CCR5AS lncRNA variation differentially regulates CCR5, influencing HIV disease outcome.

Multiple genome-wide studies have identified associations between outcome of human immunodeficiency virus (HIV) infection and polymorphisms in and around the gene encoding the HIV co-receptor CCR5, but the functional basis for the strongest of these associations, rs1015164A/G, is unknown. We found that rs1015164 marks variation in an activating transcription factor 1 binding site that controls expression of the antisense long noncoding RNA (lncRNA) CCR5AS. Knockdown or enhancement of CCR5AS expression resulted in a corresponding change in CCR5 expression on CD4+ T cells. CCR5AS interfered with interactions between the RNA-binding protein Raly and the CCR5 3' untranslated region, protecting CCR5 messenger RNA from Raly-mediated degradation. Reduction in CCR5 expression through inhibition of CCR5AS diminished infection of CD4+ T cells with CCR5-tropic HIV in vitro. These data represent a rare determination of the functional importance of a genome-wide disease association where expression of a lncRNA affects HIV infection and disease progression.

The power of genetic diversity in genome-wide association studies of lipids.

Increased blood lipid levels are heritable risk factors of cardiovascular disease with varied prevalence worldwide owing to different dietary patterns and medication use1. Despite advances in prevention and treatment, in particular through reducing low-density lipoprotein cholesterol levels2, heart disease remains the leading cause of death worldwide3. Genome-wideassociation studies (GWAS) of blood lipid levels have led to important biological and clinical insights, as well as new drug targets, for cardiovascular disease. However, most previous GWAS4-23 have been conducted in European ancestry populations and may have missed genetic variants that contribute to lipid-level variation in other ancestry groups. These include differences in allele frequencies, effect sizes and linkage-disequilibrium patterns24. Here we conduct a multi-ancestry, genome-wide genetic discovery meta-analysis of lipid levels in approximately 1.65 million individuals, including 350,000 of non-European ancestries. We quantify the gain in studying non-European ancestries and provide evidence to support the expansion of recruitment of additional ancestries, even with relatively small sample sizes. We find that increasing diversity rather than studying additional individuals of European ancestry results in substantial improvements in fine-mapping functional variants and portability of polygenic prediction (evaluated in approximately 295,000 individuals from 7 ancestry groupings). Modest gains in the number of discovered loci and ancestry-specific variants were also achieved. As GWAS expand emphasis beyond the identification of genes and fundamental biology towards the use of genetic variants for preventive and precision medicine25, we anticipate that increased diversity of participants will lead to more accurate and equitable26 application of polygenic scores in clinical practice.

Increasing diversity of functional genetics studies to advance biological discovery and human health.

In this perspective we discuss the current lack of genetic and environmental diversity in functional genomics datasets. There is a well-described Eurocentric bias in genetic and functional genomic research that has a clear impact on the benefit this research can bring to underrepresented populations. Current research focused on genetic variant-to-function experiments aims to identify molecular QTLs, but the lack of data from genetically diverse individuals has limited analyses to mostly populations of European ancestry. Although some efforts have been established to increase diversity in functional genomic studies, much remains to be done to consistently generate data for underrepresented populations from now on. We discuss the major barriers for this continuity and suggest actionable insights, aiming to empower research and researchers from underserved populations.

Studying the impact of translational genomic research: Lessons from eMERGE.

Two major goals of the Electronic Medical Record and Genomics (eMERGE) Network are to learn how best to return research results to patient/participants and the clinicians who care for them and also to assess the impact of placing these results in clinical care. Yet since its inception, the Network has confronted a host of challenges in achieving these goals, many of which had ethical, legal, or social implications (ELSIs) that required consideration. Here, we share impediments we encountered in recruiting participants, returning results, and assessing their impact, all of which affected our ability to achieve the goals of eMERGE, as well as the steps we took to attempt to address these obstacles. We divide the domains in which we experienced challenges into four broad categories: (1) study design, including recruitment of more diverse groups; (2) consent; (3) returning results to participants and their health care providers (HCPs); and (4) assessment of follow-up care of participants and measuring the impact of research on participants and their families. Since most phases of eMERGE have included children as well as adults, we also address the particular ELSI posed by including pediatric populations in this research. We make specific suggestions for improving translational genomic research to ensure that future projects can effectively return results and assess their impact on patient/participants and providers if the goals of genomic-informed medicine are to be achieved.

Unsupervised discovery of ancestry-informative markers and genetic admixture proportions in biobank-scale datasets.

Admixture estimation plays a crucial role in ancestry inference and genome-wide association studies (GWASs). Computer programs such as ADMIXTURE and STRUCTURE are commonly employed to estimate the admixture proportions of sample individuals. However, these programs can be overwhelmed by the computational burdens imposed by the 105 to 106 samples and millions of markers commonly found in modern biobanks. An attractive strategy is to run these programs on a set of ancestry-informative SNP markers (AIMs) that exhibit substantially different frequencies across populations. Unfortunately, existing methods for identifying AIMs require knowing ancestry labels for a subset of the sample. This supervised learning approach creates a chicken and the egg scenario. In this paper, we present an unsupervised, scalable framework that seamlessly carries out AIM selection and likelihood-based estimation of admixture proportions. Our simulated and real data examples show that this approach is scalable to modern biobank datasets. OpenADMIXTURE, our Julia implementation of the method, is open source and available for free.

Human pangenome analysis of sequences missing from the reference genome reveals their widespread evolutionary, phenotypic, and functional roles.

Nonreference sequences (NRSs) are DNA sequences present in global populations but absent in the current human reference genome. However, the extent and functional significance of NRSs in the human genomes and populations remains unclear. Here, we de novo assembled 539 genomes from five genetically divergent human populations using long-read sequencing technology, resulting in the identification of 5.1 million NRSs. These were merged into 45284 unique NRSs, with 29.7% being novel discoveries. Among these NRSs, 38.7% were common across the five populations, and 35.6% were population specific. The use of a graph-based pangenome approach allowed for the detection of 565 transcript expression quantitative trait loci on NRSs, with 426 of these being novel findings. Moreover, 26 NRS candidates displayed evidence of adaptive selection within human populations. Genes situated in close proximity to or intersecting with these candidates may be associated with metabolism and type 2 diabetes. Genome-wide association studies revealed 14 NRSs to be significantly associated with eight phenotypes. Additionally, 154 NRSs were found to be in strong linkage disequilibrium with 258 phenotype-associated SNPs in the GWAS catalogue. Our work expands the understanding of human NRSs and provides novel insights into their functions, facilitating evolutionary and biomedical researches.

Eligibility criteria and enrollment of a diverse racial and ethnic population in multiple myeloma clinical trials.

The narrow eligibility criteria may contribute to the underrepresentation of racial and ethnic subgroups in cancer clinical trials. We conducted a retrospective pooled analysis of multicenter global clinical trials submitted to the US Food and Drug Administration between 2006 and 2019 to support the approval of the use of multiple myeloma (MM) therapies that analyze the rates and reasons for trial ineligibility based on race and ethnicity in MM clinical trials. Race and ethnicity were coded per Office of Management and Budget standards. Patients flagged as having screen failures were identified as ineligible. Ineligibility rates were calculated as the percentage of patients who were ineligible compared with the screened population within the respective racial and ethnic subgroups. Trial eligibility criteria were grouped into specific categories to analyze the reasons for trial ineligibility. Black patients (24%) and other (23%) race subgroups had higher ineligibility rates than White patients (17%). The Asian race had the lowest ineligibility rate (12%) among all racial subgroups. Failure to meet the hematologic laboratory criteria (19%) and treatment-related criteria (17%) were the most common reasons for ineligibility among Black patients and were more common in Black patients than in other races. Failure to meet disease-related criteria was the most common reason for ineligibility among White (28%) and Asian (29%) participants. Our analysis indicates that specific eligibility criteria may contribute to enrollment disparities for racial and ethnic subgroups in MM clinical trials. However, the small number of screened patients in the underrepresented racial and ethnic subgroups limits definitive conclusions.

Estimating the timing of multiple admixture events using 3-locus linkage disequilibrium.

Estimating admixture histories is crucial for understanding the genetic diversity we see in present-day populations. Allele frequency or phylogeny-based methods are excellent for inferring the existence of admixture or its proportions. However, to estimate admixture times, spatial information from admixed chromosomes of local ancestry or the decay of admixture linkage disequilibrium (ALD) is used. One popular method, implemented in the programs ALDER and ROLLOFF, uses two-locus ALD to infer the time of a single admixture event, but is only able to estimate the time of the most recent admixture event based on this summary statistic. To address this limitation, we derive analytical expressions for the expected ALD in a three-locus system and provide a new statistical method based on these results that is able to resolve more complicated admixture histories. Using simulations, we evaluate the performance of this method on a range of different admixture histories. As an example, we apply the method to the Colombian and Mexican samples from the 1000 Genomes project. The implementation of our method is available at https://github.com/Genomics-HSE/LaNeta.

Historical representations of social groups across 200 years of word embeddings from Google Books.

Using word embeddings from 850 billion words in English-language Google Books, we provide an extensive analysis of historical change and stability in social group representations (stereotypes) across a long timeframe (from 1800 to 1999), for a large number of social group targets (Black, White, Asian, Irish, Hispanic, Native American, Man, Woman, Old, Young, Fat, Thin, Rich, Poor), and their emergent, bottom-up associations with 14,000 words and a subset of 600 traits. The results provide a nuanced picture of change and persistence in stereotypes across 200 y. Change was observed in the top-associated words and traits: Whether analyzing the top 10 or 50 associates, at least 50% of top associates changed across successive decades. Despite this changing content of top-associated words, the average valence (positivity/negativity) of these top stereotypes was generally persistent. Ultimately, through advances in the availability of historical word embeddings, this study offers a comprehensive characterization of both change and persistence in social group representations as revealed through books of the English-speaking world from 1800 to 1999.

Social disadvantage, economic inequality, and life expectancy in nine Indian states.

SignificanceIndia is one of the most hierarchical societies in the world. Because vital statistics are incomplete, mortality disparities are not quantified. Using survey data on more than 20 million individuals from nine Indian states representing about half of India's population, we estimate and decompose life expectancy differences between higher-caste Hindus, comprising other backward classes and high castes, and three marginalized social groups: Adivasis (indigenous peoples), Dalits (oppressed castes), and Muslims. The three marginalized groups experience large disadvantages in life expectancy at birth relative to higher-caste Hindus. Economic status explains less than half of these gaps. These large disparities underscore parallels between diverse systems of discrimination akin to racism. They highlight the global significance of addressing social inequality in India.

Balancing openness with Indigenous data sovereignty: An opportunity to leave no one behind in the journey to sequence all of life.

The field of genomics has benefited greatly from its "openness" approach to data sharing. However, with the increasing volume of sequence information being created and stored and the growing number of international genomics efforts, the equity of openness is under question. The United Nations Convention of Biodiversity aims to develop and adopt a standard policy on access and benefit-sharing for sequence information across signatory parties. This standardization will have profound implications on genomics research, requiring a new definition of open data sharing. The redefinition of openness is not unwarranted, as its limitations have unintentionally introduced barriers of engagement to some, including Indigenous Peoples. This commentary provides an insight into the key challenges of openness faced by the researchers who aspire to protect and conserve global biodiversity, including Indigenous flora and fauna, and presents immediate, practical solutions that, if implemented, will equip the genomics community with both the diversity and inclusivity required to respectfully protect global biodiversity.

Lewis a-b- histo-blood group antigen phenotype is predictive of severe COVID-19 in the black South African population group.

Several risk factors have been associated with SARS-CoV-2 infections and severity of COVID-19 disease it causes. This study investigated whether variations in histo-blood group antigen (HBGA) expression can predispose individuals to SARS-CoV-2 infections and severity of the disease. Nasopharyngeal swabs, randomly selected from SARS-CoV-2 positive and SARS-CoV-2 negative individuals, were tested for Lewis and H-type 1 HBGA phenotypes by ELISA using monoclonal antibodies specific to Lewis a, Lewis b and H type 1 antigens. The most common Lewis HBGA phenotype among all study participants was Lewis a-b+ (46%), followed by Lewis a-b- (24%), Lewis a+b- and Lewis a+b+ (15% each), while 55% of the study participants were H-type 1. Although SARS-CoV-2 negative individuals had a lower likelihood of having a Lewis a-b- phenotype compared to their SARS-CoV-2 positives counterparts (OR: 0.53, 95% C.I: 0.255-1.113), it did not reach statistical significance (P = 0.055). The frequency of Lewis a+b+, Lewis a+B-, Lewis a-b+, H type 1 positive and H type 1 negative were consistent between SARS-CoV-2 positive and SARS-CoV-2 negative individuals. When stratified according to severity of the disease, individuals with Lewis a+b- phenotype had a higher likelihood of developing mild COVID-19 symptoms (OR: 3.27, 95% CI; 0.9604-11.1), but was not statistically significant (P = 0.055), while Lewis a-b- phenotype was predictive of severe COVID-19 symptoms (OR: 4.3, 95% CI: 1.274-14.81), P = 0.016. In conclusion, individuals with Lewis a-b- phenotype were less likely to be infected by SARS-CoV-2, but when infected, they were at risk of severe COVID-19.

Utility and Diversity: Challenges for Genomic Medicine.

Genomic information is poised to play an increasing role in clinical care, extending beyond highly penetrant genetic conditions to less penetrant genotypes and common disorders. But with this shift, the question of clinical utility becomes a major challenge. A collaborative effort is necessary to determine the information needed to evaluate different uses of genomic information and then acquire that information. Another challenge must also be addressed if that process is to provide equitable benefits: the lack of diversity of genomic data. Current genomic knowledge comes primarily from populations of European descent, which poses the risk that most of the human population will be shortchanged when health benefits of genomics emerge. These two challenges have defined my career as a geneticist and have taught me that solutions must start with dialogue across disciplinary and social divides.

GENLIB: new function to simulate haplotype transmission in large complex genealogies.

SUMMARY: Founder populations with deep genealogical data are well suited for investigating genetic variants contributing to diseases. Here, we present a major update of the genealogical analysis R package GENLIB, centered around a new function which can simulate the transmission of haplotypes from founders to probands along very large and complex user-specified genealogies. AVAILABILITY AND IMPLEMENTATION: The latest update of the GENLIB package (v1.1.9) contains the new gen.simuHaplo() function and is available on the CRAN repository and from https://github.com/R-GENLIB/GENLIB. Examples can be accessed at https://github.com/R-GENLIB/simuhaplo_functions.

networkGWAS: a network-based approach to discover genetic associations.

MOTIVATION: While the search for associations between genetic markers and complex traits has led to the discovery of tens of thousands of trait-related genetic variants, the vast majority of these only explain a small fraction of the observed phenotypic variation. One possible strategy to overcome this while leveraging biological prior is to aggregate the effects of several genetic markers and to test entire genes, pathways or (sub)networks of genes for association to a phenotype. The latter, network-based genome-wide association studies, in particular suffer from a vast search space and an inherent multiple testing problem. As a consequence, current approaches are either based on greedy feature selection, thereby risking that they miss relevant associations, or neglect doing a multiple testing correction, which can lead to an abundance of false positive findings. RESULTS: To address the shortcomings of current approaches of network-based genome-wide association studies, we propose networkGWAS, a computationally efficient and statistically sound approach to network-based genome-wide association studies using mixed models and neighborhood aggregation. It allows for population structure correction and for well-calibrated P-values, which are obtained through circular and degree-preserving network permutations. networkGWAS successfully detects known associations on diverse synthetic phenotypes, as well as known and novel genes in phenotypes from Saccharomycescerevisiae and Homo sapiens. It thereby enables the systematic combination of gene-based genome-wide association studies with biological network information. AVAILABILITY AND IMPLEMENTATION: https://github.com/BorgwardtLab/networkGWAS.git.

Metric evaluation of the anterior nasal spine to estimate sex and population group in South African individuals.

INTRODUCTION: The anterior nasal spine is a pointed, midline projection of the maxilla. This bony structure dictates the overlying soft tissues providing the phenotypic features of the nose and upper lip and determines the differences in the mid-face morphology. Little data is available on the metric features of the Anterior nasal spine (ANS). This study aimed to perform metric evaluations of the ANS of white and black South African males and females to ascertain if morphological variations exist and if the differences are viable for the use in sex and population identification. MATERIALS AND METHODS: The sample included 100 CBCT images for each population and sex group. Linear and angular measurements of the ANS were recorded in both the sagittal and axial planes. RESULTS: Classification decision trees (pruned) were fitted to ascertain the relationship between population group, sex and the ANS measurements including and excluding age. For population group, all the ANS measurements were statistically significant for females but in males, all the ANS measurements were significant when performed individually. However, when fitted to the classification tree, Sagittal 2 did not show any statistical significance. When considering sex, only 2 of the ANS measurements (Sagittal 2 and Axial 1) were found to be significant. The results did not differ significantly when comparing the decision trees including and excluding age. CONCLUSIONS: White South African individuals presented with a longer ANS that produced a more acute angle whereas black South African individuals presented with a shorter ANS and a more obtuse angle. Additionally, males presented with a longer ANS compared to females. ANS measurements were found to be more relevant for population discernment than for sex.

Health disparities in mortality among individuals with HIV-associated dementia in South Carolina.

HIV disproportionately affects the South compared to other regions of the US. Some people living with HIV (PLWH) may acquire HIV-associated neurocognitive disorders (HAND), of which HIV-associated dementia (HAD) is the most severe form. This study aimed to examine the disparities in mortality among individuals with HAD. Data were obtained from the South Carolina Alzheimer's Disease and Related Dementias Registry from 2010 to 2016 (HAD: n = 505; N = 164,982). Logistic regression and Cox proportional hazards models were used to determine mortality related to HIV-associated dementia and potential sociodemographic differences. Adjusted models controlled for age, gender, race, rurality, and place of diagnosis. Individuals diagnosed in a nursing facility were three times more likely to die with HAD compared to those diagnosed in the community (OR: 3.25; 95% CI: 2.08-5.08). Black populations were more likely to die with HAD compared to White populations (OR: 1.52; 95% CI: 0.953-2.42). Disparities in mortality among patients with HAD were found in place of diagnosis and by race. Future research should determine if mortality among individuals with HAD were as a result of HAD or non-HIV related decline.

Preference-based measures of health-related quality of life in Indigenous people: a systematic review.

PURPOSE: In many countries, there are calls to address health inequalities experienced by Indigenous people. Preference-based measures (PBMs) provide a measurement of health-related quality of life and can support resource allocation decisions. This review aimed to identify, summarize, and appraise the literature reporting the use and performance of PBMs with Indigenous people. METHODS: Eleven major databases were searched from inception to August 31, 2022. Records in English that (1) assessed any measurement property of PBMs, (2) directly elicited health preferences, (3) reported the development or translation of PBMs for Indigenous people, or (4) measured health-related quality of life (HRQL) using PBMs were included. Ethically engaged research with Indigenous people was considered as an element of methodological quality. Data was synthesized descriptively (PROSPERO ID: CRD42020205239). RESULTS: Of 3139 records identified, 81 were eligible, describing psychometric evaluation (n = 4), preference elicitation (n = 4), development (n = 4), translation (n = 2), and HRQL measurement (n = 71). 31 reported ethically engaged research. Reports originated primarily from Australia (n = 38), New Zealand (n = 20), USA (n = 9) and Canada (n = 6). Nearly all (n = 73) reported indirect, multi-attribute PBMs, the most common of which was the EQ-5D (n = 50). CONCLUSION: A large number of recent publications from diverse disciplines report the use of PBMs with Indigenous people, despite little evidence on measurement properties in these populations. Understanding the measurement properties of PBMs with Indigenous people is important to better understand how these measures might, or might not, be used in policy and resource decisions affecting Indigenous people. (Funding: EuroQoL Research Foundation).

Community-based rehabilitation services implemented by multidisciplinary teams among adults with stroke: a scoping review with a focus on Chinese experience.

BACKGROUND: Despite the growing interest in hospital rehabilitation services for communities, studies on existing community-based rehabilitation (CBR) services remain scarce owing to limitations in the development of community health services and regional cultural diversity. As a guaranteed measure for ensuring the quality of rehabilitation services and achieving the desired service outcomes, clear roles and responsibilities in multidisciplinary teams and effective service delivery are particularly important. OBJECTIVE: This scoping review aimed to determine the scope of community stroke rehabilitation programs involving existing multidisciplinary teams and to analyze the implementation content and implementers' functional roles to provide guidance for future CBR programs. METHODS: The scoping review design followed the methodology of the Joanna Briggs Institute and was based on the normative scoping review framework proposed by Arksey and O'Malley. The comprehensive CBR framework was proposed by World Health Organization-guided data charting and analysis. RESULTS: Of the 22,849 identified citations, 74 studies were included, consisting of 6,809 patients with stroke and 49 primary caregivers, most of whom were from China. The most common working mode in CBR programs was a dual approach involving both healthcare professionals in medical institutions and community healthcare professionals. The number of programs in each discipline was in the following descending order: nursing, medical care, rehabilitation, psychology, nutrition, and public health. Among these, multidisciplinary teams comprising medical, nursing, and rehabilitation disciplines were the most common, with a total of 29 programs. Disciplinary members were mainly responsible for implementing their respective disciplinary content, with physicians providing guidance for the programs. More than 82.4% of the studies reported 2-4 intervention strategies. The intervention forms of rehabilitation content were the most diverse, whereas preventive interventions were more homogeneous than others. Physical function and socio-psychological measurements were the most commonly reported outcomes. CONCLUSION: CBR services implemented by multidisciplinary teams can effectively achieve functional and emotional improvement in patients with stroke, and nurses are the most involved in implementation, especially in community settings. The results further emphasize the importance of strengthening the exploration of nurses' maximum potential to implement CBR plans in future practice. TRIAL REGISTRATION: The registration information for this scoping review can be found at osf.io/pv7tg.

Psychosocial risk factors of youth suicide in the Western Pacific: a scoping review.

INTRODUCTION:  The Western Pacific region accounts for 25% of global suicide rates globally. In the last decade, however, there is a rising concern over the rate of youth suicides in the region. In line with the regional vision of reducing the rate of non-communicable diseases by 2025, the study contributes to the literature by utilizing a scoping review approach to identify psychosocial risk factors associated with youth suicide in the region. METHOD: Publications on youth suicide in the Western Pacific region between 2010 and 2021 were reviewed. A total of 43 publications met the inclusion criteria and were read in full. RESULTS: Psychosocial risk factors associated with suicide in each publication were identified and thematically classified into five themes: interpersonal factors, history of abuse, academic factors, work factors, and minority status. DISCUSSION: Findings showed discrepancies in youth suicide research across member nations in the Western Pacific. Implications for regional policies on suicide prevention and future research were discussed.