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Kakourou G, Sofocleous C, Mamas T, Vrettou C, Traeger-Synodinos J. The current clinical applications of preimplantation genetic testing (PGT): acknowledging the limitations of biology and technology. Expert Rev Mol Diagn 2024:1-9. [PMID: 39107971 DOI: 10.1080/14737159.2024.2390187] [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: 01/20/2024] [Accepted: 08/05/2024] [Indexed: 08/13/2024]
Abstract
INTRODUCTION Preimplantation Genetic Testing (PGT) is a cutting-edge test used to detect genetic abnormalities in embryos fertilized through Medically Assisted Reproduction (MAR). PGT aims to ensure that embryos selected for transfer are free of specific genetic conditions or chromosome abnormalities, thereby reducing chances for unsuccessful MAR cycles, complicated pregnancies, and genetic diseases in future children. AREAS COVERED In PGT, genetics, embryology, and technology progress and evolve together. Biological and technological limitations are described and addressed to highlight complexity and knowledge constraints and draw attention to concerns regarding safety of procedures, clinical validity, and utility, extent of applications and overall ethical implications for future families and society. EXPERT OPINION Understanding the genetic basis of diseases along with advanced technologies applied in embryology and genetics contribute to faster, cost-effective, and more efficient PGT. Next Generation Sequencing-based techniques, enhanced by improved bioinformatics, are expected to upgrade diagnostic accuracy. Complicating findings such as mosaicism, mt-DNA variants, variants of unknown significance, or variants related to late-onset or polygenic diseases will however need further appraisal. Emphasis on monitoring such emerging data is crucial for evidence-based counseling while standardized protocols and guidelines are essential to ensure clinical value and respect of Ethical, Legal and Societal Issues.
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Affiliation(s)
- Georgia Kakourou
- Laboratory of Medical Genetics, Medical School, National and Kapodistrian University of Athens, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Christalena Sofocleous
- Laboratory of Medical Genetics, Medical School, National and Kapodistrian University of Athens, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Thalia Mamas
- Laboratory of Medical Genetics, Medical School, National and Kapodistrian University of Athens, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Christina Vrettou
- Laboratory of Medical Genetics, Medical School, National and Kapodistrian University of Athens, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Joanne Traeger-Synodinos
- Laboratory of Medical Genetics, Medical School, National and Kapodistrian University of Athens, "Aghia Sophia" Children's Hospital, Athens, Greece
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2
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Zhang S, Pei Z, Xiao M, Zhou J, Hu B, Zhu S, Sun X, Wu J, Lei C, Xu C. Comprehensive preimplantation genetic testing for balanced insertional translocation carriers. J Med Genet 2024; 61:794-802. [PMID: 38802138 DOI: 10.1136/jmg-2024-109851] [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: 01/03/2024] [Accepted: 05/12/2024] [Indexed: 05/29/2024]
Abstract
BACKGROUND Balanced insertional translocations (BITs) can increase the risk of infertility, recurrent miscarriages or neonatal birth defects due to chromosomal imbalances in gametes. However, studies on preimplantation genetic testing (PGT) for patients carrying BITs are inadequate. METHODS A preimplantation genetic genotyping and haplotype analysis approach was developed and implemented in this study. Genome-wide SNP genotyping was performed, followed by core family-based haplotype analysis. The balanced insertion segments in euploid embryos were inferred from the haplotypes inherited from the carrier parent. RESULTS A total of 10 BIT carrier couples were enrolled in our study. 15 in vitro fertilisation cycles were conducted, resulting in 73 blastocysts biopsied and subjected to PGT analysis. Among these, 20 blastocysts displayed rearrangement-related imbalances, 13 exhibited de novo aneuploidies, 15 presented a complex anomaly involving both imbalances and additional aneuploidies, while 25 were euploid. Within the euploid embryos, 12 were balanced carrier embryos and 13 were non-carrier embryos. To date, eight non-carrier and one carrier embryos have been transferred, resulting in seven clinical pregnancies. All pregnancies were recommended to perform prenatal diagnosis, our date revealed complete concordance between fetal genetic testing results and PGT results. Presently, five infants have been born from these pregnancies, and two pregnancies are still ongoing. CONCLUSION The proposed method facilitates comprehensive chromosome screening and the concurrent identification of balanced insertions or normal karyotypes in embryos. This study offers an effective and universally applicable strategy for BIT carriers to achieve a healthy pregnancy and prevent the transmission of BITs to their offspring.
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Affiliation(s)
- Shuo Zhang
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, Shanghai, China
| | - Zhenle Pei
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, Shanghai, China
| | - Min Xiao
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, Shanghai, China
| | - Jing Zhou
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, Shanghai, China
| | - Bin Hu
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, Shanghai, China
| | - Saijuan Zhu
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, Shanghai, China
| | - Xiaoxi Sun
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, Shanghai, China
- Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, Shanghai, China
| | - Junping Wu
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, Shanghai, China
| | - Caixia Lei
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, Shanghai, China
| | - Congjian Xu
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, Shanghai, China
- Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, Shanghai, China
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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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Ariad D, Madjunkova S, Madjunkov M, Chen S, Abramov R, Librach C, McCoy RC. Aberrant landscapes of maternal meiotic crossovers contribute to aneuploidies in human embryos. Genome Res 2024; 34:70-84. [PMID: 38071472 PMCID: PMC10903951 DOI: 10.1101/gr.278168.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 11/21/2023] [Indexed: 12/19/2023]
Abstract
Meiotic recombination is crucial for human genetic diversity and chromosome segregation accuracy. Understanding its variation across individuals and the processes by which it goes awry are long-standing goals in human genetics. Current approaches for inferring recombination landscapes rely either on population genetic patterns of linkage disequilibrium (LD)-capturing a time-averaged view-or on direct detection of crossovers in gametes or multigeneration pedigrees, which limits data set scale and availability. Here, we introduce an approach for inferring sex-specific recombination landscapes using data from preimplantation genetic testing for aneuploidy (PGT-A). This method relies on low-coverage (<0.05×) whole-genome sequencing of in vitro fertilized (IVF) embryo biopsies. To overcome the data sparsity, our method exploits its inherent relatedness structure, knowledge of haplotypes from external population reference panels, and the frequent occurrence of monosomies in embryos, whereby the remaining chromosome is phased by default. Extensive simulations show our method's high accuracy, even at coverages as low as 0.02×. Applying this method to PGT-A data from 18,967 embryos, we mapped 70,660 recombination events with ∼150 kbp resolution, replicating established sex-specific recombination patterns. We observed a reduced total length of the female genetic map in trisomies compared with disomies, as well as chromosome-specific alterations in crossover distributions. Based on haplotype configurations in pericentromeric regions, our data indicate chromosome-specific propensities for different mechanisms of meiotic error. Our results provide a comprehensive view of the role of aberrant meiotic recombination in the origins of human aneuploidies and offer a versatile tool for mapping crossovers in low-coverage sequencing data from multiple siblings.
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Affiliation(s)
- Daniel Ariad
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA;
| | - Svetlana Madjunkova
- CReATe Fertility Centre, Toronto, Ontario M5G 1N8, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | | | - Siwei Chen
- CReATe Fertility Centre, Toronto, Ontario M5G 1N8, Canada
| | - Rina Abramov
- CReATe Fertility Centre, Toronto, Ontario M5G 1N8, Canada
| | - Clifford Librach
- CReATe Fertility Centre, Toronto, Ontario M5G 1N8, Canada
- Department of Obstetrics and Gynecology, University of Toronto, Toronto, Ontario M5G 1E2, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Rajiv C McCoy
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA;
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De Coster T, Zhao Y, Tšuiko O, Demyda-Peyrás S, Van Soom A, Vermeesch JR, Smits K. Genome-wide equine preimplantation genetic testing enabled by simultaneous haplotyping and copy number detection. Sci Rep 2024; 14:2003. [PMID: 38263320 PMCID: PMC10805710 DOI: 10.1038/s41598-023-48103-7] [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: 06/28/2023] [Accepted: 11/22/2023] [Indexed: 01/25/2024] Open
Abstract
In different species, embryonic aneuploidies and genome-wide errors are a major cause of developmental failure. The increasing number of equine embryos being produced worldwide provides the opportunity to characterize and rank or select embryos based on their genetic profile prior to transfer. Here, we explored the possibility of generic, genome-wide preimplantation genetic testing concurrently for aneuploidies (PGT-A) and monogenic (PGT-M) traits and diseases in the horse, meanwhile assessing the incidence and spectrum of chromosomal and genome-wide errors in in vitro-produced equine embryos. To this end, over 70,000 single nucleotide polymorphism (SNP) positions were genotyped in 14 trophectoderm biopsies and corresponding biopsied blastocysts, and in 26 individual blastomeres from six arrested cleavage-stage embryos. Subsequently, concurrent genome-wide copy number detection and haplotyping by haplarithmisis was performed and the presence of aneuploidies and genome-wide errors and the inherited parental haplotypes for four common disease-associated genes with high carrier frequency in different horse breeds (GBE1, PLOD1, B3GALNT2, MUTYH), and for one color coat-associated gene (STX17) were compared in biopsy-blastocyst combinations. The euploid (n = 12) or fully aneuploid (n = 2) state and the inherited parental haplotypes for 42/45 loci of interest of the biopsied blastocysts were predicted by the biopsy samples in all successfully analyzed biopsy-blastocyst combinations (n = 9). Two biopsies showed a loss of maternal chromosome 28 and 31, respectively, which were confirmed in the corresponding blastocysts. In one of those biopsies, additional complex aneuploidies not present in the blastocyst were found. Five out of six arrested embryos contained chromosomal and/or genome-wide errors in most of their blastomeres, demonstrating their contribution to equine embryonic arrest in vitro. The application of the described PGT strategy would allow to select equine embryos devoid of genetic errors and pathogenetic variants, and with the variants of interest, which will improve foaling rate and horse quality. We believe this approach will be a gamechanger in horse breeding.
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Affiliation(s)
- T De Coster
- Department of Internal Medicine, Reproduction and Population Medicine, Ghent University, Merelbeke, Belgium.
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
| | - Y Zhao
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - O Tšuiko
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - S Demyda-Peyrás
- Department of Genetics, University of Córdoba, Córdoba, Spain
- Department of Animal Production, Veterinary School, National University of La Plata, La Plata, Argentina
| | - A Van Soom
- Department of Internal Medicine, Reproduction and Population Medicine, Ghent University, Merelbeke, Belgium
| | - J R Vermeesch
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - K Smits
- Department of Internal Medicine, Reproduction and Population Medicine, Ghent University, Merelbeke, Belgium.
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Hornak M, Bezdekova K, Kubicek D, Navratil R, Hola V, Balcova M, Bohmova M, Weisova K, Vesela K. OneGene PGT: comprehensive preimplantation genetic testing method utilizing next-generation sequencing. J Assist Reprod Genet 2024; 41:185-192. [PMID: 38062333 PMCID: PMC10789686 DOI: 10.1007/s10815-023-02998-3] [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: 05/11/2023] [Accepted: 11/24/2023] [Indexed: 01/17/2024] Open
Abstract
PURPOSE Preimplantation genetic testing for monogenic disorders (PGT-M) allows early diagnosis in embryos conceived in vitro. PGT-M helps to prevent known genetic disorders in affected families and ensures that pathogenic variants in the male or female partner are not passed on to offspring. The trend in genetic testing of embryos is to provide a comprehensive platform that enables robust and reliable testing for the causal pathogenic variant(s), as well as chromosomal abnormalities that commonly occur in embryos. In this study, we describe PGT protocol that allows direct mutation testing, haplotyping, and aneuploidy screening. METHODS Described PGT protocol called OneGene PGT allows direct mutation testing, haplotyping, and aneuploidy screening using next-generation sequencing (NGS). Whole genome amplification product is combined with multiplex PCR used for SNP enrichment. Dedicated bioinformatic tool enables mapping, genotype calling, and haplotyping of informative SNP markers. A commercial software was used for aneuploidy calling. RESULTS OneGenePGT has been implemented for seven of the most common monogenic disorders, representing approximately 30% of all PGT-M indications at our IVF centre. The technique has been thoroughly validated, focusing on direct pathogenic variant testing, haplotype identification, and chromosome abnormality detection. Validation results show full concordance with Sanger sequencing and karyomapping, which were used as reference methods. CONCLUSION OneGene PGT is a comprehensive, robust, and cost-effective method that can be established for any gene of interest. The technique is particularly suitable for common monogenic diseases, which can be performed based on a universal laboratory protocol without the need for set-up or pre-testing.
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Affiliation(s)
| | | | - David Kubicek
- REPROMEDA, Studentska 812/6, 625 00, Brno, Czech Republic
| | | | - Veronika Hola
- REPROMEDA, Studentska 812/6, 625 00, Brno, Czech Republic
| | - Maria Balcova
- REPROMEDA, Studentska 812/6, 625 00, Brno, Czech Republic
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Ariad D, Madjunkova S, Madjunkov M, Chen S, Abramov R, Librach C, McCoy RC. Aberrant landscapes of maternal meiotic crossovers contribute to aneuploidies in human embryos. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.07.543910. [PMID: 37333422 PMCID: PMC10274764 DOI: 10.1101/2023.06.07.543910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Meiotic recombination is crucial for human genetic diversity and chromosome segregation accuracy. Understanding its variation across individuals and the processes by which it goes awry are long-standing goals in human genetics. Current approaches for inferring recombination landscapes either rely on population genetic patterns of linkage disequilibrium (LD)-capturing a time-averaged view-or direct detection of crossovers in gametes or multi-generation pedigrees, which limits dataset scale and availability. Here, we introduce an approach for inferring sex-specific recombination landscapes using data from preimplantation genetic testing for aneuploidy (PGT-A). This method relies on low-coverage (<0.05×) whole-genome sequencing of in vitro fertilized (IVF) embryo biopsies. To overcome the data sparsity, our method exploits its inherent relatedness structure, knowledge of haplotypes from external population reference panels, as well as the frequent occurrence of monosomies in embryos, whereby the remaining chromosome is phased by default. Extensive simulations demonstrate our method's high accuracy, even at coverages as low as 0.02×. Applying this method to PGT-A data from 18,967 embryos, we mapped 70,660 recombination events with ~150 kbp resolution, replicating established sex-specific recombination patterns. We observed a reduced total length of the female genetic map in trisomies compared to disomies, as well as chromosome-specific alterations in crossover distributions. Based on haplotype configurations in pericentromeric regions, our data indicate chromosome-specific propensities for different mechanisms of meiotic error. Our results provide a comprehensive view of the role of aberrant meiotic recombination in the origins of human aneuploidies and offer a versatile tool for mapping crossovers in low-coverage sequencing data from multiple siblings.
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Affiliation(s)
- Daniel Ariad
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Svetlana Madjunkova
- CReATe Fertility Centre, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | | | - Siwei Chen
- CReATe Fertility Centre, Toronto, Canada
| | | | - Clifford Librach
- CReATe Fertility Centre, Toronto, Canada
- Department of Obstetrics and Gynecology, University of Toronto, Toronto, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, Canada
- Department of Physiology, University of Toronto, Toronto, Canada
| | - Rajiv C. McCoy
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
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Backenroth D, Altarescu G, Zahdeh F, Mann T, Murik O, Renbaum P, Segel R, Zeligson S, Hakam-Spector E, Carmi S, Zeevi DA. SHaploseek is a sequencing-only, high-resolution method for comprehensive preimplantation genetic testing. Sci Rep 2023; 13:18036. [PMID: 37865712 PMCID: PMC10590366 DOI: 10.1038/s41598-023-45292-z] [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: 06/15/2023] [Accepted: 10/18/2023] [Indexed: 10/23/2023] Open
Abstract
Recent advances in genomic technologies expand the scope and efficiency of preimplantation genetic testing (PGT). We previously developed Haploseek, a clinically-validated, variant-agnostic comprehensive PGT solution. Haploseek is based on microarray genotyping of the embryo's parents and relatives, combined with low-pass sequencing of the embryos. Here, to increase throughput and versatility, we aimed to develop a sequencing-only implementation of Haploseek. Accordingly, we developed SHaploseek, a universal PGT method to determine genome-wide haplotypes of each embryo based on low-pass (≤ 5x) sequencing of the parents and relative(s) along with ultra-low-pass (0.2-0.4x) sequencing of the embryos. We used SHaploseek to analyze five single lymphoblast cells and 31 embryos. We validated the genome-wide haplotype predictions against either bulk DNA, Haploseek, or, at focal genomic sites, PCR-based PGT results. SHaploseek achieved > 99% concordance with bulk DNA in two families from which single cells were derived from grown-up children. In embryos from 12 PGT families, all of SHaploseek's focal site haplotype predictions were concordant with clinical PCR-based PGT results. Genome-wide, there was > 99% median concordance between Haploseek and SHaploseek's haplotype predictions. Concordance remained high at all assayed sequencing depths ≥ 2x, as well as with only 1ng of parental DNA input. In subtelomeric regions, significantly more haplotype predictions were high-confidence in SHaploseek compared to Haploseek. In summary, SHaploseek constitutes a single-platform, accurate, and cost-effective comprehensive PGT solution.
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Affiliation(s)
- Daniel Backenroth
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gheona Altarescu
- PGT Unit, Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
- Faculty of Medicine, Hebrew University, Jerusalem, Israel
| | - Fouad Zahdeh
- Translational Genomics Lab, Medical Genetics Institute, Shaare Zedek Medical Center, Bayit Str. 12, P.O.Box 3235, 91031, Jerusalem, Israel
| | - Tzvia Mann
- Translational Genomics Lab, Medical Genetics Institute, Shaare Zedek Medical Center, Bayit Str. 12, P.O.Box 3235, 91031, Jerusalem, Israel
| | - Omer Murik
- Translational Genomics Lab, Medical Genetics Institute, Shaare Zedek Medical Center, Bayit Str. 12, P.O.Box 3235, 91031, Jerusalem, Israel
| | - Paul Renbaum
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Reeval Segel
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Sharon Zeligson
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | | | - Shai Carmi
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - David A Zeevi
- Translational Genomics Lab, Medical Genetics Institute, Shaare Zedek Medical Center, Bayit Str. 12, P.O.Box 3235, 91031, Jerusalem, Israel.
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Bekaert B, Boel A, De Witte L, Vandenberghe W, Popovic M, Stamatiadis P, Cosemans G, Tordeurs L, De Loore AM, Chuva de Sousa Lopes SM, De Sutter P, Stoop D, Coucke P, Menten B, Heindryckx B. Retained chromosomal integrity following CRISPR-Cas9-based mutational correction in human embryos. Mol Ther 2023; 31:2326-2341. [PMID: 37376733 PMCID: PMC10422011 DOI: 10.1016/j.ymthe.2023.06.013] [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: 12/09/2022] [Revised: 04/11/2023] [Accepted: 06/22/2023] [Indexed: 06/29/2023] Open
Abstract
Human germline gene correction by targeted nucleases holds great promise for reducing mutation transmission. However, recent studies have reported concerning observations in CRISPR-Cas9-targeted human embryos, including mosaicism and loss of heterozygosity (LOH). The latter has been associated with either gene conversion or (partial) chromosome loss events. In this study, we aimed to correct a heterozygous basepair substitution in PLCZ1, related to infertility. In 36% of the targeted embryos that originated from mutant sperm, only wild-type alleles were observed. By performing genome-wide double-digest restriction site-associated DNA sequencing, integrity of the targeted chromosome (i.e., no deletions larger than 3 Mb or chromosome loss) was confirmed in all seven targeted GENType-analyzed embryos (mutant editing and absence of mutation), while short-range LOH events (shorter than 10 Mb) were clearly observed by single-nucleotide polymorphism assessment in two of these embryos. These results fuel the currently ongoing discussion on double-strand break repair in early human embryos, making a case for the occurrence of gene conversion events or partial template-based homology-directed repair.
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Affiliation(s)
- Bieke Bekaert
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Annekatrien Boel
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Lisa De Witte
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Winter Vandenberghe
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Mina Popovic
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Panagiotis Stamatiadis
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Gwenny Cosemans
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Lise Tordeurs
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Athina-Maria De Loore
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Susana Marina Chuva de Sousa Lopes
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium; Department of Anatomy and Embryology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Petra De Sutter
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Dominic Stoop
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Paul Coucke
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Björn Menten
- Center for Medical Genetics Ghent, Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Björn Heindryckx
- Ghent-Fertility and Stem Cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium.
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10
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Tsuiko O, El Ayeb Y, Jatsenko T, Allemeersch J, Melotte C, Ding J, Debrock S, Peeraer K, Vanhie A, De Leener A, Pirard C, Kluyskens C, Denayer E, Legius E, Vermeesch JR, Brems H, Dimitriadou E. Preclinical workup using long-read amplicon sequencing provides families with de novo pathogenic variants access to universal preimplantation genetic testing. Hum Reprod 2023; 38:511-519. [PMID: 36625546 DOI: 10.1093/humrep/deac273] [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: 07/11/2022] [Revised: 11/16/2022] [Indexed: 01/11/2023] Open
Abstract
STUDY QUESTION Can long-read amplicon sequencing be beneficial for preclinical preimplantation genetic testing (PGT) workup in couples with a de novo pathogenic variant in one of the prospective parents? SUMMARY ANSWER Long-read amplicon sequencing represents a simple, rapid and cost-effective preclinical PGT workup strategy that provides couples with de novo pathogenic variants access to universal genome-wide haplotyping-based PGT programs. WHAT IS KNOWN ALREADY Universal PGT combines genome-wide haplotyping and copy number profiling to select embryos devoid of both familial pathogenic variants and aneuploidies. However, it cannot be directly applied in couples with a de novo pathogenic variant in one of the partners due to the absence of affected family members required for phasing the disease-associated haplotype. STUDY DESIGN, SIZE, DURATION This is a prospective study, which includes 32 families that were enrolled in the universal PGT program at the University Hospital of Leuven between 2018 and 2022. We implemented long-read amplicon sequencing during the preclinical PGT workup to deduce the parental origin of the disease-associated allele in the affected partner, which can then be traced in embryos during clinical universal PGT cycles. PARTICIPANTS/MATERIALS, SETTING, METHODS To identify the parental origin of the disease-associated allele, genomic DNA from the carrier of the de novo pathogenic variant and his/her parent(s) was used for preclinical PGT workup. Primers flanking the de novo variant upstream and downstream were designed for each family. Following long-range PCR, amplicons that ranged 5-10 kb in size, were sequenced using Pacific Bioscience and/or Oxford Nanopore platforms. Next, targeted variant calling and haplotyping were performed to identify parental informative single-nucleotide variants (iSNVs) linked to the de novo mutation. Following the preclinical PGT workup, universal PGT via genome-wide haplotyping was performed for couples who proceeded with clinical PGT cycle. In parallel, 13 trophectoderm (TE) biopsies from three families that were analyzed by universal PGT, were also used for long-read amplicon sequencing to explore this approach for embryo direct mutation detection coupled with targeted long-read haplotyping. MAIN RESULTS AND THE ROLE OF CHANCE The parental origin of the mutant allele was identified in 24/32 affected individuals during the preclinical PGT workup stage, resulting in a 75% success rate. On average, 5.95 iSNVs (SD = 4.5) were detected per locus of interest, and the average distance of closest iSNV to the de novo variant was ∼1750 bp. In 75% of those cases (18/24), the de novo mutation occurred on the paternal allele. In the remaining eight families, the risk haplotype could not be established due to the absence of iSNVs linked to the mutation or inability to successfully target the region of interest. During the time of the study, 12/24 successfully analyzed couples entered the universal PGT program, and three disease-free children have been born. In parallel to universal PGT analysis, long-read amplicon sequencing of 13 TE biopsies was also performed, confirming the segregation of parental alleles in the embryo and the results of the universal PGT. LIMITATIONS, REASONS FOR CAUTION The main limitation of this approach is that it remains targeted with the need to design locus-specific primers. Because of the restricted size of target amplicons, the region of interest may also remain non-informative in the absence of iSNVs. WIDER IMPLICATIONS OF THE FINDINGS Targeted haplotyping via long-read amplicon sequencing, particularly using Oxford Nanopore Technologies, provides a valuable alternative for couples with de novo pathogenic variants that allows access to universal PGT. Moreover, the same approach can be used for direct mutation analysis in embryos, as a second line confirmation of the preclinical PGT result or as a potential alternative PGT procedure in couples, where additional family members are not available. STUDY FUNDING/COMPETING INTEREST(S) This work was supported by KU Leuven funding (no. C1/018 to J.R.V.) and Fonds Wetenschappelijk Onderzoek (1241121N to O.T.). J.R.V. is co-inventor of a patent ZL910050-PCT/EP2011/060211-WO/2011/157846 'Methods for haplotyping single-cells' and ZL913096-PCT/EP2014/068315-WO/2015/028576 'Haplotyping and copy number typing using polymorphic variant allelic frequencies' licensed to Agilent Technologies. All other authors have no conflict of interest to declare. TRIAL REGISTRATION NUMBER N/A.
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Affiliation(s)
- Olga Tsuiko
- Laboratory for Cytogenetics and Genome Research, Department of Human Genetics, KU Leuven, Leuven, Belgium.,Centre for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Yasmine El Ayeb
- Laboratory for Cytogenetics and Genome Research, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Tatjana Jatsenko
- Laboratory for Cytogenetics and Genome Research, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Joke Allemeersch
- Centre for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Cindy Melotte
- Centre for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Jia Ding
- Centre for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Sophie Debrock
- Leuven University Fertility Center, University Hospitals Leuven, Leuven, Belgium
| | - Karen Peeraer
- Leuven University Fertility Center, University Hospitals Leuven, Leuven, Belgium
| | - Arne Vanhie
- Leuven University Fertility Center, University Hospitals Leuven, Leuven, Belgium
| | - Anne De Leener
- Centre for Human Genetics, Cliniques Universitaires Saint Luc, UCLouvain, Brussels, Belgium
| | - Céline Pirard
- Department of Gynaecology, Cliniques Universitaires Saint Luc, UCLouvain, Brussels, Belgium
| | - Candice Kluyskens
- Department of Gynaecology, Cliniques Universitaires Saint Luc, UCLouvain, Brussels, Belgium
| | - Ellen Denayer
- Centre for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Eric Legius
- Centre for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Joris Robert Vermeesch
- Laboratory for Cytogenetics and Genome Research, Department of Human Genetics, KU Leuven, Leuven, Belgium.,Centre for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Hilde Brems
- Centre for Human Genetics, University Hospitals Leuven, Leuven, Belgium
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11
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van Dijk W, Derks K, Drüsedau M, Meekels J, Koeck R, Essers R, Dreesen J, Coonen E, de Die-Smulders C, Stevens SJC, Brunner HG, van den Wijngaard A, Paulussen ADC, Zamani Esteki M. Embryo tracking system for high-throughput sequencing-based preimplantation genetic testing. Hum Reprod 2022; 37:2700-2708. [PMID: 36149256 PMCID: PMC9627733 DOI: 10.1093/humrep/deac208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 09/01/2022] [Indexed: 12/05/2022] Open
Abstract
STUDY QUESTION Can the embryo tracking system (ETS) increase safety, efficacy and scalability of massively parallel sequencing-based preimplantation genetic testing (PGT)? SUMMARY ANSWER Applying ETS-PGT, the chance of sample switching is decreased, while scalability and efficacy could easily be increased substantially. WHAT IS KNOWN ALREADY Although state-of-the-art sequencing-based PGT methods made a paradigm shift in PGT, they still require labor intensive library preparation steps that makes PGT cost prohibitive and poses risks of human errors. To increase the quality assurance, efficiency, robustness and throughput of the sequencing-based assays, barcoded DNA fragments have been used in several aspects of next-generation sequencing (NGS) approach. STUDY DESIGN, SIZE, DURATION We developed an ETS that substantially alleviates the complexity of the current sequencing-based PGT. With (n = 693) and without (n = 192) ETS, the downstream PGT procedure was performed on both bulk DNA samples (n = 563) and whole-genome amplified (WGAed) few-cell DNA samples (n = 322). Subsequently, we compared full genome haplotype landscapes of both WGAed and bulk DNA samples containing ETS or no ETS. PARTICIPANTS/MATERIALS, SETTING, METHODS We have devised an ETS to track embryos right after whole-genome amplification (WGA) to full genome haplotype profiles. In this study, we recruited 322 WGAed DNA samples derived from IVF embryos as well as 563 bulk DNA isolated from peripheral blood of prospective parents. To determine possible interference of the ETS in the NGS-based PGT workflow, barcoded DNA fragments were added to DNA samples prior to library preparation and compared to samples without ETS. Coverages and variants were determined. MAIN RESULTS AND THE ROLE OF CHANCE Current PGT protocols are quality sensitive and prone to sample switching. To avoid sample switching and increase throughput of PGT by sequencing-based haplotyping, six control steps should be carried out manually and checked by a second person in a clinical setting. Here, we developed an ETS approach in which one step only in the entire PGT procedure needs the four-eyes principal. We demonstrate that ETS not only precludes error-prone manual checks but also has no effect on the genomic landscape of preimplantation embryos. Importantly, our approach increases efficacy and throughput of the state-of-the-art PGT methods. LIMITATIONS, REASONS FOR CAUTION Even though the ETS simplified sequencing-based PGT by avoiding potential errors in six steps in the protocol, if the initial assignment is not performed correctly, it could lead to cross-contamination. However, this can be detected in silico following downstream ETS analysis. Although we demonstrated an approach to evaluate purity of the ETS fragment, it is recommended to perform a pre-PGT quality control assay of the ETS amplicons with non-human DNA, such that the purity of each ETS molecule can be determined prior to ETS-PGT. WIDER IMPLICATIONS OF THE FINDINGS The ETS-PGT approach notably increases efficacy and scalability of PGT. ETS-PGT has broad applicative value, as it can be tailored to any single- and few-cell sequencing approach where the starting specimen is scarce, as opposed to other methods that require a large number of cells as the input. Moreover, ETS-PGT could easily be adapted to any sequencing-based diagnostic method, including PGT for structural rearrangements and aneuploidies by low-pass sequencing as well as non-invasive prenatal testing. STUDY FUNDING/COMPETING INTEREST(S) M.Z.E. is supported by the EVA (Erfelijkheid Voortplanting & Aanleg) specialty program (grant no. KP111513) of Maastricht University Medical Centre (MUMC+), and the Horizon 2020 innovation (ERIN) (grant no. EU952516) of the European Commission. TRIAL REGISTRATION NUMBER N/A.
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Affiliation(s)
- Wanwisa van Dijk
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands
| | - Kasper Derks
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands
| | - Marion Drüsedau
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands
| | - Jeroen Meekels
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands
| | - Rebekka Koeck
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands.,Department of Genetics and Cell Biology, GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Rick Essers
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands.,Department of Genetics and Cell Biology, GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Joseph Dreesen
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands.,Department of Genetics and Cell Biology, GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Edith Coonen
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands.,Center for Reproductive Medicine, Maastricht University Medical Centre+, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Christine de Die-Smulders
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands.,Department of Genetics and Cell Biology, GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Servi J C Stevens
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands.,Department of Genetics and Cell Biology, GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Han G Brunner
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands.,Department of Genetics and Cell Biology, GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands.,Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Arthur van den Wijngaard
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands.,Department of Genetics and Cell Biology, GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Aimée D C Paulussen
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands.,Department of Genetics and Cell Biology, GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
| | - Masoud Zamani Esteki
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands.,Department of Genetics and Cell Biology, GROW School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
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