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

Genetic Modulators of Diversity in the Biological Expression of Sickle Cell Anemia in Patients from Democratic Republic of Congo: Role of βs-globin Haplotypes

Background: So far, the fetal hemoglobin (HbF) level is the most recognized modulator of sickle cell anemia (SCA) clinical expression. Variability in the HbF levels is associated with the SCA haplotypes and quantitative trait loci identified by  Genome-Wide Association Studies (GWAS). Key words: sickle cell anemia, DR Congo, SCA haplotypes, HbF, single nucleotide polymorphisms  

History, Advances, and Challenges of Sickle Cell Disease Treatment

Sickle cell disease (SCD) is marked by red blood cells that deform into a sickle shape, causing severe health complications. Historic neglect and slow therapeutic progress have left many, especially African descendants, vulnerable. Recent treatment strides include novel drugs and gene therapy, promising improved management. Nonetheless, challenges persist with treatment adoption because of cost, adverse effects, and accessibility. Advancements hold hope for enhanced life quality and longevity for SCD patients.

Systematic comparison of phenome-wide admixture mapping and genome-wide association in a diverse biobank

Biobank-scale association studies that include Hispanic/Latino(a) (HL) and African American (AA) populations remain underrepresented, limiting the discovery of disease associated genetic factors in these groups. We present here a systematic comparison of phenome-wide admixture mapping (AM) and genome-wide association (GWAS) using data from the diverse Bio Me biobank in New York City. Our analysis highlights 77 genome-wide significant AM signals, 48 of which were not detected by GWAS, emphasizing the complementary nature of these two approaches. AM-tagged variants show significantly higher minor allele frequency and population differentiation (Fst) while GWAS demonstrated higher odds ratios, underscoring the distinct genetic architecture identified by each method. This study offers a comprehensive phenome-wide AM resource, demonstrating its utility in uncovering novel genetic associations in underrepresented populations, particularly for variants missed by traditional GWAS approaches.

Arab founder variants: Contributions to clinical genomics and precision medicine

BACKGROUND

Founder variants are ancestral variants shared by individuals who are not closely related. The large effect size of some of these variants in the context of Mendelian disorders offers numerous precision medicine opportunities.

METHODS

Using one of the largest datasets on Mendelian disorders in the Middle East, we identified 2,908 medically relevant founder variants derived from 18,360 exomes and genomes and investigated their contribution to the clinical annotation of the human genome.

FINDINGS

Strikingly, ∼34% of Arab founder variants are absent in gnomAD. We found a strong contribution of Arab founder variants to the identification of novel gene-disease links (n = 224) and the support/dispute (n = 81 support, n = 101 dispute) of previously reported candidate gene-disease links. The powerful segregation evidence generated by Arab founder variants allowed many ClinVar and Human Gene Mutation Database variants to be reclassified. Overall, 39.5% of diagnostic reports from our clinical lab are based on founder variants, and 19.41% of tested individuals carry at least one pathogenic founder variant. The presumptive loss-of-function mechanism that typically underlies autosomal recessive diseases means that Arab founder variants also offer unique opportunities in "druggable genome" research. Arab founder variants were also informative of migration patterns in the Middle East consistent with documented historical accounts.

CONCLUSIONS

We highlight the contribution of founder variants from an under-represented population group to precision medicine and inform future prevention programs. Our study also sheds light on the added value of these variants in supplementing other lines of research in tracing population history.

FUNDING

There is no funding for this work.

Copy-number variants differ in frequency across genetic ancestry groups

Copy-number variants (CNVs) have been implicated in a variety of neuropsychiatric and cognitive phenotypes. We found that deleterious CNVs are less prevalent in non-European ancestry groups than they are in European ancestry groups of both the UK Biobank (UKBB) and a US replication cohort (SPARK). We also identified specific recurrent CNVs that consistently differ in frequency across ancestry groups in both the UKBB and SPARK. These ancestry-related differences in CNV prevalence present in both an unselected community population and a family cohort enriched with individuals diagnosed with autism spectrum disorder (ASD) strongly suggest that genetic ancestry should be considered when probing associations between CNVs and health outcomes.

First investigation of RH gene polymorphism in patients with sickle cell disease and associated blood donors in Cameroon, Central Africa

BACKGROUND

Although genetic polymorphism of the RH blood group system is well known in sub-Saharan Africa, national/regional specificities still remain to be described precisely. For the first time in Cameroon, Central Africa, and in order to better characterize the molecular basis driving RH phenotype variability, as well as to identify the main antigens that may be potentially responsible for alloimmunization, we sought 1) to study the RH genes in a cohort of 109 patients with sickle cell disease; 2) to study the same genes in the corresponding donors whose red blood cells (RBCs) were transfused to the patients (108 donors in 98 patients); 3) to predict RH phenotype on the basis of the molecular data and compare the results with serologic testing; and 4) to identify retrospectively patients at risk for alloimmunization.

MATERIALS AND METHODS

In order to generate an exhaustive dataset, the RH genes of all patient and donor samples were systematically investigated 1) by quantitative multiplex PCR of short fluorescent fragments (QMPSF) for characterization of RHD gene zygosity and potential structural variants (SVs), and 2) by Sanger sequencing for identification of single nucleotide variants (SNVs). Subsequent to molecular analysis, the genotypes and RH phenotype were deduced and predicted, respectively, from reference databases.

RESULTS

In a total of 217 Cameroonian individuals, as many as 24 and up to 22 variant alleles were identified in the RHD and RHCE genes, respectively, in addition to the reference alleles. Interestingly, 65 patients with SCD (66.3%) were assumed to be exposed to one or more undesirable RH antigen(s) with varying degrees of clinical relevance.

DISCUSSION

Beyond the comprehensive report of the nature and distribution of RH variant alleles in a subset of Cameroonian patients treated by transfusion therapy, this work highlights the need for an extensive review of current practice, including routine serologic typing procedures, preferably in the near future.

Evaluation of a point-of-care rapid diagnostic test kit (SICKLECHECK) for screening of sickle cell diseases

Sickle cell diseases (SCD) are the most common genetic disorders with significant morbidity and mortality worldwide, including in India. The high prevalence of this disorder in many geographical regions calls for the use of a point-of-care rapid diagnostic test (RDT) for early screening and management of the diagnosed cases to reduce the allied clinical severity. In view of this, the present study was undertaken for the validation of a point-of-care RDT kit (SICKLECHECKTM) for the screening of SCD. This validation and diagnostic accuracy study was conducted among the cases advised for screening of SCD. For validation, all the recruited cases were investigated for both the SICKLECHECKTM RDT kit and HPLC (Variant-II) considering HPLC as a gold standard. A total of 400 cases were screened for both tests. For the presence and absence of sickle cell hemoglobin in the samples, SICKLECHECKTM RDT kit results showed a sensitivity and specificity of 99.39% and 98.73% respectively with references to HPLC findings. For the detection of the 'AS' pattern, the SICKLECHECKTM RDT kit has shown a sensitivity and specificity of 99.07% and 98.81% respectively. For the detection of the 'SS' pattern, the SICKLECHECKTM RDT kit has shown a sensitivity and specificity of 97.92% and 100.0% respectively. Cases with β thalassemia trait, hemoglobin E trait, hemoglobin Lepore trait and trait for hereditary-persistence-of-fetal-hemoglobin (high HbF %) diagnosed in HPLC were resulted with 'AA' pattern in SICKLECHECKTM RDT kit. The high sensitivity and specificity of the SICKLECHECKTM RDT kit insist on its use as a point-of-care screening tool for SCD especially where there is a lack of laboratory facilities as well as in hospital-based set-up requiring immediate diagnosis and management of SCD. However, for further confirmation, the samples should be analyzed with other gold standard techniques like HPLC.

Determinants of the haemoglobin level in patients with sickle cell disease living in sub-Saharan Africa: Major impact of the country of residence and independent effects of leucocyte and platelet counts and haemolysis

The degree of anaemia in sickle cell disease (SCD) is a well-known contributor to morbidity and mortality. We aimed to explore the factors affecting haemoglobin (Hb) level in African SCD patients, considering haemolysis biomarkers (LDH and bilirubin level, and reticulocyte count), leucocyte and platelet counts and socio-demographic characteristics (gender, age group, country of residence and BMI). The research was part of the CADRE multinational cohort and involved 3699 SCD patients living in Mali, Senegal, Ivory Coast, Democratic Republic of Congo, Gabon and Cameroon: 2936 SS/Sβ0, 587 SC and 176 Sβ + patients with median Hb level of 8, 11.3 and 11.2 g/dL respectively (p < 0.001). In multivariate analysis conducted in 1394 SS/Sβ0 patients, living in Cameroon, female gender, lower BMI, higher haemolysis markers (especially LDH) and higher leucocyte and platelet counts were independently associated with lower Hb level (all p < 0.05). In 497 SC and 156 Sβ + patients, female gender (p < 0.001), lower BMI (p < 0.05) and higher platelet counts (p < 0.001) were independently associated with lower Hb level. Anaemia in African SCD patients is not only associated with haemolysis but also with the country of residence, lower BMI and leucocyte or platelet counts which might reflect inflammation related to infectious burden in the region.

Sickle Cell Disease in Brazil: Current Management

Sickle cell disease (SCD) comprises inherited red blood cell disorders due to a mutation in the β-globin gene (c20A > T, pGlu6Val) and is characterized by the presence of abnormal hemoglobin, hemoglobin S, hemolysis, and vaso-occlusion. This mutation, either in a homozygous configuration or in compound states with other β-globin mutations, leads to polymerization of hemoglobin S in deoxygenated conditions, causing modifications in red blood cell shape, particularly sickling. Vaso-occlusive crisis (VOC) is the hallmark of the disease, but other severe complications may arise from repeated bouts of VOCs. SCD is considered a global health problem, and its incidence has increased in some areas of the world, particularly the Americas and Africa. Management of the disease varies according to the region of the world, mainly due to local resources and socioeconomic status. This review aimed to describe more recent data on SCD regarding available treatment options, especially in Brazil. New treatment options are expected to be available to all patients, particularly crizanlizumab, which is already approved in the country.

More evidence for widespread antagonistic pleiotropy in polymorphic disease alleles

Introduction

Many loci segregate alleles classified as "genetic diseases" due to their deleterious effects on health. However, some disease alleles have been reported to show beneficial effects under certain conditions or in certain populations. The beneficial effects of these antagonistically pleiotropic alleles may explain their continued prevalence, but the degree to which antagonistic pleiotropy is common or rare is unresolved. We surveyed the medical literature to identify examples of antagonistic pleiotropy to help determine whether antagonistic pleiotropy appears to be rare or common.

Results

We identified ten examples of loci with polymorphisms for which the presence of antagonistic pleiotropy is well supported by detailed genetic or epidemiological information in humans. One additional locus was identified for which the supporting evidence comes from animal studies. These examples complement over 20 others reported in other reviews.

Discussion

The existence of more than 30 identified antagonistically pleiotropic human disease alleles suggests that this phenomenon may be widespread. This poses important implications for both our understanding of human evolutionary genetics and our approaches to clinical treatment and disease prevention, especially therapies based on genetic modification.

The cliff edge model of the evolution of schizophrenia: Mathematical, epidemiological, and genetic evidence

How has schizophrenia, a condition that significantly reduces an individual's evolutionary fitness, remained common across generations and cultures? Numerous theories about the evolution of schizophrenia have been proposed, most of which are not consistent with modern epidemiological and genetic evidence. Here, we briefly review this evidence and explore the cliff edge model of schizophrenia. It suggests that schizophrenia is the extreme manifestation of a polygenic trait or a combination of traits that, within a normal range of variation, confer cognitive, linguistic, and/or social advantages. Only beyond a certain threshold, these traits precipitate the onset of schizophrenia and reduce fitness. We provide the first mathematical model of this qualitative concept and show that it requires only very weak positive selection of the underlying trait(s) to explain today's schizophrenia prevalence. This prediction, along with expectations about the effect size of schizophrenia risk alleles, are surprisingly well matched by empirical evidence. The cliff edge model predicts a dynamic change of selection of risk alleles, which explains the contradictory findings of evolutionary genetic studies.

Birth Prevalence of Sickle Cell Disease and County-Level Social Vulnerability - Sickle Cell Data Collection Program, 11 States, 2016-2020

Sickle cell disease (SCD) remains a public health priority in the United States because of its association with complex health needs, reduced life expectancy, lifelong disabilities, and high cost of care. A cross-sectional analysis was conducted to calculate the crude and race-specific birth prevalence for SCD using state newborn screening program records during 2016-2020 from 11 Sickle Cell Data Collection program states. The percentage distribution of birth mother residence within Social Vulnerability Index quartiles was derived. Among 3,305 newborns with confirmed SCD (including 57% with homozygous hemoglobin S or sickle β-null thalassemia across 11 states, 90% of whom were Black or African American [Black], and 4% of whom were Hispanic or Latino), the crude SCD birth prevalence was 4.83 per 10,000 (one in every 2,070) live births and 28.54 per 10,000 (one in every 350) non-Hispanic Black newborns. Approximately two thirds (67%) of mothers of newborns with SCD lived in counties with high or very high levels of social vulnerability; most mothers lived in counties with high or very high levels of vulnerability for racial and ethnic minority status (89%) and housing type and transportation (64%) themes. These findings can guide public health, health care systems, and community program planning and implementation that address social determinants of health for infants with SCD. Implementation of tailored interventions, including increasing access to transportation, improving housing, and advancing equity in high vulnerability areas, could facilitate care and improve health outcomes for children with SCD.

Acute soft head syndrome in a teenager with sickle cell anemia: A case report

Key Clinical Message

Sickle cell disease (SCD) rarely presents with acute soft head syndrome (ASHS) often posing a diagnostic dilemma. Recovery is typically spontaneous, however, in the context of lack of awareness and limited brain imaging it could potentially lead to poor outcome.

Abstract

ASHS is a rare complication of SCD, invariably occurring near puberty with hitherto elusive pathogenic mechanisms. ASHS often resolves spontaneously on conservative management, however, lack of awareness in the context of limited access to brain imaging could pose diagnostic challenges resulting in inappropriate management and untoward outcome. We present a case of a teenager who presented with subtle symptoms for which the diagnosis of sickle cell anemia (SCA) was delayed until he developed ASHS. LTM was a 16 years old boy with a history of recurrent joints pain since the age of 6 years, with a family history of SCA, but had initial negative sickling test. He presented with episodes of multiple joints pain, unprovoked scalp and left orbital swelling, low-grade fever and mild headache without any evidence for bleeding diathesis. The diagnosis of SCA was confirmed by hemoglobin electrophoresis. Computed tomography (CT) scan of the head revealed subgaleal heamatoma (SGH) and intraorbital haematoma without intracranial hemorrhage (ICH). He was managed conservatively with analgesics and hydration together with antibiotics for associated sepsis with complete resolution of clinical symptoms within 2 weeks. This case represents a rare scenario for a relatively mild SCA phenotype presenting with ASHS whose diagnosis poses an enigma in the resource-limited contex. It is therefore, prudent to recognize ASHS to avoid judicious interventions which could potentially result in untoward clinical outcome.

Simultaneous adjunctive treatment of malaria and its coevolved genetic disorder sickle cell anemia

Effective treatments for genetic disorders that coevolved with pathogens require simultaneous betterment of both conditions. Hydroxyurea (HU) offers safe and efficacious treatment for sickle cell anemia (SCA) by reducing clinical complications, transfusions, and death rates. Despite concerns that the HU treatment for SCA would increase infection risk by the human malaria Plasmodium falciparum, (the genetic driver of the sickle mutation), HU instead reduced clinical malaria. We used physiologically relevant drug exposures that mimic in vivo pharmacokinetics in humans. Under these conditions, we showed that HU and other ribonucleotide reductase (RNR) inhibitors have significant, intrinsic killing activity in vitro against schizont stages of P falciparum in both normal and sickle red blood cells. Long-term in vitro selection with HU increased the expression of Pfrnr genes but showed a low risk of eliciting stably resistant parasites or compromising the potency of current antimalarial drugs. Additive activity devoid of antagonism by HU was observed with a wide spectrum of commonly used antimalarial treatments. These data endorse broad, safe, and long-term use of HU for SCA in malaria-endemic countries and provide a novel biological model for the treatment of a genetic disorder with simultaneous, adjunct therapy of a life-threatening infection needed in a global health setting.

Silent Cerebral Infarcts in Iraqi Patients with Sickle Cell Disease

Silent ischemic infarcts have been reported to be the most frequent neurological abnormalities in sickle cell disease (SCD) in several studies worldwide. However, no previous studies investigated this neurological disorder in Iraqi SCD patients. To address this issue, a total of 52 patients with a median age of 20 years (range 10-46) and including 46.2% males were enrolled. Patients were clinically evaluated and their records were reviewed. They had full blood and reticulocyte counts, hemoglobin F estimation, serum lactic dehydrogenase and bilirubin assayed, as well as brain magnetic resonance imaging (MRI) to screen for silent cerebral infarcts. Six out of the 52 patients (11.5%) had silent cerebral infarcts, all of which were in the deep white matter, ranging from 6 to 10 mm in their largest diameters. There were no significant differences in age, sex, or sickle cell genotype between those with silent cerebral infarcts and those without it. Those with silent cerebral infarcts had lower median hemoglobin, higher reticulocytes and lower pain frequencies than those without it, yet again this was not significant. Follow up MRI in four out of the six silent infarct patients showed no additional lesions and no increase in size of the original ones after six to eight months. In conclusion, it appears that the frequency of silent cerebral infarcts in Iraqi SCD patients is lower than the bulk of the literature from other populations. Further studies to screen for genetic polymorphisms that may explain this lower rate may be informative.

The genetic legacy of African Americans from Catoctin Furnace

Few African Americans have been able to trace family lineages back to ancestors who died before the 1870 United States Census, the first in which all Black people were listed by name. We analyzed 27 individuals from Maryland's Catoctin Furnace African American Cemetery (1774-1850), identifying 41,799 genetic relatives among consenting research participants in 23andMe, Inc.'s genetic database. One of the highest concentrations of close relatives is in Maryland, suggesting that descendants of the Catoctin individuals remain in the area. We find that many of the Catoctin individuals derived African ancestry from the Wolof or Kongo groups and European ancestry from Great Britain and Ireland. This study demonstrates the power of joint analysis of historical DNA and large datasets generated through direct-to-consumer ancestry testing.

Influence of TRPM4 rs8104571 genotype on intracranial pressure and outcomes in African Americans with traumatic brain injury

The TRPM4 gene codes for a membrane ion channel subunit related to inflammation in the central nervous system. Recent investigation has identified an association between TRPM4 single nucleotide polymorphisms (SNPs) rs8104571 and rs150391806 and increased intracranial (ICP) pressure following traumatic brain injury (TBI). We assessed the influence of these genotypes on clinical outcomes and ICP in TBI patients. We included 292 trauma patients with TBI. DNA extraction and real-time PCR were used for TRPM4 rs8104571 and rs150391806 allele discrimination. Five participants were determined to have the rs8104571 homozygous variant genotype, and 20 participants were identified as heterozygotes; 24 of these 25 participants were African American. No participants had rs150391806 variant alleles, preventing further analysis of this SNP. Genotypes containing the rs8104571 variant allele were associated with decreased Glasgow outcome scale-extended (GOSE) score (P = 0.0231), which was also consistent within our African-American subpopulation (P = 0.0324). Regression analysis identified an association between rs8104571 variant homozygotes and mortality within our overall population (P = 0.0230) and among African Americans (P = 0.0244). Participants with rs8104571 variant genotypes exhibited an overall increase in ICP (P = 0.0077), although a greater frequency of ICP measurements > 25 mmHg was observed in wild-type participants (P =  < 0.0001). We report an association between the TRPM4 rs8104571 variant allele and poor outcomes following TBI. These findings can potentially be translated into a precision medicine approach for African Americans following TBI utilizing TRPM4-specific pharmaceutical interventions. Validation through larger cohorts is warranted.

Sickle Cell Anemia Associated With Increased In-Hospital Mortality in Post-Cardiac Arrest Patients

Introduction Sickle cell anemia (SCA) is a hemoglobinopathy that arises from a point mutation in the beta-globin gene, which causes the polymerization of deoxygenated hemoglobin that leads to a wide variety of clinical complications. Deaths in patients with SCA most commonly arise from renal, cardiovascular disease, infections, and stroke. In-hospital cardiac arrest has been found to be more common in older patients and those on ventilatory life support, among others. This study aims to provide more insight into how SCA affects the risk of in-hospital mortality in post-cardiac arrest patients. Methods The National Inpatient Survey database years 2016 to 2019 was utilized. The International Classification of Diseases, Tenth Revision, Procedure Coding System (ICD-10 PCS) codes for cardiopulmonary resuscitation were used to identify in-hospital cardiac arrest (IHCA) patients. ICD-10 Clinical Modification (CM) codes were used to identify SCA and other medical comorbidities. Categorical data was compared using Person's chi-square test, and continuous variables were compared using the independent samples t-test. Multinomial logistic regression was used to study the effects of SCA on post-arrest in-hospital mortality controlling for age, Charlson comorbidity score, and demographic variables. Binomial logistic regression models for dichotomous variables were utilized in the subgroup and secondary outcomes analysis. Results In patients with IHCA, patients who had SCA were found to have a significantly increased risk of in-hospital mortality adjusted for baseline characteristics and Charlson comorbidity score (OR: 1.16, 95% CI: 1.02-1.32, p=0.0025). Patient characteristics most strongly associated with an increased risk of in-hospital mortality in this cohort were found to be Black race (OR: 1.92, 95% CI: 1.87-1.97, p<0.001) and self-payer status (OR: 2.14, 95% CI: 2.06-2.22, p<0.001). Subgroup analysis revealed only patients with sickle cell disease had a statistically significant increased risk of in-hospital mortality in this cohort (OR: 4.41, 95% CI: 3.5-5.55, p<0.001), and patients with sickle cell trait did not. Conclusion In patients with IHCA, SCA is associated with an increased risk of in-hospital mortality. This risk was confined to patients with sickle cell disease and not patients with sickle cell trait.

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.

Global Distribution of Founder Variants Associated with Non-Syndromic Hearing Impairment

The genetic etiology of non-syndromic hearing impairment (NSHI) is highly heterogeneous with over 124 distinct genes identified. The wide spectrum of implicated genes has challenged the implementation of molecular diagnosis with equal clinical validity in all settings. Differential frequencies of allelic variants in the most common NSHI causal gene, gap junction beta 2 (GJB2), has been described as stemming from the segregation of a founder variant and/or spontaneous germline variant hot spots. We aimed to systematically review the global distribution and provenance of founder variants associated with NSHI. The study protocol was registered on PROSPERO, the International Prospective Register of Systematic Reviews, with the registration number "CRD42020198573". Data from 52 reports, involving 27,959 study participants from 24 countries, reporting 56 founder pathogenic or likely pathogenic (P/LP) variants in 14 genes (GJB2, GJB6, GSDME, TMC1, TMIE, TMPRSS3, KCNQ4, PJVK, OTOF, EYA4, MYO15A, PDZD7, CLDN14, and CDH23), were reviewed. Varied number short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) were used for haplotype analysis to identify the shared ancestral informative markers in a linkage disequilibrium and variants' origins, age estimates, and common ancestry computations in the reviewed reports. Asia recorded the highest number of NSHI founder variants (85.7%; 48/56), with variants in all 14 genes, followed by Europe (16.1%; 9/56). GJB2 had the highest number of ethnic-specific P/LP founder variants. This review reports on the global distribution of NSHI founder variants and relates their evolution to population migration history, bottleneck events, and demographic changes in populations linked with the early evolution of deleterious founder alleles. International migration and regional and cultural intermarriage, coupled to rapid population growth, may have contributed to re-shaping the genetic architecture and structural dynamics of populations segregating these pathogenic founder variants. We have highlighted and showed the paucity of data on hearing impairment (HI) variants in Africa, establishing unexplored opportunities in genetic traits.

The future of sickle cell disease therapeutics rests in genomics

Sickle cell disease (SCD) is the most-common monogenic recessive disease in humans, annually affecting almost 300,000 newborns worldwide, 75% of whom live in Africa. Genomics research can accelerate the development of curative therapies for SCD in three ways. First, research should explore the missing heritability of foetal haemoglobin (HbF) - the strongest known modifier of SCD clinical expression - among highly genetically heterogenous and understudied African populations, to provide novel therapeutics targets for HbF induction. Second, SCD research should invest in RNA therapies, either by using microRNA to target the production of HbF proteins by binding to the transcription machinery in a cell, or by directly mediating production of HbF or adult haemoglobin through injection of messenger RNA. Third, investigators should aim to identify currently unknown genetic risk factors for SCD cardiovascular complications, which will address mortality, particularly in adults. Now is the time for global research programs to uncover genomic keys to unlock SCD therapeutics.

Managing the Cerebrovascular Complications of Sickle Cell Disease: Current Perspectives

The importance of protecting brain function for people with sickle cell disease (SCD) cannot be overstated. SCD is associated with multiple cerebrovascular complications that threaten neurocognitive function and life. Without screening and preventive management, 11% of children at 24% of adults with SCD have ischemic or hemorrhagic strokes. Stroke screening in children with SCD is well-established using transcranial Doppler ultrasound (TCD). TCD velocities above 200 cm/s significantly increase the risk of stroke, which can be prevented using chronic red blood cell (RBC) transfusion. RBC transfusion is also the cornerstone of acute stroke management and secondary stroke prevention. Chronic transfusion requires long-term management of complications like iron overload. Hydroxyurea can replace chronic transfusions for primary stroke prevention in a select group of patients or in populations where chronic transfusions are not feasible. Silent cerebral infarction (SCI) is even more common than stroke, affecting 39% of children and more than 50% of adults with SCD; management of SCI is individualized and includes careful neurocognitive evaluation. Hematopoietic stem cell transplant prevents cerebrovascular complications, despite the short- and long-term risks. Newer disease-modifying agents like voxelotor and crizanlizumab, as well as gene therapy, may treat cerebrovascular complications, but these approaches are investigational.

Obesity Pillars Roundtable: Body mass index and body composition in Black and Female individuals. Race-relevant or racist? Sex-relevant or sexist?

Background

Body mass index (BMI or weight in kilograms/height in meters2) is the most common metric to diagnose overweight and obesity. However, a body composition analysis more thoroughly assesses adiposity, percent body fat, lean body mass (i.e., including skeletal muscle), and sometimes bone mineral density. BMI is not an accurate assessment of body fat in individuals with increased or decreased muscle mass; the diagnostic utility of BMI in individuals is also influenced by race and sex.

Methods

Previous Obesity Pillars Roundtables addressed the diagnostic limitations of BMI, the importance of android and visceral fat (especially among those with South and East Asian ancestry), and considerations of obesity among individuals who identify as Hispanic, diverse in sexual-orientation, Black, Native American, and having ancestry from the Mediterranean and Middle East regions. This roundtable examines considerations of BMI in Black and female individuals.

Results

The panelists agreed that body composition assessment was a more accurate measure of adiposity and muscle mass than BMI. When it came to matters of race and sex, one panelist felt: "race is a social construct and not a defining biology." Another felt that: "BMI should be a screening tool to prompt further evaluation of adiposity that utilizes better diagnostic tools for body composition." Regarding bias and misperceptions of resistance training in female individuals, another panelist stated: "I have spent my entire medical career taking care of women and have never seen a woman unintentionally gain 'too much' muscle mass and bulk up from moderate strength training."

Conclusions

Conveying the importance of race and sex regarding body composition has proven challenging, with the discussion sometimes devolving into misunderstandings or misinformation that may be perceived as racist or sexist. Body composition analysis is the ultimate diagnostic equalizer in addressing the inaccuracies and biases inherent in the exclusive use of BMI.

Confronting Racism in All Forms of Pain Research: Reframing Study Designs

This second paper in a 3-part series on antiracism in pain research across the translational spectrum focuses on study design factors. Although objectivity is a cornerstone value of science, subjectivity is embedded in every step of the research process as investigators make choices about who they collaborate with, which research questions they ask, how they recruit participants, which research tools they use, and how they analyze and interpret data. We present theory and evidence from disciplines such as sociology, medical anthropology, statistics, and public health to discuss 4 common study design factors, including 1) the dominant biomedical narrative of pain that restricts funding and exploration of social indicators of pain, 2) low diversity and inclusion in pain research enrollment that restricts generalizability to racialized groups, 3) the use of "race" or "ethnicity" as a statistical variable and proxy for lived experiences (eg, racism, resilience), and 4) limited modeling in preclinical research for the impact of social factors on pain physiology. The information presented in this article is intended to start conversations across stakeholders in the pain field to explore how we can come together to adopt antiracism practices in our work at large to achieve equity for racialized groups. PERSPECTIVE: This is the second paper in a 3-part series on antiracism in pain research. This part identifies common study design factors that risk hindering progress toward pain care equity. We suggest reframes using an antiracism framework for these factors to encourage all pain investigators to collectively make strides toward equity.

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.

Distribution of HbS Allele and Haplotypes in a Multi-Ethnic Population of Guinea Bissau, West Africa: Implications for Public Health Screening

BACKGROUND

Sickle Cell Disease (SCD) is an inherited condition that is widespread globally and especially in malaria-endemic West African countries. Limited epidemiological data on SCD are available for Guinea Bissau, where newborn screening is not yet implemented, routine diagnosis is not available, and care is case directed.

METHODS

Dried blood spots were collected from children accessing two hospitals managed by Italian Non-Governmental Organizations in the capital city of Bissau and sent to Padova for Hemoglobin (Hb) quantification through HPLC and molecular analysis. Beta globin gene analysis was performed in all; and Hb haplotype of the HbSS and HbSA patients was performed in South Africa. One hundred samples belonging to the most frequent ethnic groups were randomly selected for detection of G6PD mutations.

RESULTS

Samples from 848 consecutive children (498 males and 350 females, mean age 6.8 years) accessing the two hospitals were analyzed: 6.95% AS (4.42% allelic frequency), 0.94% SS, and 0.23% AC. 376G G6PD allelic frequency was 24%; 14.8% in AS individuals. The Senegal haplotype was the most prevalent (31%), and the proposition of chromosomes with the atypical haplotype was surprisingly high (56%).

CONCLUSION

Our study demonstrates a significant frequency of the HbS allele in the population of Guinea Bissau supporting the implementation of screening strategies. The differences among ethnic groups can help guide targeted interventions for SCD awareness campaigns and determine priority areas for public health interventions. The pilot analysis on haplotypes reveals a large proportion of the atypical haplotype, which may be indicative of a genetically heterogeneous population.

Falciparum malaria mortality in sub-Saharan Africa in the pretreatment era

Driven by the malaria-protective effect of sickle-cell trait, balancing selection results in hemoglobin S equilibrium allele frequencies of between 15% and 20% in areas of high Plasmodium falciparum transmission in sub-Saharan Africa. From this we estimate that the malaria-attributable childhood mortality in the pretreatment era was between 15% and 24%.

Whole-genome sequencing in diverse subjects identifies genetic correlates of leukocyte traits: The NHLBI TOPMed program

Many common and rare variants associated with hematologic traits have been discovered through imputation on large-scale reference panels. However, the majority of genome-wide association studies (GWASs) have been conducted in Europeans, and determining causal variants has proved challenging. We performed a GWAS of total leukocyte, neutrophil, lymphocyte, monocyte, eosinophil, and basophil counts generated from 109,563,748 variants in the autosomes and the X chromosome in the Trans-Omics for Precision Medicine (TOPMed) program, which included data from 61,802 individuals of diverse ancestry. We discovered and replicated 7 leukocyte trait associations, including (1) the association between a chromosome X, pseudo-autosomal region (PAR), noncoding variant located between cytokine receptor genes (CSF2RA and CLRF2) and lower eosinophil count; and (2) associations between single variants found predominantly among African Americans at the S1PR3 (9q22.1) and HBB (11p15.4) loci and monocyte and lymphocyte counts, respectively. We further provide evidence indicating that the newly discovered eosinophil-lowering chromosome X PAR variant might be associated with reduced susceptibility to common allergic diseases such as atopic dermatitis and asthma. Additionally, we found a burden of very rare FLT3 (13q12.2) variants associated with monocyte counts. Together, these results emphasize the utility of whole-genome sequencing in diverse samples in identifying associations missed by European-ancestry-driven GWASs.

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.

Child mortality from sickle cell disease in Nigeria: a model-estimated, population-level analysis of data from the 2018 Demographic and Health Survey

BACKGROUND

Child mortality from sickle cell disease in sub-Saharan Africa is presumed to be high but is not well quantified. This uncertainty contributes to the neglect of sickle cell disease and delays the prioritisation of interventions. In this study, we estimated the mortality of children in Nigeria with sickle cell disease, and the proportion of national under-5 mortality attributable to sickle cell disease.

METHODS

We did a model-estimated, population-level analysis of data from Nigeria's 2018 Demographic and Health Survey (DHS) to estimate the prevalence and geographical distribution of HbSS and HbSC genotypes assuming Hardy-Weinberg equilibrium near birth. Interviews for the survey were done between Aug 14 and Dec 29, 2018, and the embedded sickle cell disease survey was done in a randomly selected third of the overall survey's households. We developed an approach for estimating child mortality from sickle cell disease by combining information on tested children and their untested siblings. Tested children were aged 6-59 months at the time of the survey. Untested siblings born 0-14 years before the survey were also included in analyses. Testing as part of the DHS was done without regard to disease status. We analysed mortality differences using the inheritance-derived genotypic distribution of untested siblings older than the tested cohort, enabling us to estimate excess mortality from sickle cell disease for the older-sibling cohort (ie, those born between 2003 and 2013).

FINDINGS

We analysed test results for 11 186 children aged 6-59 months from 7411 households in Nigeria. The estimated average birth prevalence of HbSS was 1·21% (95% CI 1·09-1·37) and was 0·24% (0·19-0·31) for HbSC. We obtained data for estimating child mortality from 10 195 tested children (who could be matched to the individual mother survey) and 17 205 of their untested siblings. 15 227 of the siblings were in the older-sibling cohort. The group of children with sickle cell disease born between 2003 and 2013 with at least one younger sibling in the survey had about 370 excess under-5 deaths per 1000 livebirths (95% CI 150-580; p=0·0008) than children with HbAA. The estimated national average under-5 mortality for children with sickle cell disease born between 2003 and 2013 was 490 per 1000 livebirths (95% CI 270-700), 4·0 times higher (95% CI 2·1-6·0) than children with HbAA. About 4·2% (95% CI 1·7-6·9) of national under-5 mortality was attributable to excess mortality from sickle cell disease.

INTERPRETATION

The burden of child mortality from sickle cell disease in Nigeria continues to be disproportionately higher than the burden of mortality of children without sickle cell disease. Most of these deaths could be prevented if adequate resources were allocated and available focused interventions were implemented. The methods developed in this study could be used to estimate the burden of sickle cell disease elsewhere in Africa and south Asia.

FUNDING

Sickle Pan African Research Consortium, and the Bill & Melinda Gates Foundation.

Sickle Cell Trait Modulates the Proteome and Phosphoproteome of Plasmodium falciparum-Infected Erythrocytes

The high prevalence of sickle cell disease in some human populations likely results from the protection afforded against severe Plasmodium falciparum malaria and death by heterozygous carriage of HbS. P. falciparum remodels the erythrocyte membrane and skeleton, displaying parasite proteins at the erythrocyte surface that interact with key human proteins in the Ankyrin R and 4.1R complexes. Oxidative stress generated by HbS, as well as by parasite invasion, disrupts the kinase/phosphatase balance, potentially interfering with the molecular interactions between human and parasite proteins. HbS is known to be associated with abnormal membrane display of parasite antigens. Studying the proteome and the phosphoproteome of red cell membrane extracts from P. falciparum infected and non-infected erythrocytes, we show here that HbS heterozygous carriage, combined with infection, modulates the phosphorylation of erythrocyte membrane transporters and skeletal proteins as well as of parasite proteins. Our results highlight modifications of Ser-/Thr- and/or Tyr- phosphorylation in key human proteins, such as ankyrin, β-adducin, β-spectrin and Band 3, and key parasite proteins, such as RESA or MESA. Altered phosphorylation patterns could disturb the interactions within membrane protein complexes, affect nutrient uptake and the infected erythrocyte cytoadherence phenomenon, thus lessening the severity of malaria symptoms.