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Genes Aug 2021We detail the development of the ancestry informative single nucleotide polymorphisms (SNPs) panel forming part of the VISAGE Basic Tool (BT), which combines 41...
We detail the development of the ancestry informative single nucleotide polymorphisms (SNPs) panel forming part of the VISAGE Basic Tool (BT), which combines 41 appearance predictive SNPs and 112 ancestry predictive SNPs (three SNPs shared between sets) in one massively parallel sequencing (MPS) multiplex, whereas blood-based age analysis using methylation markers is run in a parallel MPS analysis pipeline. The selection of SNPs for the BT ancestry panel focused on established forensic markers that already have a proven track record of good sequencing performance in MPS, and the overall SNP multiplex scale closely matched that of existing forensic MPS assays. SNPs were chosen to differentiate individuals from the five main continental population groups of Africa, Europe, East Asia, America, and Oceania, extended to include differentiation of individuals from South Asia. From analysis of 1000 Genomes and HGDP-CEPH samples from these six population groups, the BT ancestry panel was shown to have no classification error using the Bayes likelihood calculators of the online analysis portal. The differentiation power of the component ancestry SNPs of BT was balanced as far as possible to avoid bias in the estimation of co-ancestry proportions in individuals with admixed backgrounds. The balancing process led to very similar cumulative population-specific divergence values for Africa, Europe, America, and Oceania, with East Asia being slightly below average, and South Asia an outlier from the other groups. Comparisons were made of the African, European, and Native American estimated co-ancestry proportions in the six admixed 1000 Genomes populations, using the BT ancestry panel SNPs and 572,000 Affymetrix Human Origins array SNPs. Very similar co-ancestry proportions were observed down to a minimum value of 10%, below which, low-level co-ancestry was not always reliably detected by BT SNPs. The analysis portal provides a comprehensive population dataset for the BT ancestry panel SNPs, comprising a 520-sample standardised reference dataset; 3445 additional samples from 1000 Genomes, HGDP-CEPH, Simons Foundation and Estonian Biocentre genome diversity projects; and 167 samples of six populations from in-house genotyping of individuals from Middle East, North and East African regions complementing those of the sampling regimes of the other diversity projects.
Topics: Africa; Americas; Ethnicity; Europe; Female; Forensic Genetics; Gene Frequency; Genetics, Population; Genotype; High-Throughput Nucleotide Sequencing; Humans; Male; Oceania; Polymorphism, Single Nucleotide; Racial Groups
PubMed: 34440458
DOI: 10.3390/genes12081284 -
The Lancet. Planetary Health Jan 2022Nutrient deficiencies limit human development and could be caused by the high cost of locally available foods needed to meet nutrient requirements. We aimed to identify... (Observational Study)
Observational Study
BACKGROUND
Nutrient deficiencies limit human development and could be caused by the high cost of locally available foods needed to meet nutrient requirements. We aimed to identify the populations whose nutrient needs are most difficult to meet with existing global food systems.
METHODS
In this observational study, we used the International Comparison Program 2017 collection of global food prices to measure cost per day and cost per calorie of meeting nutrient needs, based on least-cost diets within upper and lower bounds for energy and 20 nutrients for healthy populations across 20 demographic groups in 172 countries. We then analysed the composition of these least-cost diets by food groups to estimate how the affordability of foods for meeting nutrient needs varied by age, sex, and reproductive status.
FINDINGS
In 2017, the global median of diet costs per day was US$2·32 (IQR 1·95-2·76), with cost highest for adolescent boys aged 14-18 years at $2·72 (2·31-3·15). For females, median cost was highest for adolescents aged 14-18 years during pregnancy and lactation at $2·64 (2·29-3·15), exceeding the cost for adult men aged 19-30 years. The global median of diet cost per 1000 kcal was $0·94 (IQR 0·80-1·12), and was higher for females throughout the life course than for males, peaking for adolescent girls aged 9-13 years ($1·17 [95% CI 1·15-1·19]) and women older than 70 years ($1·18 [1·17-1·19]). Diet costs were most sensitive to requirements for calcium, iron, zinc, and vitamins C and E, as well as the upper bounds on carbohydrates and sodium. Total diet costs per day did not vary significantly with national income; however, in high-income countries, the composition of least-cost diets included more animal-source foods, whereas in low-income countries, diets with more pulses, nuts and seeds, and fruits and vegetables provided the most affordable way to meet nutrient requirements.
INTERPRETATION
Diets with adequate nutrients were unaffordable for many demographic groups, especially women and girls. These results could help to guide agriculture and food policy or transfer programmes to support populations at risk of inadequate intake.
FUNDING
The Bill & Melinda Gates Foundation and UKAid.
Topics: Adolescent; Animals; Diet; Eating; Female; Humans; Male; Nutrients; Population Groups; Pregnancy; Vegetables
PubMed: 34998455
DOI: 10.1016/S2542-5196(21)00285-0 -
JAMA Health Forum Oct 2022Racial and ethnic disparities in delayed medical care for reasons that are not directly associated with the cost of care remain understudied.
IMPORTANCE
Racial and ethnic disparities in delayed medical care for reasons that are not directly associated with the cost of care remain understudied.
OBJECTIVE
To describe trends in racial and ethnic disparities in barriers to timely medical care among adults during a recent 20-year period.
DESIGN, SETTING, AND PARTICIPANTS
This was a serial cross-sectional study of 590 603 noninstitutionalized adults in the US using data from the National Health Interview Survey from 1999 to 2018. Data analyses were performed from December 2021 through August 2022.
EXPOSURES
Self-reported race, ethnicity, household income, and sex.
MAIN OUTCOMES AND MEASURES
Temporal trends in disparities regarding 5 specific barriers to timely medical care: inability to get through by telephone, no appointment available soon enough, long waiting times, inconvenient office or clinic hours, and lack of transportation.
RESULTS
The study cohort comprised 590 603 adult respondents (mean [SE] age, 46.00 [0.07] years; 329 638 [51.9%] female; 27 447 [4.7%] Asian, 83 929 [11.8%] Black, 98 692 [13.8%] Hispanic/Latino, and 380 535 [69.7%] White). In 1999, the proportion of each race and ethnicity group reporting any of the 5 barriers to timely medical care was 7.3% among the Asian group; 6.9%, Black; 7.9%, Hispanic/Latino; and 7.0%, White (P > .05 for each difference compared with White individuals). From 1999 to 2018, this proportion increased across all 4 race and ethnicity groups (by 5.7, 8.0, 8.1, and 5.9 percentage points [pp] among Asian, Black, Hispanic/Latino, and White individuals, respectively; P < .001 for each), slightly increasing the disparities between groups. In 2018, compared with White individuals, the proportion reporting any barrier was 2.1 and 3.1 pp higher among Black and Hispanic/Latino individuals (P = .03 and P = .001, respectively). There was no significant difference in prevalence between Asian and White individuals. There was a significant increase in the difference in prevalence between Black individuals and White individuals who reported delaying care because of long waiting times at the clinic or medical office and because of a lack of transportation (1.5 pp and 1.8 pp; P = .03 and P = .01, respectively). In addition, the difference in prevalence between Hispanic/Latino and White individuals who reported delaying care because of long waiting times increased significantly (2.6 pp; P < .001).
CONCLUSIONS AND RELEVANCE
The findings of this serial cross-sectional study of data from the National Health Interview Survey suggest that barriers to timely medical care in the US increased for all population groups from 1999 to 2018, with associated increases in disparities among race and ethnicity groups. Interventions beyond those currently implemented are needed to improve access to medical care and to eliminate disparities among race and ethnicity groups.
Topics: Adult; Female; Humans; Middle Aged; Male; Ethnicity; Hispanic or Latino; Cross-Sectional Studies; Black People; Cohort Studies
PubMed: 36306118
DOI: 10.1001/jamahealthforum.2022.3856 -
American Journal of Primatology Nov 2013Ethnoprimatology is an important and growing discipline, studying the diverse relationships between humans and primates. However there is a danger that too great a focus...
Ethnoprimatology is an important and growing discipline, studying the diverse relationships between humans and primates. However there is a danger that too great a focus on primates as important to humans may obscure the importance of other animal groups to local people. The Waorani of Amazonian Ecuador were described by Sponsel [Sponsel (1997) New World Primates: Ecology, evolution and behavior. New York: Aldine de Gruyter. p 143-165] as the "natural place" for ethnoprimatology, because of their close relationship to primates, including primates forming a substantial part of their diet. Therefore they are an ideal group in which to examine contemporary perceptions of primates in comparison to other types of animal. We examine how Waorani living in Yasuní National Park name and categorize primates and other common mammals. Although there is some evidence that the Waorani consider primates a unique group, the non-primate kinkajou and olingo are also included as part of the group "monkeys," and no evidence was found that primates were more important than other mammals to Waorani culture. Instead, a small number of key species, in particular the woolly monkey (Lagothrix poeppigii) and white-lipped peccary (Tayassu pecari), were found to be both important in the diet and highly culturally salient. These results have implications for both ethnoprimatologists and those working with local communities towards broader conservation goals. Firstly, researchers should ensure that they and local communities are referring to the same animals when they use broad terms such as "monkey," and secondly the results caution ethnoprimatologists against imposing western taxonomic groups on indigenous peoples, rather than allowing them to define themselves which species are important.
Topics: Animals; Atelinae; Carnivora; Conservation of Natural Resources; Diet; Ecology; Ecuador; Humans; Perception; Population Groups; Primates
PubMed: 23818096
DOI: 10.1002/ajp.22173 -
PloS One 2012Uncovering population structure is important for properly conducting association studies and for examining the demographic history of a population. Here, we examined the...
Uncovering population structure is important for properly conducting association studies and for examining the demographic history of a population. Here, we examined the Japanese population substructure using data from the Japan Multi-Institutional Collaborative Cohort (J-MICC), which covers all but the northern region of Japan. Using 222 autosomal loci from 4502 subjects, we investigated population substructure by estimating F(ST) among populations, testing population differentiation, and performing principal component analysis (PCA) and correspondence analysis (CA). All analyses revealed a low but significant differentiation between the Amami Islanders and the mainland Japanese population. Furthermore, we examined the genetic differentiation between the mainland population, Amami Islanders and Okinawa Islanders using six loci included in both the Pan-Asian SNP (PASNP) consortium data and the J-MICC data. This analysis revealed that the Amami and Okinawa Islanders were differentiated from the mainland population. In conclusion, we revealed a low but significant level of genetic differentiation between the mainland population and populations in or to the south of the Amami Islands, although genetic variation between both populations might be clinal. Therefore, the possibility of population stratification must be considered when enrolling the islander population of this area, such as in the J-MICC study.
Topics: Adult; Cohort Studies; Female; Genetic Variation; Geography; Humans; Japan; Male; Middle Aged; Polymorphism, Single Nucleotide; Population Dynamics; Population Groups
PubMed: 22509376
DOI: 10.1371/journal.pone.0035000 -
Croatian Medical Journal Aug 2006To present a summary of the lifestyle, genetic origin, diet, and disease in the population of Sami, indigenous people of northern Fennoscandia. (Review)
Review
AIM
To present a summary of the lifestyle, genetic origin, diet, and disease in the population of Sami, indigenous people of northern Fennoscandia.
METHOD
A survey of the available scientific literature and preliminary results from our own study of the Swedish Sami population.
RESULTS
The Sami probably have a heterogeneous genetic origin, with a major contribution of continental or Eastern European tribes and a smaller contribution from Asia. The traditional Sami diet, high in animal products, persists in Sami groups still involved with reindeer herding, but others have adopted a diet typical of Western cultures. Early reports indicated a lower prevalence of heart disease and most cancers, except stomach cancer. Recent studies have not found a lower risk of heart disease, but have consistently shown an overall reduced cancer risk. Sami have been reported to share some specific health-related genetic polymorphisms with other European populations, but none that would explain the observed differences in disease risk.
CONCLUSION
The genetic structure of the Sami population makes it suitable for studies of the genetic and environmental factors influencing the development of common diseases. The difference in incidence of heart disease between studies may reflect the ongoing transition from a traditional to a more Westernized lifestyle. The ability to compare population segments with different lifestyles, combined with the genetic structure of the population, creates unusual possibilities for studies of the genetic and environmental factors involved in the development of common disease.
Topics: Cardiovascular Diseases; Diet; Ethnicity; Finland; Genetics, Population; Humans; Life Style; Morbidity; Neoplasms; Norway; Population Groups; Sweden
PubMed: 16909452
DOI: No ID Found -
Sensors (Basel, Switzerland) Nov 2021The global population is aging in an unprecedented manner and the challenges for improving the lives of older adults are currently both a strong priority in the...
The global population is aging in an unprecedented manner and the challenges for improving the lives of older adults are currently both a strong priority in the political and healthcare arena. In this sense, preventive measures and telemedicine have the potential to play an important role in improving the number of healthy years older adults may experience and virtual coaching is a promising research area to support this process. This paper presents COLAEVA, an interactive web application for older adult population clustering and evolution analysis. Its objective is to support caregivers in the design, validation and refinement of coaching plans adapted to specific population groups. COLAEVA enables coaching caregivers to interactively group similar older adults based on preliminary assessment data, using AI features, and to evaluate the influence of coaching plans once the final assessment is carried out for a baseline comparison. To evaluate COLAEVA, a usability test was carried out with 9 test participants obtaining an average SUS score of 71.1. Moreover, COLAEVA is available online to use and explore.
Topics: Aged; Data Mining; Humans; Internet; Mentoring; Population Groups; Telemedicine
PubMed: 34883995
DOI: 10.3390/s21237991 -
The Journal of Law, Medicine & Ethics :... Mar 2020Biomedical research using data from participants' mobile devices borrows heavily from the ethos of the "citizen science" movement, by delegating data collection and...
Biomedical research using data from participants' mobile devices borrows heavily from the ethos of the "citizen science" movement, by delegating data collection and transmission to its volunteer subjects. This engagement gives volunteers the opportunity to feel like partners in the research and retain a reassuring sense of control over their participation. These virtues, in turn, give both grass-roots citizen science initiatives and institutionally sponsored mHealth studies appealing features to flag in recruiting participants from the public. But while grass-roots citizen science projects are often community-based, mHealth research ultimately depends on the individuals who own and use mobile devices. This inflects the ethos of mHealth research towards a celebration of individual autonomy and empowerment, at the expense of its implications for the communities or groups to which its individual participants belong. But the prospects of group harms - and benefits - from mHealth research are as vivid as they are in other forms of data-intensive "precision health" research, and will be important to consider in the design of any studies using this approach.
Topics: Biomedical Research; Computers, Handheld; Data Aggregation; Digital Divide; Humans; Policy Making; Population Groups; Telemedicine
PubMed: 32342749
DOI: 10.1177/1073110520917037 -
Communications Biology Sep 2023Risk prediction models using genetic data have seen increasing traction in genomics. However, most of the polygenic risk models were developed using data from...
Risk prediction models using genetic data have seen increasing traction in genomics. However, most of the polygenic risk models were developed using data from participants with similar (mostly European) ancestry. This can lead to biases in the risk predictors resulting in poor generalization when applied to minority populations and admixed individuals such as African Americans. To address this issue, largely due to the prediction models being biased by the underlying population structure, we propose a deep-learning framework that leverages data from diverse population and disentangles ancestry from the phenotype-relevant information in its representation. The ancestry disentangled representation can be used to build risk predictors that perform better across minority populations. We applied the proposed method to the analysis of Alzheimer's disease genetics. Comparing with standard linear and nonlinear risk prediction methods, the proposed method substantially improves risk prediction in minority populations, including admixed individuals, without needing self-reported ancestry information.
Topics: Humans; Alzheimer Disease; Black or African American; Genomics; Multifactorial Inheritance; Phenotype; Genetic Predisposition to Disease; Risk Assessment; Deep Learning; Risk; European People; Minority Groups; Population Groups; Models, Statistical
PubMed: 37736834
DOI: 10.1038/s42003-023-05352-6 -
Proceedings of the National Academy of... Mar 2021Island Southeast Asia has recently produced several surprises regarding human history, but the region's complex demography remains poorly understood. Here, we report...
Island Southeast Asia has recently produced several surprises regarding human history, but the region's complex demography remains poorly understood. Here, we report ∼2.3 million genotypes from 1,028 individuals representing 115 indigenous Philippine populations and genome-sequence data from two ∼8,000-y-old individuals from Liangdao in the Taiwan Strait. We show that the Philippine islands were populated by at least five waves of human migration: initially by Northern and Southern Negritos (distantly related to Australian and Papuan groups), followed by Manobo, Sama, Papuan, and Cordilleran-related populations. The ancestors of Cordillerans diverged from indigenous peoples of Taiwan at least ∼8,000 y ago, prior to the arrival of paddy field rice agriculture in the Philippines ∼2,500 y ago, where some of their descendants remain to be the least admixed East Asian groups carrying an ancestry shared by all Austronesian-speaking populations. These observations contradict an exclusive "out-of-Taiwan" model of farming-language-people dispersal within the last four millennia for the Philippines and Island Southeast Asia. Sama-related ethnic groups of southwestern Philippines additionally experienced some minimal South Asian gene flow starting ∼1,000 y ago. Lastly, only a few lowlanders, accounting for <1% of all individuals, presented a low level of West Eurasian admixture, indicating a limited genetic legacy of Spanish colonization in the Philippines. Altogether, our findings reveal a multilayered history of the Philippines, which served as a crucial gateway for the movement of people that ultimately changed the genetic landscape of the Asia-Pacific region.
Topics: Agriculture; Asia, Southeastern; Australia; Female; Genetic Drift; Genomics; History, Ancient; Human Migration; Humans; Male; Oryza; Philippines; Population Groups; Taiwan
PubMed: 33753512
DOI: 10.1073/pnas.2026132118