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Amer K, Soliman NA, Soror S, Gad YZ, Moustafa A, Elmonem MA, Amer M, Ragheb A, Kotb A, Taha T, Ali W, Sakr M, Ghaffar KA. Egypt Genome: Towards an African new genomic era. J Adv Res 2024:S2090-1232(24)00227-3. [PMID: 38844121 DOI: 10.1016/j.jare.2024.06.003] [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: 11/07/2023] [Revised: 05/14/2024] [Accepted: 06/02/2024] [Indexed: 06/27/2024] Open
Abstract
BACKGROUND Studying the human genome is crucial to embrace precision medicine through tailoring treatment and prevention strategies to the unique genetic makeup and molecular information of individuals. After human genome project (1990-2003) generated the first full sequence of a human genome, there have been concerns towards Northern bias due to underrepresentation of other populations. Multiple countries have now established national genome projects aiming at the genomic knowledge that can be harnessed from their populations, which in turn can serve as a basis for their health care policies in the near future. AIM OF REVIEW The intention is to introduce the recently established Egypt Genome (EG) to delineate the genomics and genetics of both the modern and Ancient Egyptian populations. Leveraging genomic medicine to improve precision medicine strategies while building a solid foundation for large-scale genomic research capacity is the fundamental focus of EG. KEY SCIENTIFIC CONCEPTS EG generated genomic knowledge is predicted to enrich the existing human genome and to expand its diversity by studying the underrepresented African/Middle Eastern populations. The insightful impact of EG goes beyond Egypt and Africa as it fills the knowledge gaps in health and disease genomics towards improved and sustainable genomic-driven healthcare systems for better outcomes. Promoting the integration of genomics into clinical practice and spearheading the implementation of genomic-driven healthcare and precision medicine is therefore a key focus of EG. Mining into the wealth of Ancient Egyptian Genomics to delineate the genetic bridge between the contemporary and Ancient Egyptian populations is another excitingly unique area of EG to realize the global vision of human genome.
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Affiliation(s)
- Khaled Amer
- Egypt Center for Research and Regenerative Medicine (ECRRM), Cairo, Egypt.
| | - Neveen A Soliman
- Egypt Center for Research and Regenerative Medicine (ECRRM), Cairo, Egypt; Department of Pediatrics, Center of Pediatric Nephrology and Transplantation, Faculty of Medicine, Cairo University, Cairo, Egypt.
| | - Sameh Soror
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Helwan University, Cairo, Egypt
| | - Yehia Z Gad
- Department of Medical Molecular Genetics, Human Genetics and Genome Research Institute, National Research Center, Cairo, Egypt; Ancient DNA Laboratory, National Museum of Egyptian Civilization, Egypt
| | - Ahmed Moustafa
- Department of Biology, and Bioinformatics and Integrative Genomics Lab, American University in Cairo, Cairo, Egypt
| | - Mohamed A Elmonem
- Egypt Center for Research and Regenerative Medicine (ECRRM), Cairo, Egypt; Department of Clinical and Chemical Pathology, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - May Amer
- Egypt Center for Research and Regenerative Medicine (ECRRM), Cairo, Egypt
| | - Ameera Ragheb
- Egypt Center for Research and Regenerative Medicine (ECRRM), Cairo, Egypt
| | - Amira Kotb
- Egypt Center for Research and Regenerative Medicine (ECRRM), Cairo, Egypt; Department of Clinical and Chemical Pathology, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Tarek Taha
- Egypt Center for Research and Regenerative Medicine (ECRRM), Cairo, Egypt
| | - Wael Ali
- Egypt Center for Research and Regenerative Medicine (ECRRM), Cairo, Egypt
| | - Mahmoud Sakr
- Academy of Scientific Research & Technology, Egypt
| | - Khaled Abdel Ghaffar
- Department of Oral Medicine, Periodontolgy and Diagnosis, Faculty of Dentistry, Ain Shams University, Cairo, Egypt; Ministry of Health and Population, Cairo, Egypt
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2
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Owen GI, Cordova-Delgado M, Bustos BI, Cerpa LC, Gonzalez P, Morales-Pison S, Garcia-Bloj B, Garrido M, Miquel JF, Quiñones LA. Assessing the Occurrence and Influence of Cancer Chemotherapy-Related Pharmacogenetic Alleles in the Chilean Population. Pharmaceutics 2024; 16:561. [PMID: 38675222 PMCID: PMC11054647 DOI: 10.3390/pharmaceutics16040561] [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: 03/14/2024] [Revised: 04/02/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Pharmacogenomic knowledge as a biomarker for cancer care has transformed clinical practice, however, as current guidelines are primarily derived from Eurocentric populations, this limits their application in Latin America, particularly among Hispanic or Latino groups. Despite advancements, systemic chemotherapy still poses challenges in drug toxicity and suboptimal response. This study explores pharmacogenetic markers related to anticancer drugs in a Chilean cohort, filling a gap in Latin American research. Notably, the influence of native South American Mapuche-Huilliche ancestry. METHODS To explore pharmacogenetic markers related to anticancer drugs, we utilized an ethnically Admixed Chilean genome-wide association studies (GWAS) dataset of 1095 unrelated individuals. Pharmacogenomic markers were selected from PharmGKB, totaling 36 level 1 and 2 evidence single nucleotide polymorphisms (SNPs) and 571 level 3 SNPs. Comparative analyses involved assessing SNP frequencies across diverse populations from the 1000 Genomes Project. Haplotypes were estimated, and linkage disequilibrium was examined. Ancestry-based association analyses explored relationships between SNPs and Mapuche-Huilliche and European ancestries. Chi-square distribution with p ≤ 0.05 and Bonferroni's multiple adjustment tests determined statistical differences between allele frequencies. RESULTS Our study reveals significant disparities in SNP frequency within the Chilean population. Notably, dihydropyrimidine dehydrogenase (DPYD) variants (rs75017182 and rs67376798), linked to an increased risk of severe fluoropyrimidine toxicity, exhibit an exceptionally low frequency (minor allele frequency (MAF) < 0.005). Nudix hydrolase 15 (NUDT15) rs116855232, associated with hematological mercaptopurine toxicity, is relatively common (MAF = 0.062), and is further linked to Mapuche-Huilliche ancestry. Thiopurine methyltransferase enzyme (TPMT), implicated in severe toxicity to mercaptopurines, SNPs rs1142345 and rs1800460 of TMPT gene demonstrate higher MAFs in Admixed Americans and the Chilean population (MAF range 0.031-0.057). Finally, the variant in the UDP-glucuronosyltransferase 1 gene (UGT1A1) rs4148323, correlated with irinotecan neutropenia, exhibits the highest MAF in East Asian (MAF = 0.136) and Chilean (MAF = 0.025) populations, distinguishing them from other investigated populations. CONCLUSIONS This study provides the first comprehensive pharmacogenetic characterization of cancer therapy-related SNPs and highlights significant disparities in SNP frequencies within the Chilean population. Our findings underscore the necessity for inclusive research and personalized therapeutic strategies to ensure the equitable and effective application of precision medicine across diverse global communities.
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Affiliation(s)
- Gareth I. Owen
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (M.C.-D.); (P.G.)
- Department of Hematology and Oncology, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- Advanced Center for Chronic Diseases (ACCDiS), Santiago 8330034, Chile
- Millennium Institute on Immunology and Immunotherapy, Santiago 8331150, Chile
- Centro de Prevención y Control de Cáncer (CECAN), Santiago 8380453, Chile
| | - Miguel Cordova-Delgado
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (M.C.-D.); (P.G.)
- Department of Hematology and Oncology, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
- Faculty of Chemical and Pharmaceutical Sciences, Universidad de Chile, Santiago 8380494, Chile
| | - Bernabé I. Bustos
- Ken and Ruth Davee Department of Neurology, Simpson Querrey Center for Neurogenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA;
| | - Leslie C. Cerpa
- Laboratory of Chemical Carcinogenesis and Pharmacogenetics, Department of Basic and Clinical Oncology, Faculty of Medicine, Universidad de Chile, Santiago 8380494, Chile;
- Latin American Network for Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Santiago 8350499, Chile
| | - Pamela Gonzalez
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile; (M.C.-D.); (P.G.)
| | - Sebastián Morales-Pison
- Centro de Oncología de Precisión (COP), Facultad de Medicina y Ciencias de la Salud, Universidad Mayor, Santiago 7560908, Chile; (S.M.-P.); (B.G.-B.); (M.G.)
| | - Benjamín Garcia-Bloj
- Centro de Oncología de Precisión (COP), Facultad de Medicina y Ciencias de la Salud, Universidad Mayor, Santiago 7560908, Chile; (S.M.-P.); (B.G.-B.); (M.G.)
| | - Marcelo Garrido
- Centro de Oncología de Precisión (COP), Facultad de Medicina y Ciencias de la Salud, Universidad Mayor, Santiago 7560908, Chile; (S.M.-P.); (B.G.-B.); (M.G.)
- SAGA, Centro de Estudios Clínicos, Santiago 7610315, Chile
- Department of Oncología, Clínica Indisa, Santiago 7520440, Chile
| | - Juan Francisco Miquel
- Department of Gastroenterology, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago 8330032, Chile;
| | - Luis A. Quiñones
- Laboratory of Chemical Carcinogenesis and Pharmacogenetics, Department of Basic and Clinical Oncology, Faculty of Medicine, Universidad de Chile, Santiago 8380494, Chile;
- Latin American Network for Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Santiago 8350499, Chile
- Department of Pharmaceutical Sciences and Technology, Faculty of Chemical and Pharmaceutical Sciences, University of Chile, Santiago 8380494, Chile
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Choi J, Kim S, Kim J, Son HY, Yoo SK, Kim CU, Park YJ, Moon S, Cha B, Jeon MC, Park K, Yun JM, Cho B, Kim N, Kim C, Kwon NJ, Park YJ, Matsuda F, Momozawa Y, Kubo M, Kim HJ, Park JH, Seo JS, Kim JI, Im SW. A whole-genome reference panel of 14,393 individuals for East Asian populations accelerates discovery of rare functional variants. SCIENCE ADVANCES 2023; 9:eadg6319. [PMID: 37556544 PMCID: PMC10411914 DOI: 10.1126/sciadv.adg6319] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 07/06/2023] [Indexed: 08/11/2023]
Abstract
Underrepresentation of non-European (EUR) populations hinders growth of global precision medicine. Resources such as imputation reference panels that match the study population are necessary to find low-frequency variants with substantial effects. We created a reference panel consisting of 14,393 whole-genome sequences including more than 11,000 Asian individuals. Genome-wide association studies were conducted using the reference panel and a population-specific genotype array of 72,298 subjects for eight phenotypes. This panel yields improved imputation accuracy of rare and low-frequency variants within East Asian populations compared with the largest reference panel. Thirty-nine previously unidentified associations were found, and more than half of the variants were East Asian specific. We discovered genes with rare protein-altering variants, including LTBP1 for height and GPR75 for body mass index, as well as putative regulatory mechanisms for rare noncoding variants with cell type-specific effects. We suggest that this dataset will add to the potential value of Asian precision medicine.
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Affiliation(s)
- Jaeyong Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | | | - Juhyun Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ho-Young Son
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
| | - Seong-Keun Yoo
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Young Jun Park
- Department of Translational Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sungji Moon
- Interdisciplinary Program in Cancer Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Bukyoung Cha
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
| | - Min Chul Jeon
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kyunghyuk Park
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
| | - Jae Moon Yun
- Department of Family Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Belong Cho
- Department of Family Medicine, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Family Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | | | | | | | - Young Joo Park
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | | | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Hyun-Jin Kim
- National Cancer Control Institute, National Cancer Center, Goyang, Republic of Korea
| | - Jin-Ho Park
- Department of Family Medicine, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Family Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jeong-Sun Seo
- Macrogen Inc., Seoul, Republic of Korea
- Asian Genome Center, Seoul National University Bundang Hospital, Gyeonggi, Republic of Korea
| | - Jong-Il Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sun-Wha Im
- Department of Biochemistry and Molecular Biology, Kangwon National University School of Medicine, Gangwon, Republic of Korea
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4
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New insights from GWAS on BMI-related growth traits in a longitudinal cohort of admixed children with Native American and European ancestry. iScience 2023; 26:106091. [PMID: 36844456 PMCID: PMC9947275 DOI: 10.1016/j.isci.2023.106091] [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: 10/27/2021] [Revised: 05/04/2022] [Accepted: 01/25/2023] [Indexed: 02/02/2023] Open
Abstract
Body-mass index (BMI) is a hallmark of adiposity. In contrast with adulthood, the genetic architecture of BMI during childhood is poorly understood. The few genome-wide association studies (GWAS) on children have been performed almost exclusively in Europeans and at single ages. We performed cross-sectional and longitudinal GWAS for BMI-related traits on 904 admixed children with mostly Mapuche Native American and European ancestries. We found regulatory variants of the immune gene HLA-DQB3 strongly associated with BMI at 1.5 - 2.5 years old. A variant in the sex-determining gene DMRT1 was associated with the age at adiposity rebound (Age-AR) in girls (P = 9.8 × 10 - 9 ). BMI was significantly higher in Mapuche than in Europeans between 5.5 and 16.5 years old. Finally, Age-AR was significantly lower (P = 0.004 ) by 1.94 years and BMI at AR was significantly higher (P = 0.04 ) by 1.2 kg/ m 2 , in Mapuche children compared with Europeans.
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5
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Pedersen MW, Antunes C, De Cahsan B, Moreno-Mayar JV, Sikora M, Vinner L, Mann D, Klimov PB, Black S, Michieli CT, Braig HR, Perotti MA. Ancient human genomes and environmental DNA from the cement attaching 2,000 year-old head lice nits. Mol Biol Evol 2021; 39:6481551. [PMID: 34963129 PMCID: PMC8829908 DOI: 10.1093/molbev/msab351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Over the past few decades, there has been a growing demand for genome analysis of ancient human remains. Destructive sampling is increasingly difficult to obtain for ethical reasons, and standard methods of breaking the skull to access the petrous bone or sampling remaining teeth are often forbidden for curatorial reasons. However, most ancient humans carried head lice and their eggs abound in historical hair specimens. Here we show that host DNA is protected by the cement that glues head lice nits to the hair of ancient Argentinian mummies, 1,500–2,000 years old. The genetic affinities deciphered from genome-wide analyses of this DNA inform that this population migrated from north-west Amazonia to the Andes of central-west Argentina; a result confirmed using the mitochondria of the host lice. The cement preserves ancient environmental DNA of the skin, including the earliest recorded case of Merkel cell polyomavirus. We found that the percentage of human DNA obtained from nit cement equals human DNA obtained from the tooth, yield 2-fold compared with a petrous bone, and 4-fold to a bloodmeal of adult lice a millennium younger. In metric studies of sheaths, the length of the cement negatively correlates with the age of the specimens, whereas hair linear distance between nit and scalp informs about the environmental conditions at the time before death. Ectoparasitic lice sheaths can offer an alternative, nondestructive source of high-quality ancient DNA from a variety of host taxa where bones and teeth are not available and reveal complementary details of their history.
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Affiliation(s)
- Mikkel W Pedersen
- GLOBE Institute, Faculty of Health and Medical Science, University of Copenhagen, Denmark
| | - Catia Antunes
- Ecology and Evolutionary Biology Section, School of Biological Sciences, University of Reading, Reading, United Kingdom
| | - Binia De Cahsan
- GLOBE Institute, Faculty of Health and Medical Science, University of Copenhagen, Denmark
| | - J Víctor Moreno-Mayar
- GLOBE Institute, Faculty of Health and Medical Science, University of Copenhagen, Denmark
| | - Martin Sikora
- GLOBE Institute, Faculty of Health and Medical Science, University of Copenhagen, Denmark
| | - Lasse Vinner
- GLOBE Institute, Faculty of Health and Medical Science, University of Copenhagen, Denmark
| | - Darren Mann
- Oxford University Museum of Natural History, Oxford, United Kingdom
| | - Pavel B Klimov
- School of Natural Sciences, Bangor University, Bangor, Wales, United Kingdom.,Department of Ecology and Evolutionary Biology, University of Michigan, Museum of Zoology, Ann Arbor, USA
| | - Stuart Black
- Department of Geography and Environmental Science, Wager Building, University of Reading, Reading, United Kingdom
| | - Catalina Teresa Michieli
- Instituto de Investigaciones Arqueológicas y Museo "Prof. Mariano Gambier", Universidad Nacional de San Juan, San Juan, Argentina
| | - Henk R Braig
- School of Natural Sciences, Bangor University, Bangor, Wales, United Kingdom.,Institute and Museum of Natural Sciences, Faculty of Exact, Physical and Natural Sciences, National University of San Juan, San Juan, Argentina
| | - M Alejandra Perotti
- Ecology and Evolutionary Biology Section, School of Biological Sciences, University of Reading, Reading, United Kingdom
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6
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Vicuña L, Norambuena T, Miranda JP, Pereira A, Mericq V, Ongaro L, Montinaro F, Santos JL, Eyheramendy S. Novel loci and Mapuche genetic ancestry are associated with pubertal growth traits in Chilean boys. Hum Genet 2021; 140:1651-1661. [PMID: 34047840 PMCID: PMC8553699 DOI: 10.1007/s00439-021-02290-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 05/04/2021] [Indexed: 01/24/2023]
Abstract
Puberty is a complex developmental process that varies considerably among individuals and populations. Genetic factors explain a large proportion of the variability of several pubertal traits. Recent genome-wide association studies (GWAS) have identified hundreds of variants involved in traits that result from body growth, like adult height. However, they do not capture many genetic loci involved in growth changes over distinct growth phases. Further, such GWAS have been mostly performed in Europeans, but it is unknown how these findings relate to other continental populations. In this study, we analyzed the genetic basis of three pubertal traits; namely, peak height velocity (PV), age at PV (APV) and height at APV (HAPV). We analyzed a cohort of 904 admixed Chilean children and adolescents with European and Mapuche Native American ancestries. Height was measured on roughly a \documentclass[12pt]{minimal}
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\begin{document}$$6-$$\end{document}6-month basis from childhood to adolescence between 2006 and 2019. We predict that, in average, HAPV is 4.3 cm higher in European than in Mapuche adolescents (P = 0.042), and APV is 0.73 years later in European compared with Mapuche adolescents (P = 0.023). Further, by performing a GWAS on 774, 433 single-nucleotide polymorphisms, we identified a genetic signal harboring 3 linked variants significantly associated with PV in boys (P\documentclass[12pt]{minimal}
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\begin{document}$$< 5 \times 10^{-8}$$\end{document}<5×10-8). This signal has never been associated with growth-related traits.
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Affiliation(s)
- Lucas Vicuña
- Faculty of Engineering and Sciences, Universidad Adolfo Ibáñez, Peñalolén, Santiago, Chile.,Instituto Milenio de Investigación Sobre los Fundamentos de los Datos (IMFD), Santiago, Chile
| | - Tomás Norambuena
- Faculty of Engineering and Sciences, Universidad Adolfo Ibáñez, Peñalolén, Santiago, Chile.,Instituto Milenio de Investigación Sobre los Fundamentos de los Datos (IMFD), Santiago, Chile
| | - José Patricio Miranda
- Faculty of Engineering and Sciences, Universidad Adolfo Ibáñez, Peñalolén, Santiago, Chile
| | - Ana Pereira
- Institute of Nutrition and Food Technology, University of Chile, Santiago, Chile
| | - Veronica Mericq
- Institute of Maternal and Child Research, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Linda Ongaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Francesco Montinaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - José L Santos
- Department of Nutrition, Diabetes and Metabolism, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Susana Eyheramendy
- Faculty of Engineering and Sciences, Universidad Adolfo Ibáñez, Peñalolén, Santiago, Chile. .,Instituto Milenio de Investigación Sobre los Fundamentos de los Datos (IMFD), Santiago, Chile.
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Martin LJ, Benson DW. Focused Strategies for Defining the Genetic Architecture of Congenital Heart Defects. Genes (Basel) 2021; 12:827. [PMID: 34071175 PMCID: PMC8228798 DOI: 10.3390/genes12060827] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/24/2021] [Accepted: 05/26/2021] [Indexed: 12/14/2022] Open
Abstract
Congenital heart defects (CHD) are malformations present at birth that occur during heart development. Increasing evidence supports a genetic origin of CHD, but in the process important challenges have been identified. This review begins with information about CHD and the importance of detailed phenotyping of study subjects. To facilitate appropriate genetic study design, we review DNA structure, genetic variation in the human genome and tools to identify the genetic variation of interest. Analytic approaches powered for both common and rare variants are assessed. While the ideal outcome of genetic studies is to identify variants that have a causal role, a more realistic goal for genetic analytics is to identify variants in specific genes that influence the occurrence of a phenotype and which provide keys to open biologic doors that inform how the genetic variants modulate heart development. It has never been truer that good genetic studies start with good planning. Continued progress in unraveling the genetic underpinnings of CHD will require multidisciplinary collaboration between geneticists, quantitative scientists, clinicians, and developmental biologists.
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Affiliation(s)
- Lisa J. Martin
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH 45229, USA
| | - D. Woodrow Benson
- Department of Pediatrics, Medical College of Wisconsin, Wauwatosa, WI 53226, USA;
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8
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Lin M, Park DS, Zaitlen NA, Henn BM, Gignoux CR. Admixed Populations Improve Power for Variant Discovery and Portability in Genome-Wide Association Studies. Front Genet 2021; 12:673167. [PMID: 34108994 PMCID: PMC8181458 DOI: 10.3389/fgene.2021.673167] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/27/2021] [Indexed: 11/13/2022] Open
Abstract
Genome-wide association studies (GWAS) are primarily conducted in single-ancestry settings. The low transferability of results has limited our understanding of human genetic architecture across a range of complex traits. In contrast to homogeneous populations, admixed populations provide an opportunity to capture genetic architecture contributed from multiple source populations and thus improve statistical power. Here, we provide a mechanistic simulation framework to investigate the statistical power and transferability of GWAS under directional polygenic selection or varying divergence. We focus on a two-way admixed population and show that GWAS in admixed populations can be enriched for power in discovery by up to 2-fold compared to the ancestral populations under similar sample size. Moreover, higher accuracy of cross-population polygenic score estimates is also observed if variants and weights are trained in the admixed group rather than in the ancestral groups. Common variant associations are also more likely to replicate if first discovered in the admixed group and then transferred to an ancestral population, than the other way around (across 50 iterations with 1,000 causal SNPs, training on 10,000 individuals, testing on 1,000 in each population, p = 3.78e-6, 6.19e-101, ∼0 for FST = 0.2, 0.5, 0.8, respectively). While some of these FST values may appear extreme, we demonstrate that they are found across the entire phenome in the GWAS catalog. This framework demonstrates that investigation of admixed populations harbors significant advantages over GWAS in single-ancestry cohorts for uncovering the genetic architecture of traits and will improve downstream applications such as personalized medicine across diverse populations.
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Affiliation(s)
- Meng Lin
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Danny S Park
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, San Francisco, CA, United States
| | - Noah A Zaitlen
- Department of Neurology and Computational Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Brenna M Henn
- Department of Anthropology, Center for Population Biology and the Genome Center, University of California, Davis, Davis, CA, United States
| | - Christopher R Gignoux
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
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9
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Yilmaz F, Null M, Astling D, Yu HC, Cole J, Santorico SA, Hallgrimsson B, Manyama M, Spritz RA, Hendricks AE, Shaikh TH. Genome-wide copy number variations in a large cohort of bantu African children. BMC Med Genomics 2021; 14:129. [PMID: 34001112 PMCID: PMC8130444 DOI: 10.1186/s12920-021-00978-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 05/06/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Copy number variations (CNVs) account for a substantial proportion of inter-individual genomic variation. However, a majority of genomic variation studies have focused on single-nucleotide variations (SNVs), with limited genome-wide analysis of CNVs in large cohorts, especially in populations that are under-represented in genetic studies including people of African descent. METHODS We carried out a genome-wide copy number analysis in > 3400 healthy Bantu Africans from Tanzania. Signal intensity data from high density (> 2.5 million probes) genotyping arrays were used for CNV calling with three algorithms including PennCNV, DNAcopy and VanillaICE. Stringent quality metrics and filtering criteria were applied to obtain high confidence CNVs. RESULTS We identified over 400,000 CNVs larger than 1 kilobase (kb), for an average of 120 CNVs (SE = 2.57) per individual. We detected 866 large CNVs (≥ 300 kb), some of which overlapped genomic regions previously associated with multiple congenital anomaly syndromes, including Prader-Willi/Angelman syndrome (Type1) and 22q11.2 deletion syndrome. Furthermore, several of the common CNVs seen in our cohort (≥ 5%) overlap genes previously associated with developmental disorders. CONCLUSIONS These findings may help refine the phenotypic outcomes and penetrance of variations affecting genes and genomic regions previously implicated in diseases. Our study provides one of the largest datasets of CNVs from individuals of African ancestry, enabling improved clinical evaluation and disease association of CNVs observed in research and clinical studies in African populations.
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Affiliation(s)
- Feyza Yilmaz
- Integrative and Systems Biology Program, University of Colorado Denver, Denver, USA
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, USA
| | - Megan Null
- Department of Mathematical and Statistical Sciences, University of Colorado Denver, Denver, USA
| | - David Astling
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, USA
| | - Hung-Chun Yu
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, USA
| | - Joanne Cole
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, USA
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, USA
| | - Stephanie A Santorico
- Department of Mathematical and Statistical Sciences, University of Colorado Denver, Denver, USA
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, USA
- Biostatistics and Informatics, Colorado School of Public Health, Aurora, USA
| | - Benedikt Hallgrimsson
- Department of Cell Biology and Anatomy, Cumming School of Medicine and Alberta, Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Mange Manyama
- Anatomy in Radiology, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Richard A Spritz
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, USA
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, USA
| | - Audrey E Hendricks
- Department of Mathematical and Statistical Sciences, University of Colorado Denver, Denver, USA
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, USA
- Biostatistics and Informatics, Colorado School of Public Health, Aurora, USA
| | - Tamim H Shaikh
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, USA.
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, USA.
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Vicuña L, Klimenkova O, Norambuena T, Martinez FI, Fernandez MI, Shchur V, Eyheramendy S. Postadmixture Selection on Chileans Targets Haplotype Involved in Pigmentation, Thermogenesis and Immune Defense against Pathogens. Genome Biol Evol 2020; 12:1459-1470. [PMID: 32614437 PMCID: PMC7487163 DOI: 10.1093/gbe/evaa136] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2020] [Indexed: 12/13/2022] Open
Abstract
Detection of positive selection signatures in populations around the world is helping to uncover recent human evolutionary history as well as the genetic basis of diseases. Most human evolutionary genomic studies have been performed in European, African, and Asian populations. However, populations with Native American ancestry have been largely underrepresented. Here, we used a genome-wide local ancestry enrichment approach complemented with neutral simulations to identify postadmixture adaptations underwent by admixed Chileans through gene flow from Europeans into local Native Americans. The top significant hits (P = 2.4×10-7) are variants in a region on chromosome 12 comprising multiple regulatory elements. This region includes rs12821256, which regulates the expression of KITLG, a well-known gene involved in lighter hair and skin pigmentation in Europeans as well as in thermogenesis. Another variant from that region is associated with the long noncoding RNA RP11-13A1.1, which has been specifically involved in the innate immune response against infectious pathogens. Our results suggest that these genes were relevant for adaptation in Chileans following the Columbian exchange.
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Affiliation(s)
- Lucas Vicuña
- Faculty of Engineering and Sciences, Universidad Adolfo Ibañez, Peñalolén, Santiago, Chile
| | - Olga Klimenkova
- National Research University Higher School of Economics, Russian Federation, Moscow, Russia
| | - Tomás Norambuena
- Faculty of Engineering and Sciences, Universidad Adolfo Ibañez, Peñalolén, Santiago, Chile
| | - Felipe I Martinez
- Center for Intercultural and Indigenous Research, School of Anthropology, Faculty of Social Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Mario I Fernandez
- Department of Urology, Clínica Alemana, Santiago, Chile
- Center for Genetics and Genomics, Faculty of Medicine, Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Vladimir Shchur
- National Research University Higher School of Economics, Russian Federation, Moscow, Russia
| | - Susana Eyheramendy
- Faculty of Engineering and Sciences, Universidad Adolfo Ibañez, Peñalolén, Santiago, Chile
- Instituto Milenio de Investigación sobre los Fundamentos de los Datos (IMFD)
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