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PubMed2024

Multi-ancestry polygenic mechanisms of type 2 diabetes.

Type 2 diabetes (T2D) is a multifactorial disease with substantial genetic risk, for which the underlying biological mechanisms are not fully understood. In this study, we identified multi-ancestry T2D genetic clusters by analyzing genetic data from diverse populations in 37 published T2D genome-wide association studies representing more than 1.4 million individuals. We implemented soft clustering with 650 T2D-associated genetic variants and 110 T2D-related traits, capturing known and novel T2D clusters with distinct cardiometabolic trait associations across two independent biobanks representing diverse genetic ancestral populations (African, n = 21,906; Admixed American, n = 14,410; East Asian, n =2,422; European, n = 90,093; and South Asian, n = 1,262). The 12 genetic clusters were enriched for specific single-cell regulatory regions. Several of the polygenic scores derived from the clusters differed in distribution among ancestry groups, including a significantly higher proportion of lipodystrophy-related polygenic risk in East Asian ancestry. T2D risk was equivalent at a body mass index (BMI) of 30 kg m-2 in the European subpopulation and 24.2 (22.9-25.5) kg m-2 in the East Asian subpopulation; after adjusting for cluster-specific genetic risk, the equivalent BMI threshold increased to 28.5 (27.1-30.0) kg m-2 in the East Asian group. Thus, these multi-ancestry T2D genetic clusters encompass a broader range of biological mechanisms and provide preliminary insights to explain ancestry-associated differences in T2D risk profiles.

Humans↗

PubMed2026

Public opinion survey on heritable human genome editing in South Africa: a study protocol.

Heritable human genome editing (HHGE) presents new possibilities for the prevention of genetic diseases but also raises ethical and societal questions. While international surveys have explored public attitudes, particularly in high-income countries, there is a lack of large-scale empirical data from the Global South. In South Africa, previous work used deliberative public engagement to examine public perspectives. The present study aims to complement this by capturing public opinion through a cross-sectional survey, enabling direct comparison with deliberative findings. This study will recruit 400 adult participants residing in South Africa using targeted Facebook advertisements. A two-phase sampling process will be employed: initial screening for demographic information, followed by stratified sampling to ensure a representative South African population. The opinion survey consists of 19 HHGE scenarios, each explored through private and public moral lenses. Additionally, participants will indicate their interpretation of 'safe and effective' genome editing. Quantitative data will be analysed using descriptive statistics, chi-square tests, and logistic regression. Qualitative responses will undergo thematic analysis using both manual coding and generative AI tools under human oversight. The study includes two stages of informed consent and ensures data confidentiality through strict data handling protocols. Results will be disseminated in peer-reviewed journals and policy forums. The study will also generate a secondary dataset for evaluating AI-assisted qualitative analysis, to be conducted under separate ethical clearance.

Humans↗

PubMed2025

GWAS for Periodontitis Phenotypes Using Multi-Ancestry All of Us Research Platform.

Periodontitis is a multifactorial inflammatory disease whose pathogenesis is associated with intricate interactions between genetic and environmental factors. Leveraging electronic health records data from the All of Us Research Program, we stratified periodontitis by clinically relevant dimensions: stage, grade, and extent. Based on these phenotypes, we performed a multi-ancestry genome-wide association study, focusing on predominant ancestry populations of African, European, and Admixed American. Our study cohort comprised 3,881 periodontitis patients and a control group of 10,760 patients with dental caries and without periodontitis. Ancestry-specific GWAS revealed significant genetic associations (P<5×10-8) in periodontitis grade phenotypes at the LINC00294 and CLMN loci in the African ancestry population and also confirmed via the multi-ancestry meta-analysis. In addition, the XYLT1 locus emerged as a significant signal associated with periodontitis grade phenotype in the admixed American GWAS. Our GWAS comparing periodontitis to dental caries in the admixed American population identified several significant loci, including RABGAP1L, previously linked to immune regulation, DCHS2, a cadherin-related gene involved in bone mineralization and tissue morphogenesis, and OSTM1, known to be crucial for bone remodeling. The findings of our study highlight the potential of integrating EHR and genomic data from large-scale biobanks to achieve informative dental phenotyping, uncover novel molecular insights into periodontal disease, and personalize treatment approaches.

Journal Article↗

PubMed2024

Questioning inbreeding: Could outbreeding affect productivity in the North African catfish in Thailand?

The North African catfish (Clarias gariepinus) is a significant species in aquaculture, which is crucial for ensuring food and nutrition security. Their high adaptability to diverse environments has led to an increase in the number of farms that are available for their production. However, long-term closed breeding adversely affects their reproductive performance, leading to a decrease in production efficiency. This is possibly caused by inbreeding depression. To investigate the root cause of this issue, the genetic diversity of captive North African catfish populations was assessed in this study. Microsatellite genotyping and mitochondrial DNA D-loop sequencing were applied to 136 catfish specimens, collected from three populations captured for breeding in Thailand. Interestingly, extremely low inbreeding coefficients were obtained within each population, and distinct genetic diversity was observed among the three populations, indicating that their genetic origins are markedly different. This suggests that outbreeding depression by genetic admixture among currently captured populations of different origins may account for the low productivity of the North African catfish in Thailand. Genetic improvement of the North African catfish populations is required by introducing new populations whose origins are clearly known. This strategy should be systematically integrated into breeding programs to establish an ideal founder stock for selective breeding.

Animals↗

PubMed2025

Nested Admixture During and After the Trans-Atlantic Slave Trade on the Island of São Tomé.

Human genetic admixture, involving the contact between two or more previously isolated populations, can be a complex process influenced by social dynamics. In this study, we aim to reconstruct complex admixture histories in São Tomé, an island in the Gulf of Guinea where the Portuguese established one of the first plantation-based slave societies. Since the 15th century, migration waves from Africa and Europe, slavery, marooning, and indentured labour led to profound demographic shifts and social stratification on the island. Examining 2.5 million SNPs newly genotyped in 96 São Toméans, we observed patterns of genetic differentiation that were more complex than those of other populations descended from enslaved Africans on either side of the Atlantic. Using local ancestry inference and Identical-by-Descent methods, we identified five genetic clusters in São Tomé and reconstructed shared ancestries between each cluster and 70 African and European population samples, including an extensive sample from the Cabo Verde archipelago. Our findings align with historical records, retracing the major slave trade routes and labour-driven migrations after the abolition of slavery. We also identified gene flow between recently admixed groups that were previously isolated on the island. We call this process, creating multiple layers of genetic ancestry in admixed genomes, nested admixture. We suggest that changing social structures in São Tomé transformed the genetic structure of its population and influenced the admixture process. This study demonstrates how successive admixture and isolation events during and after the Trans-Atlantic Slave Trade shaped extant genetic diversity patterns at local scale in Africa.

Humans↗

PubMed2025

Genomic exploration of the journey of Plasmodium vivax in Latin America.

Plasmodium vivax is the predominant malaria parasite in Latin America. Its colonization history in the region is rich and complex, and is still highly debated, especially about its origin(s). Our study employed cutting-edge population genomic techniques to analyze whole genome variation from 620 P. vivax isolates, including 107 newly sequenced samples from West Africa, Middle East, and Latin America. This sampling represents nearly all potential source populations worldwide currently available. Analyses of the genetic structure, diversity, ancestry, coalescent-based inferences, including demographic scenario testing using Approximate Bayesian Computation, have revealed a more complex evolutionary history than previously envisioned. Indeed, our analyses suggest that the current American P. vivax populations predominantly stemmed from a now-extinct European lineage, with the potential contribution also from unsampled populations, most likely of West African origin. We also found evidence that P. vivax arrived in Latin America in multiple waves, initially during early European contact and later through post-colonial human migration waves in the late 19th-century. This study provides a fresh perspective on P. vivax's intricate evolutionary journey and brings insights into the possible contribution of West African P. vivax populations to the colonization history of Latin America.

Plasmodium vivax↗

PubMed2026

Large-scale admixture mapping in the All of Us Research Program improves the characterization of cross-population phenotypic differences.

Admixed individuals have been understudied in medical research largely due to their complex genetic ancestries. However, the consideration of admixture can identify ancestry-enriched genetic associations, delineating genetic underpinnings of cross-population phenotypic variation. Here, we performed admixture mapping in individuals with inferred admixture from African and European populations (N = 48,921). Across 22 traits, we identified 71 ancestry-trait associations, including loci where ancestral haplotypes explained phenotypic variation yet were missed by single-variant association testing due to their stricter multiple testing burden. One such locus where inferred local AFR ancestries are associated with increased hemoglobin A1c (HbA1c) was 12q14.3, highlighting its potential role in explaining differences between populations. Together, our results expand upon the phenotypic differences between populations and characterize loci where genetic ancestries play a critical role in the architecture of disease.

Humans↗

PubMed2026

Multi-ancestry multi-trait analysis reveals shared genetics across major psychiatric disorders and Alzheimer's disease.

The clinical overlap between major psychiatric disorders (MPDs) and Alzheimer's disease (AD) implicates complex shared etiology. Previous studies demonstrated that both diseases are genetically complex and highly heritable, suggesting that more endeavors are necessary to be made from the very bottom to understand their genetic basis. With the advance of post-genomic analysis, multi-ancestry meta-analysis allows the generalizability of the genetic architecture across different populations to uncover ancestry-specific variants, while multi-trait analysis enables the discovery of the co-colocalized risk genomic regions across diseases. Therefore, in this study, we leveraged published GWAS summary statistics from European, East Asian, Hispanic and African American populations to report schizophrenia, major depressive disorders, and Alzheimer's disease risk loci and further fine-mapping to credible sets with >95% PP inclusion of the causal variant. We distilled 2871 potential traits from publicly available and found 134 traits significantly genetically correlated with both MPDs and AD using batch LD score regression. We then prioritized the identified loci from multi-ancestry results for cross-trait colocalization analysis to assess shared genetic etiology and further nominated 2 colocalized loci across both conditions, including rs2532240 and rs6504163. In the end, we finalized our analysis by validation and functional inference of the underlying susceptibility genes as well as putative mechanisms using evidence from multiple resources, including FIVEx, Open Targets, and scQTLbase.

Humans↗

PubMed2025

Polaris: Polarization of ancestral and derived polymorphic alleles for inferences of extended haplotype homozygosity in human populations.

SUMMARY: Statistical methods that measure the extent of haplotype homozygosity on chromosomes have been highly informative for identifying episodes of recent selection. For example, the integrated haplotype score (iHS) and the extended haplotype homozygosity (EHH) statistics detect long-range haplotype structure around derived and ancestral alleles indicative of classic and soft selective sweeps, respectively. However, to our knowledge, there are currently no publicly available methods that classify ancestral and derived alleles in genomic datasets for the purpose of quantifying the extent of haplotype homozygosity. Here, we introduce the Polaris package, which polarizes chromosomal variants into ancestral and derived alleles and creates corresponding genetic maps for analysis by selscan and HaploSweep, two versatile haplotype-based programs that perform scans for selection. With the input files generated by Polaris, selscan and/or HaploSweep can produce the appropriate sign (either positive or negative) for outlier iHS statistics, enabling users to distinguish between selection on derived or ancestral alleles. In addition, Polaris can convert the numerical output of these analyses into graphical representations of selective sweeps, increasing the functionality of our software. RESULTS: To demonstrate the utility of our approach, we applied the Polaris package to Chromosome 2 in the European Finnish, Middle Eastern Bedouin, and East African Maasai populations. More specifically, we examined the regulatory sequence in intron 13 of the MCM6 gene associated with lactase persistence (i.e. the ability to digest the lactose sugar present in fresh milk), a region of intense interest to human evolutionary geneticists. Our analyses showed that derived alleles (at known enhancers for lactase expression) sit on an extended haplotype background in the Finnish, Bedouin, and Maasai consistent with a classic selective sweep model as determined by iHS and EHH statistics. Importantly, we were able to immediately identify this target allele under selection based on the information generated by our software. We also explored outlier statistics across Chromosome 2 in two distinct datasets from these populations: (i) one containing polarized alleles generated with Polaris and (ii) the other containing unpolarized alleles in the original phased vcf file. Here, we found an excess of outlier statistics on Chromosome 2 in the unpolarized datasets, raising the possibility that a subset of these "hits" of selection may be unreliable. Overall, Polaris is a versatile package that enables users to efficiently explore, interpret, and report signals of recent selection in genomic datasets. AVAILABILITY AND IMPLEMENTATION: The Polaris package is free and open source on GitHub (https://github.com/alisi1989/Polaris) and DropBox (https://www.dropbox.com/scl/fo/mlxizft5267vem9u62qkn/AAnM0qX923zPzQBlPX8iteM?rlkey=uezrp4t2waffpj0nmo1evr320&e=1&st=jaodccws&dl=0).

Haplotypes↗

PubMed2026

Characterizing features of the genetic architecture underlying autism from a multi-ancestry perspective.

Autism spectrum disorder (ASD; MIM 209850) is reported to vary globally from 0.01% in East Asian populations to 4.36% in certain Australian cohorts. Despite high heritability estimates (61-94%), the genetic architecture underlying ASD susceptibility remains poorly characterized across diverse populations, as most genomic studies have initially focused on individuals of European ancestry. To investigate ancestry-specific genetic contributions to ASD, we analyzed whole-genome sequencing data from three independent ASD cohorts. We identified admixed ASD probands (n = 1 033) and ancestry-matched controls (n = 1 033) and performed admixture mapping (AM). AM using five continental reference populations (European, African, East Asian, South Asian, and Native American) identified five ancestry-specific ASD-susceptibility loci, including one African-related locus at 1p21.2 near S1PR1 and four Native American-associated loci at chromosome 11q13.4. Three of these latter loci were contiguous and encompassed genes previously implicated in ASD, notably SHANK2 and DHCR7, with fine-mapping identifying a significantly associated variant between the two genes (rs77695321; P = 1.52 × 10⁻⁷). The fourth Native American-associated signal at 11q13.4 overlapped the folate receptor genes FOLR1 and FOLR3, with fine-mapping identifying a genome-wide significant variant (rs7950807; P = 5.21 × 10⁻⁸). A secondary admixture mapping analysis restricted to Latin American individuals, incorporating 6 487 Brazilian controls, identified 16 additional ancestry-specific loci across seven genomic regions.

Journal Article↗

PubMed2025

Discovery of Respiratory Pathogens in People Living With HIV in the African Cohort Study.

INTRODUCTION: Respiratory infection outbreaks pose a threat to the readiness of the United States and allied armed forces. Predicting and preventing such outbreaks requires understanding of the epidemiology of potential respiratory pathogens in communities where service members live and work. We conducted pan-viral surveillance of respiratory specimens from people living with HIV or without HIV but under the risk enrolled in the U.S. Military HIV Research Program's African Cohort Study to determine the prevalence and possible clinical presentation of viruses in this population. METHODS: The African Cohort Study is an open-ended prospective cohort study that enrolls people with and without HIV aged ≥15 years at 12 clinical sites in Kenya, Tanzania, Uganda, and Nigeria. The study follows participants every 6 months and collects social, demographic, clinical, and laboratory data. A total of 131 respiratory samples, collected from March 2022 to February 2023 from participants in South Rift Valley Province, Kenya, who had symptoms of respiratory illness or a positive COVID-19 test, were analyzed using a pan-viral hybridization metagenomic next-generation sequencing approach. Libraries were sequenced on the Illumina Next-generation Sequencing System NovaSeq 6000. Sample data were run through several pathogen discovery pipelines. RESULTS: Full genome and partial genome sequences were assembled for several respiratory viruses including SARS-CoV-2, human coronavirus HKU1, human adenovirus 62, human metapneumovirus, human mastadenovirus B (coinfection with SARS-CoV-2), human mastadenovirus C (coinfection with SARS-CoV-2), and human parechovirus 3 (coinfection with adenovirus 62). The results showed that SARS-CoV-2 lineages correspond with lineages circulating during March 2022 to February 2023 and revealed additional viral respiratory pathogens and viruses known to be associated with HIV. CONCLUSIONS: These preliminary results suggest that continued genomic surveillance efforts are needed for data-driven decisions on force health protection, prevention of emerging respiratory infections, and mitigation of impacts on military readiness caused by infectious diseases.

Humans↗

PubMed2026

Population genomics of Plasmodium malariae from 4 African countries.

BACKGROUNDMalaria caused by Plasmodium malariae is geographically widespread and sometimes associated with prolonged infection, yet little is known about its genomic epidemiology.METHODSWe performed hybrid capture and whole-genome sequencing of 77 isolates collected from Cameroon (n = 7), the Democratic Republic of the Congo (n = 16), Nigeria (n = 4), and Tanzania (n = 50) between 2015 and 2021, analyzing parasite genetic population structure and demography.RESULTSThere is no evidence of geographic population structure. Nucleotide diversity was significantly lower than in colocalized P. falciparum isolates, while linkage disequilibrium was significantly higher. Genome-wide selection scans identified no erythrocyte invasion ligands or antimalarial resistance orthologs as top hits; however, targeted analyses of these loci revealed evidence of selective sweeps around 4 erythrocyte invasion ligands and 6 antimalarial resistance orthologs. Demographic inference modeling suggests that African P. malariae is recovering from a bottleneck.CONCLUSIONP. malariae is genomically atypical among human Plasmodium spp. and lacks strong population structure in Africa. The low diversity has potential impacts on understanding persistent versus new infection through genomic epidemiology.FUNDINGBill & Melinda Gates Foundation (grant 002202), USAID/PMI through Jhpiego and CDC, NIH (T32AI007151, T32AI070114, R01AI107949, R01AI129812, R21 AI148579, R01AI137395, R21AI152260, R01AI132547, and K24AI134990), and the DELTAS Africa initiative (DELGEME grant 107740/Z/15/Z).

Plasmodium malariae↗

PubMed2025

The human IG heavy chain constant gene locus is enriched for large structural variants and coding polymorphisms that vary among human populations.

The human immunoglobulin heavy chain constant (IGHC) domain of antibodies (Ab) is responsible for effector functions critical to immunity. This domain is encoded by genes in the IGHC locus, where descriptions of genomic diversity remain incomplete. We utilized long-read sequencing to build an IGHC haplotype/variant catalog from 105 individuals of diverse ancestry. We discovered uncharacterized single nucleotide variants (SNV) and large structural variants (SVs, n=7), representing new genes and alleles enriched for non-synonymous substitutions, highlighting potential functional effects. Of the 221 identified IGHC alleles, 192 were novel. SNV, SV, and gene allele/genotype frequencies revealed population differentiation, including (i) hundreds of SNVs in African and East Asian populations exceeding a fixation index (FST) of 0.3, and (ii) an IGHG4 haplotype carrying coding variants uniquely enriched in Asian populations. Our results illuminate missing signatures of IGHC diversity and establish a new foundation for investigating IGHC germline variation in Ab function and disease.

Journal Article↗

PubMed2026

Assessing Hardy-Weinberg equilibrium in T2T-aligned 1000 genomes project.

Quality control of markers in genome-wide association studies often includes testing for Hardy-Weinberg equilibrium (HWE). However, this is usually implemented in a homogeneous population without stratifying by sex. Previous work indicates sex-based selection at numerous autosomal loci in cohorts with active recruitment. Sex chromosome sequences can also interfere with autosomal SNPs. These motivate a re-examination of HWE in sex-aware analyses. Using the telomere-to-telomere (T2Tv2)-aligned high-coverage whole genome sequencing data from 2,490 individuals in the 1000 Genomes Project, we examined genome-wide sex-specific deviations from HWE across five super-populations. Our analyses were restricted to bi-allelic SNPs with non-missing genotypes and minor allele frequency (MAF) ≥5% in both sexes of the five super-populations. We applied an allele-based framework to quantify both the magnitude and direction of Hardy-Weinberg disequilibrium (HWD), followed by a second-order omnibus meta-analysis that combined HWD results across populations and sexes. At a genome-wide significance threshold of p < 5e-8, 0.9% of autosomal SNPs exhibited significant deviations from HWE. The majority of these deviations were associated with genomic features indicative of poor sequence quality. Restricting the analysis to reliable genomic regions substantially reduced the number of signals, yielding 255 autosomal SNPs and one non-pseudoautosomal chromosome X SNP. Among these, 140 autosomal SNPs displayed significant heterogeneity across populations but not across sexes. Notably, eight SNPs within a 15-bp region on chromosome 14q31.3 showed excess heterozygosity in both sexes of the African super-population (AFR). Finally, we developed a multivariate predictor of HWD based on sequence features, providing a practical tool that can be integrated into existing quality control pipelines for whole genome sequencing studies.

Journal Article↗

PubMed2025

Is there are relationship between polymorphisms TSHR gene frequencies and genetic ancestry markers in patients with Primary Congenital Hypothyroidism?

The literature shows a correlation between ethnicity and pathogenic variants of the thyroid stimulating hormone receptor (TSHR) gene. Some of these polymorphisms may be risk factors for the development of primary congenital hypothyroidism (PCH). In this study, we investigated the relationship between the frequency of TSHR gene polymorphisms and the genetic influence of African, Amerindian, and European ancestry-informative markers in patients from an Amazonian population in Brazil who were diagnosed with PCH. The study was conducted on samples from 106 patients who were diagnosed with PCH. Genomic DNA was isolated from peripheral blood samples, and 10 exons from the TSHR gene were automatically sequenced. Ancestry-informative marker identification was performed using a panel of 48 markers, and the results were compared with parental Amerindian, Western European, and Sub-Saharan African populations using Structure v2.3.4 software. Four nucleotide alterations were identified among 49 patients. The distribution of tested ancestry markers among the 106 patients indicated a significant difference in the percentages of Amerindian (25.90 %), European (41.80 %), and African (32.20 %) ancestry. Logistic regression analysis revealed no significant association between the rs2075179 and rs1991517 polymorphisms and genetic ancestry. This study revealed no evidence of a relationship between polymorphic TSHR gene variants and genetic ancestry markers in patients with PCH.

Journal Article↗

PubMed2026

Kaposi Sarcoma-Associated Herpesvirus Is Not Detected in Osteosarcoma From KSHV-Endemic African Countries and the Non-Endemic United States Populations.

Osteosarcoma is an aggressive primary malignant bone tumor of poorly defined etiology that predominantly affects adolescents and young adults. A viral cause has long been proposed, and a recent study from Xinjiang, China, reported frequent detection of Kaposi sarcoma-associated herpesvirus (KSHV) in Uyghur osteosarcoma cases, suggesting a possible association in this KSHV-endemic population. Whether this association extends to broader populations remains unknown. Our study investigated the presence of KSHV in osteosarcoma specimens from KSHV-endemic African countries (Cameroon, Kenya, South Africa, Zambia) and the non-endemic United States. A total of 356 formalin-fixed paraffin-embedded and fresh-frozen specimens were retrieved or prospectively collected. In 77 selected high-quality specimens, KSHV infection was assessed by immunohistochemistry for LANA1 and by qPCR targeting 5 viral open reading frames (ORF25, ORF26, ORF37, ORF65, and ORF73). LANA1 expression was undetectable in all tumors. Using qPCR, 75/77 specimens were negative for all targets, 1/77 excluded due to insufficient remaining DNA quantity to perform the assay, and 1/77 positive across all five targets. Additionally, we studied the KSHV seroprevalence in a separate cohort comprised of 49 sera obtained from individuals with osteosarcoma from Zambia (n = 39) and the United States (n = 10). We measured by ELISA the presence of specific antibodies against four KSHV antigens: K8.1, KCP, VCA, and LANA1. KSHV seropositivity was detected in 15/39 individuals from Zambia and none from the United States. In the absence of compelling evidence, our findings could not support an association between KSHV infection and osteosarcoma in our study population.

Humans↗

PubMed2024

Genetic investigation of population structure in Atlantic chub mackerel, Scomber colias Gmelin, 1789 along the West African coast.

Sustainable management of transboundary fish stocks hinges on accurate delineation of population structure. Genetic analysis offers a powerful tool to identify potential subpopulations within a seemingly homogenous stock, facilitating the development of effective, coordinated management strategies across international borders. Along the West African coast, the Atlantic chub mackerel (Scomber colias) is a commercially important and ecologically significant species, yet little is known about its genetic population structure and connectivity. Currently, the stock is managed as a single unit in West African waters despite new research suggesting morphological and adaptive differences. Here, eight microsatellite loci were genotyped on 1,169 individuals distributed across 33 sampling sites from Morocco (27.39°N) to Namibia (22.21°S). Bayesian clustering analysis depicts one homogeneous population across the studied area with null overall differentiation (F ST = 0.0001ns), which suggests panmixia and aligns with the migratory potential of this species. This finding has significant implications for the effective conservation and management of S. colias within a wide scope of its distribution across West African waters from the South of Morocco to the North-Centre of Namibia and underscores the need for increased regional cooperation in fisheries management and conservation.

Animals↗

PubMed2026

A multi-ancestry polygenic risk score for body mass index predicts longitudinal weight change.

BACKGROUND: Identifying individuals at risk for future weight gain is challenging, partly because associations with traditional clinical risk factors may be biased by confounding and reverse causation. Polygenic risk scores (PRS) provide a stable, lifelong measure of genetic predisposition to obesity. However, existing PRS have not been evaluated for their association with longitudinal weight change in adulthood and often lack generalizability across diverse genetic ancestry groups. METHODS: We conducted ancestry-specific genome-wide association study meta-analyses of body mass index (BMI) in populations of European, African or African American, Admixed American, East Asian, and South Asian ancestries and developed ancestry-specific PRS. A multi-ancestry polygenic risk score (MAPRS) was trained using ancestry-specific PRS in a model selection dataset (N = 39,685) from the All of Us Research Program (AoU). We evaluated the MAPRS in an independent AoU model evaluation dataset (N = 158,743) for BMI prediction and in a separate AoU test dataset (N = 78,219) with repeated measurements over 1.5-2.5 years for weight change prediction. The outcomes included change in BMI and ≥ 10% or ≥ 5% total body weight (TBW) gain. We further examined the relationship between MAPRS and 12 clinical risk factors commonly comorbid with obesity in relation to weight change. RESULTS: The MAPRS captured 7.05% of the variance in measured BMI in the AoU model evaluation dataset and demonstrated improved generalizability across all non-European genetic ancestry groups. In the AoU test dataset, conditioned on baseline BMI at the second-to-last measurement, a one SD increase in MAPRS was associated with a 0.16 kg/m2 increase in future BMI (standard error = 0.012 kg/m2; p-value = 2.2 × 10-39), 1.27-fold increased odds of experiencing ≥ 10% TBW gain (95% CI: 1.24-1.31; p-value = 1.4 × 10-55), and 1.15-fold increased odds of experiencing ≥ 5% TBW gain (95% CI: 1.13-1.18; p-value = 2.8 × 10-39). These associations were observed across all genetic ancestry groups and remained highly consistent after adjustment for any clinical risk factor. In contrast, most clinical risk factors demonstrated inconsistent or weaker associations with weight change outcomes. CONCLUSIONS: We developed an MAPRS for BMI that represents a robust and generalizable risk factor for longitudinal weight gain in adulthood, providing a foundation for genetically informed risk stratification and earlier, more targeted obesity prevention strategies.

Humans↗