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Haffener PE, Al-Riyami AZ, Al-Zadjali S, Al-Rawahi M, Al Hosni S, Al Marhoobi A, Al Sheriyani A, Leffler EM. Characterization of Blood Group Variants in an Omani Population by Comparison of Whole Genome Sequencing and Serology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.17.599396. [PMID: 38948735 PMCID: PMC11212902 DOI: 10.1101/2024.06.17.599396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Although blood group variation was first described over a century ago, our understanding of the genetic variation affecting antigenic expression on the red blood cell surface in many populations is lacking. This deficit limits the ability to accurately type patients, especially as serological testing is not available for all described blood groups, and targeted genotyping panels may lack rare or population-specific variants. Here, we perform serological assays across 24 antigens and whole genome sequencing on 100 Omanis, a population underrepresented in genomic databases. We inferred blood group phenotypes using the most commonly typed genetic variants. The comparison of serological to inferred phenotypes resulted in an average concordance of 96.9%. Among the 22 discordances, we identify seven known variants in four blood groups that, to our knowledge, have not been previously reported in Omanis. Incorporating these variants for phenotype inference, concordance increases to 98.8%. Additionally, we describe five candidate variants in the Lewis, Lutheran, MNS, and P1 blood groups that may affect antigenic expression, although further functional confirmation is required. Notably, we identify several blood group alleles most common in African populations, likely introduced to Oman by gene flow over the last thousand years. These findings highlight the need to evaluate individual populations and their population history when considering variants to include in genotype panels for blood group typing. This research will inform future work in blood banks and transfusion services.
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Affiliation(s)
- Paige E. Haffener
- Department of Human Genetics, The University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Arwa Z. Al-Riyami
- Department of Hematology, Sultan Qaboos University Hospital, University Medical City, Muscat, Oman
| | - Shoaib Al-Zadjali
- Sultan Qaboos Comprehensive Cancer Center, University Medical City, Muscat, Oman
| | - Mohammed Al-Rawahi
- Department of Hematology, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Saif Al Hosni
- Department of Hematology, Sultan Qaboos University Hospital, University Medical City, Muscat, Oman
| | - Ali Al Marhoobi
- Department of Hematology, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | | | - Ellen M. Leffler
- Department of Human Genetics, The University of Utah School of Medicine, Salt Lake City, UT, USA
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Quilodrán CS, Rio J, Tsoupas A, Currat M. Past human expansions shaped the spatial pattern of Neanderthal ancestry. SCIENCE ADVANCES 2023; 9:eadg9817. [PMID: 37851812 PMCID: PMC10584333 DOI: 10.1126/sciadv.adg9817] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 09/11/2023] [Indexed: 10/20/2023]
Abstract
The worldwide expansion of modern humans (Homo sapiens) started before the extinction of Neanderthals (Homo neanderthalensis). Both species coexisted and interbred, leading to slightly higher introgression in East Asians than in Europeans. This distinct ancestry level has been argued to result from selection, but range expansions of modern humans could provide an alternative explanation. This hypothesis would lead to spatial introgression gradients, increasing with distance from the expansion source. We investigate the presence of Neanderthal introgression gradients after past human expansions by analyzing Eurasian paleogenomes. We show that the out-of-Africa expansion resulted in spatial gradients of Neanderthal ancestry that persisted through time. While keeping the same gradient orientation, the expansion of early Neolithic farmers contributed decisively to reducing the Neanderthal introgression in European populations compared to Asian populations. This is because Neolithic farmers carried less Neanderthal DNA than preceding Paleolithic hunter-gatherers. This study shows that inferences about past human population dynamics can be made from the spatiotemporal variation in archaic introgression.
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Affiliation(s)
| | - Jérémy Rio
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Alexandros Tsoupas
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Mathias Currat
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, Geneva, Switzerland
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Tobler R, Souilmi Y, Huber CD, Bean N, Turney CSM, Grey ST, Cooper A. The role of genetic selection and climatic factors in the dispersal of anatomically modern humans out of Africa. Proc Natl Acad Sci U S A 2023; 120:e2213061120. [PMID: 37220274 PMCID: PMC10235988 DOI: 10.1073/pnas.2213061120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 03/14/2023] [Indexed: 05/25/2023] Open
Abstract
The evolutionarily recent dispersal of anatomically modern humans (AMH) out of Africa (OoA) and across Eurasia provides a unique opportunity to examine the impacts of genetic selection as humans adapted to multiple new environments. Analysis of ancient Eurasian genomic datasets (~1,000 to 45,000 y old) reveals signatures of strong selection, including at least 57 hard sweeps after the initial AMH movement OoA, which have been obscured in modern populations by extensive admixture during the Holocene. The spatiotemporal patterns of these hard sweeps provide a means to reconstruct early AMH population dispersals OoA. We identify a previously unsuspected extended period of genetic adaptation lasting ~30,000 y, potentially in the Arabian Peninsula area, prior to a major Neandertal genetic introgression and subsequent rapid dispersal across Eurasia as far as Australia. Consistent functional targets of selection initiated during this period, which we term the Arabian Standstill, include loci involved in the regulation of fat storage, neural development, skin physiology, and cilia function. Similar adaptive signatures are also evident in introgressed archaic hominin loci and modern Arctic human groups, and we suggest that this signal represents selection for cold adaptation. Surprisingly, many of the candidate selected loci across these groups appear to directly interact and coordinately regulate biological processes, with a number associated with major modern diseases including the ciliopathies, metabolic syndrome, and neurodegenerative disorders. This expands the potential for ancestral human adaptation to directly impact modern diseases, providing a platform for evolutionary medicine.
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Affiliation(s)
- Raymond Tobler
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, SA5005, Australia
| | - Yassine Souilmi
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, SA5005, Australia
- Environment Institute, The University of Adelaide, Adelaide, SA5005, Australia
| | - Christian D. Huber
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, SA5005, Australia
| | - Nigel Bean
- Australian Research Council Centre of Excellence for Mathematical and Statistical Frontiers, The University of Adelaide, Adelaide, SA5005, Australia
- School of Mathematical Sciences, The University of Adelaide, Adelaide, SA5005, Australia
| | - Chris S. M. Turney
- Division of Research, University of Technology Sydney, Ultimo, NSW2007, Australia
| | - Shane T. Grey
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW2052, Australia
- Transplantation Immunology Group, Translation Science Pillar, Garvan Institute of Medical Research, Darlinghurst, NSW2010, Australia
| | - Alan Cooper
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, SA5005, Australia
- Blue Sky Genetics, Ashton, SA5137, Australia
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Ferreira JC, Alshamali F, Pereira L, Fernandes V. Characterization of Arabian Peninsula whole exomes: Contributing to the catalogue of human diversity. iScience 2022; 25:105336. [DOI: 10.1016/j.isci.2022.105336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 08/01/2022] [Accepted: 10/10/2022] [Indexed: 11/24/2022] Open
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Circum-Saharan Prehistory through the Lens of mtDNA Diversity. Genes (Basel) 2022; 13:genes13030533. [PMID: 35328086 PMCID: PMC8951852 DOI: 10.3390/genes13030533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 12/04/2022] Open
Abstract
African history has been significantly influenced by the Sahara, which has represented a barrier for migrations of all living beings, including humans. Major exceptions were the gene flow events that took place between North African and sub-Saharan populations during the so-called African Humid Periods, especially in the Early Holocene (11.5 to 5.5 thousand years ago), and more recently in connection with trans-Saharan commercial routes. In this study, we describe mitochondrial DNA (mtDNA) diversity of human populations from both sides of the Sahara Desert, i.e., both from North Africa and the Sahel/Savannah belt. The final dataset of 7213 mtDNA sequences from 134 African populations encompasses 470 newly collected and 6743 previously published samples, which were analyzed using descriptive methods and Bayesian statistics. We completely sequenced 26 mtDNAs from sub-Saharan samples belonging to the Eurasian haplogroup N1. Analyses of these N1 mitogenomes revealed their possible routes to the Sahel, mostly via Bab el-Mandab. Our results indicate that maternal gene flow must have been important in this circum-Saharan space, not only within North Africa and the Sahel/Savannah belt but also between these two regions.
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Saad M, Mokrab Y, Halabi N, Shan J, Razali R, Kunji K, Syed N, Temanni R, Subramanian M, Ceccarelli M, Rafii Tabrizi A, Bedognetti D, Chouchane L. Genetic predisposition to cancer across people of different ancestries in Qatar: a population-based, cohort study. Lancet Oncol 2022; 23:341-352. [DOI: 10.1016/s1470-2045(21)00752-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/12/2021] [Accepted: 12/15/2021] [Indexed: 12/22/2022]
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