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Sun F, Li H, Sun D, Fu S, Gu L, Shao X, Wang Q, Dong X, Duan B, Xing F, Wu J, Xiao M, Zhao F, Han JDJ, Liu Q, Fan X, Li C, Wang C, Shi T. Single-cell omics: experimental workflow, data analyses and applications. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2561-0. [PMID: 39060615 DOI: 10.1007/s11427-023-2561-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/18/2024] [Indexed: 07/28/2024]
Abstract
Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular features. Our exploration of how the genomes orchestrate the formation and maintenance of each cell, and control the cellular phenotypes of various organismsis, is both captivating and intricate. Since the inception of the first single-cell RNA technology, technologies related to single-cell sequencing have experienced rapid advancements in recent years. These technologies have expanded horizontally to include single-cell genome, epigenome, proteome, and metabolome, while vertically, they have progressed to integrate multiple omics data and incorporate additional information such as spatial scRNA-seq and CRISPR screening. Single-cell omics represent a groundbreaking advancement in the biomedical field, offering profound insights into the understanding of complex diseases, including cancers. Here, we comprehensively summarize recent advances in single-cell omics technologies, with a specific focus on the methodology section. This overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.
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Affiliation(s)
- Fengying Sun
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China
| | - Haoyan Li
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Dongqing Sun
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Shaliu Fu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China
| | - Lei Gu
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xin Shao
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314103, China
| | - Qinqin Wang
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xin Dong
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Bin Duan
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China
| | - Feiyang Xing
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jun Wu
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Minmin Xiao
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China.
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, 100871, China.
| | - Qi Liu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China.
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China.
| | - Xiaohui Fan
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314103, China.
- Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China.
| | - Chen Li
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Chenfei Wang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Tieliu Shi
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China.
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
- Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE, School of Statistics, East China Normal University, Shanghai, 200062, China.
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Ginod P, Dahan MH. Preimplantation Genetic Testing for Polygenetic Conditions: A Legal, Ethical, and Scientific Challenge. Semin Reprod Med 2024; 42:60-68. [PMID: 38519038 DOI: 10.1055/s-0044-1782618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2024]
Abstract
The recent commercialization of the Embryo Health Score (EHS), determined through preimplantation genetic testing for polygenic conditions, offers the potential to select embryos with lower disease risk, thus potentially enhancing offspring longevity and health. Lately, Orchid Health company increased testing from less than 20 diseases to more than 900+ conditions for birth defects. However, the "geneticization" of phenotype estimates to a health state erases the environmental part, including the in vitro fertilization potential risks, questioning its scientific usefulness. EHS is utilized in countries with minimal regulatory oversight and will likely expand, while it remains illegal in other countries due to ethical and legal dilemmas it raises about reproductive autonomy, discrimination, impacts on family dynamics, and genetic diversity. The shift toward commercialized polygenic embryo screening (PES) redefines healthcare relationships, turning prospective parents into consumers and altering the physician's role. Moreover, PES could increase social inequalities, stigmatize those not born following PES, and encourage "desirable" phenotypic or behavioral traits selection, leading to ethical drift. Addressing these issues is essential before further implementation and requires a collaborative approach involving political, governmental, and public health, alongside geneticists, ethicists, and fertility specialists, focusing on the societal implications and acceptability of testing for polygenic traits for embryo selection.
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Affiliation(s)
- Perrine Ginod
- MUHC Reproductive Centre, McGill University, Montréal, Quebec, Canada
- CHU Dijon Bourgogne, Service de Gynécologie-Obstétrique et Assistance Médicale à la Procréation, Dijon, France
| | - Michael H Dahan
- MUHC Reproductive Centre, McGill University, Montréal, Quebec, Canada
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, McGill University, Montréal, Quebec, Canada
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Wu X, Pan J, Zhu Y, Huang H. Research progress and challenges of preimplantation genetic testing for polygenic diseases. Zhejiang Da Xue Xue Bao Yi Xue Ban 2023; 53:280-287. [PMID: 37987034 PMCID: PMC11348693 DOI: 10.3724/zdxbyxb-2023-0440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 10/29/2023] [Indexed: 11/22/2023]
Abstract
Preimplantation genetic testing is an important part in assisted reproductive technology, which can block the intergenerational inheritance of a single gene or chromosomal diseases. Preimplantation genetic testing for polygenic disease risk (PGT-P) is one of the latest developments in the field. With the development of artificial intelligence and genetic detection technology, PGT-P can be used to analyze genetic material, calculate polygenic risk scores and convert these into incidence probability. Embryos with relatively low incidence probability can be screened for transfer, in order to reduce the possibility that the offspring suffers from the disease in the future. This has significant clinical and social significance. At present, PGT-P has been applied clinically and made phased progress at home and abroad. But as a developing technology, PGT-P still has some technical limitations as unstable results, environmental influences and racial differences cannot be ruled out. From the ethical perspective, if the screening indications are not strictly regulated, it is likely to cause new social problems. In this paper, we review the technical details and recent progress in PGT-P, and discuss the prospects of its future development, especially how to establish a complete and suitable screening model for Chinese population.
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Affiliation(s)
- Xiaojing Wu
- Zhejiang University School of Medicine, Hangzhou 310058, China.
- Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China.
| | - Jiexue Pan
- Department of Reproductive Medicine, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200090, China
| | - Yimin Zhu
- Zhejiang University School of Medicine, Hangzhou 310058, China.
- Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China.
- Ministry of Education Key Laboratory of Reproductive Genetics, Department of Reproductive Endocrinology, Zhejiang University School of Medicine, Hangzhou 310006, China.
| | - Hefeng Huang
- Zhejiang University School of Medicine, Hangzhou 310058, China.
- Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310006, China.
- Department of Reproductive Medicine, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200090, China.
- Ministry of Education Key Laboratory of Reproductive Genetics, Department of Reproductive Endocrinology, Zhejiang University School of Medicine, Hangzhou 310006, China.
- Shanghai Key Laboratory of Embryo Original Diseases, Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai 200030, China.
- Institute of Reproduction and Development, Obstetrics and Gynecology Hospital, Fudan University, Shanghai 200030, China.
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Chang L, Jiao H, Chen J, Wu G, Liu P, Li R, Guo J, Long W, Tang X, Lu B, Xu H, Wu H. Single-cell whole-genome sequencing, haplotype analysis in prenatal diagnosis of monogenic diseases. Life Sci Alliance 2023; 6:e202201761. [PMID: 36810160 PMCID: PMC9947115 DOI: 10.26508/lsa.202201761] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 02/10/2023] [Accepted: 02/10/2023] [Indexed: 02/24/2023] Open
Abstract
Monogenic inherited diseases are common causes of congenital disabilities, leading to severe economic and mental burdens on affected families. In our previous study, we demonstrated the validity of cell-based noninvasive prenatal testing (cbNIPT) in prenatal diagnosis by single-cell targeted sequencing. The present research further explored the feasibility of single-cell whole-genome sequencing (WGS) and haplotype analysis of various monogenic diseases with cbNIPT. Four families were recruited: one with inherited deafness, one with hemophilia, one with large vestibular aqueduct syndrome (LVAS), and one with no disease. Circulating trophoblast cells (cTBs) were obtained from maternal blood and analyzed by single-cell 15X WGS. Haplotype analysis showed that CFC178 (deafness family), CFC616 (hemophilia family), and CFC111 (LVAS family) inherited haplotypes from paternal and/or maternal pathogenic loci. Amniotic fluid or fetal villi samples from the deafness and hemophilia families confirmed these results. WGS performed better than targeted sequencing in genome coverage, allele dropout (ADO), and false-positive (FP) ratios. Our findings suggest that cbNIPT by WGS and haplotype analysis have great potential for use in prenatally diagnosing various monogenic diseases.
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Affiliation(s)
- Liang Chang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Haining Jiao
- Department of Obstetrics and Gynecology, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiucheng Chen
- Unimed Biotech (Shanghai) Co., Ltd., Shanghai, China
| | - Guanlin Wu
- Unimed Biotech (Shanghai) Co., Ltd., Shanghai, China
| | - Ping Liu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Rong Li
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Jianying Guo
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Wenqing Long
- Department of Obstetrics and Gynecology, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaojian Tang
- Department of Obstetrics and Gynecology, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bingjie Lu
- Unimed Biotech (Shanghai) Co., Ltd., Shanghai, China
| | - Haibin Xu
- Unimed Biotech (Shanghai) Co., Ltd., Shanghai, China
| | - Han Wu
- Unimed Biotech (Shanghai) Co., Ltd., Shanghai, China
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Kumar A, Im K, Banjevic M, Ng PC, Tunstall T, Garcia G, Galhardo L, Sun J, Schaedel ON, Levy B, Hongo D, Kijacic D, Kiehl M, Tran ND, Klatsky PC, Rabinowitz M. Whole-genome risk prediction of common diseases in human preimplantation embryos. Nat Med 2022; 28:513-516. [PMID: 35314819 PMCID: PMC8938270 DOI: 10.1038/s41591-022-01735-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 02/04/2022] [Indexed: 12/14/2022]
Abstract
Preimplantation genetic testing (PGT) of in-vitro-fertilized embryos has been proposed as a method to reduce transmission of common disease; however, more comprehensive embryo genetic assessment, combining the effects of common variants and rare variants, remains unavailable. Here, we used a combination of molecular and statistical techniques to reliably infer inherited genome sequence in 110 embryos and model susceptibility across 12 common conditions. We observed a genotype accuracy of 99.0–99.4% at sites relevant to polygenic risk scoring in cases from day-5 embryo biopsies and 97.2–99.1% in cases from day-3 embryo biopsies. Combining rare variants with polygenic risk score (PRS) magnifies predicted differences across sibling embryos. For example, in a couple with a pathogenic BRCA1 variant, we predicted a 15-fold difference in odds ratio (OR) across siblings when combining versus a 4.5-fold or 3-fold difference with BRCA1 or PRS alone. Our findings may inform the discussion of utility and implementation of genome-based PGT in clinical practice. A computational approach combining whole-genome sequencing of parental genomes and genotyping of preimplantation embryos allows accurate prediction of the inherited genomes of embryos and calculation of polygenic risk scores.
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Affiliation(s)
| | - Kate Im
- MyOme, Inc., Menlo Park, CA, USA
| | | | | | | | | | | | | | | | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | | | | | | | - Nam D Tran
- Spring Fertility, San Francisco, CA, USA
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Wang X, Liu Y, Liu H, Pan W, Ren J, Zheng X, Tan Y, Chen Z, Deng Y, He N, Chen H, Li S. Recent advances and application of whole genome amplification in molecular diagnosis and medicine. MedComm (Beijing) 2022; 3:e116. [PMID: 35281794 PMCID: PMC8906466 DOI: 10.1002/mco2.116] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 11/30/2022] Open
Abstract
Whole genome amplification (WGA) is a technology for non-selective amplification of the whole genome sequence, first appearing in 1992. Its primary purpose is to amplify and reflect the whole genome of trace tissues and single cells without sequence bias and to provide sufficient DNA template for subsequent multigene and multilocus analysis, along with comprehensive genome research. WGA provides a method to obtain a large amount of genetic information from a small amount of DNA and provides a valuable tool for preserving limited samples in molecular biology. WGA technology is especially suitable for forensic identification and genetic disease research, along with new technologies such as next-generation sequencing (NGS). In addition, WGA is also widely used in single-cell sequencing. Due to the small amount of DNA in a single cell, it is often unable to meet the amount of samples needed for sequencing, so WGA is generally used to achieve the amplification of trace samples. This paper reviews WGA methods based on different principles, summarizes both amplification principle and amplification quality, and discusses the application prospects and challenges of WGA technology in molecular diagnosis and medicine.
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Affiliation(s)
- Xiaoyu Wang
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Yapeng Liu
- School of Early‐Childhood Education, Nanjing Xiaozhuang UniversityNanjingChina
| | - Hongna Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Wenjing Pan
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Jie Ren
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Xiangming Zheng
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Yimin Tan
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Nongyue He
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
- State Key Laboratory of BioelectronicsSoutheast UniversityNanjingChina
| | - Hui Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and DevicesHunan University of TechnologyZhuzhouChina
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8
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9
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Lencz T, Backenroth D, Granot-Hershkovitz E, Green A, Gettler K, Cho JH, Weissbrod O, Zuk O, Carmi S. Utility of polygenic embryo screening for disease depends on the selection strategy. eLife 2021; 10:e64716. [PMID: 34635206 PMCID: PMC8510582 DOI: 10.7554/elife.64716] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 08/09/2021] [Indexed: 12/13/2022] Open
Abstract
Polygenic risk scores (PRSs) have been offered since 2019 to screen in vitro fertilization embryos for genetic liability to adult diseases, despite a lack of comprehensive modeling of expected outcomes. Here we predict, based on the liability threshold model, the expected reduction in complex disease risk following polygenic embryo screening for a single disease. A strong determinant of the potential utility of such screening is the selection strategy, a factor that has not been previously studied. When only embryos with a very high PRS are excluded, the achieved risk reduction is minimal. In contrast, selecting the embryo with the lowest PRS can lead to substantial relative risk reductions, given a sufficient number of viable embryos. We systematically examine the impact of several factors on the utility of screening, including: variance explained by the PRS, number of embryos, disease prevalence, parental PRSs, and parental disease status. We consider both relative and absolute risk reductions, as well as population-averaged and per-couple risk reductions, and also examine the risk of pleiotropic effects. Finally, we confirm our theoretical predictions by simulating 'virtual' couples and offspring based on real genomes from schizophrenia and Crohn's disease case-control studies. We discuss the assumptions and limitations of our model, as well as the potential emerging ethical concerns.
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Affiliation(s)
- Todd Lencz
- Departments of Psychiatry and Molecular Medicine, Zucker School of Medicine at Hofstra/NorthwellHempsteadUnited States
- Department of Psychiatry, Division of Research, The Zucker Hillside Hospital Division of Northwell HealthGlen OaksUnited States
- Institute for Behavioral Science, The Feinstein Institutes for Medical ResearchManhassetUnited States
| | - Daniel Backenroth
- Braun School of Public Health and Community Medicine, The Hebrew University of JerusalemJerusalemIsrael
| | - Einat Granot-Hershkovitz
- Braun School of Public Health and Community Medicine, The Hebrew University of JerusalemJerusalemIsrael
| | - Adam Green
- Braun School of Public Health and Community Medicine, The Hebrew University of JerusalemJerusalemIsrael
| | - Kyle Gettler
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Judy H Cho
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount SinaiNew YorkUnited States
- Department of Medicine, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Omer Weissbrod
- Department of Epidemiology, Harvard T.H. Chan School of Public HealthBostonUnited States
| | - Or Zuk
- Department of Statistics and Data Science, The Hebrew University of JerusalemJerusalemIsrael
| | - Shai Carmi
- Braun School of Public Health and Community Medicine, The Hebrew University of JerusalemJerusalemIsrael
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Abstract
Over the past decade, genomic analyses of single cells-the fundamental units of life-have become possible. Single-cell DNA sequencing has shed light on biological questions that were previously inaccessible across diverse fields of research, including somatic mutagenesis, organismal development, genome function, and microbiology. Single-cell DNA sequencing also promises significant future biomedical and clinical impact, spanning oncology, fertility, and beyond. While single-cell approaches that profile RNA and protein have greatly expanded our understanding of cellular diversity, many fundamental questions in biology and important biomedical applications require analysis of the DNA of single cells. Here, we review the applications and biological questions for which single-cell DNA sequencing is uniquely suited or required. We include a discussion of the fields that will be impacted by single-cell DNA sequencing as the technology continues to advance.
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Affiliation(s)
- Gilad D Evrony
- Center for Human Genetics and Genomics, Grossman School of Medicine, New York University, New York, NY 10016, USA;
| | - Anjali Gupta Hinch
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom;
| | - Chongyuan Luo
- Department of Human Genetics, University of California, Los Angeles, California 90095, USA;
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11
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Tellier LCAM, Eccles J, Treff NR, Lello L, Fishel S, Hsu S. Embryo Screening for Polygenic Disease Risk: Recent Advances and Ethical Considerations. Genes (Basel) 2021; 12:1105. [PMID: 34440279 PMCID: PMC8393569 DOI: 10.3390/genes12081105] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/25/2021] [Accepted: 07/06/2021] [Indexed: 11/16/2022] Open
Abstract
Machine learning methods applied to large genomic datasets (such as those used in GWAS) have led to the creation of polygenic risk scores (PRSs) that can be used identify individuals who are at highly elevated risk for important disease conditions, such as coronary artery disease (CAD), diabetes, hypertension, breast cancer, and many more. PRSs have been validated in large population groups across multiple continents and are under evaluation for widespread clinical use in adult health. It has been shown that PRSs can be used to identify which of two individuals is at a lower disease risk, even when these two individuals are siblings from a shared family environment. The relative risk reduction (RRR) from choosing an embryo with a lower PRS (with respect to one chosen at random) can be quantified by using these sibling results. New technology for precise embryo genotyping allows more sophisticated preimplantation ranking with better results than the current method of selection that is based on morphology. We review the advances described above and discuss related ethical considerations.
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Affiliation(s)
- Laurent C. A. M. Tellier
- Department of Physics and Astronomy, Michigan State University, East Lansing, MI 48824, USA; (L.C.A.M.T.); (S.H.)
- Genomic Prediction, Inc., North Brunswick, NJ 08902, USA; (J.E.); (N.R.T.)
| | - Jennifer Eccles
- Genomic Prediction, Inc., North Brunswick, NJ 08902, USA; (J.E.); (N.R.T.)
| | - Nathan R. Treff
- Genomic Prediction, Inc., North Brunswick, NJ 08902, USA; (J.E.); (N.R.T.)
| | - Louis Lello
- Department of Physics and Astronomy, Michigan State University, East Lansing, MI 48824, USA; (L.C.A.M.T.); (S.H.)
- Genomic Prediction, Inc., North Brunswick, NJ 08902, USA; (J.E.); (N.R.T.)
| | - Simon Fishel
- CARE Fertility Group, Nottingham NG8 6PZ, UK;
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool L2 2QP, UK
| | - Stephen Hsu
- Department of Physics and Astronomy, Michigan State University, East Lansing, MI 48824, USA; (L.C.A.M.T.); (S.H.)
- Genomic Prediction, Inc., North Brunswick, NJ 08902, USA; (J.E.); (N.R.T.)
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12
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Lázaro-Muñoz G, Pereira S, Carmi S, Lencz T. Screening embryos for polygenic conditions and traits: ethical considerations for an emerging technology. Genet Med 2020; 23:432-434. [PMID: 33106616 PMCID: PMC7936952 DOI: 10.1038/s41436-020-01019-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/10/2020] [Accepted: 10/13/2020] [Indexed: 12/11/2022] Open
Affiliation(s)
- Gabriel Lázaro-Muñoz
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX, USA.
| | - Stacey Pereira
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX, USA
| | - Shai Carmi
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Todd Lencz
- Departments of Psychiatry and Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA.,Department of Psychiatry, Division of Research, The Zucker Hillside Hospital, Glen Oaks, NY, USA.,Institute for Behavioral Science, The Feinstein Institutes for Medical Research, Manhasset, NY, USA
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13
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de Melo-Martin I. Germline Gene Editing: Minding the Past and the Future. THE AMERICAN JOURNAL OF BIOETHICS : AJOB 2020; 20:36-38. [PMID: 32762628 DOI: 10.1080/15265161.2020.1782521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
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14
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Preimplantation Genetic Testing for Chromosomal Abnormalities: Aneuploidy, Mosaicism, and Structural Rearrangements. Genes (Basel) 2020; 11:genes11060602. [PMID: 32485954 PMCID: PMC7349251 DOI: 10.3390/genes11060602] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 05/25/2020] [Accepted: 05/27/2020] [Indexed: 12/18/2022] Open
Abstract
There is a high incidence of chromosomal abnormalities in early human embryos, whether they are generated by natural conception or by assisted reproductive technologies (ART). Cells with chromosomal copy number deviations or chromosome structural rearrangements can compromise the viability of embryos; much of the naturally low human fecundity as well as low success rates of ART can be ascribed to these cytogenetic defects. Chromosomal anomalies are also responsible for a large proportion of miscarriages and congenital disorders. There is therefore tremendous value in methods that identify embryos containing chromosomal abnormalities before intrauterine transfer to a patient being treated for infertility—the goal being the exclusion of affected embryos in order to improve clinical outcomes. This is the rationale behind preimplantation genetic testing for aneuploidy (PGT-A) and structural rearrangements (-SR). Contemporary methods are capable of much more than detecting whole chromosome abnormalities (e.g., monosomy/trisomy). Technical enhancements and increased resolution and sensitivity permit the identification of chromosomal mosaicism (embryos containing a mix of normal and abnormal cells), as well as the detection of sub-chromosomal abnormalities such as segmental deletions and duplications. Earlier approaches to screening for chromosomal abnormalities yielded a binary result of normal versus abnormal, but the new refinements in the system call for new categories, each with specific clinical outcomes and nuances for clinical management. This review intends to give an overview of PGT-A and -SR, emphasizing recent advances and areas of active development.
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15
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Ginoza MEC, Isasi R. Regulating Preimplantation Genetic Testing across the World: A Comparison of International Policy and Ethical Perspectives. Cold Spring Harb Perspect Med 2020; 10:cshperspect.a036681. [PMID: 31506325 DOI: 10.1101/cshperspect.a036681] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Preimplantation genetic testing (PGT) is a reproductive technology that, in the course of in vitro fertilization (IVF), allows prospective parents to select their future offspring based on genetic characteristics. PGT could be seen as an exercise of reproductive liberty, thus potentially raising significant socioethical and legal controversy. In this review, we examine-from a comparative perspective-variations in policy approaches to the regulation of PGT. We draw on a sample of 19 countries (Australia, Austria, Belgium, Brazil, Canada, China, France, Germany, India, Israel, Italy, Japan, Mexico, Netherlands, Singapore, South Korea, Switzerland, United Kingdom, and the United States) to provide a global landscape of the spectrum of policy and legislative approaches (e.g., restrictive to permissive, public vs. private models). We also explore central socioethical and policy issues and contentious applications, including permissibility criteria (e.g., medical necessity), nonmedical sex selection, and reproductive tourism. Finally, we further outline genetic counseling requirements across policy approaches.
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Affiliation(s)
| | - Rosario Isasi
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida 33136, USA
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16
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Murphy NM, Samarasekera TS, Macaskill L, Mullen J, Rombauts LJF. Genome sequencing of human in vitro fertilisation embryos for pathogenic variation screening. Sci Rep 2020; 10:3795. [PMID: 32123222 PMCID: PMC7052235 DOI: 10.1038/s41598-020-60704-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 02/13/2020] [Indexed: 12/22/2022] Open
Abstract
Whole-genome sequencing of preimplantation human embryos to detect and screen for genetic diseases is a technically challenging extension to preconception screening. Combining preconception genetic screening with preimplantation testing of human embryos facilitates the detection of de novo mutations and self-validates transmitted variant detection in both the reproductive couple and the embryo’s samples. Here we describe a trio testing workflow that involves whole-genome sequencing of amplified DNA from biopsied embryo trophectoderm cells and genomic DNA from both parents. Variant prediction software and annotation databases were used to assess variants of unknown significance and previously not described de novo variants in five single-gene preimplantation genetic testing couples and eleven of their embryos. Pathogenic variation, tandem repeat, copy number and structural variations were examined against variant calls for compound heterozygosity and predicted disease status was ascertained. Multiple trio testing showed complete concordance with known variants ascertained by single-nucleotide polymorphism array and uncovered de novo and transmitted pathogenic variants. This pilot study describes a method of whole-genome sequencing and analysis for embryo selection in high-risk couples to prevent early life fatal genetic conditions that adversely affect the quality of life of the individual and families.
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Affiliation(s)
- Nicholas M Murphy
- Genetic Technologies Ltd., Victoria, Australia. .,Monash IVF, Clayton, Victoria, Australia. .,GenEmbryomics Pty. Ltd., Victoria, Australia. .,Drug Delivery Disposition and Dynamics, Faculty of Pharmacy and Pharmaceutical Sciences, Parkville, Melbourne, Victoria, Australia.
| | | | | | | | - Luk J F Rombauts
- Monash IVF, Clayton, Victoria, Australia.,Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Obstetrics and Gynaecology, Monash University, Clayton, Victoria, Australia.,Monash Women's & Newborn Program, Monash Health, Victoria, Australia
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17
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Genomic Medicine-Progress, Pitfalls, and Promise. Cell 2020; 177:45-57. [PMID: 30901547 DOI: 10.1016/j.cell.2019.02.003] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 01/31/2019] [Accepted: 02/01/2019] [Indexed: 02/07/2023]
Abstract
In the wake of the Human Genome Project (HGP), strong expectations were set for the timeline and impact of genomics on medicine-an anticipated transformation in the diagnosis, treatment, and prevention of disease. In this Perspective, we take stock of the nascent field of genomic medicine. In what areas, if any, is genomics delivering on this promise, or is the path to success clear? Where are we falling short, and why? What have been the unanticipated developments? Overall, we argue that the optimism surrounding the transformational potential of genomics on medicine remains justified, albeit with a considerably different form and timescale than originally projected. We also argue that the field needs to pivot back to basics, as understanding the entirety of the genotype-to-phenotype equation is a likely prerequisite for delivering on the full potential of the human genome to advance the human condition.
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18
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Yan Z, Zhu X, Wang Y, Nie Y, Guan S, Kuo Y, Chang D, Li R, Qiao J, Yan L. scHaplotyper: haplotype construction and visualization for genetic diagnosis using single cell DNA sequencing data. BMC Bioinformatics 2020; 21:41. [PMID: 32007105 PMCID: PMC6995221 DOI: 10.1186/s12859-020-3381-5] [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: 10/07/2019] [Accepted: 01/22/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Haplotyping reveals chromosome blocks inherited from parents to in vitro fertilized (IVF) embryos in preimplantation genetic diagnosis (PGD), enabling the observation of the transmission of disease alleles between generations. However, the methods of haplotyping that are suitable for single cells are limited because a whole genome amplification (WGA) process is performed before sequencing or genotyping in PGD, and true haplotype profiles of embryos need to be constructed based on genotypes that can contain many WGA artifacts. RESULTS Here, we offer scHaplotyper as a genetic diagnosis tool that reconstructs and visualizes the haplotype profiles of single cells based on the Hidden Markov Model (HMM). scHaplotyper can trace the origin of each haplotype block in the embryo, enabling the detection of carrier status of disease alleles in each embryo. We applied this method in PGD in two families affected with genetic disorders, and the result was the healthy live births of two children in the two families, demonstrating the clinical application of this method. CONCLUSION Next generation sequencing (NGS) of preimplantation embryos enable genetic screening for families with genetic disorders, avoiding the birth of affected babies. With the validation and successful clinical application, we showed that scHaplotyper is a convenient and accurate method to screen out embryos. More patients with genetic disorder will benefit from the genetic diagnosis of embryos. The source code of scHaplotyper is available at GitHub repository: https://github.com/yzqheart/scHaplotyper.
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Affiliation(s)
- Zhiqiang Yan
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, 100191, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Xiaohui Zhu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, 100191, China
| | - Yuqian Wang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, 100191, China
| | - Yanli Nie
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, 100191, China
| | - Shuo Guan
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, 100191, China
| | - Ying Kuo
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, 100191, China
| | - Di Chang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, 100191, China
| | - Rong Li
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, 100191, China
| | - Jie Qiao
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, 100191, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China.,Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, 100871, China
| | - Liying Yan
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, China. .,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing, 100191, China. .,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproduction, Beijing, 100191, China.
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19
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Karavani E, Zuk O, Zeevi D, Barzilai N, Stefanis NC, Hatzimanolis A, Smyrnis N, Avramopoulos D, Kruglyak L, Atzmon G, Lam M, Lencz T, Carmi S. Screening Human Embryos for Polygenic Traits Has Limited Utility. Cell 2019; 179:1424-1435.e8. [PMID: 31761530 PMCID: PMC6957074 DOI: 10.1016/j.cell.2019.10.033] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 09/11/2019] [Accepted: 10/25/2019] [Indexed: 12/19/2022]
Abstract
The increasing proportion of variance in human complex traits explained by polygenic scores, along with progress in preimplantation genetic diagnosis, suggests the possibility of screening embryos for traits such as height or cognitive ability. However, the expected outcomes of embryo screening are unclear, which undermines discussion of associated ethical concerns. Here, we use theory, simulations, and real data to evaluate the potential gain of embryo screening, defined as the difference in trait value between the top-scoring embryo and the average embryo. The gain increases very slowly with the number of embryos but more rapidly with the variance explained by the score. Given current technology, the average gain due to screening would be ≈2.5 cm for height and ≈2.5 IQ points for cognitive ability. These mean values are accompanied by wide prediction intervals, and indeed, in large nuclear families, the majority of children top-scoring for height are not the tallest.
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Affiliation(s)
- Ehud Karavani
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Or Zuk
- Department of Statistics, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel
| | - Danny Zeevi
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Nir Barzilai
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Genetics, Institute for Aging Research, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Nikos C Stefanis
- Department of Psychiatry, National and Kapodistrian University of Athens Medical School, Eginition Hospital, 115 28 Athens, Greece; University Mental Health Research Institute, 115 27 Athens, Greece; Neurobiology Research Institute, Theodor-Theohari Cozzika Foundation, 115 21 Athens, Greece
| | - Alex Hatzimanolis
- Department of Psychiatry, National and Kapodistrian University of Athens Medical School, Eginition Hospital, 115 28 Athens, Greece; Neurobiology Research Institute, Theodor-Theohari Cozzika Foundation, 115 21 Athens, Greece
| | - Nikolaos Smyrnis
- Department of Psychiatry, National and Kapodistrian University of Athens Medical School, Eginition Hospital, 115 28 Athens, Greece; University Mental Health Research Institute, 115 27 Athens, Greece
| | - Dimitrios Avramopoulos
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Leonid Kruglyak
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Gil Atzmon
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Genetics, Institute for Aging Research, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Biology, Faculty of Natural Sciences, University of Haifa, Haifa 3498838, Israel
| | - Max Lam
- Division of Psychiatry Research, Zucker Hillside Hospital, Glen Oaks, NY 11004, USA; Institute of Behavioral Science, Feinstein Institutes of Medical Research, Manhasset, NY 11030, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Todd Lencz
- Division of Psychiatry Research, Zucker Hillside Hospital, Glen Oaks, NY 11004, USA; Institute of Behavioral Science, Feinstein Institutes of Medical Research, Manhasset, NY 11030, USA; Department of Psychiatry, 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 9112102, Israel.
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20
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McCoy RC, Newnham LJ, Ottolini CS, Hoffmann ER, Chatzimeletiou K, Cornejo OE, Zhan Q, Zaninovic N, Rosenwaks Z, Petrov DA, Demko ZP, Sigurjonsson S, Handyside AH. Tripolar chromosome segregation drives the association between maternal genotype at variants spanning PLK4 and aneuploidy in human preimplantation embryos. Hum Mol Genet 2019; 27:2573-2585. [PMID: 29688390 DOI: 10.1093/hmg/ddy147] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/18/2018] [Indexed: 12/22/2022] Open
Abstract
Aneuploidy is prevalent in human embryos and is the leading cause of pregnancy loss. Many aneuploidies arise during oogenesis, increasing with maternal age. Superimposed on these meiotic aneuploidies are frequent errors occurring during early mitotic divisions, contributing to widespread chromosomal mosaicism. Here we reanalyzed a published dataset comprising preimplantation genetic testing for aneuploidy in 24 653 blastomere biopsies from day-3 cleavage-stage embryos, as well as 17 051 trophectoderm biopsies from day-5 blastocysts. We focused on complex abnormalities that affected multiple chromosomes simultaneously, seeking insights into their formation. In addition to well-described patterns such as triploidy and haploidy, we identified 4.7% of blastomeres possessing characteristic hypodiploid karyotypes. We inferred this signature to have arisen from tripolar chromosome segregation in normally fertilized diploid zygotes or their descendant diploid cells. This could occur via segregation on a tripolar mitotic spindle or by rapid sequential bipolar mitoses without an intervening S-phase. Both models are consistent with time-lapse data from an intersecting set of 77 cleavage-stage embryos, which were enriched for the tripolar signature among embryos exhibiting abnormal cleavage. The tripolar signature was strongly associated with common maternal genetic variants spanning the centrosomal regulator PLK4, driving the association we previously reported with overall mitotic errors. Our findings are consistent with the known capacity of PLK4 to induce tripolar mitosis or precocious M-phase upon dysregulation. Together, our data support tripolar chromosome segregation as a key mechanism generating complex aneuploidy in cleavage-stage embryos and implicate maternal genotype at a quantitative trait locus spanning PLK4 as a factor influencing its occurrence.
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Affiliation(s)
- Rajiv C McCoy
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.,Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Louise J Newnham
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | | | - Eva R Hoffmann
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK.,Department of Cellular and Molecular Medicine, DNRF Center for Chromosome Stability, University of Copenhagen, Copenhagen N, Denmark
| | - Katerina Chatzimeletiou
- Section of Reproductive Medicine, First Department of Obstetrics & Gynaecology, Aristotle University Medical School, Papageorgiou General Hospital, Thessaloniki, Greece
| | - Omar E Cornejo
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Qiansheng Zhan
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Nikica Zaninovic
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Zev Rosenwaks
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, CA, USA
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21
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Backenroth D, Zahdeh F, Kling Y, Peretz A, Rosen T, Kort D, Zeligson S, Dror T, Kirshberg S, Burak E, Segel R, Levy-Lahad E, Zangen D, Altarescu G, Carmi S, Zeevi DA. Haploseek: a 24-hour all-in-one method for preimplantation genetic diagnosis (PGD) of monogenic disease and aneuploidy. Genet Med 2018; 21:1390-1399. [DOI: 10.1038/s41436-018-0351-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 10/25/2018] [Indexed: 11/09/2022] Open
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22
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Zhu W, Zhang XY, Marjani SL, Zhang J, Zhang W, Wu S, Pan X. Next-generation molecular diagnosis: single-cell sequencing from bench to bedside. Cell Mol Life Sci 2017; 74:869-880. [PMID: 27738745 PMCID: PMC11107533 DOI: 10.1007/s00018-016-2368-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 08/31/2016] [Accepted: 09/14/2016] [Indexed: 02/05/2023]
Abstract
Single-cell sequencing (SCS) is a fast-growing, exciting field in genomic medicine. It enables the high-resolution study of cellular heterogeneity, and reveals the molecular basis of complicated systems, which facilitates the identification of new biomarkers for diagnosis and for targeting therapies. It also directly promotes the next generation of genomic medicine because of its ultra-high resolution and sensitivity that allows for the non-invasive and early detection of abnormalities, such as aneuploidy, chromosomal translocation, and single-gene disorders. This review provides an overview of the current progress and prospects for the diagnostic applications of SCS, specifically in pre-implantation genetic diagnosis/screening, non-invasive prenatal diagnosis, and analysis of circulating tumor cells. These analyses will accelerate the early and precise control of germline- or somatic-mutation-based diseases, particularly single-gene disorders, chromosome abnormalities, and cancers.
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Affiliation(s)
- Wanjun Zhu
- Department of Genetics, School of Medicine, Yale University, New Haven, CT, 06520, USA
- College of Veterinary Medicine, University of Minnesota, Twin Cities, Saint Paul, MN, 55108, USA
| | - Xiao-Yan Zhang
- Hangzhou Cancer Institution, Hangzhou Cancer Hospital, Hangzhou, 310002, Zhejiang, People's Republic of China
| | - Sadie L Marjani
- Department of Biology, Central Connecticut State University, New Britain, CT, 06050, USA
| | - Jialing Zhang
- Department of Genetics, School of Medicine, Yale University, New Haven, CT, 06520, USA
| | - Wengeng Zhang
- Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Shixiu Wu
- Hangzhou Cancer Institution, Hangzhou Cancer Hospital, Hangzhou, 310002, Zhejiang, People's Republic of China.
| | - Xinghua Pan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Guangdong Province Key Laboratory of Biochip Technology, Southern Medical University, Guangzhou, 510515, Guangdong, People's Republic of China.
- Department of Genetics, School of Medicine, Yale University, New Haven, CT, 06520, USA.
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23
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Abstract
Genome editing allows for the versatile genetic modification of somatic cells, germ cells and embryos. In particular, CRISPR/Cas9 is worldwide used in biomedical research. Although the first report on Cas9-mediated gene modification in human embryos focused on the prevention of a genetic disease in offspring, it raised profound ethical and social concerns over the safety of subsequent generations and the potential misuse of genome editing for human enhancement. The present article considers germ line genome editing approaches from various clinical and ethical viewpoints and explores its objectives. The risks and benefits of the following three likely objectives are assessed: the prevention of monogenic diseases, personalized assisted reproductive technology (ART) and genetic enhancement. Although genetic enhancement should be avoided, the international regulatory landscape suggests the inevitability of this misuse at ART centers. Under these circumstances, possible regulatory responses and the potential roles of public dialogue are discussed.
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24
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Araki M, Ishii T. Providing Appropriate Risk Information on Genome Editing for Patients. Trends Biotechnol 2016; 34:86-90. [PMID: 26802361 DOI: 10.1016/j.tibtech.2015.12.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 10/14/2015] [Accepted: 12/07/2015] [Indexed: 12/25/2022]
Abstract
Genome editing, represented by CRISPR/Cas9, facilitates somatic and germline gene modifications in many species, including humans. However, one of key issues, off-target mutation deserves special consideration prior to clinical applications. We herein discuss the importance of risk information on genome editing for obtaining legitimate patient consent and social acceptance.
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Affiliation(s)
- Motoko Araki
- Office of Health and Safety, Hokkaido University, Sapporo Hokkaido, 060-0808, Japan
| | - Tetsuya Ishii
- Office of Health and Safety, Hokkaido University, Sapporo Hokkaido, 060-0808, Japan.
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25
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Breman AM, Chow JC, U'Ren L, Normand EA, Qdaisat S, Zhao L, Henke DM, Chen R, Shaw CA, Jackson L, Yang Y, Vossaert L, Needham RHV, Chang EJ, Campton D, Werbin JL, Seubert RC, Van den Veyver IB, Stilwell JL, Kaldjian EP, Beaudet AL. Evidence for feasibility of fetal trophoblastic cell-based noninvasive prenatal testing. Prenat Diagn 2016; 36:1009-1019. [PMID: 27616633 PMCID: PMC5129580 DOI: 10.1002/pd.4924] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 08/09/2016] [Accepted: 09/05/2016] [Indexed: 12/13/2022]
Abstract
Objective The goal was to develop methods for detection of chromosomal and subchromosomal abnormalities in fetal cells in the mother's circulation at 10–16 weeks' gestation using analysis by array comparative genomic hybridization (CGH) and/or next‐generation sequencing (NGS). Method Nucleated cells from 30 mL of blood collected at 10–16 weeks' gestation were separated from red cells by density fractionation and then immunostained to identify cytokeratin positive and CD45 negative trophoblasts. Individual cells were picked and subjected to whole genome amplification, genotyping, and analysis by array CGH and NGS. Results Fetal cells were recovered from most samples as documented by Y chromosome PCR, short tandem repeat analysis, array CGH, and NGS including over 30 normal male cells, one 47,XXY cell from an affected fetus, one trisomy 18 cell from an affected fetus, nine cells from a trisomy 21 case, three normal cells and one trisomy 13 cell from a case with confined placental mosaicism, and two chromosome 15 deletion cells from a case known by CVS to have a 2.7 Mb de novo deletion. Conclusion We believe that this is the first report of using array CGH and NGS whole genome sequencing to detect chromosomal abnormalities in fetal trophoblastic cells from maternal blood. © 2016 The Authors. Prenatal Diagnosis published by John Wiley & Sons, Ltd. What's already known about this topic?
Analysis of cell‐free DNA for noninvasive prenatal testing (NIPT) is widely practiced, and the frequency of amniocentesis and CVS has decreased. However, cell‐free NIPT is not adequate for detecting smaller deletions and duplications with high specificity, sensitivity, and positive predictive value. Although fetal nucleated red blood cells and trophoblastic cells are known to be present in the maternal circulation, it has not been possible to develop a reliable cytogenetic cell‐based form of NIPT.
What does this study add?
Fetal cytotrophoblasts were successfully recovered from maternal blood. Although a clinical test has not been validated, for the first time, the feasibility of using array comparative genomic hybridization and next generation sequencing to detect chromosomal and subchromosomal abnormalities is demonstrated. The results suggest the possibility of developing a cell‐based form of NIPT with ability to detect abnormalities with a similar accuracy as can currently be obtained with amniocentesis and CVS.
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Affiliation(s)
- Amy M Breman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | | | - Elizabeth A Normand
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sadeem Qdaisat
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Li Zhao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - David M Henke
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Laird Jackson
- Department of Obstetrics and Gynecology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Liesbeth Vossaert
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | | | | | | | | | - Ignatia B Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, USA.,Texas Children's Hospital, Houston, TX, USA
| | | | | | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Texas Children's Hospital, Houston, TX, USA
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Beaudet AL. Using fetal cells for prenatal diagnosis: History and recent progress. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2016; 172:123-7. [PMID: 27133782 DOI: 10.1002/ajmg.c.31487] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The potential to use fetal cells in the mother's circulation during the first or second trimester for prenatal diagnosis was described in 1968, but it has not been possible do develop a routine clinical prenatal test despite extensive commercial and academic research efforts. Early attention focused on the detection of aneuploidy, but more recent technology opens the possibility of high resolution detection of copy number abnormalities and even whole genome or exome sequencing to detect both inherited and de novo mutations. In the interim, cell-free noninvasive prenatal testing NIPT has allowed improved detection of aneuploidy, but this has led to a sharp reduction in the number of amniocentesis and chorionic villus sampling (CVS) procedures, which inevitably implies reduced detection of serious de novo deletion abnormalities. Attention has focused of both fetal nucleated red blood cells (fnRBCs) and trophoblasts. Recent progress presented at meetings, but not yet published, suggests that it will soon be possible to perform genome-wide relatively high resolution detection of deletions and duplications by recovering fetal trophoblasts during the first trimester and analyzing them by whole gene genome amplification followed by copy number analysis using arrays or next generation sequencing. © 2016 Wiley Periodicals, Inc.
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