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Malbos M, Vera G, Sheth H, Schnur RE, Juven A, Brehin AC, Sheth J, Gandhi A, Shapiro FL, Bruel AL, Marguet F, Begtrup A, Monaghan KG, Safraou H, Brasseur-Daudruy M, Mau-Them FT, Duffourd Y, Faivre L, Thauvin-Robinet C, Benke PJ, Philippe C. SCYL2-related autosomal recessive neurodevelopmental disorders: Arthrogryposis multiplex congenita-4 and beyond? Clin Genet 2024. [PMID: 39169672 DOI: 10.1111/cge.14608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 07/07/2024] [Accepted: 08/05/2024] [Indexed: 08/23/2024]
Abstract
SCY1-like protein 2 (SCYL2) is a member of the SCY1-like pseudokinase family which regulates secretory protein trafficking. It plays a crucial role in the nervous system by suppressing excitotoxicity in the developing brain. Scyl2 knockout mice have excess prenatal mortality and survivors show severe neurological dysfunction. Bi-allelic loss-of-function (LOF) variants in SCYL2 were recently associated with arthrogryposis multiplex congenita-4 (AMC4) following the report of 6 individuals from two consanguineous unrelated families. The AMC4 phenotype described included severe arthrogryposis, corpus callosum agenesis, epilepsy and frequently, early death. We describe here two additional similarly affected individuals with AMC4, including one diagnosed in the prenatal period, with bi-allelic LOF variants in SCYL2, and two individuals homozygous for missense variants in the protein kinase domain of SCYL2 and presenting with developmental delay only. Our study confirms the association of SCYL2 with AMC4 and suggests a milder phenotype can occur, extending the phenotypic spectrum of autosomal recessive SCYL2-related disorders.
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Affiliation(s)
- Marlène Malbos
- CRMRs "Anomalies du Développement et syndromes malformatifs" et "Déficiences Intellectuelles de causes rares", FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
- Laboratoire de Génomique Médicale, UF Innovation en diagnostic génomique des maladies rares, CHU Dijon Bourgogne, Dijon, France
| | - Gabriella Vera
- Department of Pathology, Department of Genetics and Reference Center for Developmental Abnormalities, Univ Rouen Normandie, Normandie Univ, Inserm U1245 and CHU Rouen, Rouen, France
| | - Harsh Sheth
- FRIGE's Institute of Human Genetics, Ahmedabad, India
| | - Rhonda E Schnur
- Cooper Medical School of Rowan University/Cooper University Health Care, Camden, New Jersey, USA
| | - Aurélien Juven
- CRMRs "Anomalies du Développement et syndromes malformatifs" et "Déficiences Intellectuelles de causes rares", FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
- Laboratoire de Génomique Médicale, UF Innovation en diagnostic génomique des maladies rares, CHU Dijon Bourgogne, Dijon, France
| | - Anne-Claire Brehin
- Department of Pathology, Department of Genetics and Reference Center for Developmental Abnormalities, Univ Rouen Normandie, Normandie Univ, Inserm U1245 and CHU Rouen, Rouen, France
| | - Jayesh Sheth
- FRIGE's Institute of Human Genetics, Ahmedabad, India
| | - Ajit Gandhi
- FRIGE's Institute of Human Genetics, Ahmedabad, India
| | - Faye L Shapiro
- Cooper Medical School of Rowan University/Cooper University Health Care, Camden, New Jersey, USA
| | - Ange-Line Bruel
- Laboratoire de Génomique Médicale, UF Innovation en diagnostic génomique des maladies rares, CHU Dijon Bourgogne, Dijon, France
- Inserm UMR1231 GAD, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
| | - Florent Marguet
- Department of Pathology, Department of Genetics and Reference Center for Developmental Abnormalities, Univ Rouen Normandie, Normandie Univ, Inserm U1245 and CHU Rouen, Rouen, France
| | | | | | - Hana Safraou
- Laboratoire de Génomique Médicale, UF Innovation en diagnostic génomique des maladies rares, CHU Dijon Bourgogne, Dijon, France
- Inserm UMR1231 GAD, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
| | | | - Frédéric Tran Mau-Them
- Laboratoire de Génomique Médicale, UF Innovation en diagnostic génomique des maladies rares, CHU Dijon Bourgogne, Dijon, France
- Inserm UMR1231 GAD, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
| | - Yannis Duffourd
- Laboratoire de Génomique Médicale, UF Innovation en diagnostic génomique des maladies rares, CHU Dijon Bourgogne, Dijon, France
| | - Laurence Faivre
- CRMRs "Anomalies du Développement et syndromes malformatifs" et "Déficiences Intellectuelles de causes rares", FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
- Laboratoire de Génomique Médicale, UF Innovation en diagnostic génomique des maladies rares, CHU Dijon Bourgogne, Dijon, France
| | - Christel Thauvin-Robinet
- CRMRs "Anomalies du Développement et syndromes malformatifs" et "Déficiences Intellectuelles de causes rares", FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
- Laboratoire de Génomique Médicale, UF Innovation en diagnostic génomique des maladies rares, CHU Dijon Bourgogne, Dijon, France
| | - Paul J Benke
- Division of Clinical Genetics, Joe DiMaggio Children's Hospital, Hollywood, Florida, USA
| | - Christophe Philippe
- Laboratoire de Génomique Médicale, UF Innovation en diagnostic génomique des maladies rares, CHU Dijon Bourgogne, Dijon, France
- Inserm UMR1231 GAD, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
- Laboratoire de Génétique, CHR Metz-Thionville, Hôpital Mercy, Metz, France
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Zhang C, Ma W, Xu M, Li T, Han G, Gu L, Chen M, Zhang M, Cheng B, Zhang X. Identification and Functional Characterization of ZmSCYL2 Involved in Phytosterol Accumulation in Plants. Int J Mol Sci 2023; 24:10411. [PMID: 37373558 DOI: 10.3390/ijms241210411] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 06/11/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
Phytosterols are natural active substances widely found in plants and play an important role in hypolipidemia, antioxidants, antitumor, immunomodulation, plant growth, and development. In this study, phytosterols were extracted and identified from the seed embryos of 244 maize inbred lines. Based on this, a genome-wide association study (GWAS) was used to predict the possible candidate genes responsible for phytosterol content; 9 SNPs and 32 candidate genes were detected, and ZmSCYL2 was identified to be associated with phytosterol accumulation. We initially confirmed its functions in transgenic Arabidopsis and found that mutation of ZmSCYL2 resulted in slow plant growth and a significant reduction in sterol content, while overexpression of ZmSCYL2 accelerated plant growth and significantly increased sterol content. These results were further confirmed in transgenic tobacco and suggest that ZmSCYL2 was closely related to plant growth; overexpression of ZmSCYL2 not only facilitated plant growth and development but also promoted the accumulation of phytosterols.
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Affiliation(s)
- Chenchen Zhang
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Wanlu Ma
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Minyan Xu
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Tao Li
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Guomin Han
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Longjiang Gu
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Meng Chen
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Mengting Zhang
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Beijiu Cheng
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Xin Zhang
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
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Sobahy TM, Motwalli O, Alazmi M. AllelePred: A Simple Allele Frequencies Ensemble Predictor for Different Single Nucleotide Variants. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:796-801. [PMID: 35239491 DOI: 10.1109/tcbb.2022.3155659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
BACKGROUND & OBJECTIVE Genomic medicine stands to be revolutionized by understanding single nucleotide variants (SNVs) and their expression in single-gene disorders (Mendelian diseases). Computational tools can play a vital role in the exploration of such variations and their pathogenicity. Consequently, we developed the ensemble prediction tool AllelePred to identify deleterious SNVs and disease causative genes. RESULTS The model utilizes different population genetics backgrounds and restricted criteria for features selection to help generate high accuracy results. In comparison to other tools, such as Eigen, PROVEAN, and fathmm-MKL our classifier achieves higher accuracy (98%), precision (96%), F1 score (93%), and coverage (100%) for different types of coding variants. The new method was also compared against a bioinformatics analytical workflow, which uses gnomAD overall AFs (less than 1%) and CADD (scaled C-score of at least 15). Furthermore, this research highlights the stature of genetic variant sharing and curation. We accumulated a list of highly probable deleterious variants and recommended further experimental validation before medical diagnostic usage. CONCLUSIONS The ensemble prediction tool AllelePred enables increased accuracy in recognizing deleterious SNVs and the genetic determinants in real clinical data.
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The diagnostic yield, candidate genes, and pitfalls for a genetic study of intellectual disability in 118 middle eastern families. Sci Rep 2022; 12:18862. [PMID: 36344539 PMCID: PMC9640568 DOI: 10.1038/s41598-022-22036-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/07/2022] [Indexed: 11/09/2022] Open
Abstract
Global Developmental Delay/Intellectual disability (ID) is the term used to describe various disorders caused by abnormal brain development and characterized by impairments in cognition, communication, behavior, or motor skills. In the past few years, whole-exome sequencing (WES) has been proven to be a powerful, robust, and scalable approach for candidate gene discoveries in consanguineous populations. In this study, we recruited 215 patients affected with ID from 118 Middle Eastern families. Whole-exome sequencing was completed for 188 individuals. The average age at which WES was completed was 8.5 years. Pathogenic or likely pathogenic variants were detected in 32/118 families (27%). Variants of uncertain significance were seen in 33/118 families (28%). The candidate genes with a possible association with ID were detected in 32/118 (27%) with a total number of 64 affected individuals. These genes are novel, were previously reported in a single family, or cause strikingly different phenotypes with a different mode of inheritance. These genes included: AATK, AP1G2, CAMSAP1, CCDC9B, CNTROB, DNAH14, DNAJB4, DRG1, DTNBP1, EDRF1, EEF1D, EXOC8, EXOSC4, FARSB, FBXO22, FILIP1, INPP4A, P2RX7, PRDM13, PTRHD1, SCN10A, SCYL2, SMG8, SUPV3L1, TACC2, THUMPD1, XPR1, ZFYVE28. During the 5 years of the study and through gene matching databases, several of these genes have now been confirmed as causative of ID. In conclusion, understanding the causes of ID will help understand biological mechanisms, provide precise counseling for affected families, and aid in primary prevention.
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Biswas A, Nath SD, Ahsan T, Hossain MM, Akhteruzzaman S, Sajib AA. TTN as a candidate gene for distal arthrogryposis type 10 pathogenesis. J Genet Eng Biotechnol 2022; 20:119. [PMID: 35951140 PMCID: PMC9372250 DOI: 10.1186/s43141-022-00405-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 07/04/2022] [Indexed: 11/10/2022]
Abstract
Background Arthrogryposis is a medical term used to describe congenital contractures which often affect multiple limbs. Distal arthrogryposis (DA) is one of the major categories of arthrogryposis that primarily affects the distal parts of the body, i.e., the hands and the legs. Although ten different types and several subtypes of DAs have been described, the genes associated with each of these DAs are yet to be characterized. Distal arthrogryposis type 10 (DA10) is a rare genetic disease, which is distinguished from the other arthrogryposis types by plantar flexion contractures resulting in toe-walking during infancy as well as variability in contractures of the hip, hamstring, elbow, wrist and finger joints with no ocular or neurological abnormalities. Symptoms of DA10 indicate impairment specifically in the musculoskeletal system. DA10 is still poorly studied. Aim The objective of this study was to identify the candidate gene for DA10 by scrutinizing the protein-protein interaction (PPI) networks using in silico tools. Results Among the genes that reside within the previously reported genomic coordinates (human chromosome assembly 38 or GRCh38 coordinates 2:179,700,000–188,500,000) of the causative agent of DA10, only TTN (the gene that codes for the protein Titin or TTN) follows the expression pattern similar to the other known DA associated genes and its expression is predominant in the skeletal and heart muscles. Titin also participates in biological pathways and processes relevant to arthrogryposes. TTN-related known skeletal muscle disorders follow the autosomal-dominant pattern of inheritance, which is a common characteristic of distal arthrogryposes as well. Conclusion Based on the findings of the analyses and their correlation with previous reports, TTN appears to be the candidate gene for DA10. Our attempt to discover a potential candidate gene may eventually lead to an understanding of disease mechanism and possible treatment strategies, as well as demonstrate the suitability of PPI in the search for candidate genes. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-022-00405-5.
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Affiliation(s)
- Anik Biswas
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Sudipta Deb Nath
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Tamim Ahsan
- Molecular Biotechnology Division, National Institute of Biotechnology, Savar, Dhaka, 1349, Bangladesh
| | - M Monir Hossain
- Department of Neonatal Medicine, Bangladesh Institute of Child Health, Dhaka, 1207, Bangladesh
| | - Sharif Akhteruzzaman
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Abu Ashfaqur Sajib
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, 1000, Bangladesh.
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Cassidy AM, Kuliyev E, Thomas DB, Chen H, Pelletier S. Dissecting protein function in vivo: Engineering allelic series in mice using CRISPR-Cas9 technology. Methods Enzymol 2022; 667:775-812. [PMID: 35525561 DOI: 10.1016/bs.mie.2022.03.053] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Allelic series are extremely valuable genetic tools to study gene function and identify essential structural features of gene products. In mice, allelic series have been engineered using conventional gene targeting in embryonic stem cells or chemical mutagenesis. While these approaches have provided valuable information about the function of genes, they remain cumbersome. Modern approaches such as CRISPR-Cas9 technologies now allow for the precise and cost-effective generation of mouse models with specific mutations, facilitating the development of allelic series. Here, we describe procedures for the generation of three types of mutations used to dissect protein function in vivo using CRISPR-Cas9 technology. This step-by-step protocol describes the generation of missense mutations, large in-frame deletions, and insertions of genetic material using SCY1-like 1 (Scyl1) as a model gene.
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Affiliation(s)
- Annelise M Cassidy
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Emin Kuliyev
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Destinée B Thomas
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Hanying Chen
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Stephane Pelletier
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States.
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Latypova X, Creadore SG, Dahan-Oliel N, Gustafson AG, Wei-Hung Hwang S, Bedard T, Shazand K, van Bosse HJP, Giampietro PF, Dieterich K. A Genomic Approach to Delineating the Occurrence of Scoliosis in Arthrogryposis Multiplex Congenita. Genes (Basel) 2021; 12:genes12071052. [PMID: 34356068 PMCID: PMC8305424 DOI: 10.3390/genes12071052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 12/15/2022] Open
Abstract
Arthrogryposis multiplex congenita (AMC) describes a group of conditions characterized by the presence of non-progressive congenital contractures in multiple body areas. Scoliosis, defined as a coronal plane spine curvature of ≥10 degrees as measured radiographically, has been reported to occur in approximately 20% of children with AMC. To identify genes that are associated with both scoliosis as a clinical outcome and AMC, we first queried the DECIPHER database for copy number variations (CNVs). Upon query, we identified only two patients with both AMC and scoliosis (AMC-SC). The first patient contained CNVs in three genes (FBN2, MGF10, and PITX1), while the second case had a CNV in ZC4H2. Looking into small variants, using a combination of Human Phenotype Ontogeny and literature searching, 908 genes linked with scoliosis and 444 genes linked with AMC were identified. From these lists, 227 genes were associated with AMC-SC. Ingenuity Pathway Analysis (IPA) was performed on the final gene list to gain insight into the functional interactions of genes and various categories. To summarize, this group of genes encompasses a diverse group of cellular functions including transcription regulation, transmembrane receptor, growth factor, and ion channels. These results provide a focal point for further research using genomics and animal models to facilitate the identification of prognostic factors and therapeutic targets for AMC.
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Affiliation(s)
- Xenia Latypova
- Grenoble Institut Neurosciences, Université Grenoble Alpes, Inserm, U1216, CHU Grenoble Alpes, 38000 Grenoble, France;
| | | | - Noémi Dahan-Oliel
- Shriners Hospitals for Children, Montreal, QC H4A 0A9, Canada;
- School of Physical & Occupational Therapy, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC H3G 2M1, Canada
| | | | - Steven Wei-Hung Hwang
- Shriners Hospitals for Children, Philadelphia, PA 19140, USA; (S.W.-H.H.); (H.J.P.v.B.)
| | - Tanya Bedard
- Alberta Congenital Anomalies Surveillance System, Alberta Health Services, Edmonton, AB T5J 3E4, Canada;
| | - Kamran Shazand
- Shriners Hospitals for Children Headquarters, Tampa, FL 33607, USA; (S.G.C.); (A.G.G.); (K.S.)
| | | | - Philip F. Giampietro
- Department of Pediatrics, University of Illinois-Chicago, Chicago, IL 60607, USA
- Correspondence: (P.F.G.); (K.D.)
| | - Klaus Dieterich
- Institut of Advanced Biosciences, Université Grenoble Alpes, Inserm, U1209, CHU Grenoble Alpes, 38000 Grenoble, France
- Correspondence: (P.F.G.); (K.D.)
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Mulindwa J, Noyes H, Ilboudo H, Pagani L, Nyangiri O, Kimuda MP, Ahouty B, Asina OF, Ofon E, Kamoto K, Kabore JW, Koffi M, Ngoyi DM, Simo G, Chisi J, Sidibe I, Enyaru J, Simuunza M, Alibu P, Jamonneau V, Camara M, Tait A, Hall N, Bucheton B, MacLeod A, Hertz-Fowler C, Matovu E, Matovu E, Sidibe I, Mumba D, Koffi M, Simo G, Chisi J, Alibu VP, Macleod A, Bucheton B, Hertzfowler C, Elliot A, Camara M, Bishop O, Mulindwa J, Nyangiri O, Kimuda MP, Ofon E, Ahouty B, Kabore J. High Levels of Genetic Diversity within Nilo-Saharan Populations: Implications for Human Adaptation. Am J Hum Genet 2020; 107:473-486. [PMID: 32781046 PMCID: PMC7477016 DOI: 10.1016/j.ajhg.2020.07.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 07/13/2020] [Indexed: 12/23/2022] Open
Abstract
Africa contains more human genetic variation than any other continent, but the majority of the population-scale analyses of the African peoples have focused on just two of the four major linguistic groups, the Niger-Congo and Afro-Asiatic, leaving the Nilo-Saharan and Khoisan populations under-represented. In order to assess genetic variation and signatures of selection within a Nilo-Saharan population and between the Nilo-Saharan and Niger-Congo and Afro-Asiatic, we sequenced 50 genomes from the Nilo-Saharan Lugbara population of North-West Uganda and 250 genomes from 6 previously unsequenced Niger-Congo populations. We compared these data to data from a further 16 Eurasian and African populations including the Gumuz, another putative Nilo-Saharan population from Ethiopia. Of the 21 million variants identified in the Nilo-Saharan population, 3.57 million (17%) were not represented in dbSNP and included predicted non-synonymous mutations with possible phenotypic effects. We found greater genetic differentiation between the Nilo-Saharan Lugbara and Gumuz populations than between any two Afro-Asiatic or Niger-Congo populations. F3 tests showed that Gumuz contributed a genetic component to most Niger-Congo B populations whereas Lugabara did not. We scanned the genomes of the Lugbara for evidence of selective sweeps. We found selective sweeps at four loci (SLC24A5, SNX13, TYRP1, and UVRAG) associated with skin pigmentation, three of which already have been reported to be under selection. These selective sweeps point toward adaptations to the intense UV radiation of the Sahel.
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