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Capalbo A, de Wert G, Mertes H, Klausner L, Coonen E, Spinella F, Van de Velde H, Viville S, Sermon K, Vermeulen N, Lencz T, Carmi S. Screening embryos for polygenic disease risk: a review of epidemiological, clinical, and ethical considerations. Hum Reprod Update 2024:dmae012. [PMID: 38805697 DOI: 10.1093/humupd/dmae012] [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: 01/10/2024] [Revised: 03/25/2024] [Indexed: 05/30/2024] Open
Abstract
BACKGROUND The genetic composition of embryos generated by in vitro fertilization (IVF) can be examined with preimplantation genetic testing (PGT). Until recently, PGT was limited to detecting single-gene, high-risk pathogenic variants, large structural variants, and aneuploidy. Recent advances have made genome-wide genotyping of IVF embryos feasible and affordable, raising the possibility of screening embryos for their risk of polygenic diseases such as breast cancer, hypertension, diabetes, or schizophrenia. Despite a heated debate around this new technology, called polygenic embryo screening (PES; also PGT-P), it is already available to IVF patients in some countries. Several articles have studied epidemiological, clinical, and ethical perspectives on PES; however, a comprehensive, principled review of this emerging field is missing. OBJECTIVE AND RATIONALE This review has four main goals. First, given the interdisciplinary nature of PES studies, we aim to provide a self-contained educational background about PES to reproductive specialists interested in the subject. Second, we provide a comprehensive and critical review of arguments for and against the introduction of PES, crystallizing and prioritizing the key issues. We also cover the attitudes of IVF patients, clinicians, and the public towards PES. Third, we distinguish between possible future groups of PES patients, highlighting the benefits and harms pertaining to each group. Finally, our review, which is supported by ESHRE, is intended to aid healthcare professionals and policymakers in decision-making regarding whether to introduce PES in the clinic, and if so, how, and to whom. SEARCH METHODS We searched for PubMed-indexed articles published between 1/1/2003 and 1/3/2024 using the terms 'polygenic embryo screening', 'polygenic preimplantation', and 'PGT-P'. We limited the review to primary research papers in English whose main focus was PES for medical conditions. We also included papers that did not appear in the search but were deemed relevant. OUTCOMES The main theoretical benefit of PES is a reduction in lifetime polygenic disease risk for children born after screening. The magnitude of the risk reduction has been predicted based on statistical modelling, simulations, and sibling pair analyses. Results based on all methods suggest that under the best-case scenario, large relative risk reductions are possible for one or more diseases. However, as these models abstract several practical limitations, the realized benefits may be smaller, particularly due to a limited number of embryos and unclear future accuracy of the risk estimates. PES may negatively impact patients and their future children, as well as society. The main personal harms are an unindicated IVF treatment, a possible reduction in IVF success rates, and patient confusion, incomplete counselling, and choice overload. The main possible societal harms include discarded embryos, an increasing demand for 'designer babies', overemphasis of the genetic determinants of disease, unequal access, and lower utility in people of non-European ancestries. Benefits and harms will vary across the main potential patient groups, comprising patients already requiring IVF, fertile people with a history of a severe polygenic disease, and fertile healthy people. In the United States, the attitudes of IVF patients and the public towards PES seem positive, while healthcare professionals are cautious, sceptical about clinical utility, and concerned about patient counselling. WIDER IMPLICATIONS The theoretical potential of PES to reduce risk across multiple polygenic diseases requires further research into its benefits and harms. Given the large number of practical limitations and possible harms, particularly unnecessary IVF treatments and discarded viable embryos, PES should be offered only within a research context before further clarity is achieved regarding its balance of benefits and harms. The gap in attitudes between healthcare professionals and the public needs to be narrowed by expanding public and patient education and providing resources for informative and unbiased genetic counselling.
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Affiliation(s)
- Antonio Capalbo
- Juno Genetics, Department of Reproductive Genetics, Rome, Italy
- Center for Advanced Studies and Technology (CAST), Department of Medical Genetics, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Guido de Wert
- Department of Health, Ethics & Society, CAPHRI-School for Public Health and Primary Care and GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Heidi Mertes
- Department of Philosophy and Moral Sciences, Ghent University, Ghent, Belgium
- Department of Public Health and Primary Care, Ghent University, Ghent, Belgium
| | - Liraz Klausner
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Edith Coonen
- Departments of Clinical Genetics and Reproductive Medicine, Maastricht University Medical Centre, Maastricht, The Netherlands
- School for Oncology and Developmental Biology, GROW, Maastricht University, Maastricht, The Netherlands
| | - Francesca Spinella
- Eurofins GENOMA Group Srl, Molecular Genetics Laboratories, Department of Scientific Communication, Rome, Italy
| | - Hilde Van de Velde
- Research Group Genetics Reproduction and Development (GRAD), Vrije Universiteit Brussel, Brussel, Belgium
- Brussels IVF, UZ Brussel, Brussel, Belgium
| | - Stephane Viville
- Laboratoire de Génétique Médicale LGM, Institut de Génétique Médicale d'Alsace IGMA, INSERM UMR 1112, Université de Strasbourg, France
- Laboratoire de Diagnostic Génétique, Unité de Génétique de l'infertilité (UF3472), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Karen Sermon
- Research Group Genetics Reproduction and Development (GRAD), Vrije Universiteit Brussel, Brussel, Belgium
| | | | - Todd Lencz
- Institute of Behavioral Science, Feinstein Institutes for Medical Research, Manhasset, NY, USA
- Departments of Psychiatry and Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, USA
| | - Shai Carmi
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
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Cahoon JL, Rui X, Tang E, Simons C, Langie J, Chen M, Lo YC, Chiang CWK. Imputation accuracy across global human populations. Am J Hum Genet 2024; 111:979-989. [PMID: 38604166 PMCID: PMC11080279 DOI: 10.1016/j.ajhg.2024.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 04/13/2024] Open
Abstract
Genotype imputation is now fundamental for genome-wide association studies but lacks fairness due to the underrepresentation of references from non-European ancestries. The state-of-the-art imputation reference panel released by the Trans-Omics for Precision Medicine (TOPMed) initiative improved the imputation of admixed African-ancestry and Hispanic/Latino samples, but imputation for populations primarily residing outside of North America may still fall short in performance due to persisting underrepresentation. To illustrate this point, we imputed the genotypes of over 43,000 individuals across 123 populations around the world and identified numerous populations where imputation accuracy paled in comparison to that of European-ancestry populations. For instance, the mean imputation r-squared (Rsq) for variants with minor allele frequencies between 1% and 5% in Saudi Arabians (n = 1,061), Vietnamese (n = 1,264), Thai (n = 2,435), and Papua New Guineans (n = 776) were 0.79, 0.78, 0.76, and 0.62, respectively, compared to 0.90-0.93 for comparable European populations matched in sample size and SNP array content. Outside of Africa and Latin America, Rsq appeared to decrease as genetic distances to European-ancestry reference increased, as predicted. Using sequencing data as ground truth, we also showed that Rsq may over-estimate imputation accuracy for non-European populations more than European populations, suggesting further disparity in accuracy between populations. Using 1,496 sequenced individuals from Taiwan Biobank as a second reference panel to TOPMed, we also assessed a strategy to improve imputation for non-European populations with meta-imputation, but this design did not improve accuracy across frequency spectra. Taken together, our analyses suggest that we must ultimately strive to increase diversity and size to promote equity within genetics research.
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Affiliation(s)
- Jordan L Cahoon
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, Los Angeles, CA 90033, USA; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, Los Angeles, CA 90089, USA; Department of Computer Science, University of Southern California, Los Angeles, Los Angeles, CA 90089, USA
| | - Xinyue Rui
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, Los Angeles, CA 90033, USA
| | - Echo Tang
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, Los Angeles, CA 90089, USA
| | - Christopher Simons
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, Los Angeles, CA 90089, USA
| | - Jalen Langie
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, Los Angeles, CA 90033, USA
| | - Minhui Chen
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, Los Angeles, CA 90033, USA
| | - Ying-Chu Lo
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, Los Angeles, CA 90033, USA
| | - Charleston W K Chiang
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, Los Angeles, CA 90033, USA; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, Los Angeles, CA 90089, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, Los Angeles, CA 90033, USA.
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3
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de Smith AJ, Wahlster L, Jeon S, Kachuri L, Black S, Langie J, Cato LD, Nakatsuka N, Chan TF, Xia G, Mazumder S, Yang W, Gazal S, Eng C, Hu D, Burchard EG, Ziv E, Metayer C, Mancuso N, Yang JJ, Ma X, Wiemels JL, Yu F, Chiang CWK, Sankaran VG. A noncoding regulatory variant in IKZF1 increases acute lymphoblastic leukemia risk in Hispanic/Latino children. CELL GENOMICS 2024; 4:100526. [PMID: 38537633 PMCID: PMC11019360 DOI: 10.1016/j.xgen.2024.100526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 12/11/2023] [Accepted: 02/27/2024] [Indexed: 04/04/2024]
Abstract
Hispanic/Latino children have the highest risk of acute lymphoblastic leukemia (ALL) in the US compared to other racial/ethnic groups, yet the basis of this remains incompletely understood. Through genetic fine-mapping analyses, we identified a new independent childhood ALL risk signal near IKZF1 in self-reported Hispanic/Latino individuals, but not in non-Hispanic White individuals, with an effect size of ∼1.44 (95% confidence interval = 1.33-1.55) and a risk allele frequency of ∼18% in Hispanic/Latino populations and <0.5% in European populations. This risk allele was positively associated with Indigenous American ancestry, showed evidence of selection in human history, and was associated with reduced IKZF1 expression. We identified a putative causal variant in a downstream enhancer that is most active in pro-B cells and interacts with the IKZF1 promoter. This variant disrupts IKZF1 autoregulation at this enhancer and results in reduced enhancer activity in B cell progenitors. Our study reveals a genetic basis for the increased ALL risk in Hispanic/Latino children.
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Affiliation(s)
- Adam J de Smith
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA.
| | - Lara Wahlster
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Soyoung Jeon
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Linda Kachuri
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Susan Black
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jalen Langie
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Liam D Cato
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Tsz-Fung Chan
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Guangze Xia
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Soumyaa Mazumder
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Wenjian Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Steven Gazal
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Celeste Eng
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Bioengineering and Biotherapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Donglei Hu
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Esteban González Burchard
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Bioengineering and Biotherapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Elad Ziv
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Catherine Metayer
- School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Nicholas Mancuso
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Jun J Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Xiaomei Ma
- Yale School of Public Health, New Haven, CT 06520, USA
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Fulong Yu
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou National Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Charleston W K Chiang
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA; USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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4
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Zhao Y, Chukanova M, Kentistou KA, Fairhurst-Hunter Z, Siegert AM, Jia RY, Dowsett GKC, Gardner EJ, Lawler K, Day FR, Kaisinger LR, Tung YCL, Lam BYH, Chen HJC, Wang Q, Berumen-Campos J, Kuri-Morales P, Tapia-Conyer R, Alegre-Diaz J, Barroso I, Emberson J, Torres JM, Collins R, Saleheen D, Smith KR, Paul DS, Merkle F, Farooqi IS, Wareham NJ, Petrovski S, O'Rahilly S, Ong KK, Yeo GSH, Perry JRB. Protein-truncating variants in BSN are associated with severe adult-onset obesity, type 2 diabetes and fatty liver disease. Nat Genet 2024; 56:579-584. [PMID: 38575728 PMCID: PMC11018524 DOI: 10.1038/s41588-024-01694-x] [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: 06/05/2023] [Accepted: 02/21/2024] [Indexed: 04/06/2024]
Abstract
Obesity is a major risk factor for many common diseases and has a substantial heritable component. To identify new genetic determinants, we performed exome-sequence analyses for adult body mass index (BMI) in up to 587,027 individuals. We identified rare loss-of-function variants in two genes (BSN and APBA1) with effects substantially larger than those of well-established obesity genes such as MC4R. In contrast to most other obesity-related genes, rare variants in BSN and APBA1 were not associated with normal variation in childhood adiposity. Furthermore, BSN protein-truncating variants (PTVs) magnified the influence of common genetic variants associated with BMI, with a common variant polygenic score exhibiting an effect twice as large in BSN PTV carriers than in noncarriers. Finally, we explored the plasma proteomic signatures of BSN PTV carriers as well as the functional consequences of BSN deletion in human induced pluripotent stem cell-derived hypothalamic neurons. Collectively, our findings implicate degenerative processes in synaptic function in the etiology of adult-onset obesity.
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Affiliation(s)
- Yajie Zhao
- MRC Epidemiology Unit and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Maria Chukanova
- Metabolic Research Laboratories, MRC Metabolic Diseases Unit and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Katherine A Kentistou
- MRC Epidemiology Unit and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Zammy Fairhurst-Hunter
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Anna Maria Siegert
- Metabolic Research Laboratories, MRC Metabolic Diseases Unit and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Raina Y Jia
- MRC Epidemiology Unit and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Georgina K C Dowsett
- Metabolic Research Laboratories, MRC Metabolic Diseases Unit and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Eugene J Gardner
- MRC Epidemiology Unit and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Katherine Lawler
- Metabolic Research Laboratories, MRC Metabolic Diseases Unit and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Felix R Day
- MRC Epidemiology Unit and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Lena R Kaisinger
- MRC Epidemiology Unit and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Yi-Chun Loraine Tung
- Metabolic Research Laboratories, MRC Metabolic Diseases Unit and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Brian Yee Hong Lam
- Metabolic Research Laboratories, MRC Metabolic Diseases Unit and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Hsiao-Jou Cortina Chen
- Metabolic Research Laboratories, MRC Metabolic Diseases Unit and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Quanli Wang
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Jaime Berumen-Campos
- Experimental Medicine Research Unit, Faculty of Medicine, National Autonomous University of Mexico, Copilco Universidad, Mexico City, Mexico
| | - Pablo Kuri-Morales
- Experimental Medicine Research Unit, Faculty of Medicine, National Autonomous University of Mexico, Copilco Universidad, Mexico City, Mexico
- Instituto Tecnológico de Estudios Superiores de Monterrey, Tecnológico, Monterrey, Mexico
| | - Roberto Tapia-Conyer
- Experimental Medicine Research Unit, Faculty of Medicine, National Autonomous University of Mexico, Copilco Universidad, Mexico City, Mexico
| | - Jesus Alegre-Diaz
- Experimental Medicine Research Unit, Faculty of Medicine, National Autonomous University of Mexico, Copilco Universidad, Mexico City, Mexico
| | - Inês Barroso
- Exeter Centre of Excellence for Diabetes Research (EXCEED), University of Exeter Medical School, Exeter, UK
| | - Jonathan Emberson
- MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Clinical Trial Service Unit & Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Jason M Torres
- MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Clinical Trial Service Unit & Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Rory Collins
- Clinical Trial Service Unit & Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Danish Saleheen
- Center for Non-Communicable Diseases, Karachi, Pakistan
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Katherine R Smith
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Dirk S Paul
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Florian Merkle
- Institute of Metabolic Science and Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - I Sadaf Farooqi
- Metabolic Research Laboratories, MRC Metabolic Diseases Unit and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Nick J Wareham
- MRC Epidemiology Unit and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Slavé Petrovski
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Stephen O'Rahilly
- Metabolic Research Laboratories, MRC Metabolic Diseases Unit and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Ken K Ong
- MRC Epidemiology Unit and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Giles S H Yeo
- Metabolic Research Laboratories, MRC Metabolic Diseases Unit and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - John R B Perry
- MRC Epidemiology Unit and NIHR Cambridge Biomedical Research Centre, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK.
- Metabolic Research Laboratories, MRC Metabolic Diseases Unit and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK.
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5
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Faundes V, Repetto GM, Valdivia LE. Discovery of novel genetic syndromes in Latin America: Opportunities and challenges. Genet Mol Biol 2024; 47Suppl 1:e20230318. [PMID: 38466870 DOI: 10.1590/1678-4685-gmb-2023-0318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 02/06/2024] [Indexed: 03/13/2024] Open
Abstract
Latin America (LatAm) has a rich and historically significant role in delineating both novel and well-documented genetic disorders. However, the ongoing advancements in the field of human genetics pose challenges to the relatively slow adaption of LatAm in the field. Here, we describe past and present contributions of LatAm to the discovery of novel genetic disorders, often referred as novel gene-disease associations (NGDA). We also describe the current methodologies for discovery of NGDA, taking into account the latest developments in genomics. We provide an overview of opportunities and challenges for NGDA research in LatAm considering the steps currently performed to identify and validate such associations. Given the multiple and diverse needs of populations and countries in LatAm, it is imperative to foster collaborations amongst patients, indigenous people, clinicians and scientists. Such collaborative effort is essential for sustaining and enhancing the LatAm´s contributions to the field of NGDA.
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Affiliation(s)
- Víctor Faundes
- Universidad de Chile, Instituto de Nutrición y Tecnología de los Alimentos, Laboratorio de Genética y Enfermedades Metabólicas, Santiago, Chile
| | - Gabriela M Repetto
- Universidad del Desarrollo, Facultad de Medicina, Instituto de Ciencias e Innovación en Medicina, Centro de Genética y Genómica, Programa de Enfermedades Raras, Santiago, Chile
| | - Leonardo E Valdivia
- Universidad Mayor, Facultad de Ciencias, Centro de Biología Integrativa, Santiago, Chile
- Universidad Mayor, Facultad de Ciencias, Escuela de Biotecnología, Santiago, Chile
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6
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de Smith AJ, Jiménez-Morales S, Mejía-Aranguré JM. The genetic risk of acute lymphoblastic leukemia and its implications for children of Latin American origin. Front Oncol 2024; 13:1299355. [PMID: 38264740 PMCID: PMC10805326 DOI: 10.3389/fonc.2023.1299355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 12/12/2023] [Indexed: 01/25/2024] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common cancer in children, and disproportionately affects children of Hispanic/Latino ethnicity in the United States, who have the highest incidence of disease compared with other racial/ethnic groups. Incidence of childhood ALL is similarly high in several Latin American countries, notably in Mexico, and of concern is the rising incidence of childhood ALL in some Hispanic/Latino populations that may further widen this disparity. Prior studies have implicated common germline genetic variants in the increased risk of ALL among Hispanic/Latino children. In this review, we describe the known disparities in ALL incidence as well as patient outcomes that disproportionately affect Hispanic/Latino children across the Americas, and we focus on the role of genetic variation as well as Indigenous American ancestry in the etiology of these disparities. Finally, we discuss future avenues of research to further our understanding of the causes of the disparities in ALL incidence and outcomes in children of Latin American origin, which will be required for future precision prevention efforts.
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Affiliation(s)
- Adam J. de Smith
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California Keck School of Medicine, Los Angeles, CA, United States
- USC Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, CA, United States
| | - Silvia Jiménez-Morales
- Laboratorio de Innovación y Medicina de Precisión, Núcleo A, Instituto Nacional de Medicina Genómica, Ciudad de México, Mexico
| | - Juan Manuel Mejía-Aranguré
- Laboratorio de Genómica Funcional del Cáncer, Instituto Nacional de Medicina Genómica, Ciudad de México, Mexico
- Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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Sohail M, Moreno-Estrada A. The Mexican Biobank Project promotes genetic discovery, inclusive science and local capacity building. Dis Model Mech 2024; 17:dmm050522. [PMID: 38299665 PMCID: PMC10855211 DOI: 10.1242/dmm.050522] [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] [Indexed: 02/02/2024] Open
Abstract
Diversifying genotype-phenotype databases is essential to understanding complex trait and disease etiology across different environments and genetic ancestries. The rise of biobanks across the world is helping reveal the genetic and environmental architecture of multiple disease traits but the diversity they capture remains limited. To help close this gap, the Mexican Biobank (MXB) Project was recently generated, and has already revealed fine-scale genetic ancestries and demographic histories across the country, and their impact on trait-relevant genetic variation. This will help guide future genetic epidemiology and public health efforts, and has also improved polygenic prediction for several traits in Mexican populations compared with using data from other genome-wide association studies, such as the UK Biobank. The MXB illustrates the importance of transnational initiatives and funding calls that prioritize local leadership and capacity building to move towards inclusive genomic science.
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Affiliation(s)
- Mashaal Sohail
- Genómica Computacional, Centro de Ciencias Genómicas (CCG), Universidad Nacional Autónoma de México (UNAM), 62209 Cuernavaca, Morelos, México
| | - Andrés Moreno-Estrada
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN (Cinvestav), 36821 Irapuato, Guanajuato, México
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Maldonado BL, Piqué DG, Kaplan RC, Claw KG, Gignoux CR. Genetic risk prediction in Hispanics/Latinos: milestones, challenges, and social-ethical considerations. J Community Genet 2023; 14:543-553. [PMID: 37962783 PMCID: PMC10725387 DOI: 10.1007/s12687-023-00686-4] [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: 12/01/2022] [Accepted: 10/18/2023] [Indexed: 11/15/2023] Open
Abstract
Genome-wide association studies (GWAS) have allowed the identification of disease-associated variants, which can be leveraged to build polygenic scores (PGSs). Even though PGSs can be a valuable tool in personalized medicine, their predictive power is limited in populations of non-European ancestry, particularly in admixed populations. Recent efforts have focused on increasing racial and ethnic diversity in GWAS, thus, addressing some of the limitations of genetic risk prediction in these populations. Even with these efforts, few studies focus exclusively on Hispanics/Latinos. Additionally, Hispanic/Latino populations are often considered a single population despite varying admixture proportions between and within ethnic groups, diverse genetic heterogeneity, and demographic history. Combined with highly heterogeneous environmental and socioeconomic exposures, this diversity can reduce the transferability of genetic risk prediction models. Given the recent increase of genomic studies that include Hispanics/Latinos, we review the milestones and efforts that focus on genetic risk prediction, summarize the potential for improving PGS transferability, and highlight the challenges yet to be addressed. Additionally, we summarize social-ethical considerations and provide ideas to promote genetic risk prediction models that can be implemented equitably.
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Affiliation(s)
- Betzaida L Maldonado
- Human Medical Genetics & Genomics Graduate Program, University of Colorado-Anschutz Medical Campus, Aurora, CO, USA.
- Colorado Center for Personalized Medicine, University of Colorado-Anschutz Medical Campus, Aurora, CO, USA.
- Department of Biomedical Informatics, University of Colorado-Anschutz Medical Campus, Aurora, CO, USA.
| | - Daniel G Piqué
- Colorado Center for Personalized Medicine, University of Colorado-Anschutz Medical Campus, Aurora, CO, USA
- Section of Genetics and Metabolism, Department of Pediatrics, Children's Hospital Colorado, Aurora, CO, USA
| | - Robert C Kaplan
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Katrina G Claw
- Human Medical Genetics & Genomics Graduate Program, University of Colorado-Anschutz Medical Campus, Aurora, CO, USA
- Colorado Center for Personalized Medicine, University of Colorado-Anschutz Medical Campus, Aurora, CO, USA
- Department of Biomedical Informatics, University of Colorado-Anschutz Medical Campus, Aurora, CO, USA
| | - Christopher R Gignoux
- Human Medical Genetics & Genomics Graduate Program, University of Colorado-Anschutz Medical Campus, Aurora, CO, USA
- Colorado Center for Personalized Medicine, University of Colorado-Anschutz Medical Campus, Aurora, CO, USA
- Department of Biomedical Informatics, University of Colorado-Anschutz Medical Campus, Aurora, CO, USA
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