestry from genotype: a comparison of classifiers." International Journal of Legal Medicine 131, no. 4 (December 20, 2016): 901–12. http://dx.doi.org/10.1007/s00414-016-1504-3.

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18

Crum, Tamar E., Robert D. Schnabel, Jared E. Decker, Luciana C. A. Regitano, and Jeremy F. Taylor. "CRUMBLER: A tool for the prediction of ancestry in cattle." PLOS ONE 14, no. 8 (August 26, 2019): e0221471. http://dx.doi.org/10.1371/journal.pone.0221471.

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19

De, Tanima, C. Sehwan Park, and Minoli A. Perera. "Cardiovascular Pharmacogenomics: Does It Matter If You're Black or White?" Annual Review of Pharmacology and Toxicology 59, no. 1 (January 6, 2019): 577–603. http://dx.doi.org/10.1146/annurev-pharmtox-010818-021154.

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Race and ancestry have long been associated with differential risk and outcomes to disease as well as responses to medications. These differences in drug response are multifactorial with some portion associated with genomic variation. The field of pharmacogenomics aims to predict drug response in patients prior to medication administration and to uncover the biological underpinnings of drug response. The field of human genetics has long recognized that genetic variation differs in frequency between ancestral populations, with some single nucleotide polymorphisms found solely in one population. Thus far, most pharmacogenomic studies have focused on individuals of European and East Asian ancestry, resulting in a substantial disparity in the clinical utility of genetic prediction for drug response in US minority populations. In this review, we discuss the genetic factors that underlie variability to drug response and known pharmacogenomic associations and how these differ between populations, with an emphasis on the current knowledge in cardiovascular pharmacogenomics.
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Ramani, Anantharaman, Yongxun Wong, Si Zhen Tan, Bing Hong Shue, and Christopher Syn. "Ancestry prediction in Singapore population samples using the Illumina ForenSeq kit." Forensic Science International: Genetics 31 (November 2017): 171–79. http://dx.doi.org/10.1016/j.fsigen.2017.08.013.

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21

Chugh, Sumeet S., and Kyndaron Reinier. "Ancestry and the Promise of Improved Risk Prediction for Sudden Death." Journal of the American College of Cardiology 72, no. 20 (November 2018): 2440–42. http://dx.doi.org/10.1016/j.jacc.2018.09.016.

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22

Chen, Chia-Yen, Jiali Han, David J. Hunter, Peter Kraft, and Alkes L. Price. "Explicit Modeling of Ancestry Improves Polygenic Risk Scores and BLUP Prediction." Genetic Epidemiology 39, no. 6 (May 21, 2015): 427–38. http://dx.doi.org/10.1002/gepi.21906.

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23

Sari O, Ilksen, Sumeyye Zulal Simsek, Gonul Filoglu, and Ozlem Bulbul. "Predicting Eye and Hair Color in a Turkish Population Using the HIrisPlex System." Genes 13, no. 11 (November 11, 2022): 2094. http://dx.doi.org/10.3390/genes13112094.

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Forensic DNA Phenotyping (FDP) can reveal the appearance of an unknown individual by predicting the ancestry, phenotype (i.e., hair, eye, skin color), and age from DNA obtained at the crime scene. The HIrisPlex system has been developed to simultaneously predict eye and hair color. However, the prediction accuracy of the system needs to be assessed for the tested population before implementing FDP in casework. In this study, we evaluated the performance of the HIrisPlex system on 149 individuals from the Turkish population. We applied the single-based extension (SNaPshot chemistry) method and used the HIrisPlex online tool to test the prediction of the eye and hair colors. The accuracy of the HIrisPlex system was assessed through the calculation of the area under the receiver characteristic operating curves (AUC), sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). The results showed that the proposed method successfully predicted the eye and hair color, especially for blue (100%) and brown (95.60%) eye and black (95.23) and brown (98.94) hair colors. As observed in previous studies, the system failed to predict intermediate eye color, representing 25% in our cohort. The majority of incorrect predictions were observed for blond hair color (40.7%). Previous HIrisPlex studies have also noted difficulties with these phenotypes. Our study shows that the HIrisPlex system can be applied to forensic casework in Turkey with careful interpretation of the data, particularly intermediate eye color and blond hair color.
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Rauf, Sobiah, Jeremy J. Austin, Denice Higgins, and Muhammad Ramzan Khan. "Unveiling forensically relevant biogeographic, phenotype and Y-chromosome SNP variation in Pakistani ethnic groups using a customized hybridisation enrichment forensic intelligence panel." PLOS ONE 17, no. 2 (February 17, 2022): e0264125. http://dx.doi.org/10.1371/journal.pone.0264125.

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Massively parallel sequencing following hybridisation enrichment provides new opportunities to obtain genetic data for various types of forensic testing and has proven successful on modern as well as degraded and ancient DNA. A customisable forensic intelligence panel that targeted 124 SNP markers (67 ancestry informative markers, 23 phenotype markers from the HIrisplex panel, and 35 Y-chromosome SNPs) was used to examine biogeographic ancestry, phenotype and sex and Y-lineage in samples from different ethnic populations of Pakistan including Pothwari, Gilgit, Baloach, Pathan, Kashmiri and Siraiki. Targeted sequencing and computational data analysis pipeline allowed filtering of variants across the targeted loci. Study samples showed an admixture between East Asian and European ancestry. Eye colour was predicted accurately based on the highest p-value giving overall prediction accuracy of 92.8%. Predictions were consistent with reported hair colour for all samples, using the combined highest p-value approach and step-wise model incorporating probability thresholds for light or dark shade. Y-SNPs were successfully recovered only from male samples which indicates the ability of this method to identify biological sex and allow inference of Y-haplogroup. Our results demonstrate practicality of using hybridisation enrichment and MPS to aid in human intelligence gathering and will open many insights into forensic research in South Asia.
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Fleckhaus, Jan, Ana Freire-Aradas, Markus A. Rothschild, and Peter M. Schneider. "Impact of genetic ancestry on chronological age prediction using DNA methylation analysis." Forensic Science International: Genetics Supplement Series 6 (December 2017): e399-e400. http://dx.doi.org/10.1016/j.fsigss.2017.09.162.

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Jin, Xiao‐Ye, Wei Cui, Chong Chen, Yu‐Xin Guo, Yong‐Wei Tao, Qiong Lan, Ting‐Ting Kong, and Bo‐Feng Zhu. "Biogeographic origin prediction of three continental populations through 42 ancestry informative SNPs." ELECTROPHORESIS 41, no. 3-4 (November 29, 2019): 235–45. http://dx.doi.org/10.1002/elps.201900241.

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Hùng, Nguyễn Trần Thế, and Lê Đức Hậu. "Development and Implementation of Polygenic Risk Score in Vietnamese Population." Journal of Research and Development on Information and Communication Technology 2019, no. 2 (December 31, 2019): 75–83. http://dx.doi.org/10.32913/mic-ict-research.v2019.n2.893.

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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.
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Thompson, Ken A., Catherine L. Peichel, Diana J. Rennison, Matthew D. McGee, Arianne Y. K. Albert, Timothy H. Vines, Anna K. Greenwood, et al. "Analysis of ancestry heterozygosity suggests that hybrid incompatibilities in threespine stickleback are environment dependent." PLOS Biology 20, no. 1 (January 10, 2022): e3001469. http://dx.doi.org/10.1371/journal.pbio.3001469.

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Hybrid incompatibilities occur when interactions between opposite ancestry alleles at different loci reduce the fitness of hybrids. Most work on incompatibilities has focused on those that are “intrinsic,” meaning they affect viability and sterility in the laboratory. Theory predicts that ecological selection can also underlie hybrid incompatibilities, but tests of this hypothesis using sequence data are scarce. In this article, we compiled genetic data for F2 hybrid crosses between divergent populations of threespine stickleback fish (Gasterosteus aculeatus L.) that were born and raised in either the field (seminatural experimental ponds) or the laboratory (aquaria). Because selection against incompatibilities results in elevated ancestry heterozygosity, we tested the prediction that ancestry heterozygosity will be higher in pond-raised fish compared to those raised in aquaria. We found that ancestry heterozygosity was elevated by approximately 3% in crosses raised in ponds compared to those raised in aquaria. Additional analyses support a phenotypic basis for incompatibility and suggest that environment-specific single-locus heterozygote advantage is not the cause of selection on ancestry heterozygosity. Our study provides evidence that, in stickleback, a coarse—albeit indirect—signal of environment-dependent hybrid incompatibility is reliably detectable and suggests that extrinsic incompatibilities can evolve before intrinsic incompatibilities.
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Wen, Jia, Munan Xie, Bryce Rowland, Jonathan D. Rosen, Quan Sun, Jiawen Chen, Amanda L. Tapia, et al. "Transcriptome-Wide Association Study of Blood Cell Traits in African Ancestry and Hispanic/Latino Populations." Genes 12, no. 7 (July 8, 2021): 1049. http://dx.doi.org/10.3390/genes12071049.

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Background: Thousands of genetic variants have been associated with hematological traits, though target genes remain unknown at most loci. Moreover, limited analyses have been conducted in African ancestry and Hispanic/Latino populations; hematological trait associated variants more common in these populations have likely been missed. Methods: To derive gene expression prediction models, we used ancestry-stratified datasets from the Multi-Ethnic Study of Atherosclerosis (MESA, including n = 229 African American and n = 381 Hispanic/Latino participants, monocytes) and the Depression Genes and Networks study (DGN, n = 922 European ancestry participants, whole blood). We then performed a transcriptome-wide association study (TWAS) for platelet count, hemoglobin, hematocrit, and white blood cell count in African (n = 27,955) and Hispanic/Latino (n = 28,324) ancestry participants. Results: Our results revealed 24 suggestive signals (p < 1 × 10−4) that were conditionally distinct from known GWAS identified variants and successfully replicated these signals in European ancestry subjects from UK Biobank. We found modestly improved correlation of predicted and measured gene expression in an independent African American cohort (the Genetic Epidemiology Network of Arteriopathy (GENOA) study (n = 802), lymphoblastoid cell lines) using the larger DGN reference panel; however, some genes were well predicted using MESA but not DGN. Conclusions: These analyses demonstrate the importance of performing TWAS and other genetic analyses across diverse populations and of balancing sample size and ancestry background matching when selecting a TWAS reference panel.
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Du, Zhaohui, Guimin Gao, Babatunde Adedokun, Thomas Ahearn, Kathryn L. Lunetta, Gary Zirpoli, Melissa A. Troester, et al. "Evaluating Polygenic Risk Scores for Breast Cancer in Women of African Ancestry." JNCI: Journal of the National Cancer Institute 113, no. 9 (March 26, 2021): 1168–76. http://dx.doi.org/10.1093/jnci/djab050.

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Abstract Background Polygenic risk scores (PRSs) have been demonstrated to identify women of European, Asian, and Latino ancestry at elevated risk of developing breast cancer (BC). We evaluated the performance of existing PRSs trained in European ancestry populations among women of African ancestry. Methods We assembled genotype data for women of African ancestry, including 9241 case subjects and 10 193 control subjects. We evaluated associations of 179- and 313-variant PRSs with overall and subtype-specific BC risk. PRS discriminatory accuracy was assessed using area under the receiver operating characteristic curve. We also evaluated a recalibrated PRS, replacing the index variant with variants in each region that better captured risk in women of African ancestry and estimated lifetime absolute risk of BC in African Americans by PRS category. Results For overall BC, the odds ratio per SD of the 313-variant PRS (PRS313) was 1.27 (95% confidence interval [CI] = 1.23 to 1.31), with an area under the receiver operating characteristic curve of 0.571 (95% CI = 0.562 to 0.579). Compared with women with average risk (40th-60th PRS percentile), women in the top decile of PRS313 had a 1.54-fold increased risk (95% CI = 1.38-fold to 1.72-fold). By age 85 years, the absolute risk of overall BC was 19.6% for African American women in the top 1% of PRS313 and 6.7% for those in the lowest 1%. The recalibrated PRS did not improve BC risk prediction. Conclusion The PRSs stratify BC risk in women of African ancestry, with attenuated performance compared with that reported in European, Asian, and Latina populations. Future work is needed to improve BC risk stratification for women of African ancestry.
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Palencia-Madrid, Leire, Catarina Xavier, María de la Puente, Carsten Hohoff, Christopher Phillips, Manfred Kayser, and Walther Parson. "Evaluation of the VISAGE Basic Tool for Appearance and Ancestry Prediction Using PowerSeq Chemistry on the MiSeq FGx System." Genes 11, no. 6 (June 26, 2020): 708. http://dx.doi.org/10.3390/genes11060708.

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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.
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Diepenbroek, Marta, Birgit Bayer, Kristina Schwender, Roberta Schiller, Jessica Lim, Robert Lagacé, and Katja Anslinger. "Evaluation of the Ion AmpliSeq™ PhenoTrivium Panel: MPS-Based Assay for Ancestry and Phenotype Predictions Challenged by Casework Samples." Genes 11, no. 12 (November 25, 2020): 1398. http://dx.doi.org/10.3390/genes11121398.

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As the field of forensic DNA analysis has started to transition from genetics to genomics, new methods to aid in crime scene investigations have arisen. The development of informative single nucleotide polymorphism (SNP) markers has led the forensic community to question if DNA can be a reliable “eye-witness” and whether the data it provides can shed light on unknown perpetrators. We have developed an assay called the Ion AmpliSeq™ PhenoTrivium Panel, which combines three groups of markers: 41 phenotype- and 163 ancestry-informative autosomal SNPs together with 120 lineage-specific Y-SNPs. Here, we report the results of testing the assay’s sensitivity and the predictions obtained for known reference samples. Moreover, we present the outcome of a blind study performed on real casework samples in order to understand the value and reliability of the information that would be provided to police investigators. Furthermore, we evaluated the accuracy of admixture prediction in Converge™ Software. The results show the panel to be a robust and sensitive assay which can be used to analyze casework samples. We conclude that the combination of the obtained predictions of phenotype, biogeographical ancestry, and male lineage can serve as a potential lead in challenging police investigations such as cold cases or cases with no suspect.
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Costa, Beatrice, Claudia Manzoni, Manuel Bernal-Quiros, Demis A. Kia, Miquel Aguilar, Ignacio Alvarez, Victoria Alvarez, et al. "C9orf72, age at onset, and ancestry help discriminate behavioral from language variants in FTLD cohorts." Neurology 95, no. 24 (September 17, 2020): e3288-e3302. http://dx.doi.org/10.1212/wnl.0000000000010914.

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ObjectiveWe sought to characterize C9orf72 expansions in relation to genetic ancestry and age at onset (AAO) and to use these measures to discriminate the behavioral from the language variant syndrome in a large pan-European cohort of frontotemporal lobar degeneration (FTLD) cases.MethodsWe evaluated expansions frequency in the entire cohort (n = 1,396; behavioral variant frontotemporal dementia [bvFTD] [n = 800], primary progressive aphasia [PPA] [n = 495], and FTLD–motor neuron disease [MND] [n = 101]). We then focused on the bvFTD and PPA cases and tested for association between expansion status, syndromes, genetic ancestry, and AAO applying statistical tests comprising Fisher exact tests, analysis of variance with Tukey post hoc tests, and logistic and nonlinear mixed-effects model regressions.ResultsWe found C9orf72 pathogenic expansions in 4% of all cases (56/1,396). Expansion carriers differently distributed across syndromes: 12/101 FTLD-MND (11.9%), 40/800 bvFTD (5%), and 4/495 PPA (0.8%). While addressing population substructure through principal components analysis (PCA), we defined 2 patients groups with Central/Northern (n = 873) and Southern European (n = 523) ancestry. The proportion of expansion carriers was significantly higher in bvFTD compared to PPA (5% vs 0.8% [p = 2.17 × 10−5; odds ratio (OR) 6.4; confidence interval (CI) 2.31–24.99]), as well as in individuals with Central/Northern European compared to Southern European ancestry (4.4% vs 1.8% [p = 1.1 × 10−2; OR 2.5; CI 1.17–5.99]). Pathogenic expansions and Central/Northern European ancestry independently and inversely correlated with AAO. Our prediction model (based on expansions status, genetic ancestry, and AAO) predicted a diagnosis of bvFTD with 64% accuracy.ConclusionsOur results indicate correlation between pathogenic C9orf72 expansions, AAO, PCA-based Central/Northern European ancestry, and a diagnosis of bvFTD, implying complex genetic risk architectures differently underpinning the behavioral and language variant syndromes.
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Kamariza, Mireille, Kristin Tsuo, Zan Koenig, Benjamin Neale, Mark Daly, Alicia Martin, and Elizabeth Atkinson. "53. LOCAL ANCESTRY ALLOWS FOR IMPROVED GENOMIC PREDICTION IN UNDERREPRESENTED AND ADMIXED POPULATIONS." European Neuropsychopharmacology 51 (October 2021): e68-e69. http://dx.doi.org/10.1016/j.euroneuro.2021.07.142.

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Freire-Aradas, A., Y. Ruiz, C. Phillips, O. Maroñas, J. Söchtig, A. Gómez Tato, J. Álvarez Dios, et al. "Exploring iris colour prediction and ancestry inference in admixed populations of South America." Forensic Science International: Genetics 13 (November 2014): 3–9. http://dx.doi.org/10.1016/j.fsigen.2014.06.007.

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Sun, Kuan, Libing Yun, Chen Zhang, Chengchen Shao, Tianzhen Gao, Ziqin Zhao, Yiping Hou, Jianhui Xie, and Qiqun Tang. "Evaluation of 12 Multi-InDel markers for forensic ancestry prediction in Asian populations." Forensic Science International: Genetics 43 (November 2019): 102155. http://dx.doi.org/10.1016/j.fsigen.2019.102155.

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Bulbul, O., G. Filoglu, H. Altuncul, A. Freire Aradas, Y. Ruiz, M. Fondevila, C. Phillips, Á. Carracedo, A. K. Kriegel, and P. M. Schneider. "A SNP multiplex for the simultaneous prediction of biogeographic ancestry and pigmentation type." Forensic Science International: Genetics Supplement Series 3, no. 1 (December 2011): e500-e501. http://dx.doi.org/10.1016/j.fsigss.2011.10.001.

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Bigdeli, Tim B., Giulio Genovese, Penelope Georgakopoulos, Jacquelyn L. Meyers, Roseann E. Peterson, Conrad O. Iyegbe, Helena Medeiros, et al. "Contributions of common genetic variants to risk of schizophrenia among individuals of African and Latino ancestry." Molecular Psychiatry 25, no. 10 (October 7, 2019): 2455–67. http://dx.doi.org/10.1038/s41380-019-0517-y.

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Abstract Schizophrenia is a common, chronic and debilitating neuropsychiatric syndrome affecting tens of millions of individuals worldwide. While rare genetic variants play a role in the etiology of schizophrenia, most of the currently explained liability is within common variation, suggesting that variation predating the human diaspora out of Africa harbors a large fraction of the common variant attributable heritability. However, common variant association studies in schizophrenia have concentrated mainly on cohorts of European descent. We describe genome-wide association studies of 6152 cases and 3918 controls of admixed African ancestry, and of 1234 cases and 3090 controls of Latino ancestry, representing the largest such study in these populations to date. Combining results from the samples with African ancestry with summary statistics from the Psychiatric Genomics Consortium (PGC) study of schizophrenia yielded seven newly genome-wide significant loci, and we identified an additional eight loci by incorporating the results from samples with Latino ancestry. Leveraging population differences in patterns of linkage disequilibrium, we achieve improved fine-mapping resolution at 22 previously reported and 4 newly significant loci. Polygenic risk score profiling revealed improved prediction based on trans-ancestry meta-analysis results for admixed African (Nagelkerke’s R2 = 0.032; liability R2 = 0.017; P < 10−52), Latino (Nagelkerke’s R2 = 0.089; liability R2 = 0.021; P < 10−58), and European individuals (Nagelkerke’s R2 = 0.089; liability R2 = 0.037; P < 10−113), further highlighting the advantages of incorporating data from diverse human populations.
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Lyons, Roger E. "378 Making-Do When Big Data Isn’t Big Enough: Limitations and pathways of possible development in the prediction of Thoroughbred racing performance as a breeding outcome." Journal of Animal Science 98, Supplement_4 (November 3, 2020): 140–43. http://dx.doi.org/10.1093/jas/skaa278.259.

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Abstract A performance genetics model adapted to real-world data of Thoroughbred racing and breeding will be presented. The continuity of ancestry and performance is documented in the annals of pedigree, not as functional counterparts, but as corresponding signs of market value. Pedigree invites chronic misprision of highly diverse genetic resources competing for scarce opportunity in the racing economy, resulting in samples that are often small and of dubious composition. Data is specialized for competing “pedigree analysis” that packages the system of signification to meet market demand for meaning. Given statistical deficits, this data is a necessary inferential asset of the model. The model’s premise is that predictability is optimized if racing performance is defined as the function of an indivisible relation between parents. Statistical data consists of 6-generation ancestries of mares that produced offspring by a subject stallion. Comparison of proportions is used to identify effects resulting from his relation to individual ancestors of the subject mare. Expected performance by the sire’s offspring is defined as the proportion of mares that produced a superior runner by him. Each ancestor of a subject mare also has descendants among the mares that produced offspring by the stallion. For each of those groups, the proportion of mares that produced a superior runner is compared with the stallion’s expected performance using a t-test of statistical significance at the .10 level. Probable effect is further tested by case study involving such variables as racing class, generational distance, sex-linkage, inbreeding, and an ancestor’s pattern of effect across the stallion population. Stallions with the highest prevalence of positive effects are preferred for the subject mare. This model, under the trade name LyonScore®, has been used since 2012 by Werk Thoroughbred Constultants, Inc. as a component of its client services. Table 1: The data, listed in tabular format below, is graphically displayed for actual use on an ancestry tree whose nodes are numbered by relation to a subject mare (“Position”). Each statistical data item in the table is derived from the stud record of a stallion named Distorted Humor and corresponds with an ancestor of a mare named Positively Royal. Each ancestor of this mare is also an ancestor of a group of mares that produced offspring of Distorted Humor and were at least three years of age as of 2019. A proportion of each of those groups of mares produced at least one superior runner. Proportions that differ significantly from Distorted Humor’s expected proportion are so indicated. Only ancestors involving a group of at least 18 mares are considered to have inferential value on statistical grounds. Table 2: The sire Danzig is an ancestor of Positively Royal, along with 75 mares that produced foals by Distorted Humor, only five of which produced a superior runner by him, significantly fewer than expected. However, since Distorted Humor’s dam is by Danzig, the question of generational distance is relevant as a variable to the effect of inbreeding. The table below shows Danzig’s proportional distribution by genetic relation to those 75 mares as indicated by “Position.” Of the 64 mares in descent of Danzig within three generations, three mares produced a superior runner. It’s notable, though, that 2 of 6 mares with the same relation to Danzig as Positively Royal produced superior runners. Since Danzig is the only ancestor with a negative effect, further consideration is warranted. Table 3: In a population that tends to slough off unprofitable genetic resources, overspecialization is the main risk of close inbreeding. Some generational variations of an ancestor’s contribution can turn inbreeding to less specialized effect, but this depends on generational distance. Distorted Humor’s earliest opportunity with mares in descent of Danzig involved offspring closely inbred to Danzig, but later in his career he encountered mares for which variation was more likely. As the table shows, two of six mares descending from Danzig in position 25 (4th generation) produced Distorted Humor’s best runners inbred to Danzig, so it is of some interest that Positively Royal, the subject mare, is also a postion-25 descendant of Danzig. However, that those two mares happen to be full sisters whose breeding has little else in common with that of Positively Royal leaves the question of Distorted Humor’s fitness for this mare less certain than would be preferred.
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Sampaio, Rafaella, Jessica Mauer, Lucas Ito, Julia Antonieto, Vanessa Ota, Rodrigo Bressan, Ary Gadelha, et al. "T11. USING LOCAL ANCESTRY INFERENCE TO IMPROVE POLYGENIC RISK SCORE PREDICTION IN ADMIXED POPULATIONS." European Neuropsychopharmacology 63 (October 2022): e173-e174. http://dx.doi.org/10.1016/j.euroneuro.2022.07.315.

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Gettings, Katherine Butler, Ronald Lai, Joni L. Johnson, Michelle A. Peck, Jessica A. Hart, Heather Gordish-Dressman, Moses S. Schanfield, and Daniele S. Podini. "A 50-SNP assay for biogeographic ancestry and phenotype prediction in the U.S. population." Forensic Science International: Genetics 8, no. 1 (January 2014): 101–8. http://dx.doi.org/10.1016/j.fsigen.2013.07.010.

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Jordan, Bertrand. "ADN et portait-robot : où en est-on ?" médecine/sciences 36, no. 8-9 (August 2020): 813–16. http://dx.doi.org/10.1051/medsci/2020146.

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The prediction of a person’s aspect from analysis of an anonymous DNA sample has made significant progress in the last decade. Pigmentation (eyes, hair and, more recently, skin colour) can now be determined with good accuracy; face shape is still not amenable to prediction (except, in general lines, from ancestry). Age can apparently also be determined from methylation profiles. Police forces are, understandably, very interested in this technology, with a tendency to over-estimate its accuracy. Legislation varies greatly, with some nations opting for complete prohibition (Germany) and others allowing wide application of the approach (United Kingdom).
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Minnier, Jessica, Nallakkandi Rajeevan, Lina Gao, Byung Park, Saiju Pyarajan, Paul Spellman, Sally G. Haskell, Cynthia A. Brandt, and Shiuh-Wen Luoh. "Polygenic Breast Cancer Risk for Women Veterans in the Million Veteran Program." JCO Precision Oncology, no. 5 (July 2021): 1178–91. http://dx.doi.org/10.1200/po.20.00541.

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PURPOSE Accurate breast cancer (BC) risk assessment allows personalized screening and prevention. Prospective validation of prediction models is required before clinical application. Here, we evaluate clinical- and genetic-based BC prediction models in a prospective cohort of women from the Million Veteran Program. MATERIALS AND METHODS Clinical BC risk prediction models were validated in combination with a genetic polygenic risk score of 313 (PRS313) single-nucleotide polymorphisms in genetic females without prior BC diagnosis (n = 35,130, mean age 49 years) with 30% non-Hispanic African ancestry (AA). Clinical risk models tested were Breast and Prostate Cancer Cohort Consortium, literature review, and Breast Cancer Risk Assessment Tool, and implemented with or without PRS313. Prediction accuracy and association with incident breast cancer was evaluated with area under the receiver operating characteristic curve (AUC), hazard ratios, and proportion with high absolute lifetime risk. RESULTS Three hundred thirty-eight participants developed incident breast cancers with a median follow-up of 3.9 years (2.5 cases/1,000 person-years), with 196 incident cases in women of European ancestry and 112 incident cases in AA women. Individualized Coherent Absolute Risk Estimator-literature review in combination with PRS313 had an AUC of 0.708 (95% CI, 0.659 to 0.758) in women with European or non-African ancestries and 0.625 (0.539 to 0.711) in AA women. Breast Cancer Risk Assessment Tool with PRS313 had an AUC of 0.695 (0.62 to 0.729) in European or non-AA and 0.675 (0.626 to 0.723) in AA women. Incorporation of PRS313 with clinical models improved prediction in European but not in AA women. Models estimated up to 9% of European and 18% of AA women with absolute lifetime risk > 20%. CONCLUSION Clinical and genetic BC risk models predict incident BC in a large prospective multiracial cohort; however, more work is needed to improve genetic risk estimation in AA women.
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Lambert, Samuel A., Gad Abraham, and Michael Inouye. "Towards clinical utility of polygenic risk scores." Human Molecular Genetics 28, R2 (July 31, 2019): R133—R142. http://dx.doi.org/10.1093/hmg/ddz187.

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Abstract Prediction of disease risk is an essential part of preventative medicine, often guiding clinical management. Risk prediction typically includes risk factors such as age, sex, family history of disease and lifestyle (e.g. smoking status); however, in recent years, there has been increasing interest to include genomic information into risk models. Polygenic risk scores (PRS) aggregate the effects of many genetic variants across the human genome into a single score and have recently been shown to have predictive value for multiple common diseases. In this review, we summarize the potential use cases for seven common diseases (breast cancer, prostate cancer, coronary artery disease, obesity, type 1 diabetes, type 2 diabetes and Alzheimer’s disease) where PRS has or could have clinical utility. PRS analysis for these diseases frequently revolved around (i) risk prediction performance of a PRS alone and in combination with other non-genetic risk factors, (ii) estimation of lifetime risk trajectories, (iii) the independent information of PRS and family history of disease or monogenic mutations and (iv) estimation of the value of adding a PRS to specific clinical risk prediction scenarios. We summarize open questions regarding PRS usability, ancestry bias and transferability, emphasizing the need for the next wave of studies to focus on the implementation and health-economic value of PRS testing. In conclusion, it is becoming clear that PRS have value in disease risk prediction and there are multiple areas where this may have clinical utility.
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Al-Sannaa, Nouriya Abbas, Alexander Pepler, Hind Y. Al-Abdulwahed, Sami I. Al-Majed, Rifat F. Abdi, Moritz Menzel, and Saskia Biskup. "Webb–Dattani Syndrome: Report of a Saudi Arabian Family with a Novel Homozygous Mutation in the ARNT2 Gene." Journal of Pediatric Neurology 17, no. 02 (February 7, 2018): 071–76. http://dx.doi.org/10.1055/s-0037-1621720.

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AbstractWebb–Dattani syndrome (WEDAS) is an autosomal recessive disorder caused by mutation in the ARNT2 gene characterized by frontotemporal hypoplasia, globally delayed development, and pituitary and hypothalamic insufficiency. The condition is reported to be associated with consanguinity and with Saudi Arabian ancestry. Here we describe a family of three affected siblings born to healthy second cousin parents of Saudi Arabian ancestry. The children presented at 3 months of age with congenital central hypotonia and hypoventilation, central diabetes insipidus, multiple pituitary hormone deficiency, severe developmental delay, acquired microcephaly, cortical blindness with normal retinal examination, seizures, and gastroesophageal reflux. Whole exome sequencing detected a homozygous unclear variant (c.378C>T; p.G126G) in the ARNT2 gene in both the affected twins. According to splice prediction programs, this variant results in the creation of a cryptic donor splice site, possibly leading to a loss of function. These data support the role of the detected mutation in the ARNT2 gene in causing the described phenotype.
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Alshehhi, Aamer, Aliya Almarzooqi, Khadija Alhammadi, Naoufel Werghi, Guan K. Tay, and Habiba Alsafar. "Advancement in Human Face Prediction Using DNA." Genes 14, no. 1 (January 3, 2023): 136. http://dx.doi.org/10.3390/genes14010136.

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The rapid improvements in identifying the genetic factors contributing to facial morphology have enabled the early identification of craniofacial syndromes. Similarly, this technology can be vital in forensic cases involving human identification from biological traces or human remains, especially when reference samples are not available in the deoxyribose nucleic acid (DNA) database. This review summarizes the currently used methods for predicting human phenotypes such as age, ancestry, pigmentation, and facial features based on genetic variations. To identify the facial features affected by DNA, various two-dimensional (2D)- and three-dimensional (3D)-scanning techniques and analysis tools are reviewed. A comparison between the scanning technologies is also presented in this review. Face-landmarking techniques and face-phenotyping algorithms are discussed in chronological order. Then, the latest approaches in genetic to 3D face shape analysis are emphasized. A systematic review of the current markers that passed the threshold of a genome-wide association (GWAS) of single nucleotide polymorphism (SNP)-face traits from the GWAS Catalog is also provided using the preferred reporting items for systematic reviews and meta-analyses (PRISMA), approach. Finally, the current challenges in forensic DNA phenotyping are analyzed and discussed.
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Moore, Jay A., Andrew M. Evens, Justin Newberg, Eric A. Severson, Jennifer Mills, Jordan Carter, Rahul Matnani, Jo-Anne Vergilio, Sally E. Trabucco, and Shridar Ganesan. "Genomic Ancestry in B Cell Lymphoid Malignancies." Blood 136, Supplement 1 (November 5, 2020): 5–6. http://dx.doi.org/10.1182/blood-2020-137533.

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Introduction: B cell lymphoma/leukemias (BCL) are a diverse set of malignancies. The genomic landscape of many BCL subtypes have been described. However, genomic ancestry has rarely been investigated. We applied SNP-based genomic ancestry prediction to comprehensive genomic profiling (CGP) data to identify significant enrichment of ancestry by subtype. We also explored enrichment of genomic alterations (GAs) by ancestry. Methods: During routine clinical care, 2834 unique patient (pt) samples of BCLs underwent CGP for 406 DNA genes and 265 RNA genes to detect all classes of GAs on the FoundationOne® Heme platform. This dataset was enriched for relapsed/refractory pts as they are more likely to have genomic testing as part of clinical care (referral bias). Each pt was assigned an ancestry of American (AMR), African (AFR), East Asian (EAS), European (EUR), or South Asian (SAS) using a SNP-based machine learning methodology (J. Newberg et al., AACR 2019). AMR was defined using a mix of Hispanic and Latin American populations. Enrichment analyses were performed using Fisher's exact test with FDR correction. Results: We compared the ancestry composition of each BCL subtype to the overall ancestry composition of the rest of the sample set (Fig 1A). Pts of AFR ancestry were overrepresented in plasmablastic lymphoma (PBL) (OR=7.2, P&lt;0.05); EAS pts were overrepresented in Burkitt lymphoma (BL) (OR=4.99, P&lt;0.05); and AMR pts were overrepresented in acute B-cell lymphoblastic leukemia/lymphoma (B-ALL) (OR=3.2, P&lt;0.001). AMR SNPs have been associated with increased risk of B-ALL and worse prognosis (PMID: 21297632). We also investigated GAs enriched in specific ancestries. B-ALL AMR pts were enriched for GAs in IL7R, IGH, CRLF2, JAK2, and IKZF1 compared to other ancestries in B-ALL (Fig 1B). These genes were associated with the high-risk Philadelphia chromosome-like ALL (Ph-like ALL) molecular subtype of B-ALL (PMID: 30181314). We found 33% of all B-ALL contained GAs consistent with Ph-like ALL (PMID: 30181314). While we noted enrichment of AMR pts in the overall B-ALL cohort, we identified additional enrichment in the Ph-like B-ALL cohort with 47% of Ph-like B-ALL pts being of AMR ancestry (OR=1.85, p&lt;0.001). AMR pts accounted for almost half the Ph-ALL pts in this cohort; however, even in B-ALL pts without Ph-like genomic features, 32% were of AMR ancestry suggesting this enrichment is not simply due to increased CGP testing in Ph-ALL. In diffuse large B cell lymphoma (DLBCL), we found pts to be primarily of EUR ancestry, however we identified ancestry bias in GAs (Fig 1C). CD79B alterations were enriched in DLBCL pts of SAS ancestry, although not significant after FDR correction, consistent with previous reports of increased Activate B-Cell (ABC) cell of origin (COO) subtype and BTK signaling in pts from South East Asia (PMID: 31189540). CDKN2A, also frequently altered in ABC COO subtype, trended towards enrichment in EAS ancestry. CUX1, a tumor suppressor involved in PI3K signaling, was strongly enriched in AFR pts in both DLBCL and B-ALL. One CUX1 insertion variant (G870_G871insSGG) was particularly common in AFR pts with BCL (7/9 AFR, 2/9 AMR), which has been reported previously in Myelodysplastic syndromes (PMID: 24030381). CUX1 alterations have been reported to be associated with increased PI3K signaling suggesting in part PI3K inhibitor trials should proactively include pts of AFR ancestry (PMID: 24316979). Finally, EZH2 alterations were slightly enriched in AMR DLBCL pts, but showed no ancestry bias in follicular lymphoma (FL) pts, of interest given the recent EZH2 inhibitor approval in FL. Conclusions: This study described multiple important genomic differences in BCL using genomic ancestry rather than patient-reported descriptive variables. Enrichment of AMR ancestry was observed in B-ALL overall, and in Ph-like B-ALL. In addition, enrichment of CUX1 alterations was observed in both DLBCL and B-ALL of AFR ancestry. While precision medicine holds the promise to advance cancer care, many acknowledge the potential to unintentionally deepen existing health disparities (PMID: 31112478). Further analysis of ancestry informative markers in BCL, including enrichment of ancestry markers in specific cancer subtypes and ancestry-associated enrichment of specific GAs, may lead to insights into cancer biology and contribute to ongoing cancer health disparities research. Disclosures Moore: Foundation Medicine, Inc: Current Employment; Roche Holdings: Current equity holder in publicly-traded company. Evens:Abbvie: Consultancy, Honoraria; Mylteni: Consultancy, Honoraria; Research To Practice: Honoraria, Speakers Bureau; MorphoSys: Consultancy, Honoraria; Novartis: Consultancy, Honoraria; Pharmacyclics: Consultancy, Honoraria; Merck: Consultancy, Honoraria, Research Funding; Epizyme: Consultancy, Honoraria, Research Funding; Seattle Genetics: Consultancy, Honoraria, Research Funding. Newberg:Roche Holdings: Current equity holder in publicly-traded company; Foundation Medicine, Inc: Current Employment. Severson:Foundation Medicine, Inc: Current Employment; Roche Holdings: Current equity holder in publicly-traded company. Mills:Foundation Medicine, Inc: Current Employment; Abbvie: Current equity holder in publicly-traded company; Roche Holdings: Current equity holder in publicly-traded company; Abbott: Current equity holder in publicly-traded company; Merck: Current equity holder in publicly-traded company. Vergilio:Roche Holdings: Current equity holder in publicly-traded company; Foundation Medicine, Inc: Current Employment. Trabucco:F. Hoffmann-La Roche, Bristol-Myers Squibb Co., BioNTech: Current equity holder in publicly-traded company; Patent pending with Foundation Medicine and Genentech: Patents & Royalties: Patent pending; Foundation Medicine, Inc.: Current Employment; Bristol-Myers Squibb Co: Current equity holder in publicly-traded company; BioNTech: Current equity holder in publicly-traded company; Loxo Oncology: Divested equity in a private or publicly-traded company in the past 24 months. Ganesan:M2GEN: Research Funding; Foundation Medicine, Inc: Consultancy; Inspirata: Consultancy; Merck: Consultancy, Current Employment, Current equity holder in publicly-traded company; Silagene: Consultancy; Foghorn Therapeutics: Consultancy; Roche: Consultancy; Novartis: Consultancy.
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Oliveira, Marisa, Joana Ferreira, Verónica Fernandes, Anavaj Sakuntabhai, and Luisa Pereira. "Host ancestry and dengue fever: from mapping of candidate genes to prediction of worldwide genetic risk." Future Virology 13, no. 9 (September 2018): 647–55. http://dx.doi.org/10.2217/fvl-2018-0073.

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Hatoum, Alexander S., Frank R. Wendt, Marco Galimberti, Renato Polimanti, Benjamin Neale, Henry R. Kranzler, Joel Gelernter, Howard J. Edenberg, and Arpana Agrawal. "Ancestry may confound genetic machine learning: Candidate-gene prediction of opioid use disorder as an example." Drug and Alcohol Dependence 229 (December 2021): 109115. http://dx.doi.org/10.1016/j.drugalcdep.2021.109115.

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Wang, Shengfeng, Frank Qian, Yonglan Zheng, Temidayo Ogundiran, Oladosu Ojengbede, Wei Zheng, William Blot, et al. "Genetic variants demonstrating flip-flop phenomenon and breast cancer risk prediction among women of African ancestry." Breast Cancer Research and Treatment 168, no. 3 (January 4, 2018): 703–12. http://dx.doi.org/10.1007/s10549-017-4638-1.

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