Whole-Genome-Sequence-Based Haplotypes Reveal Single Origin of the Sickle Allele during the Holocene Wet Phase

The effect on the equilibrium sickle cell allele frequency of the probable protection conferred by malaria and sickle cell gene against other infectious diseases

If a mutated gene with heterozygous advantage against malaria, e.g., hemoglobin S (HbS) gene, is introduced in a small tribe, the gene (allele) frequency (fgene) increases until it reaches a steady state value (feq) where the total mortality from malaria and sickle cell disease is a minimum. This is a classic example of balanced-polymorphism named malaria hypothesis. In a previous in silico study, assuming realistic initial conditions, it has been shown that the feq is around 14%, far less than the fgene observed in certain parts of Africa, 24%. It seems that the malaria hypothesis, per se, could not explain such a high fgene, unless it is assumed that malaria and HbS gene can provide protection against other diseases. Using Monte-Carlo simulation, the current study was conducted to examine the effect on feq of five scenarios was examined. The studied scenarios consisted of different combinations of mortality of other diseases and the possible amounts of protections conferred by malaria and HbS gene against the diseases. Taking into account other diseases causing mortality in the population makes the fgene rate of change steeper over generations. feq is an increasing function of the amount of protection conferred by HbS gene against other diseases. The effect of protection provided by malaria against other diseases on feq, is however, variable-depending on the amount of protection conferred by HbS gene against other diseases, it may increase or decrease feq. If malaria and HbS gene provide protections of 1.5-fold and threefold against other diseases, respectively, the feq is around 24%, the amount reported in certain tribes of Africa. Under certain scenarios, the feq attained is even higher.

On the feasibility of malaria hypothesis

In 1954, Allison proposed that hemoglobin S (HbS) gene causes protection against fatal malaria. This would explain the high HbS gene frequency observed in certain regions hyperendemic for malaria, so-called "malaria hypothesis". This in silico study was conducted to examine the feasibility of the hypothesis under more realistic initial conditions, where a mutant gene with heterozygous advantage against malaria (e.g., HbS) was introduced in a group of Neolithic hunter-gatherers who decided to start agriculture nearby water where malaria killed a proportion of population. The tribe population size, number of children born to each woman in each generation, mortality from malaria and sickle cell disease, the protection factor provided by the gene carriers against malaria, the probability of mating between the members of the parent and offspring populations, population growth, and increased fertility in women heterozygous for HbS, were also considered. For effectively confer protection against malaria within the shortest possible period, the mutation needs to be happened in a small population. For a large population, the process would take around 100 generations (~ 2500 years) or more to provide an effective protection. Even then, the probability that the new gene could survive and propagate to future generations is about 35%. Conventional population genetics equations with differential or difference equations, give totally incorrect estimates of the gene frequency in small populations; discrete mathematics should be used, instead. After introduction of the advantageous mutation, the gene frequency increased until a steady state value. This value is far less than the gene frequency reported in certain tribes of Africa. It seems that the malaria hypothesis, per se, could not explain such a high observed gene frequency, unless HbS is associated with lower mortality from other causes too.

Effects of genetic variation on the structure of RNA and protein

Changes in the structure of RNA and protein, have an important impact on biological functions and are even important determinants of disease pathogenesis and treatment. Some genetic variations, including copy number variation, single nucleotide variation, and so on, can lead to changes in biological function and increased susceptibility to certain diseases by changing the structure of RNA or protein. With the development of structural biology and sequencing technology, a large amount of RNA and protein structure data and genetic variation data resources has emerged to be used to explain biological processes. Here, we reviewed the effects of genetic variation on the structure of RNAs and proteins, and investigated their impact on several diseases. An online resource (http://www.onethird-lab.com/gems/) to support convenient retrieval of common tools is also built. Finally, the challenges and future development of the effects of genetic variation on RNA and protein were discussed.

Molecular characterisation of sickle cell disease and classification of major haplotypes associated with the β-globin cluster (HBB gene) by means of SNP marker sequencing in a group of samples from Bolívar, Colombia

BACKGROUND

Colombia has a mestizo population and the prevalence of haemoglobin variants varies according to each region, but heterozygous carriers can be found in all of them.

AIM

To characterise sickle cell disease (SCD) haematologically, biochemically, and molecularly, and detect classic haplotypes by DNA sequencing in a group of samples from Bolívar, Colombia.

SUBJECTS AND METHODS

Blood samples were collected after informed consent from volunteers from eight communities in the Bolívar department, plus samples from the Pacific region, Providencia Island, and Bogotá were included. Data were obtained from: (1) haematological analyses; (2) biochemical tests: dHPLC was used to determine haemoglobin (Hb); and (3) DNA sequencing data through five SNPs.

RESULTS

101 samples were identified by rs334 through Sanger's Sequencing, structural haemoglobinopathies HbAS (34.65%), HbSS (2.97%) and HbAC (1.98%) were found. When contrasting the Hb identification results between SNP rs334 Vs. dHPLC/Isoelectric Focusing (IEF), a coincidence was found in 39/43 samples analysed, therefore, when comparing these techniques, a significant correlation was found (Pearson's correlation coefficient r = 0.998). 26 samples previously analysed by rs334 were classified into classical haplotypes CAR (50.0%), BEN (30.76%), CAM (7.69%), SEN (3.84%), and ATP-I (7.69%).

CONCLUSIONS

SCD characterisation and SNPs-based classification through Sanger's DNA sequencing have not been performed before in Colombia. The results of this work will make it possible to expand the data or records of carriers and those affected, which will benefit patients and their families.

JASPER: fast, powerful, multitrait association testing in structured samples gives insight on pleiotropy in gene expression

Joint association analysis of multiple traits with multiple genetic variants can provide insight into genetic architecture and pleiotropy, improve trait prediction and increase power for detecting association. Furthermore, some traits are naturally high-dimensional, e.g., images, networks or longitudinally measured traits. Assessing significance for multitrait genetic association can be challenging, especially when the sample has population sub-structure and/or related individuals. Failure to adequately adjust for sample structure can lead to power loss and inflated type 1 error, and commonly used methods for assessing significance can work poorly with a large number of traits or be computationally slow. We developed JASPER, a fast, powerful, robust method for assessing significance of multitrait association with a set of genetic variants, in samples that have population sub-structure, admixture and/or relatedness. In simulations, JASPER has higher power, better type 1 error control, and faster computation than existing methods, with the power and speed advantage of JASPER increasing with the number of traits. JASPER is potentially applicable to a wide range of association testing applications, including for multiple disease traits, expression traits, image-derived traits and microbiome abundances. It allows for covariates, ascertainment and rare variants and is robust to phenotype model misspecification. We apply JASPER to analyze gene expression in the Framingham Heart Study, where, compared to alternative approaches, JASPER finds more significant associations, including several that indicate pleiotropic effects, some of which replicate previous results, while others have not previously been reported. Our results demonstrate the promise of JASPER for powerful multitrait analysis in structured samples.

A Journey from Blood Cells to Genes and Back

I was attracted to hematology because by combining clinical findings with the use of a microscope and simple laboratory tests, one could often make a diagnosis. I was attracted to genetics when I learned about inherited blood disorders, at a time when we had only hints that somatic mutations were also important. It seemed clear that if we understood not only what genetic changes caused what diseases but also the mechanisms through which those genetic changes contribute to cause disease, we could improve management. Thus, I investigated many aspects of the glucose-6-phosphate dehydrogenase system, including cloning of the gene, and in the study of paroxysmal nocturnal hemoglobinuria (PNH), I found that it is a clonal disorder; subsequently, we were able to explain how a nonmalignant clone can expand, and I was involved in the first trial of PNH treatment by complement inhibition. I was fortunate to do clinical and research hematology in five countries; in all of them, I learned from mentors, from colleagues, and from patients.

The perception of pediatric sickle cell anemia patient's caregivers toward hematopoietic stem cell transplantation (single-center experience, Saudi Arabia)

Background

Sickle cell disease (SCD) is a relatively common genetic disorder in Saudi Arabia characterized by the predominance of sickle hemoglobin (HbS). Although multiple supportive care options exist for patients with SCD, hematopoietic stem cell transplantation (HSCT) is the only cure available and has become highly successful, with an almost 91% overall survival rate. However, pursuing this procedure is still restrained as a curative treatment option. Therefore, this study aimed to evaluate the perception of parents' caregivers at the National Guard Hospital pediatric hematology clinic regarding using HSCT as a curative approach for their children with SCD.

Methods

This is a cross-sectional study of the interviewer-administered survey distributed utilizing electronic devices to caregivers of pediatric patients with SCD. Subjects were recruited from Pediatric Hematology & Oncology clinics at National Guard Hospital Affairs in King Abdulaziz Medical City, Jeddah, Saudi Arabia. An estimated sample size of 100 was initially calculated out of 140 pediatric SCD patients; 72 responses were collected from participants. All study participants gave informed consent. All results were analyzed using SPSS; moreover, statistics were set at a CI of 95% and a p < 0.05. In addition, inferential and descriptive statistics were done.

Results

Of all respondents, 42 (67.8%) would accept HSCT if their hematologist recommended it. However, approximately 7 (11.3%) were not interested in the procedure, and the rest, 13 (21%), were uncertain. The most reported reasons for HSCT rejection among all respondents were attributed to side effects 31 (50.8%), lack of knowledge 8 (13.1%), and misconception toward the procedure 22 (36.1%).

Conclusion

The results of this study were consistent with the fact that most caregivers would follow along with HSCT if it seemed to be fit and was recommended by their hematologists. However, to the best of our knowledge, our study being the first of its kind in the region, further research in the kingdom on the perception of HSCT is needed. Nonetheless, further patient education, an increase in caregivers' knowledge, and enlightenment of the medical team on HSCT as a curative option for sickle cell disease are vital.

Ancestry, diversity, and genetics of health-related traits in African-derived communities (quilombos) from Brazil

Brazilian quilombos are communities formed by enslaved Africans and their descendants all over the country during slavery and shortly after its abolition. Quilombos harbor a great fraction of the largely unknown genetic diversity of the African diaspora in Brazil. Thus, genetic studies in quilombos have the potential to provide important insights not only into the African roots of the Brazilian population but also into the genetic bases of complex traits and human adaptation to diverse environments. This review summarizes the main results of genetic studies performed on quilombos so far. Here, we analyzed the patterns of African, Amerindian, European, and subcontinental ancestry (within Africa) of quilombos from the five different geographic regions of Brazil. In addition, uniparental markers (from the mtDNA and the Y chromosome) studies are analyzed together to reveal demographic processes and sex-biased admixture that occurred during the formation of these unique populations. Lastly, the prevalence of known malaria-adaptive African mutations and other African-specific variants discovered in quilombos, as well as the genetic bases of health-related traits, are discussed here, together with their implication for the health of populations of African descent.

Ancestral reconstruction and correlation of the frequencies of the hemoglobin S allele and the Duffy blood group alleles in human populations

OBJECTIVES

Malaria is an important selective force for human genetic adaptation due to the sustained, lethal impact it has had on populations worldwide. High frequencies of both hemoglobin S and the null allele FYB^ES of the Duffy blood group have been found in areas where this disease is endemic, attributed to the protective action of the carriers of these variants against malaria infection. The objective of this work was to perform ancestral reconstruction and analyze the correlation of the frequencies of these alleles throughout the phylogeny of 24 human populations.

METHODS

A tree topology and the allelic frequencies reported in the literature for the 24 populations were used. The ancestral frequencies for the two alleles were reconstructed using the maximum likelihood method and the Brownian model of evolution (CI = 95%), and the correlation analysis was performed using phylogenetically independent contrasts (PICs). Statistical analyses were performed with the statistical software R version 3.4.1.

RESULTS

For both alleles, a correspondence was found in the reconstruction of the ancestral frequencies, and a significant statistical correlation (p = .001) was observed between the S and FYB^ES alleles.

CONCLUSIONS

These results provide evidence of an epistatic relationship between the two alleles, which may influence the fitness of the individuals who present with them when they are subjected to a selective force such as malaria.

Infrastructure for bioinformatics applications in Tanzania: Lessons from the Sickle Cell Programme

Sickle cell disease (SCD) is a common genetic disorder in Africa. Some ongoing work in SCD research includes the analysis and comparisons of variation in phenotypic presentations and disease outcomes with the genotypic signatures. This has contributed to the observed growth of molecular and genetic data in SCD. However, while the "omics" data continues to pile, the capacity to interpret and turn the genetic findings into clinical practice is still underdeveloped, especially in the developing region. Building bioinformatics infrastructure and capacity in the region is key to bridging the gap. This paper seeks to illustrate how the Sickle Cell Programme (SCP) at the Muhimbili University of Health and Allied Sciences (MUHAS) in Tanzania, modeled the integration of infrastructure for bioinformatics and clinical research while running day-to-day clinical care for SCD in Tanzania.

Sickle Cell Disease in Children and Adolescents: A Review of the Historical, Clinical, and Public Health Perspective of Sub-Saharan Africa and Beyond

Sickle cell disease (SCD) is an umbrella term for a group of life-long debilitating autosomal recessive disorders that are caused by a single-point mutation (Glu→Val) that results in polymerization of hemoglobin (Hb) and reversible sickle-shape deformation of erythrocytes. This leads to increased hemolysis of erythrocytes and microvascular occlusion, ischemia-reperfusion injury, and tissue infarction, ultimately causing multisystem end-organ complications. Sickle cell anemia (HbSS) is the most common and most severe genotype of SCD, followed by HbSC, HbSβ⁰thalassemia, HbSβ+thalassemia, and rare and benign genotypes. Clinical manifestations of SCD occur early in life, are variable, and are modified by several genetic and environmental factors. Nearly 500 children with SCD continue to die prematurely every day, due to delayed diagnosis and/or lack of access to comprehensive care in sub-Saharan Africa (SSA), a trend that needs to be urgently reversed. Despite proven efficacy in developed countries, newborn screening programs are not universal in SSA. This calls for a consolidated effort to make this possible, through the use of rapid, accurate, and cheap point-of-care test kits which require minimal training. For almost two decades, hydroxyurea (hydroxycarbamide), a century-old drug, was the only disease-modifying therapy approved by the U.S. Food and Drug Administration. Recently, the list expanded to L-glutamine, crizanlizumab, and voxelotor, with several promising novel therapies in the pipeline. Despite its several limitations, hematopoietic stem cell transplant (HSCT) remains the only curative intervention for SCD. Meanwhile, recent advances in gene therapy trials offer a glimpse of hope for the near future, although its use maybe limited to developed countries for several decades.

Importance of Including Non-European Populations in Large Human Genetic Studies to Enhance Precision Medicine

One goal of genomic medicine is to uncover an individual's genetic risk for disease, which generally requires data connecting genotype to phenotype, as done in genome-wide association studies (GWAS). While there may be clinical promise to employing prediction tools such as polygenic risk scores (PRS), it currently stands that individuals of non-European ancestry may not reap the benefits of genomic medicine because of underrepresentation in large-scale genetics studies. Here, we discuss why this inequity poses a problem for genomic medicine and the reasons for the low transferability of PRS across populations. We also survey the ancestry representation of published GWAS and investigate how estimates of ancestry diversity in GWASparticipants might be biased. We highlight the importance of expanding genetic research in Africa, one of the most underrepresented regions in human genomics research, and discuss issues of ethics, resources, and technology for equitable advancement of genomic medicine.

[Acute chest syndrome in adult sickle cell patients]

Sickle cell disease is a frequent genetic condition, due to a mutation of the β-globin gene, leading to the production of an abnormal S hemoglobin and characterized by multiple vaso-occlusive events. The acute chest syndrome is a severe complication associated with a significant disability and mortality. It is defined by the association of one or more clinical respiratory manifestations and a new infiltrate on lung imaging. Its pathophysiology is complex and implies vaso-occlusive phenomena (pulmonary vascular thrombosis, fat embolism), infection, and alveolar hypoventilation. S/S or S/β⁰-thalassemia genotype, a history of vaso-occlusive crisis or acute chest syndrome, a low F hemoglobin level (<5%), a high steady-state hemoglobin level (> 10 g/dL), or a high steady-state leukocytosis (>10 G/L) are the main risk factors. Febrile chest pain, dyspnea, sometimes cough with expectorations are its main clinical manifestations, and bi-basal crackles are found at auscultation. Inferior alveolar opacities with or without pleural effusions are identified on chest X-ray or CT-scan. Management of the acute chest syndrome should be prompt and implies, besides the recognition of severity signs, a multimodal analgesia, oxygen supplementation, sometimes a parenteral antibiotic treatment and the frequent use of blood transfusions especially in the most severe cases. Prevention is important and includes a regular monitoring of hospitalized patients and the use of incentive spirometry.

Determinants of severity in sickle cell disease

Sickle cell disease is a very variable condition, with outcomes ranging from death in childhood to living relatively symptom free into the 8^th decade. Much of this variability is unexplained. The co-inheritance of α thalassaemia and factors determining HbF levels significantly modify the phenotype, but few other significant genetic variants have been identified, despite extensive studies. Environmental factors are undoubtedly important, with socio-economics and access to basic medical care explaining the huge differences in outcomes between many low- and high-income countries. Exposure to cold and windy weather seems to precipitate acute complications in many people, although these effects are unpredictable and vary with geography. Many studies have tried to identify prognostic factors which can be used to predict outcomes, particularly when applied in infancy. Overall, low haemoglobin, low haemoglobin F percentage and high reticulocytes in childhood are associated with worse outcomes, although again these effects are fairly weak and inconsistent.

High level of heterozygous haplotype of hemoglobin in Abidjan population with mild malaria

Background

Sickle cell disease (SCD) is a hemoglobin disorders that concern 300,000 newborns each year around the world. There are hemoglobin haplotypes that affect SCD clinic expression.

Methods

Our goal was to identify the hemoglobin’s haplotypes among individuals with mild malaria independently of SCD status in Côte d’Ivoire. To determine these haplotypes, specific restriction enzyme (RE) is used after PCR amplification with each primer. According to the digestion of PCR product by RE, five hemoglobin’s haplotypes are found in the world.

Results

In Côte d’Ivoire, no study has yet deeply described the distribution of haplotypes. Four different “classical” haplotypes of hemoglobin were detected: Benin (56.5%), Bantou (28.5%), Senegal (4%), Cameroun (1%); and 10% of atypical profiles. Heterozygous haplotype (69%) were more frequent than homozygous haplotype (31%).

Conclusions

In this preliminary study, we note a high prevalence of atypical and heterozygous haplotype. Benin haplotype that is associated with severity of SCD was most predominant in our studied population.

Five Priorities of African Genomics Research: The Next Frontier

To embrace the prospects of accurately diagnosing thousands of monogenic conditions, predicting disease risks for complex traits or diseases, tailoring treatment to individuals' pharmacogenetic profiles, and potentially curing some diseases, research into African genomic variation is a scientific imperative. African genomes harbor millions of uncaptured variants accumulated over 300,000 years of modern humans' evolutionary history, with successive waves of admixture, migration, and natural selection combining with extensive ecological diversity to create a broad and exceptional genomic complexity. Harnessing African genomic complexity, therefore, will require sustained commitment and equitable collaboration from the scientific community and funding agencies. African governments must support academic public research and industrial partnerships that build the necessary genetic medicine workforce, utilize the emerging genomic big data to develop expertise in computer science and bioinformatics, and evolve national and global governance frameworks that recognize the ethical implications of data-driven genomic research and empower its application in African social, cultural, economic, and religious contexts. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Protocol for "Genetic composition of sickle cell disease in the Arab population: A systematic review"

Background

Sickle Cell Disease (SCD) is a global health issue in hematology with a progressively increasing prevalence. There are recent advances in the management of SCD, with new drugs being introduced. It is essential to analyze the genetic makeup of SCD regionally to anticipate the effectiveness of management modalities. This systematic review's main objectives are (a) to combine the existing knowledge of the genetic composition of SCD in the Arab population and (b) to analyze the various phenotypes of SCD prevalent in the Arab population.

Methods

We will perform a systematic review and search multiple electronic databases predefined search terms to identify eligible articles. Eligible studies should report findings on the genetic testing of Sickle Cell disease in the 22 Arab countries. Case reports, case series, observational studies with cross‐sectional or prospective research design, case‐control studies, and experimental studies will be included. Study quality will be independently evaluated by two reviewers using the statistical methodology and categories guided by the Cochrane Collaboration Handbook and PRISMA guidelines.

Discussion

This review will explore and integrate the evidence available on the various genotypes and phenotypes of SCD in the Arab population. By acquiring and summarizing data about the genetic and phenotypic variants of the SCD patient population, this study will add to the knowledge and help find more precise treatments.

Systematic review registration

The protocol is registered at the International Prospective Register of Systematic Reviews (PROSPERO; registration number: CRD42020218666).

The Determination of Distinctive Single Nucleotide Polymorphism Sets for the Diagnosis of Behçet's Disease

Behçet's Disease (BD) is a multi-system inflammatory disorder in which the etiology remains unclear. The most probable hypothesis is that genetic tendency and environmental factors play roles in the development of BD. In order to find the essential reasons, genetic changes on thousands of genes should be analyzed. Besides, there is a need for extra analysis to find out which genetic factor affects the disease. Machine learning approaches have high potential for extracting the knowledge from genomics and selecting the representative Single Nucleotide Polymorphisms (SNPs) as the most effective features for the clinical diagnosis process. In this study, we have attempted to identify representative SNPs using feature selection methods, incorporating biological information and aimed to develop a machine-learning model for diagnosing Behçet's disease. By combining biological information and machine learning classifiers, up to 99.64 percent accuracy of disease prediction is achieved using only 13,611 out of 311,459 SNPs. In addition, we revealed the SNPs that are most distinctive by performing repeated feature selection in cross-validation experiments.

Phenotypic variation in sickle cell disease: the role of beta globin haplotype, alpha thalassaemia and fetal haemoglobin in HbSS

INTRODUCTION

The haematological and clinical feature vary markedly between the different genotypes of sickle cell disease. Even within the single genotype of homozygous sickle cell disease (HbSS), there is marked variability which is presumed to result from interacting genetic and environmental factors.

AREAS COVERED

The classification of the different genotypes of sickle cell disease with approximate prevalence at birth in different communities and some of the major clinical and haematological differences. This assessment includes three potential genetic factors influencing haematology and clinical outcome in HbSS, the beta globin haplotype, alpha thalassaemia and persistence of fetal haemoglobin (HbF).

EXPERT OPINION

The author is a clinician with experience of sickle cell disease primarily in Jamaica but also in Greece, Uganda, Saudi Arabia and India. It is therefore necessarily an account of clinical data and does not address current debates on molecular mechanisms. Most data derive from Jamaica where efforts have been made to reduce any symptomatic bias by long term follow-up of patients all over the island and further reduced by a cohort study based on newborn screening which has been in operation for over 48 years.

Disrupting Essentialism in Medical Genetics Education

Many traditional practices in medical genetics education need review to counteract messages of essentialism, or the belief in an underlying natural structure differentiating social categories. While genomics research increasingly disproves a genetic foundation for race, research from educational scholars demonstrates that current medical genetics instruction may actually reinforce racial bias in learners. In this monograph, we outline seven recommendations for medical educators to actively counteract essentialism, racial, and otherwise, in the genetics classroom. In particular, we emphasize the importance of engaging learners in nuanced discussions around stereotyping and its negative consequences for both accurate diagnoses and promoting health equity.

Revisiting the malaria hypothesis: accounting for polygenicity and pleiotropy

The malaria hypothesis predicts local, balancing selection of deleterious alleles that confer strong protection from malaria. Three protective variants, recently discovered in red cell genes, are indeed more common in African than European populations. Still, up to 89% of the heritability of severe malaria is attributed to many genome-wide loci with individually small effects. Recent analyses of hundreds of genome-wide association studies (GWAS) in humans suggest that most functional, polygenic variation is pleiotropic for multiple traits. Interestingly, GWAS alleles and red cell traits associated with small reductions in malaria risk are not enriched in African populations. We propose that other selective and neutral forces, in addition to malaria prevalence, explain the global distribution of most genetic variation impacting malaria risk.

Sickle cell disease in sub-Saharan Africa: transferable strategies for prevention and care

Sickle cell disease can be life-threatening or chronically debilitating for both children and adults. Worldwide, more than 300 000 children are born with sickle cell disease every year, over 75% of whom in sub-Saharan Africa. Increased awareness and early interventions, such as neonate screening and comprehensive care, have led to considerable reductions in mortality in children younger than 5 years in high-income countries. However, sickle cell disease prevention and care have largely been neglected in Africa. Without intervention, 50-90% of affected children in many sub-Saharan African countries die before their fifth birthday. Fortunately, increasing initiatives in sub-Saharan Africa are piloting interventions such as neonate screening and comprehensive care, and as mortality declines, quality of life and increased life expectancy become major targets for interventions. Hydroxyurea (hydroxycarbamide) and haematopoietic stem-cell transplantation have already been shown to be effective therapies in high-income countries, but are either not widely accessible or too expensive for most African populations. These challenges are being alleviated by numerous networks evolving through international collaborations that are positively changing the outlook of sickle cell disease management in sub-Saharan Africa. In this Series paper, we describe the epidemiology, pathophysiology, clinicobiological profile, and psychosocial effects of sickle cell disease in sub-Saharan Africa. We highlight transferable strategies already used for the successful management of the condition and key strategies and recommendations for affordable and comprehensive care on the continent. TRANSLATION: For the French translation of the abstract see Supplementary Materials section.

Retained Splenic Function in an Indian Population with Homozygous Sickle Cell Disease May Have Important Clinical Significance

BACKGROUND AND OBJECTIVES

To determine whether the persistence of splenomegaly characteristic of the Asian haplotype of homozygous sickle cell (SS) disease is associated with continued splenic function, a comparison of patients from Odisha, India, and Jamaica.

MATERIALS AND METHODS

Indian patients were examined in a cross-sectional study and compared with the Jamaican Cohort Study from birth. Splenomegaly was assessed in both populations with standard methods. Splenic function was assessed in both by counts of pitted red blood cells determined by differential interference contrast microscopy in the same laboratory.

RESULTS

In Jamaica, the spleen became palpable in 55% of patients during the 1^st year of life and the prevalence declined thereafter, whereas in Indian patients, the prevalence rose steeply after the age of 4 years. Raised pitted red cell counts, consistent with loss of splenic function, were common after 2 years in Jamaicans but did not increase in Indians until after the age of 5 years.

INTERPRETATION AND CONCLUSIONS

The maximal risk of invasive pneumococcal infection in SS disease falls sharply after the age of 3 years, and persistence of splenic function in Odisha patients beyond this age may explain the apparent absence of pneumococcal septicemia in Indian patients and questions the role of pneumococcal prophylaxis.

The Phenotypic Consequences of Genetic Divergence between Admixed Latin American Populations: Antioquia and Chocó, Colombia

Genome-wide association studies have uncovered thousands of genetic variants that are associated with a wide variety of human traits. Knowledge of how trait-associated variants are distributed within and between populations can provide insight into the genetic basis of group-specific phenotypic differences, particularly for health-related traits. We analyzed the genetic divergence levels for 1) individual trait-associated variants and 2) collections of variants that function together to encode polygenic traits, between two neighboring populations in Colombia that have distinct demographic profiles: Antioquia (Mestizo) and Chocó (Afro-Colombian). Genetic ancestry analysis showed 62% European, 32% Native American, and 6% African ancestry for Antioquia compared with 76% African, 10% European, and 14% Native American ancestry for Chocó, consistent with demography and previous results. Ancestry differences can confound cross-population comparison of polygenic risk scores (PRS); however, we did not find any systematic bias in PRS distributions for the two populations studied here, and population-specific differences in PRS were, for the most part, small and symmetrically distributed around zero. Both genetic differentiation at individual trait-associated single nucleotide polymorphisms and population-specific PRS differences between Antioquia and Chocó largely reflected anthropometric phenotypic differences that can be readily observed between the populations along with reported disease prevalence differences. Cases where population-specific differences in genetic risk did not align with observed trait (disease) prevalence point to the importance of environmental contributions to phenotypic variance, for both infectious and complex, common disease. The results reported here are distributed via a web-based platform for searching trait-associated variants and PRS divergence levels at http://map.chocogen.com (last accessed August 12, 2020).

The trans-ancestral genomic architecture of glycemic traits

Glycemic traits are used to diagnose and monitor type 2 diabetes and cardiometabolic health. To date, most genetic studies of glycemic traits have focused on individuals of European ancestry. Here we aggregated genome-wide association studies comprising up to 281,416 individuals without diabetes (30% non-European ancestry) for whom fasting glucose, 2-h glucose after an oral glucose challenge, glycated hemoglobin and fasting insulin data were available. Trans-ancestry and single-ancestry meta-analyses identified 242 loci (99 novel; P < 5 × 10-8), 80% of which had no significant evidence of between-ancestry heterogeneity. Analyses restricted to individuals of European ancestry with equivalent sample size would have led to 24 fewer new loci. Compared with single-ancestry analyses, equivalent-sized trans-ancestry fine-mapping reduced the number of estimated variants in 99% credible sets by a median of 37.5%. Genomic-feature, gene-expression and gene-set analyses revealed distinct biological signatures for each trait, highlighting different underlying biological pathways. Our results increase our understanding of diabetes pathophysiology by using trans-ancestry studies for improved power and resolution.

Evolutionary history of sickle-cell mutation: implications for global genetic medicine

Resistance afforded by the sickle-cell trait against severe malaria has led to high frequencies of the sickle-cell mutation [HBB; c.20T>A, p.Glu6Val; OMIM: 141900 (HBB-βS)] in most parts of Africa. High-coverage sequencing and genotype data have now confirmed the single African origin of the sickle-cell gene variant [HBB; c.20T>A, p.Glu6Val; OMIM: 141900 (HBB-βS)]. Nevertheless, the classical HBB-like genes cluster haplotypes remain a rich source of HBB-βS evolutionary information. The overlapping distribution of HBB-βS and other disease-associated variants means that their evolutionary genetics must be investigated concurrently. In this review: (1) we explore the evolutionary history of HBB-βS and its implications in understanding human migration within and out of Africa: e.g. HBB haplotypes and recent migration paths of the Bantu expansion, occurrence of ~7% of the Senegal haplotype in Angola reflecting changes in population/SCD dynamics, and existence of all five classical HBB haplotype in Cameroon and Egypt suggesting a much longer presence of HBB-βS in these regions; (2) we discuss the time estimates of the emergence of HBB-βS in Africa and finally, (3) we discuss implications for genetic medicine in understanding complex epistatic interactions between HBB-βS and other gene variants selected under environmental pressure in Africa e.g. variants in HBB, HBA, G6PD, APOL1, APOE, OSBPL10 and RXRA.

Three Signatures of Adaptive Polymorphism Exemplified by Malaria-Associated Genes

Malaria has been one of the strongest selective pressures on our species. Many of the best-characterized cases of adaptive evolution in humans are in genes tied to malaria resistance. However, the complex evolutionary patterns at these genes are poorly captured by standard scans for nonneutral evolution. Here, we present three new statistical tests for selection based on population genetic patterns that are observed more than once among key malaria resistance loci. We assess these tests using forward-time evolutionary simulations and apply them to global whole-genome sequencing data from humans, and thus we show that they are effective at distinguishing selection from neutrality. Each test captures a distinct evolutionary pattern, here called Divergent Haplotypes, Repeated Shifts, and Arrested Sweeps, associated with a particular period of human prehistory. We clarify the selective signatures at known malaria-relevant genes and identify additional genes showing similar adaptive evolutionary patterns. Among our top outliers, we see a particular enrichment for genes involved in erythropoiesis and for genes previously associated with malaria resistance, consistent with a major role for malaria in shaping these patterns of genetic diversity. Polymorphisms at these genes are likely to impact resistance to malaria infection and contribute to ongoing host-parasite coevolutionary dynamics.

Fetal hemoglobin in sickle cell anemia

Fetal hemoglobin (HbF) can blunt the pathophysiology, temper the clinical course, and offer prospects for curative therapy of sickle cell disease. This review focuses on (1) HbF quantitative trait loci and the geography of β-globin gene haplotypes, especially those found in the Middle East; (2) how HbF might differentially impact the pathophysiology and many subphenotypes of sickle cell disease; (3) clinical implications of person-to-person variation in the distribution of HbF among HbF-containing erythrocytes; and (4) reactivation of HbF gene expression using both pharmacologic and cell-based therapeutic approaches. A confluence of detailed understanding of the molecular basis of HbF gene expression, coupled with the ability to precisely target by genomic editing most areas of the genome, is producing important preliminary therapeutic results that could provide new options for cell-based therapeutics with curative intent.

Human ancient DNA analyses reveal the high burden of tuberculosis in Europeans over the last 2,000 years

Tuberculosis (TB), usually caused by Mycobacterium tuberculosis bacteria, is the first cause of death from an infectious disease at the worldwide scale, yet the mode and tempo of TB pressure on humans remain unknown. The recent discovery that homozygotes for the P1104A polymorphism of TYK2 are at higher risk to develop clinical forms of TB provided the first evidence of a common, monogenic predisposition to TB, offering a unique opportunity to inform on human co-evolution with a deadly pathogen. Here, we investigate the history of human exposure to TB by determining the evolutionary trajectory of the TYK2 P1104A variant in Europe, where TB is considered to be the deadliest documented infectious disease. Leveraging a large dataset of 1,013 ancient human genomes and using an approximate Bayesian computation approach, we find that the P1104A variant originated in the common ancestors of West Eurasians ∼30,000 years ago. Furthermore, we show that, following large-scale population movements of Anatolian Neolithic farmers and Eurasian steppe herders into Europe, P1104A has markedly fluctuated in frequency over the last 10,000 years of European history, with a dramatic decrease in frequency after the Bronze Age. Our analyses indicate that such a frequency drop is attributable to strong negative selection starting ∼2,000 years ago, with a relative fitness reduction on homozygotes of 20%, among the highest in the human genome. Together, our results provide genetic evidence that TB has imposed a heavy burden on European health over the last two millennia.

Sickle cell disease is a global prototype for integrative research and healthcare

Differences in health outcomes and treatment responses within and between global populations have been well documented. There is growing recognition of the need to move beyond simple inventories and descriptions of these differences and our linear explanations for them, and gain a better understanding of the multifaceted systems and networks underlying them in order to develop more precise and effective remedies. Typical targets for such integrative research have been common multifactorial diseases. We propose sickle cell disease, one of the most common monogenic diseases, as an ideal candidate for elucidating the complexity of the influences of endogenous and exogenous factors on disease pathophysiology, phenotypic diversity, and variations in responses to treatments at both the individual and population levels. We provide data-informed representations of diverse contributors to sickle cell disease complications that could guide innovative efforts to advance scientific knowledge, clinical practice, and policy formulation related to the disease; help improve outcomes for people worldwide with sickle cell disease; and inform approaches to studying and addressing other diseases.

Race Based Medicine, Colorblind Disease: How Racism in Medicine Harms Us All

The genome between socially constructed racial groups is 99.5%-99.9% identical; the 0.1%-0.5% variation between any two unrelated individuals is greatest between individuals in the same racial group; and there are no identifiable racial genomic clusters. Nevertheless, race continues to be used as a biological reality in health disparities research, medical guidelines, and standards of care reinforcing the notion that racial and ethnic minorities are inferior, while ignoring the health problems of Whites. This article discusses how the continued misuse of race in medicine and the identification of Whites as the control group, which reinforces this racial hierarchy, are examples of racism in medicine that harm all us. To address this problem, race should only be used as a factor in medicine when explicitly connected to racism or to fulfill diversity and inclusion efforts.

Sub-Saharan African information potential to unveil adaptations to infectious disease

Sub-Saharan Africa is the most promising region of the world to conduct high-throughput studies to unveil adaptations to infectious diseases due to several reasons, namely, the longest evolving time-depth in the Homo sapiens phylogenetic tree (at least two-third older than any other worldwide region); the continuous burden of infectious diseases (still number one in health/life threat); and the coexistence of populations practising diverse subsistence modes (nomadic or seminomadic hunter-gatherers and agropastoralists, and sedentary agriculturalists, small urban and megacity groups). In this review, we will present the most up-to-date results that shed light on three main hypotheses related with this adaptation. One is the hypothesis of coevolution between host and pathogen, given enough time for the establishment of this highly dynamic relationship. The second hypothesis enunciates that the agricultural transition was responsible for the increase of the infectious disease burden, due to the huge expansion of the sedentary human population and the cohabitation with domesticates as main reservoirs of pathogens. The third hypothesis states that the boosting of our immune system against pathogens by past selection may have resulted in maladaptation of the developed hygienic societies, leading to an increase of allergic, inflammatory and autoimmune disorders. Further work will enlighten the biological mechanisms behind these main adaptations, which can be insightful for translation into diagnosis, prognosis and treatment interventions.

Fine scale human genetic structure in three regions of Cameroon reveals episodic diversifying selection

Inferences from genetic association studies rely largely on the definition and description of the underlying populations that highlight their genetic similarities and differences. The clustering of human populations into subgroups (population structure) can significantly confound disease associations. This study investigated the fine-scale genetic structure within Cameroon that may underlie disparities observed with Cameroonian ethnicities in malaria genome-wide association studies in sub-Saharan Africa. Genotype data of 1073 individuals from three regions and three ethnic groups in Cameroon were analyzed using measures of genetic proximity to ascertain fine-scale genetic structure. Model-based clustering revealed distinct ancestral proportions among the Bantu, Semi-Bantu and Foulbe ethnic groups, while haplotype-based coancestry estimation revealed possible longstanding and ongoing sympatric differentiation among individuals of the Foulbe ethnic group, and their Bantu and Semi-Bantu counterparts. A genome scan found strong selection signatures in the HLA gene region, confirming longstanding knowledge of natural selection on this genomic region in African populations following immense disease pressure. Signatures of selection were also observed in the HBB gene cluster, a genomic region known to be under strong balancing selection in sub-Saharan Africa due to its co-evolution with malaria. This study further supports the role of evolution in shaping genomes of Cameroonian populations and reveals fine-scale hierarchical structure among and within Cameroonian ethnicities that may impact genetic association studies in the country.

Evolutionary genetics and acclimatization in nephrology

Evolutionary processes, including mutation, migration and natural selection, have influenced the prevalence and distribution of various disorders in humans. However, despite a few well-known examples, such as the APOL1 variants - which have undergone positive genetic selection for their ability to confer resistance to Trypanosoma brucei infection but confer a higher risk of chronic kidney disease - little is known about the effects of evolutionary processes that have shaped genetic variation on kidney disease. An understanding of basic concepts in evolutionary genetics provides an opportunity to consider how findings from ancient and archaic genomes could inform our knowledge of evolution and provide insights into how population migration and genetic admixture have shaped the current distribution and landscape of human kidney-associated diseases. Differences in exposures to infectious agents, environmental toxins, dietary components and climate also have the potential to influence the evolutionary genetics of kidneys. Of note, selective pressure on loci associated with kidney disease is often from non-kidney diseases, and thus it is important to understand how the link between genome-wide selected loci and kidney disease occurs in relation to secondary nephropathies.

Current modalities of sickle cell disease management

Sickle cell disease (SCD) affects nearly 100,000 people in the United States of America and the sickle gene is present in approximately 8% of black Americans. Among Africans, the prevalence of sickle cell trait (heterozygosity) is as high as 30%. While SCD occurs among varying racial and ethnic groups, it is more commonly prevalent in individuals of African or African-American descent. This inherited blood disorder causes varying symptoms and complications among affected children and adults and early diagnosis and treatment are essential to help reduce mortality rates. Because there is no cure for SCD, management is vital to survival. Hence, there are different approaches in use to aid those living with SCD; thus, this paper provides insight into the current methods that are implemented in the management and maintenance of this disease.

High Levels of Genetic Diversity within Nilo-Saharan Populations: Implications for Human Adaptation

Africa contains more human genetic variation than any other continent, but the majority of the population-scale analyses of the African peoples have focused on just two of the four major linguistic groups, the Niger-Congo and Afro-Asiatic, leaving the Nilo-Saharan and Khoisan populations under-represented. In order to assess genetic variation and signatures of selection within a Nilo-Saharan population and between the Nilo-Saharan and Niger-Congo and Afro-Asiatic, we sequenced 50 genomes from the Nilo-Saharan Lugbara population of North-West Uganda and 250 genomes from 6 previously unsequenced Niger-Congo populations. We compared these data to data from a further 16 Eurasian and African populations including the Gumuz, another putative Nilo-Saharan population from Ethiopia. Of the 21 million variants identified in the Nilo-Saharan population, 3.57 million (17%) were not represented in dbSNP and included predicted non-synonymous mutations with possible phenotypic effects. We found greater genetic differentiation between the Nilo-Saharan Lugbara and Gumuz populations than between any two Afro-Asiatic or Niger-Congo populations. F3 tests showed that Gumuz contributed a genetic component to most Niger-Congo B populations whereas Lugabara did not. We scanned the genomes of the Lugbara for evidence of selective sweeps. We found selective sweeps at four loci (SLC24A5, SNX13, TYRP1, and UVRAG) associated with skin pigmentation, three of which already have been reported to be under selection. These selective sweeps point toward adaptations to the intense UV radiation of the Sahel.

The road ahead in genetics and genomics

In celebration of the 20th anniversary of Nature Reviews Genetics, we asked 12 leading researchers to reflect on the key challenges and opportunities faced by the field of genetics and genomics. Keeping their particular research area in mind, they take stock of the current state of play and emphasize the work that remains to be done over the next few years so that, ultimately, the benefits of genetic and genomic research can be felt by everyone.

To celebrate the first 20 years of Nature Reviews Genetics, we asked 12 leading scientists to reflect on the key challenges and opportunities faced by the field of genetics and genomics.

Amy L. McGuire is the Leon Jaworski Professor of Biomedical Ethics and Director of the Center for Medical Ethics and Health Policy at Baylor College of Medicine. She has received numerous teaching awards at Baylor College of Medicine, was recognized by the Texas Executive Women as a Woman on the Move in 2016 and was invited to give a TedMed talk titled “There is No Genome for the Human Spirit” in 2014. In 2020, she was elected as a Hastings Center Fellow. Her research focuses on ethical and policy issues related to emerging technologies, with a particular focus on genomic research, personalized medicine and the clinical integration of novel neurotechnologies.

Stacey Gabriel is the Senior Director of the Genomics Platform at the Broad Institute since 2012 and has led platform development, execution and operation since its founding. She is Chair of Institute Scientists and serves on the institute’s executive leadership team. She is widely recognized as a leader in genomic technology and project execution. She has led the Broad’s contributions to numerous flagship projects in human genetics, including the International HapMap Project, the 1000 Genomes Project, The Cancer Genome Atlas, the National Heart, Lung, and Blood Institute’s Exome Sequencing Project and the TOPMed programme. She is Principal Investigator of the Broad’s All of Us (AoU) Genomics Center and serves on the AoU Program Steering Committee.

Sarah A. Tishkoff is the David and Lyn Silfen University Associate Professor in Genetics and Biology at the University of Pennsylvania, Philadelphia, USA, and holds appointments in the School of Medicine and the School of Arts and Sciences. She is a member of the US National Academy of Sciences and a recipient of an NIH Pioneer Award, a David and Lucile Packard Career Award, a Burroughs/Wellcome Fund Career Award and an American Society of Human Genetics Curt Stern Award. Her work focuses on genomic variation in Africa, human evolutionary history, the genetic basis of adaptation and phenotypic variation in Africa, and the genetic basis of susceptibility to infectious disease in Africa.

Ambroise Wonkam is Professor of Medical Genetics, Director of GeneMAP (Genetic Medicine of African Populations Research Centre) and Deputy Dean Research in the Faculty of Health Sciences, University of Cape Town, South Africa. He has successfully led numerous NIH- and Wellcome Trust-funded projects over the past decade to investigate clinical variability in sickle cell disease, hearing impairment genetics and the return of individual findings in genetic research in Africa. He won the competitive Clinical Genetics Society International Award for 2014 from the British Society of Genetic Medicine. He is president of the African Society of Human Genetics.

Aravinda Chakravarti is Director of the Center for Human Genetics and Genomics, the Muriel G. and George W. Singer Professor of Neuroscience and Physiology, and Professor of Medicine at New York University School of Medicine. He is an elected member of the US National Academy of Sciences, the US National Academy of Medicine and the Indian National Science Academy. He has been a key participant in the Human Genome Project, the International HapMap Project and the 1000 Genomes Project. His research attempts to understand the molecular basis of multifactorial disease. He was awarded the 2013 William Allan Award by the American Society of Human Genetics and the 2018 Chen Award by the Human Genome Organization.

Eileen E. M. Furlong is Head of the Genome Biology Department at the European Molecular Biology Laboratory (EMBL) and a member of the EMBL Directorate. She is an elected member of the European Molecular Biology Organization (EMBO) and the Academia Europaea, and a European Research Council (ERC) advanced investigator. Her group dissects fundamental principles of how the genome is regulated and how it drives cell fate decisions during embryonic development, including how developmental enhancers are organized and function within the 3D nucleus. Her work combines genetics, (single-cell) genomics, imaging and computational approaches to understand these processes. Her research has advanced the development of genomic methods for use in complex multicellular organisms.

Barbara Treutlein is Associate Professor of Quantitative Developmental Biology in the Department of Biosystems Science and Engineering of ETH Zurich in Basel, Switzerland. Her group uses and develops single-cell genomics approaches in combination with stem cell-based 2D and 3D culture systems to study how human organs develop and regenerate and how cell fate is regulated. For her work, Barbara has received multiple awards, including the Friedmund Neumann Prize of the Schering Foundation, the Dr. Susan Lim Award for Outstanding Young Investigator of the International Society of Stem Cell Research and the EMBO Young Investigator Award.

Alexander Meissner is a scientific member of the Max Planck Society and currently Managing Director of the Max Planck Institute (MPI) for Molecular Genetics in Berlin, Germany. He heads the Department of Genome Regulation and is a visiting scientist in the Department of Stem Cell and Regenerative Biology at Harvard University. Before his move to the MPI, he was a tenured professor at Harvard University and a senior associate member of the Broad Institute, where he co-directed the epigenomics programme. In 2018, he was elected as an EMBO member. His laboratory uses genomic tools to study developmental and disease biology with a particular focus on epigenetic regulation.

Howard Y. Chang is the Virginia and D. K. Ludwig Professor of Cancer Genomics at Stanford University and an investigator at the Howard Hughes Medical Institute. He is a physician–scientist who has focused on deciphering the hidden information in the non-coding genome. His laboratory is best known for studies of long non-coding RNAs in gene regulation and development of new epigenomic technologies. He is an elected member of the US National Academy of Sciences, the US National Academy of Medicine, and the American Academy of Arts and Sciences.

Núria López-Bigas is ICREA research Professor at the Institute for Research in Biomedicine and Associate Professor at the University Pompeu Fabra. She obtained an ERC Consolidator Grant in 2015 and was elected as an EMBO member in 2016. Her work has been recognized with the prestigious Banc de Sabadell Award for Research in Biomedicine, the Catalan National Award for Young Research Talent and the Career Development Award from the Human Frontier Science Program. Her research focuses on the identification of cancer driver mutations, genes and pathways across tumour types and in understanding the mutational processes that lead to the accumulation of mutations in cancer cells.

Eran Segal is Professor in the Department of Computer Science and Applied Mathematics at the Weizmann Institute of Science, heading a multidisciplinary laboratory with extensive experience in machine learning, computational biology and analysis of heterogeneous high-throughput genomic data. His research focuses on the microbiome, nutrition and genetics, and their effect on health and disease and aims to develop personalized medicine based on big data from human cohorts. He has published more than 150 publications and received several awards and honours for his work, including the Overton and the Michael Bruno awards. He was recently elected as an EMBO member and as a member of the Israel Young Academy.

Jin-Soo Kim is Director of the Center for Genome Engineering in the Institute for Basic Science in Daejon, South Korea. He has received numerous awards, including the 2017 Asan Award in Medicine, the 2017 Yumin Award in Science and the 2019 Research Excellence Award (Federation of Asian and Oceanian Biochemists and Molecular Biologists). He was featured as one of ten Science Stars of East Asia in Nature (558, 502–510 (2018)) and has been recognized as a highly cited researcher by Clarivate Analytics since 2018. His work focuses on developing tools for genome editing in biomedical research.

Whole genome sequence-based haplotypes reveal a single origin of the 1393 bp HBB deletion

BACKGROUND

Mutations of HBB give rise to two prevalent haemoglobin disorders-sickle cell disease (SCD) and β-thalassaemia. While SCD is caused by a single base substitution, nearly 300 mutations that downregulate expression of HBB have been described. The vast majority of β-thalassaemia alleles are point mutations or small insertion/deletions within the HBB gene; deletions causing β-thalassaemia are very rare. We have identified three individuals with haemoglobin Sβ0-thalassaemia in which the β0-thalassaemia mutation is caused by a large deletion.

OBJECTIVE

To use whole genome sequence data to determine whether these deletions arose from a single origin.

METHODS

We used two approaches to confirm unrelatedness: pairwise comparison of SNPs and identity by descent analysis. Eagle, V.2.4, was used to generate phased haplotypes for the 683 individuals. The Neighbor-Net method implemented in SplitsTree V.4.13.1 was used to construct the network of haplotypes.

RESULTS

All three deletions involved 1393 bp, encompassing the β-promoter, exons 1 and 2, and part of intron 2, with identical breakpoints. The cases were confirmed to be unrelated. Haplotypes based on 29 SNPs in the HBB cluster showed that the three individuals harboured different βS haplotypes. In contrast, the haplotype harbouring the 1393 bp deletion was the same in all three individuals.

CONCLUSION

We suggest that all the reported cases of the 1393 bp HBB deletion, including the three cases here, are likely to be of the same ancestral origin.

Genetic modifiers of long-term survival in sickle cell anemia

BACKGROUND

Sickle cell anemia (SCA) is a clinically heterogeneous, monogenic disorder. Medical care has less-than-optimal impact on clinical outcomes in SCA in Africa due to several factors, including patient accessibility, poor access to resources, and non-availability of specific effective interventions for SCA.

METHODS

Against this background, we investigated 192 African participants who underwent whole exome sequencing. Participants included 105 SCA patients spanning variable clinical expression: a "long survivor" group (age over 40 years), a "stroke" group (at least one episode of overt stroke), and a "random" group (patients younger than 40 years without overt cerebrovascular disease). Fifty-eight ethnically matched homozygous hemoglobin A controls were also studied. Findings were validated in an independently recruited sample of 29 SCA patients. Statistical significance of the mutational burden of deleterious and loss-of-function variants per gene against a null model was estimated for each group, and gene-set association tests were conducted to test differences between groups.

RESULTS

In the "long survivor" group, deleterious/loss-of-function variants were enriched in genes including CLCN6 (a voltage-dependent chloride channel for which rare deleterious variants have been associated with lower blood pressure) and OGHDL (important in arginine metabolism, which is a therapeutic target in SCA). In the "stroke" group, significant genes implicated were associated with increased activity of the blood coagulation cascade and increased complement activation, for example, SERPINC1, which encodes antithrombin. Oxidative stress and glutamate biosynthesis pathways were enriched in "long survivors" group. Published transcriptomic evidence provides functional support for the role of the identified pathways.

CONCLUSIONS

This study provides new gene sets that contribute to variability in clinical expression of SCA. Identified genes and pathways suggest new avenues for other interventions.

Prevalence and Diversity of Haplotypes of Sickle Cell Disease in the Eastern Province of Saudi Arabia

Hb F modulates sickle cell disease. Five major haplotypes of the β-globin gene cluster are associated with sickle cell disease. In the Eastern Province of Saudi Arabia, the Arab-Indian (AI) is most common. Single nucleotide polymorphism (SNP) genotyping (rs3834466, rs28440105, rs10128556, and rs968857) was carried out by nuclease allelic discrimination assay with target-specific forward and reverse primers, TaqMan probes, labeled with VIC and FAM. In 778 patients with sickle cell disease from the Eastern Province, a haplotype was assigned to 90.9% of all samples; 9.1% were classified as compound heterozygotes for the AI and an atypical haplotype. The distribution of haplotypes for 746 Hb S (HBB: c.20A > T) homozygotes was: 614 AI/AI, nine SEN/SEN (Senegal), 42 SEN/AI, nine CAM/CAM (Cameroon), one CAR (Central African Republic)/BEN (Benin), 71 AI/atypical. In Hb S/β-thalassemia (Hb S/β-thal), the distribution of Hb S haplotypes was: 22 AI/AI, one CAM/CAM, four AI/SEN, five AI/atypical. Mean Hb F in the haplotypes was: AI/AI 16.6 ± 7.5%, CAM/CAM 8.0 ± 4.1%, SEN/SEN 11.0 ± 5.1%, SEN/AI 15.1 ± 4.6%, AI/atypical 16.2 ± 6.5%. The presence of the SEN and CAM haplotypes was unexpected due to the apparent homogeneity of the population of the Eastern Province. We have successfully classified sickle cell disease haplotypes using the relatively inexpensive TaqMan assay for the first time. In addition, we have previously shown that children with AI haplotype have Hb F of 30.0% and mild disease, while in our cohort of adult AI patients, which might be the largest yet reported, Hb F was about 16.6%.

The Sickle Cell Disease Ontology: enabling universal sickle cell-based knowledge representation

Sickle cell disease (SCD) is one of the most common monogenic diseases in humans with multiple phenotypic expressions that can manifest as both acute and chronic complications. Although described more than a century ago, challenges in comprehensive disease management and collaborative research on this disease are compounded by the complex molecular and clinical phenotypes of SCD, environmental and psychosocial factors, limited therapeutic options and ambiguous terminology. This ambiguous terminology has hampered the integration and interoperability of existing SCD knowledge, and SCD research translation. The SCD Ontology (SCDO), which is a community-driven integrative and universal knowledge representation system for SCD, overcomes this issue by providing a controlled vocabulary developed by a group of experts in both SCD and ontology design. SCDO is the first and most comprehensive standardized human- and machine-readable resource that unambiguously represents terminology and concepts about SCD for researchers, patients and clinicians. It is built around the central concept ‘hemoglobinopathy’, allowing inclusion of non-SCD haemoglobinopathies, such as thalassaemias, which may interfere with or influence SCD phenotypic manifestations. This collaboratively developed ontology constitutes a comprehensive knowledge management system and standardized terminology of various SCD-related factors. The SCDO will promote interoperability of different research datasets, facilitate seamless data sharing and collaborations, including meta-analyses within the SCD community, and support the development and curation of data-basing and clinical informatics in SCD.

Genetic susceptibility to severe childhood asthma and rhinovirus-C maintained by balancing selection in humans for 150 000 years

Selective pressures imposed by pathogens have varied among human populations throughout their evolution, leading to marked inter-population differences at some genes mediating susceptibility to infectious and immune-related diseases. Here, we investigated the evolutionary history of a common polymorphism resulting in a Y529 versus C529 change in the cadherin related family member 3 (CDHR3) receptor which underlies variable susceptibility to rhinovirus-C infection and is associated with severe childhood asthma. The protective variant is the derived allele and is found at high frequency worldwide (69-95%). We detected genome-wide significant signatures of natural selection consistent with a rapid increase of the haplotypes carrying the allele, suggesting that non-neutral processes have acted on this locus across all human populations. However, the allele has not fixed in any population despite multiple lines of evidence suggesting that the mutation predates human migrations out of Africa. Using an approximate Bayesian computation method, we estimate the age of the mutation while explicitly accounting for past demography and positive or frequency-dependent balancing selection. Our analyses indicate a single emergence of the mutation in anatomically modern humans ~150 000 years ago and indicate that balancing selection has maintained the beneficial allele at high equilibrium frequencies worldwide. Apart from the well-known cases of the MHC and ABO genes, this study provides the first evidence that negative frequency-dependent selection plausibly acted on a human disease susceptibility locus, a form of balancing selection compatible with typical transmission dynamics of communicable respiratory viruses that might exploit CDHR3.

A Comprehensive Review of the Treatment and Management of Pain in Sickle Cell Disease

PURPOSE OF REVIEW

Sickle cell disease (SCD) is a hematological disorder which leads to serious complications in multiple organ systems. While significant research has addressed many of the effects of acute pain episodes and end-organ damage connected to this disease, little has approached the chronic pain state associated with this condition.

RECENT FINDINGS

Associated chronic pain represents a significant detractor from the quality of life experienced by these patients, affecting over half of those with SCD on more days than not. Current treatment typically is centered upon preventing and responding to acute vasoocclusive crises, presumably because this is the most common reason for hospitalization in these patients. The lack of management of chronic pain symptoms leaves many with SCD in a state of suffering. In this review, the treatment methodologies of SCD patients are examined including alternative treatments, both pharmaceutical and non-pharmaceutical, as well as procedural approaches specifically aimed at reducing chronic pain in these patients.

Comparison between Adult Patients with Sickle Cell Disease of Sub-Saharan African Origin Born in Metropolitan France and in Sub-Saharan Africa

Sickle cell disease (SCD) prevalence has increased rapidly in Europe as a result of an increase in the life expectancy of these patients and the arrival of SCD migrants from Africa. The aim of our study was to compare the phenotypes of adult patients born in Sub-Saharan Africa (SSA) who migrated to France with those of patients with the same origin who were born in France. This single-center observational study compared the demographic, clinical and biological characteristics of SCD adult patients of SSA origin who were born in France or SSA. Data were collected from computerized medical charts. Groups were compared using multivariate logistic regression with adjustment for age, gender and type of SCD. Of the 323 SCD patients followed in our center, 235 were enrolled, including 111 patients born in France and 124 patients born in SSA. SCD genotypes were balanced between groups. Patients born in Africa were older (median age 32.1 (24.4-39) vs. 25.6 (22.1-30.5) years, p < 0.001) and more often women (n = 75 (60.5%) vs. 48 (43.2%), p = 0.008). The median age at arrival in France was 18 years (13-23). The median height was lower among patients born in SSA (169 (163-175) vs. 174.5 cm (168-179), p < 0.001). Over their lifetimes, patients born in France had more acute chest syndromes (median number 2 (1-4) vs. 1 (0-3), p = 0.002), with the first episode occurring earlier (19 (11.6-22.3) vs. 24 (18.4-29.5) years, p < 0.007), and were admitted to intensive care units more often (53.3% vs. 34.9%, p = 0.006). This difference was more pronounced in the SS/Sβ0 population. Conversely, patients born in SSA had more skin ulcers (19.4% vs. 6.3%, p = 0.03). No significant differences were found in social and occupational insertion or other complications between the two groups. Patients born in SSA had a less severe disease phenotype regardless of their age than those born in France. This difference could be related to a survival bias occurring in Africa during childhood and migration to Europe that selected the least severe phenotypes.

THE EXPOSOME IN HUMAN EVOLUTION: FROM DUST TO DIESEL

Global exposures to air pollution and cigarette smoke are novel in human evolutionary history and are associated with about 16 million premature deaths per year. We investigate the history of the human exposome for relationships between novel environmental toxins and genetic changes during human evolution in six phases. Phase I: With increased walking on savannas, early human ancestors inhaled crustal dust, fecal aerosols, and spores; carrion scavenging introduced new infectious pathogens. Phase II: Domestic fire exposed early Homo to novel toxins from smoke and cooking. Phases III and IV: Neolithic to preindustrial Homo sapiens incurred infectious pathogens from domestic animals and dense communities with limited sanitation. Phase V: Industrialization introduced novel toxins from fossil fuels, industrial chemicals, and tobacco at the same time infectious pathogens were diminishing. Thereby, pathogen-driven causes of mortality were replaced by chronic diseases driven by sterile inflammogens, exogenous and endogenous. Phase VI: Considers future health during global warming with increased air pollution and infections. We hypothesize that adaptation to some ancient toxins persists in genetic variations associated with inflammation and longevity.

Not all red cells sickle the same: Contributions of the reticulocyte to disease pathology in sickle cell anemia

Sickle cell anemia (SCA) is associated with morbidity and early death. While the switch from fetal to sickle hemoglobin during the first months of life results in hemolytic anemia with reticulocytosis, the role of the reticulocyte in the pathophysiology and prognosis of SCA is not well-defined. Reticulocytes have unique cytoskeletal and membrane components that allow them to be distinguished from mature sickle erythrocytes in the circulation. Reticulocytes in patients with SCA are less dense than more mature and 'sickled' erythrocytes, and have increased adhesive properties. The circulating reticulocyte number in peripheral blood may assist in predicting disease severity in SCA; characterization of patient-specific reticulocyte properties during infancy and childhood may assist in predicting therapeutic response to therapies. Here, we review the biological and clinical data regarding reticulocytes and their potential impact on SCA pathophysiology and disease severity.

Impact of Rare and Common Genetic Variants on Diabetes Diagnosis by Hemoglobin A1c in Multi-Ancestry Cohorts: The Trans-Omics for Precision Medicine Program

Hemoglobin A1c (HbA1c) is widely used to diagnose diabetes and assess glycemic control in individuals with diabetes. However, nonglycemic determinants, including genetic variation, may influence how accurately HbA1c reflects underlying glycemia. Analyzing the NHLBI Trans-Omics for Precision Medicine (TOPMed) sequence data in 10,338 individuals from five studies and four ancestries (6,158 Europeans, 3,123 African-Americans, 650 Hispanics, and 407 East Asians), we confirmed five regions associated with HbA1c (GCK in Europeans and African-Americans, HK1 in Europeans and Hispanics, FN3K and/or FN3KRP in Europeans, and G6PD in African-Americans and Hispanics) and we identified an African-ancestry-specific low-frequency variant (rs1039215 in HBG2 and HBE1, minor allele frequency (MAF) = 0.03). The most associated G6PD variant (rs1050828-T, p.Val98Met, MAF = 12% in African-Americans, MAF = 2% in Hispanics) lowered HbA1c (-0.88% in hemizygous males, -0.34% in heterozygous females) and explained 23% of HbA1c variance in African-Americans and 4% in Hispanics. Additionally, we identified a rare distinct G6PD coding variant (rs76723693, p.Leu353Pro, MAF = 0.5%; -0.98% in hemizygous males, -0.46% in heterozygous females) and detected significant association with HbA1c when aggregating rare missense variants in G6PD. We observed similar magnitude and direction of effects for rs1039215 (HBG2) and rs76723693 (G6PD) in the two largest TOPMed African American cohorts, and we replicated the rs76723693 association in the UK Biobank African-ancestry participants. These variants in G6PD and HBG2 were monomorphic in the European and Asian samples. African or Hispanic ancestry individuals carrying G6PD variants may be underdiagnosed for diabetes when screened with HbA1c. Thus, assessment of these variants should be considered for incorporation into precision medicine approaches for diabetes diagnosis.