scholarly journals Sharing genetic admixture and diversity of public biomedical datasets

2017 ◽  
Author(s):  
Olivier Harismendy ◽  
Jihoon Kim ◽  
Xiaojun Xu ◽  
Lucila Ohno-Machado
Keyword(s):  
Race And Ethnicity ◽  
Human Genetics ◽  
Disease Risk ◽  
Human Subjects ◽  
Analytical Framework ◽  
Global Scale ◽  
The Cancer Genome Atlas ◽  
Genetic Admixture ◽  
Data Repositories ◽  
Genetics Research

AbstractGenetic ancestry and admixture are critical co-factors to study phenotype-genotype associations using cohorts of human subjects. Most publically available molecular datasets – genomes, exomes or transcriptomes - are however missing this information or only share self-reported ancestry. This represents a limitation to identify and re-purpose datasets to investigate the contribution of race and ethnicity to diseases and traits. we propose an analytical framework to enrich the meta-data from publically available cohorts with admixture information and a resulting diversity score at continental resolution, calculated directly from the data. We illustrate the utility and versatility of the framework using The Cancer Genome Atlas datasets indexed and searched through the DataMed Data Discovery Index. Data repositories or data contributors can use this framework to provide, as metadata, admixture for controlled access datasets, minimizing the work involved in requesting a dataset that may ultimately prove inadequate for a researcher’s purpose. With the increasingly global scale of human genetics research, research on disease risk and susceptibility would benefit greatly from the adequate estimation and sharing of admixture data following a framework such as the one presented.

scholarly journals Evaluating and sharing global genetic ancestry in biomedical datasets

2019 ◽  
Vol 26 (5) ◽  
pp. 457-461 ◽  
Author(s):  
Olivier Harismendy ◽  
Jihoon Kim ◽  
Xiaojun Xu ◽  
Lucila Ohno-Machado
Keyword(s):  
Genetic Diversity ◽  
Race And Ethnicity ◽  
Human Genetics ◽  
Disease Risk ◽  
Human Subjects ◽  
Analytical Framework ◽  
Global Scale ◽  
Genetic Ancestry ◽  
The Cancer Genome Atlas ◽  
Data Repositories

Abstract Genetic ancestry is a critical co-factor to study phenotype-genotype associations using cohorts of human subjects. Most publicly available molecular datasets are, however, missing this information or only share self-reported race and ethnicity, representing a limitation to identify and repurpose datasets to investigate the contribution of ancestry to diseases and traits. We propose an analytical framework to enrich the metadata from publicly available cohorts with genetic ancestry information and a resulting diversity score at continental resolution, calculated directly from the data. We illustrate this framework using The Cancer Genome Atlas datasets searched through the DataMed Data Discovery Index. Data repositories and contributors can use this framework to provide genetic diversity measurements for controlled access datasets, minimizing the work involved in requesting a dataset that may ultimately prove inadequate for a researcher’s purpose. With the increasing global scale of human genetics research, studies on disease risk and susceptibility would benefit greatly from the adequate estimation and sharing of genetic diversity in publicly available datasets following a framework such as the one presented.

Race and Ethnicity in Medical Research: Requirements Meet Reality

2006 ◽  
Vol 34 (3) ◽  
pp. 520-525 ◽  
Author(s):  
Margaret A. Winker
Keyword(s):  
Socioeconomic Status ◽  
Medical Research ◽  
Socioeconomic Factors ◽  
Biomedical Research ◽  
Race And Ethnicity ◽  
Careful Consideration ◽  
Biomedical Literature ◽  
Genetics Research ◽  
Race Ethnicity ◽  
Policy And Procedure

Race and ethnicity are commonly reported variables in biomedical research, but how they were initially determined is often not described and the rationale for analyzing them is often not provided. JAMA improved the reporting of these factors by implementing a policy and procedure for doing so. However, still lacking are careful consideration of what is actually being measured when race/ethnicity is described, consistent terminology, hypothesis-driven justification for analyzing race/ethnicity, and a consistent and generalizable measurement of socioeconomic status. Furthermore, some studies continue to use race/ethnicity as a proxy for genetics. Research into appropriate measures of race/ethnicity and socioeconomic factors, as well as education of researchers regarding issues of race/ethnicity, is necessary to clarify the meaning of race/ethnicity in the biomedical literature.

scholarly journals APOL1 polymorphisms and kidney disease: loss-of-function or gain-of-function?

2019 ◽  
Vol 316 (1) ◽  
pp. F1-F8 ◽  
Author(s):  
Leslie A. Bruggeman ◽  
John F. O’Toole ◽  
John R. Sedor
Keyword(s):  
Kidney Disease ◽  
Human Genetics ◽  
Disease Risk ◽  
Kidney Diseases ◽  
Expression Patterns ◽  
Model Systems ◽  
Recessive Trait ◽  
Loss Of Function ◽  
Allele Expression ◽  
Basic Biology

The mechanism that explains the association of APOL1 variants with nondiabetic kidney diseases in African Americans remains unclear. Kidney disease risk is inherited as a recessive trait, and many studies investigating the intracellular function of APOL1 have indicated the APOL1 variants G1 and G2 are associated with cytotoxicity. Whether cytotoxicity results from the absence of a protective effect conferred by the G0 allele or is induced by a deleterious effect of variant allele expression has not be conclusively established. A central issue hampering basic biology studies is the lack of model systems that authentically replicate APOL1 expression patterns. APOL1 is present in humans and a few other primates and appears to have important functions in the kidney, as the kidney is the primary target for disease associated with the genetic variance. There have been no studies to date assessing the function of untagged APOL1 protein under native expression in human or primate kidney cells, and no studies have examined the heterozygous state, a disease-free condition in humans. A second major issue is the chronic kidney disease (CKD)-associated APOL1 variants are conditional mutations, where the disease-inducing function is only evident under the appropriate environmental stimulus. In addition, it is possible there may be more than one mechanism of pathogenesis that is dependent on the nature of the stressor or other genetic variabilities. Studies addressing the function of APOL1 and how the CKD-associated APOL1 variants cause kidney disease are challenging and remain to be fully investigated under conditions that faithfully model known human genetics and physiology.

scholarly journals Trade and Deforestation Predict Rat Lungworm Disease, an Invasive-Driven Zoonosis, at Global and Regional Scales

2021 ◽  
Vol 9 ◽  
Author(s):  
Luz A. de Wit ◽  
Taylor H. Ricketts
Keyword(s):  
Land Use ◽  
Environmental Change ◽  
Human Health ◽  
Native Species ◽  
Disease Risk ◽  
Zoonotic Disease ◽  
Global Scale ◽  
Country Level ◽  
Rat Lungworm ◽  
Land Use Policies

The introduction of non-native species and deforestation are both important drivers of environmental change that can also facilitate the geographic spread of zoonotic pathogens and increase disease risk in humans. With ongoing trends in globalization and land-use conversions, introduced species and deforestation are ever more likely to pose threats to human health. Here, we used rat lungworm disease, an emerging zoonotic disease caused by Angiostrongylus cantonensis and maintained by invasive rats and snails, to explore how these two forms of environmental change can impact zoonotic disease risk. We used logistic regressions to examine the role of global trade in the introduction of A. cantonensis at a country level and used model estimates to predict the probability of introduction as a function of trade. We then used hurdle-based regression models to examine the association between deforestation and rat lungworm disease in two regions where A. cantonensis is already established: Hawaii and Thailand. At the global scale, we found the trade of horticultural products to be an important driver in the spread of A. cantonensis and that the majority of countries at high risk of future A. cantonensis introduction are islands. At country scales, we found deforestation to increase the per-capita risk of A. cantonensis exposure in Hawaii and Thailand. Our study provides a preliminary view of the associations between species introductions, deforestation, and risk of A. cantonensis exposure in people. Better understanding how these two widespread and overlapping forms of environmental change affect human health can inform international biosecurity protocols, invasive species management, and land-use policies.

scholarly journals Intestinal microbiota, obesity and prebiotics

2015 ◽  
Vol 64 (2) ◽  
pp. 93-100 ◽  
Author(s):  
R. BARCZYNSKA ◽  
K. BANDURSKA ◽  
K. SLIZEWSKA ◽  
M. LITWIN ◽  
M. SZALECKI ◽  
...  
Keyword(s):  
Body Weight ◽  
Gut Microbiota ◽  
Disease Risk ◽  
Global Scale ◽  
Weight One ◽  
Prevalence Of Obesity ◽  
Normal Body Weight ◽  
Healthy Body Weight ◽  
Treatment Of Obesity

Over the past few decades there has been a significant increase in the prevalence of obesity in both children and adults. Obesity is a disease that has reached epidemic levels on a global scale. The development of obesity is associated with both environmental and genetic factors. Recent studies indicate that intestinal microorganisms play an important function in maintaining normal body weight. One of the objectives in the gut microbiota research is to determine the role it plays and can it be a reliable biomarker of disease risk, including the predisposition to obesity. This article discusses (1) the role of prebiotics and gut microbiota in maintaining a healthy body weight and (2) potential influence on the gut microbiota in the prevention and treatment of obesity.

scholarly journals Mosquito diversity and dog heartworm prevalence in suburban areas

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Meredith R. Spence Beaulieu ◽  
Jennifer L. Federico ◽  
Michael H. Reiskind
Keyword(s):  
Disease Transmission ◽  
Disease Risk ◽  
Mosquito Species ◽  
Negative Relationship ◽  
Global Scale ◽  
Vector Borne Diseases ◽  
Suburban Areas ◽  
Host Seeking ◽  
Vector Borne ◽  
Wake County

Abstract Background Urbanization is occurring rapidly on a global scale and is altering mosquito communities, creating assemblages that are characteristically less diverse. Despite high rates of urbanization and ample examples of vector-borne diseases transmitted by multiple species, the effects of urbanization-driven mosquito diversity losses on disease transmission has not been well explored. We investigated this question using the dog heartworm, a filarial parasite vectored by numerous mosquito species. Methods We trapped host-seeking mosquitoes in undeveloped areas and neighborhoods of different ages in Wake County, North Carolina, USA, analyzing captured mosquitoes for heartworm DNA. We compared within-mosquito heartworm infection across land-use types by Kruskal–Wallis and likelihood ratio tests. Using zip code level data acquired from dogs in a local shelter, we performed linear regressions of within-host heartworm prevalence by within-mosquito heartworm prevalence as well as by three mosquito diversity measures. We also determined the best predictor of host-level prevalence among models including within-mosquito infection, mosquito diversity and abundance, and socioeconomic status as variables. Results Suburban areas had lower within-mosquito heartworm prevalence and lower likelihood of heartworm-positive mosquitoes than did undeveloped field sites, although no differences were seen between suburban and undeveloped wooded sites. No relationships were noted between within-mosquito and within-host heartworm prevalence. However, mosquito diversity metrics were positively correlated with host heartworm prevalence. Model selection revealed within-host prevalence was best predicted by a positive relationship with mosquito Shannon–Wiener diversity and a negative relationship with household income. Conclusions Our results demonstrate that decreases in mosquito diversity due to urbanization alter vector-borne disease risk. With regard to dog heartworm disease, this loss of mosquito diversity is associated with decreased heartworm prevalence within both the vector and the host. Although the response is likely different for diseases transmitted by one or few species, mosquito diversity losses leading to decreased transmission could be generalizable to other pathogens with multiple vectors. This study contributes to better understanding of the effects of urbanization and the role of vector diversity in multi-vectored pathosystems.

scholarly journals CausalMGM: an interactive web-based causal discovery tool

2020 ◽  
Vol 48 (W1) ◽  
pp. W597-W602 ◽  
Author(s):  
Xiaoyu Ge ◽  
Vineet K Raghu ◽  
Panos K Chrysanthis ◽  
Panayiotis V Benos
Keyword(s):  
Observational Data ◽  
High Throughput Sequencing ◽  
Graphical Model ◽  
The Cancer Genome Atlas ◽  
Causal Discovery ◽  
Automated Identification ◽  
Online Data ◽  
Data Repositories ◽  
Web Based ◽  
Cause And Effect

Abstract High-throughput sequencing and the availability of large online data repositories (e.g. The Cancer Genome Atlas and Trans-Omics for Precision Medicine) have the potential to revolutionize systems biology by enabling researchers to study interactions between data from different modalities (i.e. genetic, genomic, clinical, behavioral, etc.). Currently, data mining and statistical approaches are confined to identifying correlates in these datasets, but researchers are often interested in identifying cause-and-effect relationships. Causal discovery methods were developed to infer such cause-and-effect relationships from observational data. Though these algorithms have had demonstrated successes in several biomedical applications, they are difficult to use for non-experts. So, there is a need for web-based tools to make causal discovery methods accessible. Here, we present CausalMGM (http://causalmgm.org/), the first web-based causal discovery tool that enables researchers to find cause-and-effect relationships from observational data. Web-based CausalMGM consists of three data analysis tools: (i) feature selection and clustering; (ii) automated identification of cause-and-effect relationships via a graphical model; and (iii) interactive visualization of the learned causal (directed) graph. We demonstrate how CausalMGM enables an end-to-end exploratory analysis of biomedical datasets, giving researchers a clearer picture of its capabilities.

scholarly journals Methods for Modeling Ecosystem Services: A Review

2015 ◽  
Vol 7 (1) ◽  
pp. 5-12 ◽  
Author(s):  
Horea Olosutean
Keyword(s):  
Ecosystem Services ◽  
Rapid Development ◽  
Secondary Data ◽  
Analytical Framework ◽  
Global Scale ◽  
Homogeneous Distribution ◽  
Flow Equations ◽  
Future Supply ◽  
Data Banks ◽  
Scale Types

Abstract Modeling ecosystem services (ES) is an essential tool for the development of strategies that will ensure their future supply, provision and quantification. Given the rapid development in this area of research, a review of the different approaches used to model ES was performed, using an analytical framework based on five criteria for comparing the existing methodological approaches: the types of ES, availability of data sources, spatial scale, types of models used and the possible outcomes of the models. Regulating services were the most commonly modeled, followed by provisioning, cultural, and supporting services. The most frequently used data for modeling were secondary data (already available from scientific literature or data banks). Most studies were performed at the regional or at a global scale. Mechinicist models, based on state and flow equations, were the most commonly used method, but the survey showed a relatively homogeneous distribution of all the identified types of modeling. The synthesis reveals that the majority of studies are based on secondary data, applied at broad scales, without validation techniques, similar to the existing information regarding the mapping of ESs.

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