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Su H, Wang M, Li X, Duan S, Sun Q, Sun Y, Wang Z, Yang Q, Huang Y, Zhong J, Chen J, Jiang X, Ma J, Yang T, Liu Y, Luo L, Liu Y, Yang J, Chen G, Liu C, Cai Y, He G. Population genetic admixture and evolutionary history in the Shandong Peninsula inferred from integrative modern and ancient genomic resources. BMC Genomics 2024; 25:611. [PMID: 38890579 PMCID: PMC11184692 DOI: 10.1186/s12864-024-10514-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 06/11/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Ancient northern East Asians (ANEA) from the Yellow River region, who pioneered millet cultivation, play a crucial role in understanding the origins of ethnolinguistically diverse populations in modern China and the entire landscape of deep genetic structure and variation discovery in modern East Asians. However, the direct links between ANEA and geographically proximate modern populations, as well as the biological adaptive processes involved, remain poorly understood. RESULTS Here, we generated genome-wide SNP data for 264 individuals from geographically different Han populations in Shandong. An integrated genomic resource encompassing both modern and ancient East Asians was compiled to examine fine-scale population admixture scenarios and adaptive traits. The reconstruction of demographic history and hierarchical clustering patterns revealed that individuals from the Shandong Peninsula share a close genetic affinity with ANEA, indicating long-term genetic continuity and mobility in the lower Yellow River basin since the early Neolithic period. Biological adaptive signatures, including those related to immune and metabolic pathways, were identified through analyses of haplotype homozygosity and allele frequency spectra. These signatures are linked to complex traits such as height and body mass index, which may be associated with adaptations to cold environments, dietary practices, and pathogen exposure. Additionally, allele frequency trajectories over time and a haplotype network of two highly differentiated genes, ABCC11 and SLC10A1, were delineated. These genes, which are associated with axillary odor and bilirubin metabolism, respectively, illustrate how local adaptations can influence the diversification of traits in East Asians. CONCLUSIONS Our findings provide a comprehensive genomic dataset that elucidates the fine-scale genetic history and evolutionary trajectory of natural selection signals and disease susceptibility in Han Chinese populations. This study serves as a paradigm for integrating spatiotemporally diverse ancient genomes in the era of population genomic medicine.
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Affiliation(s)
- Haoran Su
- Genetic and Prenatal Diagnosis Center, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637007, Sichuan, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637007, Sichuan, China
| | - Mengge Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China.
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China.
- Research Center for Genomic Medicine, North Sichuan Medical College, Nanchong, 637100, China.
| | - Xiangping Li
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Shuhan Duan
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Research Center for Genomic Medicine, North Sichuan Medical College, Nanchong, 637100, China
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Genetic and Prenatal Diagnosis Center, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637007, Sichuan, China
| | - Qiuxia Sun
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
| | - Yuntao Sun
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Zhiyong Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Qingxin Yang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Yuguo Huang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
| | - Jie Zhong
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
| | - Jing Chen
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030001, China
| | - Xiucheng Jiang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Research Center for Genomic Medicine, North Sichuan Medical College, Nanchong, 637100, China
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Genetic and Prenatal Diagnosis Center, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637007, Sichuan, China
| | - Jinyue Ma
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Research Center for Genomic Medicine, North Sichuan Medical College, Nanchong, 637100, China
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Genetic and Prenatal Diagnosis Center, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637007, Sichuan, China
| | - Ting Yang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Yunhui Liu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
| | - Lintao Luo
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
| | - Yan Liu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Research Center for Genomic Medicine, North Sichuan Medical College, Nanchong, 637100, China
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Genetic and Prenatal Diagnosis Center, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637007, Sichuan, China
| | - Junbao Yang
- Research Center for Genomic Medicine, North Sichuan Medical College, Nanchong, 637100, China
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Genetic and Prenatal Diagnosis Center, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637007, Sichuan, China
| | - Gang Chen
- Hunan Key Laboratory of Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, 410075, China
| | - Chao Liu
- Anti-Drug Technology Center of Guangdong Province, Guangzhou, 510230, China.
| | - Yan Cai
- Genetic and Prenatal Diagnosis Center, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637007, Sichuan, China.
| | - Guanglin He
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China.
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China.
- Research Center for Genomic Medicine, North Sichuan Medical College, Nanchong, 637100, China.
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Kirkham JK, Estepp JH, Weiss MJ, Rashkin SR. Genetic Variation and Sickle Cell Disease Severity: A Systematic Review and Meta-Analysis. JAMA Netw Open 2023; 6:e2337484. [PMID: 37851445 PMCID: PMC10585422 DOI: 10.1001/jamanetworkopen.2023.37484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/30/2023] [Indexed: 10/19/2023] Open
Abstract
Importance Sickle cell disease (SCD) is a monogenic disorder, yet clinical outcomes are influenced by additional genetic factors. Despite decades of research, the genetics of SCD remain poorly understood. Objective To assess all reported genetic modifiers of SCD, evaluate the design of associated studies, and provide guidelines for future analyses according to modern genetic study recommendations. Data Sources PubMed, Web of Science, and Scopus were searched through May 16, 2023, identifying 5290 publications. Study Selection At least 2 reviewers identified 571 original, peer-reviewed English-language publications reporting genetic modifiers of human SCD phenotypes, wherein the outcome was not treatment response, and the comparison was not between SCD subtypes or including healthy controls. Data Extraction and Synthesis Data relevant to all genetic modifiers of SCD were extracted, evaluated, and presented following STREGA and PRISMA guidelines. Weighted z score meta-analyses and pathway analyses were conducted. Main Outcomes and Measures Outcomes were aggregated into 25 categories, grouped as acute complications, chronic conditions, hematologic parameters or biomarkers, and general or mixed measures of SCD severity. Results The 571 included studies reported on 29 670 unique individuals (50% ≤ 18 years of age) from 43 countries. Of the 17 757 extracted results (4890 significant) in 1552 genes, 3675 results met the study criteria for meta-analysis: reported phenotype and genotype, association size and direction, variability measure, sample size, and statistical test. Only 173 results for 62 associations could be cross-study combined. The remaining associations could not be aggregated because they were only reported once or methods (eg, study design, reporting practice) and genotype or phenotype definitions were insufficiently harmonized. Gene variants regulating fetal hemoglobin and α-thalassemia (important markers for SCD severity) were frequently identified: 19 single-nucleotide variants in BCL11A, HBS1L-MYB, and HBG2 were significantly associated with fetal hemoglobin (absolute value of Z = 4.00 to 20.66; P = 8.63 × 10-95 to 6.19 × 10-5), and α-thalassemia deletions were significantly associated with increased hemoglobin level and reduced risk of albuminuria, abnormal transcranial Doppler velocity, and stroke (absolute value of Z = 3.43 to 5.16; P = 2.42 × 10-7 to 6.00 × 10-4). However, other associations remain unconfirmed. Pathway analyses of significant genes highlighted the importance of cellular adhesion, inflammation, oxidative and toxic stress, and blood vessel regulation in SCD (23 of the top 25 Gene Ontology pathways involve these processes) and suggested future research areas. Conclusions and Relevance The findings of this comprehensive systematic review and meta-analysis of all published genetic modifiers of SCD indicated that implementation of standardized phenotypes, statistical methods, and reporting practices should accelerate discovery and validation of genetic modifiers and development of clinically actionable genetic profiles.
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Affiliation(s)
- Justin K. Kirkham
- Department of Oncology, St Jude Children’s Research Hospital, Memphis, Tennessee
| | - Jeremie H. Estepp
- Department of Hematology, St Jude Children’s Research Hospital, Memphis, Tennessee
- Department of Global Pediatric Medicine, St Jude Children’s Research Hospital, Memphis, Tennessee
- Now with Agios Pharmaceuticals, Cambridge, Massachusetts
| | - Mitch J. Weiss
- Department of Hematology, St Jude Children’s Research Hospital, Memphis, Tennessee
| | - Sara R. Rashkin
- Department of Hematology, St Jude Children’s Research Hospital, Memphis, Tennessee
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Salah NY, Ali HGA, Bassiouny N, Salem L, Taha SI, Youssef MK, Annaka L, Barakat NM. BCL11A Polymorphism in Egyptian Children with β-Thalassemia: Relation to Phenotypic Heterogeneity. J Pediatr Genet 2021; 12:16-22. [PMID: 36684548 PMCID: PMC9848767 DOI: 10.1055/s-0041-1728744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/10/2021] [Indexed: 01/25/2023]
Abstract
Fetal hemoglobin (HbF) is a potent genetic modifier of β-thalassemia phenotype. B-cell lymphoma 11A ( BCL11A ) gene results in significant silencing of HbF. The aim of this study was to assess the prevalence of different BCL11A genotypes among a cohort of Egyptian children with β-thalassemia and to correlate them to HbF and clinical severity score. Eighty-two children with β-thalassemia (aged 12.95 ± 3.63 years) were recruited from the Pediatric Hematology Clinic, Ain Shams University. They were divided based on the clinical severity of β-thalassemia into three subgroups: 20 mild (24.4%), 24 moderate (29.3%), and 38 severe (46.3%). Age, gender, age of diagnosis, initial HbF level, transfusion history, and history of splenectomy were assessed. Anthropometric measures, signs of anemia and hemosiderosis, and the severity score were determined. Laboratory investigations such as complete blood picture, ferritin, and single gene polymorphism genotyping of the rs11886868 were also performed. Our findings showed that 16 children had CC genotype (19.5%), 38 had TC genotype (46.3%), and 28 had TT genotype (34.1%) of the rs#. β-thalassemia children with TT genotype had significantly higher severity scoring than the other two groups ( p < 0.001). Moreover, mean initial HbF was found to be lower in children with TT genotype followed by TC and CC genotypes ( p < 0.001). Increased γ-globin expression associated with BCL11A gene polymorphism is associated with better clinical severity of β-thalassemia.
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Affiliation(s)
- Nouran Y. Salah
- Department of Pediatrics, Faculty of Medicine, Ain Shams University, Cairo, Egypt,Address for correspondence Nouran Yousef Salah, MD Department of Pediatrics, Faculty of Medicine, Ain Shams University25 Korash Street, Nasr City, Cairo 11375Egypt
| | - Heba G. A. Ali
- Department of Pediatrics, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Noha Bassiouny
- Department of Clinical Pathology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Lamya Salem
- Department of Clinical Pathology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Sara I. Taha
- Department of Clinical Pathology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Mariam K. Youssef
- Department of Clinical Pathology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Layla Annaka
- Department of Clinical Pathology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Noha M. Barakat
- Department of Pediatrics, Faculty of Medicine, Ain Shams University, Cairo, Egypt
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