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Kutteh WH, Papas RS, Maisenbacher MK, Dahdouh EM. Role of genetic analysis of products of conception and PGT in managing early pregnancy loss. Reprod Biomed Online 2024; 49:103738. [PMID: 38701633 DOI: 10.1016/j.rbmo.2023.103738] [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: 09/27/2023] [Revised: 11/11/2023] [Accepted: 11/15/2023] [Indexed: 05/05/2024]
Abstract
This article considers the addition of comprehensive 24-chromosomal microarray (CMA) analysis of products of conception (POC) to a standard evaluation for recurrent pregnancy loss (RPL) to help direct treatment towards expectant management versus IVF with preimplantation genetic testing for aneuploidies (PGT-A). The review included retrospective data from 65,333 miscarriages, a prospective evaluation of 378 couples with RPL who had CMA testing of POC and the standard workup, and data from an additional 1020 couples who were evaluated for RPL but did not undergo CMA testing of POC. Aneuploidy in POC explained the pregnancy loss in 57.7% (218/378) of cases. In contrast, the full RPL evaluation recommended by the American Society for Reproductive Medicine identified a potential cause in only 42.9% (600/1398). Combining the data from the RPL evaluation and the results of genetic testing of POC provides a probable explanation for the loss in over 90% (347/378) of women. Couples with an unexplained loss after the standard evaluation with POC aneuploidy accounted for 41% of cases; PGT-A may be considered after expectant management. Conversely, PGT-A would have a limited role in those with a euploid loss and a possible explanation after the standard workup. Categorizing a pregnancy loss as an explained versus unexplained loss after the standard evaluation combined with the results of CMA testing of POC may help identify patients who would benefit from expectant management versus PGT-A.
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Affiliation(s)
- William H Kutteh
- Natera, Inc., San Carlos, CA, USA.; Department of Obstetrics and Gynecology, University of Tennessee Health Sciences Center, Memphis, TN, USA..
| | - Ralph S Papas
- Department of Obstetrics and Gynecology, University of Balamand, Beirut, Lebanon
| | | | - Elias M Dahdouh
- ART Center, CHU Sainte-Justine, Department of Obstetrics and Gynecology, Université de Montréal, Montreal, Canada
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2
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Zhang X, Zheng PS. Mechanism of chromosomal mosaicism in preimplantation embryos and its effect on embryo development. J Assist Reprod Genet 2024; 41:1127-1141. [PMID: 38386118 PMCID: PMC11143108 DOI: 10.1007/s10815-024-03048-2] [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: 09/11/2023] [Accepted: 01/30/2024] [Indexed: 02/23/2024] Open
Abstract
Aneuploidy is one of the main causes of miscarriage and in vitro fertilization failure. Mitotic abnormalities in preimplantation embryos are the main cause of mosaicism, which may be influenced by several endogenous factors such as relaxation of cell cycle control mechanisms, defects in chromosome cohesion, centrosome aberrations and abnormal spindle assembly, and DNA replication stress. In addition, incomplete trisomy rescue is a rare cause of mosaicism. However, there may be a self-correcting mechanism in mosaic embryos, which allows some mosaicisms to potentially develop into normal embryos. At present, it is difficult to accurately diagnose mosaicism using preimplantation genetic testing for aneuploidy. Therefore, in clinical practice, embryos diagnosed as mosaic should be considered comprehensively based on the specific situation of the patient.
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Affiliation(s)
- Xue Zhang
- Department of Reproductive Medicine, The First Affiliated Hospital, Xi'an Jiaotong University of Medical School, Xi'an, 710061, Shanxi, P.R. China
| | - Peng-Sheng Zheng
- Department of Reproductive Medicine, The First Affiliated Hospital, Xi'an Jiaotong University of Medical School, Xi'an, 710061, Shanxi, P.R. China.
- Section of Cancer Stem Cell Research, Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education of People's Republic of China, Xi'an, 710061, Shanxi, P.R. China.
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3
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Budrewicz J, Chavez SL. Insights into embryonic chromosomal instability: mechanisms of DNA elimination during mammalian preimplantation development. Front Cell Dev Biol 2024; 12:1344092. [PMID: 38374891 PMCID: PMC10875028 DOI: 10.3389/fcell.2024.1344092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 01/15/2024] [Indexed: 02/21/2024] Open
Abstract
Mammalian preimplantation embryos often contend with aneuploidy that arose either by the inheritance of meiotic errors from the gametes, or from mitotic mis-segregation events that occurred following fertilization. Regardless of the origin, mis-segregated chromosomes become encapsulated in micronuclei (MN) that are spatially isolated from the main nucleus. Much of our knowledge of MN formation comes from dividing somatic cells during tumorigenesis, but the error-prone cleavage-stage of early embryogenesis is fundamentally different. One unique aspect is that cellular fragmentation (CF), whereby small subcellular bodies pinch off embryonic blastomeres, is frequently observed. CF has been detected in both in vitro and in vivo-derived embryos and likely represents a response to chromosome mis-segregation since it only appears after MN formation. There are multiple fates for MN, including sequestration into CFs, but the molecular mechanism(s) by which this occurs remains unclear. Due to nuclear envelope rupture, the chromosomal material contained within MN and CFs becomes susceptible to double stranded-DNA breaks. Despite this damage, embryos may still progress to the blastocyst stage and exclude chromosome-containing CFs, as well as non-dividing aneuploid blastomeres, from participating in further development. Whether these are attempts to rectify MN formation or eliminate embryos with poor implantation potential is unknown and this review will discuss the potential implications of DNA removal by CF/blastomere exclusion. We will also extrapolate what is known about the intracellular pathways mediating MN formation and rupture in somatic cells to preimplantation embryogenesis and how nuclear budding and DNA release into the cytoplasm may impact overall development.
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Affiliation(s)
- Jacqueline Budrewicz
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, United States
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Beaverton, OR, United States
| | - Shawn L. Chavez
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, United States
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Beaverton, OR, United States
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, OR, United States
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, United States
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Korkidakis A, Albert AY, Jiang I, Terry J, AbdelHafez FF, Bedaiwy MA. The Clinical Significance of Embryonic Chromosomal Errors in Recurrent Pregnancy Loss: an Analysis of 1107 Miscarriages. Reprod Sci 2023; 30:3019-3026. [PMID: 37129829 DOI: 10.1007/s43032-023-01239-3] [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: 12/29/2022] [Accepted: 04/06/2023] [Indexed: 05/03/2023]
Abstract
The objective of this study was to characterize the relationship between embryonic chromosomal errors in the products of conception (POC) and maternal age, gestational age (GA) of pregnancy loss, and findings on routine recurrent pregnancy loss (RPL) workup. This is a retrospective cohort study of women with a history of ≥ 2 pregnancy losses and who underwent cytogenetic testing on the POC of a subsequent pregnancy loss at an academic tertiary RPL referral center. The association between the odds of embryonic chromosomal errors in POC and maternal age, GA of pregnancy loss, as well as RPL work up findings was investigated. A total of 1107 miscarriages were analyzed from 741 women. There was an overall linear relationship between embryonic chromosomal errors and maternal age, with a nearly twofold increase in the odds of chromosomal error with every 5-year increase in maternal age (P < 0.0001). The association between chromosomal errors and GA was also linear (P = 0.0001), with most losses having no chromosomal errors after 13 weeks' gestation. Women with ≥ 1 positive findings on routine RPL diagnostic workup had lower odds of embryonic chromosomal errors compared to those with a normal workup [OR 0.57 (95% CI = 0.41-0.80)]. Notably, the estimated prevalence of chromosomal error remained high (> 60%) in women ≥ 35 years old irrespective of findings on routine evaluation. While embryonic chromosomal errors were associated with advanced maternal age, early GA of loss, and a negative routine RPL evaluation, the prevalence of chromosomal errors remained high in all subpopulations. These findings suggest that primary cytogenetic testing on POCs should be offered at the time of second and subsequent pregnancy losses in all RPL patients.
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Affiliation(s)
- Ann Korkidakis
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, University of British Columbia, 4500 Oak Street, Vancouver, BC, V6H 3N1, Canada
| | - Arianne Y Albert
- Women's Health Research Institute, BC Women's Hospital and Health Centre, 4500 Oak Street, Vancouver, BC, V6H 3N1, Canada
| | - Irene Jiang
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, University of British Columbia, 4500 Oak Street, Vancouver, BC, V6H 3N1, Canada
| | - Jefferson Terry
- Department of Pathology, BC Children's Hospital, 4480 Oak Street, Vancouver, BC, V6H 3V4, Canada
| | - Faten F AbdelHafez
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, University of British Columbia, 4500 Oak Street, Vancouver, BC, V6H 3N1, Canada
- Department of Obstetrics and Gynecology, Assiut University, Assiut, Egypt
| | - Mohamed A Bedaiwy
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, University of British Columbia, 4500 Oak Street, Vancouver, BC, V6H 3N1, Canada.
- Women's Health Research Institute, BC Women's Hospital and Health Centre, 4500 Oak Street, Vancouver, BC, V6H 3N1, Canada.
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Samarasekera T, Willats E, Green MP, Hardy T, Rombauts L, Zander-Fox D. Impact of male age on paternal aneuploidy: single-nucleotide polymorphism microarray outcomes following blastocyst biopsy. Reprod Biomed Online 2023; 47:103245. [PMID: 37619516 DOI: 10.1016/j.rbmo.2023.06.002] [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: 01/23/2023] [Revised: 04/20/2023] [Accepted: 06/06/2023] [Indexed: 08/26/2023]
Abstract
RESEARCH QUESTION Does advanced paternal age (APA; ≥40 years) contribute to a higher incidence of paternal origin aneuploidy in preimplantation embryos? DESIGN This was a multicentre retrospective study of single-nucleotide polymorphism (SNP) microarray (Natera and Karyomapping) preimplantation genetic testing (PGT) outcomes of blastocyst-stage embryos. Whole-chromosome aneuploidy analysis was performed on 2409 embryos from 389 male patients undertaking 681 assisted reproductive technology (ART) cycles between 2012-2021. Segmental aneuploidy analysis was performed on 867 embryos from 140 men undertaking 242 ART cycles between 2016-2021. Embryos were grouped based on paternal age at sperm collection: <35, 35-39 and ≥40 years. Paternal and maternal origin aneuploidy rates were compared between groups using chi-squared and/or Fisher's exact tests. RESULTS There was no significant difference across groups in paternal origin whole-chromosome aneuploidy rate, overall (P=0.7561) or when segregated by type (trisomy and monosomy: P=0.2235 and 0.8156) or complexity (single versus 2, 3 or ≥4 aneuploidies: P=0.9733, 0.7517, 0.669 and 0.1481). Conversely, maternal origin whole-chromosome aneuploidy rate differed across groups (P<0.0001) in alignment with differing mean maternal age (P<0.001). Paternal origin deletions were 2.9-fold higher than maternal origin deletions (P=0.0084), independent of age stratification. No significant difference in paternal origin deletions was observed with APA ≥40 compared with the younger age groups (4.8% versus 2.5% and 2.8%, P=0.5292). Individual chromosome aneuploidy rates were too low to perform statistical comparisons. CONCLUSIONS No significant association was found between APA and the incidence of paternal origin aneuploidy in preimplantation embryos, irrespective of type or complexity. Thus, APA may not be an indication for PGT.
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Affiliation(s)
| | | | - Mark P Green
- Monash IVF, Melbourne, Australia.; School of Biosciences, Faculty of Science, University of Melbourne, Melbourne, Australia
| | | | - Luk Rombauts
- Monash IVF, Melbourne, Australia.; Monash Health, Melbourne, Australia.; Biomedicine Discovery Institute, Faculty of Biomedical Sciences, Monash University, Melbourne, Australia
| | - Deirdre Zander-Fox
- Monash IVF, Melbourne, Australia.; Biomedicine Discovery Institute, Faculty of Biomedical Sciences, Monash University, Melbourne, Australia.; School of Biomedicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, Australia
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6
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Damour G, Baumer K, Legardeur H, Hall D. Early noninvasive prenatal paternity testing by targeted fetal DNA analysis. Sci Rep 2023; 13:12139. [PMID: 37495669 PMCID: PMC10372148 DOI: 10.1038/s41598-023-39367-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 07/21/2023] [Indexed: 07/28/2023] Open
Abstract
Today the challenge in paternity testing is to provide an accurate noninvasive assay that can be performed early during pregnancy. This requires the use of novel analytical methods capable of detecting the low fraction of circulating fetal DNA in maternal blood. We previously showed that forensic compound markers such as deletion/insertion polymorphisms-short tandem repeats (DIP-STR) can efficiently resolve complex mixed biological evidence including the target analysis of paternally inherited fetal alleles. In this study, we describe for the first time the validation of this type of markers in the first trimester of pregnancies, in addition to defining the statistical framework to evaluate paternity. To do so, we studied 47 DIP-STRs in 87 cases, with blood samples collected throughout gestation starting from the seven weeks of amenorrhea. Fetal DNA detection in the first trimester shows a false negative rate as low as 6%. The combined paternity index (CPI) results indicate that seven markers with fully informative genotypes are sufficient to determine the paternity. This study demonstrates that DIP-STR markers can be used from early pregnancy and that a small set of markers (about 40) is sufficient to address the question of paternity. The novel method offers substantial improvements over similar approaches in terms of reduced number of markers, lower costs and increased accuracy.
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Affiliation(s)
- Géraldine Damour
- Unité de Génétique Forensique, Centre Universitaire Romand de Médecine Légale, Centre Hospitalier Universitaire Vaudois et Université de Lausanne, Ch. de Vulliette 4, 1000, Lausanne, Switzerland
| | - Karine Baumer
- Unité de Génétique Forensique, Centre Universitaire Romand de Médecine Légale, Centre Hospitalier Universitaire Vaudois et Université de Lausanne, Ch. de Vulliette 4, 1000, Lausanne, Switzerland
| | - Hélène Legardeur
- Woman-Mother-Child Department, Lausanne University Hospital, Lausanne, Switzerland
| | - Diana Hall
- Unité de Génétique Forensique, Centre Universitaire Romand de Médecine Légale, Centre Hospitalier Universitaire Vaudois et Université de Lausanne, Ch. de Vulliette 4, 1000, Lausanne, Switzerland.
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7
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Bouwman AC, Hulsegge I, Hawken RJ, Henshall JM, Veerkamp RF, Schokker D, Kamphuis C. Classifying aneuploidy in genotype intensity data using deep learning. J Anim Breed Genet 2023; 140:304-315. [PMID: 36806175 DOI: 10.1111/jbg.12760] [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: 09/20/2022] [Accepted: 01/10/2023] [Indexed: 02/23/2023]
Abstract
Aneuploidy is the loss or gain of one or more chromosomes. Although it is a rare phenomenon in liveborn individuals, it is observed in livestock breeding populations. These breeding populations are often routinely genotyped and the genotype intensity data from single nucleotide polymorphism (SNP) arrays can be exploited to identify aneuploidy cases. This identification is a time-consuming and costly task, because it is often performed by visual inspection of the data per chromosome, usually done in plots of the intensity data by an expert. Therefore, we wanted to explore the feasibility of automated image classification to replace (part of) the visual detection procedure for any diploid species. The aim of this study was to develop a deep learning Convolutional Neural Network (CNN) classification model based on chromosome level plots of SNP array intensity data that can classify the images into disomic, monosomic and trisomic cases. A multispecies dataset enriched for aneuploidy cases was collected containing genotype intensity data of 3321 disomic, 1759 monosomic and 164 trisomic chromosomes. The final CNN model had an accuracy of 99.9%, overall precision was 1, recall was 0.98 and the F1 score was 0.99 for classifying images from intensity data. The high precision assures that cases detected are most likely true cases, however, some trisomy cases may be missed (the recall of the class trisomic was 0.94). This supervised CNN model performed much better than an unsupervised k-means clustering, which reached an accuracy of 0.73 and had especially difficult to classify trisomic cases correctly. The developed CNN classification model provides high accuracy to classify aneuploidy cases based on images of plotted X and Y genotype intensity values. The classification model can be used as a tool for routine screening in large diploid populations that are genotyped to get a better understanding of the incidence and inheritance, and in addition, avoid anomalies in breeding candidates.
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Affiliation(s)
- Aniek C Bouwman
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, The Netherlands
| | - Ina Hulsegge
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, The Netherlands
| | | | | | - Roel F Veerkamp
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, The Netherlands
| | - Dirkjan Schokker
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, The Netherlands
| | - Claudia Kamphuis
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, The Netherlands
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Yu EJ, Kim MJ, Park EA, Kang IS. Preimplantation genetic testing for aneuploidy: The management of mosaic embryos. Clin Exp Reprod Med 2022; 49:159-167. [PMID: 36097731 PMCID: PMC9468697 DOI: 10.5653/cerm.2022.05393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/24/2022] [Indexed: 11/22/2022] Open
Abstract
As the resolution and accuracy of diagnostic techniques for preimplantation genetic testing for aneuploidy (PGT-A) are improving, more mosaic embryos are being identified. Several studies have provided evidence that mosaic embryos have reproductive potential for implantation and healthy live birth. Notably, mosaic embryos with less than 50% aneuploidy have yielded a live birth rate similar to euploid embryos. This concept has led to a major shift in current PGT-A practice, but further evidence and theoretically relevant data are required. Proper guidelines for selecting mosaic embryos suitable for transfer will reduce the number of discarded embryos and increase the chances of successful embryo transfer. We present an updated review of clinical outcomes and practice recommendations for the transfer of mosaic embryos using PGT-A.
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Affiliation(s)
- Eun Jeong Yu
- Department of Obstetrics and Gynecology, CHA Fertility Center Seoul Station, CHA University School of Medicine, Seoul, Republic of Korea
| | - Min Jee Kim
- Department of Biomedical Sciences, College of Life Sciences, CHA University, Seongnam, Republic of Korea
- Laboratory of Reproductive Genetics, CHA Biotech, Seongnam, Republic of Korea
| | - Eun A Park
- Department of Biomedical Sciences, College of Life Sciences, CHA University, Seongnam, Republic of Korea
- Fertility Research Lab, CHA Fertility Center Seoul Station, Seoul, Republic of Korea
| | - Inn Soo Kang
- Department of Obstetrics and Gynecology, CHA Fertility Center Daegu, CHA University School of Medicine, Daegu, Republic of Korea
- Corresponding author: Inn Soo Kang Department of Obstetrics and Gynecology, CHA Fertility Center Daegu, CHA University School of Medicine, 2095 Dalgubeol-daero, Jung-gu, Daegu 41936, Korea Tel: +82-53-222-4200, Fax: +82-53-214-6611 E-mail:
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9
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Wang J, Thomas HR, Chen Y, Percival SM, Waldrep SC, Ramaker RC, Thompson RG, Cooper SJ, Chong Z, Parant JM. Reduced sister chromatid cohesion acts as a tumor penetrance modifier. PLoS Genet 2022; 18:e1010341. [PMID: 35994499 PMCID: PMC9436123 DOI: 10.1371/journal.pgen.1010341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 09/01/2022] [Accepted: 07/14/2022] [Indexed: 11/23/2022] Open
Abstract
Sister chromatid cohesion (SCC) is an important process in chromosome segregation. ESCO2 is essential for establishment of SCC and is often deleted/altered in human cancers. We demonstrate that esco2 haploinsufficiency results in reduced SCC and accelerates the timing of tumor onset in both zebrafish and mouse p53 heterozygous null models, but not in p53 homozygous mutant or wild-type animals. These data indicate that esco2 haploinsufficiency accelerates tumor onset in a loss of heterozygosity (LOH) sensitive background. Analysis of The Cancer Genome Atlas (TCGA) confirmed ESCO2 deficient tumors have elevated number of LOH events throughout the genome. Further, we demonstrated heterozygous loss of sgo1, important in maintaining SCC, also results in reduced SCC and accelerated tumor formation in a p53 heterozygous background. Surprisingly, while we did observe elevated levels of chromosome missegregation and micronuclei formation in esco2 heterozygous mutant animals, this chromosomal instability did not contribute to the accelerated tumor onset in a p53 heterozygous background. Interestingly, SCC also plays a role in homologous recombination, and we did observe elevated levels of mitotic recombination derived p53 LOH in tumors from esco2 haploinsufficient animals; as well as elevated levels of mitotic recombination throughout the genome of human ESCO2 deficient tumors. Together these data suggest that reduced SCC contributes to accelerated tumor penetrance through elevated mitotic recombination. Tumorigenesis often involves the inactivation of tumor suppressor genes. This often encompasses an inactivation mutation in one allele and loss of the other wild-type allele, referred to as loss of heterozygosity (LOH). The rate at which the cells lose the wild-type allele can influence the timing of tumor onset, and therefore an indicator of a patient’s risk of cancer. Factors that influence this process could be used as a predictive indicator of cancer risk, however these factors are still unclear. We demonstrate that partial impairment of sister chromatid cohesion (SCC), a fundamental component of the chromosome segregation in mitosis and homologous recombination repair, enhanced tumorigenesis. Our data suggest this is through elevated levels of mitotic recombination derived p53 LOH. This study emphasizes the importance of understanding how impaired SCC, mitotic recombination rates, and LOH rates influence cancer risk.
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Affiliation(s)
- Jun Wang
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama, United States of America
| | - Holly R. Thomas
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama, United States of America
| | - Yu Chen
- Department of Genetics, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama, United States of America
- Informatics Institute, University of Alabama at Birmingham Heersink School of Medicine, Alabama, United States of America
| | - Stefanie M. Percival
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama, United States of America
| | - Stephanie C. Waldrep
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama, United States of America
| | - Ryne C. Ramaker
- Hudson Alpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Robert G. Thompson
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama, United States of America
| | - Sara J. Cooper
- Hudson Alpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Zechen Chong
- Department of Genetics, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama, United States of America
- Informatics Institute, University of Alabama at Birmingham Heersink School of Medicine, Alabama, United States of America
| | - John M. Parant
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham Heersink School of Medicine, Birmingham, Alabama, United States of America
- * E-mail:
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10
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Bonus ML, McQueen DB, Ruderman R, Hughes L, Merrion K, Maisenbacher MK, Feinberg E, Boots C. Relationship between paternal factors and embryonic aneuploidy of paternal origin. Fertil Steril 2022; 118:281-288. [DOI: 10.1016/j.fertnstert.2022.04.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 04/13/2022] [Accepted: 04/13/2022] [Indexed: 12/13/2022]
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11
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Regin M, Spits C, Sermon K. On the origins and fate of chromosomal abnormalities in human preimplantation embryos: an unsolved riddle. Mol Hum Reprod 2022; 28:6566308. [DOI: 10.1093/molehr/gaac011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/30/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
About 8 out of 10 human embryos obtained in vitro harbour chromosomal abnormalities of either meiotic or mitotic origin. Abnormalities of mitotic origin lead to chromosomal mosaicism, a phenomenon which has sparked much debate lately as it confounds results obtained through preimplantation genetic testing for aneuploidy (PGT-A). PGT-A in itself is still highly debated, not only on the modalities of its execution, but also on whether it should be offered to patients at all.
We will focus on post-zygotic chromosomal abnormalities leading to mosaicism. First, we will summarize what is known of the rates of chromosomal abnormalities at different developmental stages. Next, based on the current understanding of the origin and cellular consequences of chromosomal abnormalities, which is largely based on studies on cancer cells and model organisms, we will offer a number of hypotheses on which mechanisms may be at work in early human development. Finally, and very briefly, we will touch upon the impact our current knowledge has on the practice of PGT-A. What is the level of abnormal cells that an embryo can tolerate before it loses its potential for full development? And is blastocyst biopsy as harmless as it seems?
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Affiliation(s)
- Marius Regin
- Research group Reproduction and Genetics, Vrije Universiteit Brussel, Brussels, 1090, Belgium
| | - Claudia Spits
- Research group Reproduction and Genetics, Vrije Universiteit Brussel, Brussels, 1090, Belgium
| | - Karen Sermon
- Research group Reproduction and Genetics, Vrije Universiteit Brussel, Brussels, 1090, Belgium
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12
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Maternal body mass index is not associated with increased rates of maternal embryonic aneuploidy. Fertil Steril 2022; 117:783-789. [PMID: 35105446 DOI: 10.1016/j.fertnstert.2021.12.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 12/21/2021] [Accepted: 12/29/2021] [Indexed: 01/01/2023]
Abstract
OBJECTIVE To evaluate the relationship between maternal body mass index (BMI) and embryonic aneuploidy of maternal origin. DESIGN Retrospective cohort analysis. SETTING University hospital-based reproductive center. PATIENTS Maternal origin of aneuploidy was available for 453 cycles and 1,717 embryos. INTERVENTIONS Data regarding BMI were collected before egg retrieval. Comparison groups included underweight (BMI, <18.5 kg/m2), normal weight (BMI, 18.5-24.9 kg/m2), overweight (BMI, 25-29.9 kg/m2), and obese (BMI, ≥30 kg/m2). Overall embryonic aneuploidy and maternal aneuploidy rates were compared. The aneuploidy rate was the number of embryos with either maternal or mixed (maternal and paternal) aneuploidy divided by the total number of embryos tested. MAIN OUTCOME MEASURES Overall embryonic aneuploidy and maternal aneuploidy rates. RESULTS Maternal aneuploidy rate was 51.5% for BMI of ≥30 kg/m2 and 39.3% for BMI of <30 kg/m2. Female age as well as several in vitro fertilization characteristics were significantly different across groups and were included in the adjusted model. Both the overall embryonic aneuploidy rate (odds ratio [OR], 1.3; 95% confidence interval [CI], 1.11-1.59) and the maternal aneuploidy rate (OR, 1.64; 95% CI, 1.25-2.16) increased with increasing maternal BMI. However, after controlling for significant confounders, BMI did not significantly predict the rate of maternal aneuploidy (OR, 1.16; 95% CI, 0.85-1.59). CONCLUSIONS Maternal BMI did not correlate with embryonic aneuploidy of maternal origin after adjusting for confounders.
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Doll B, De Castro MJ, Fries MH, Pock AR, Seibert D, Yang W. Precision Medicine-A Demand Signal for Genomics Education. Mil Med 2021; 187:40-46. [PMID: 34967402 DOI: 10.1093/milmed/usab406] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/04/2021] [Accepted: 10/13/2021] [Indexed: 11/12/2022] Open
Abstract
Pressed by the accumulating knowledge in genomics and the proven success of the translation of cancer genomics to clinical practice in oncology, the Obama administration unveiled a $215 million commitment for the Precision Medicine Initiative (PMI) in 2016, a pioneering research effort to improve health and treat disease using a new model of patient-powered research. The objectives of the initiative include more effective treatments for cancer and other diseases, creation of a voluntary national research cohort, adherence to privacy protections for maintaining data sharing and use, modernization of the regulatory framework, and forging public-private partnerships to facilitate these objectives. Specifically, the DoD Military Health System joined other agencies to execute a comprehensive effort for PMI. Of the many challenges to consider that may contribute to the implementation of genomics-lack of familiarity and understanding, poor access to genomic medicine expertise, needs for extensive informatics and infrastructure to integrate genomic results, privacy and security, and policy development to address the unique requirements of military medical practice-we will focus on the need to establish education in genomics appropriate to the provider's responsibilities. Our hypothesis is that there is a growing urgency for the development of educational experiences, formal and informal, to enable clinicians to acquire competency in genomics commensurate with their level of practice. Several educational approaches, both in practice and in development, are presented to inform decision-makers and empower military providers to pursue courses of action that respond to this need.
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Affiliation(s)
- Bruce Doll
- Office of the Vice President for Research, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | | | - Melissa H Fries
- Medstar Washington Hospital Center, Georgetown University School of Medicine, Washington, DC 20010, USA
| | - Arnyce R Pock
- E. Edward Hebert School of Medicine, Uniformed Services University, Bethesda, MD 20814, USA
| | - Diane Seibert
- Daniel K Inouye Graduate School of Nursing, Uniformed Services University, Bethesda, MD 20814, USA
| | - Wendy Yang
- E. Edward Hebert School of Medicine, Uniformed Services University, Bethesda, MD 20814, USA
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14
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Haplotype-aware inference of human chromosome abnormalities. Proc Natl Acad Sci U S A 2021; 118:2109307118. [PMID: 34772814 DOI: 10.1073/pnas.2109307118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2021] [Indexed: 12/25/2022] Open
Abstract
Extra or missing chromosomes-a phenomenon termed aneuploidy-frequently arise during human meiosis and embryonic mitosis and are the leading cause of pregnancy loss, including in the context of in vitro fertilization (IVF). While meiotic aneuploidies affect all cells and are deleterious, mitotic errors generate mosaicism, which may be compatible with healthy live birth. Large-scale abnormalities such as triploidy and haploidy also contribute to adverse pregnancy outcomes, but remain hidden from standard sequencing-based approaches to preimplantation genetic testing for aneuploidy (PGT-A). The ability to reliably distinguish meiotic and mitotic aneuploidies, as well as abnormalities in genome-wide ploidy, may thus prove valuable for enhancing IVF outcomes. Here, we describe a statistical method for distinguishing these forms of aneuploidy based on analysis of low-coverage whole-genome sequencing data, which is the current standard in the field. Our approach overcomes the sparse nature of the data by leveraging allele frequencies and linkage disequilibrium (LD) measured in a population reference panel. The method, which we term LD-informed PGT-A (LD-PGTA), retains high accuracy down to coverage as low as 0.05 × and at higher coverage can also distinguish between meiosis I and meiosis II errors based on signatures spanning the centromeres. LD-PGTA provides fundamental insight into the origins of human chromosome abnormalities, as well as a practical tool with the potential to improve genetic testing during IVF.
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15
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Chaperon JL, Wemmer NM, McKanna TA, Clark DM, Westemeyer MA, Gauthier P, Bai Y, Coleman JM. Preimplantation Genetic Testing for Kidney Disease-Related Genes: A Laboratory's Experience. Am J Nephrol 2021; 52:684-690. [PMID: 34515037 DOI: 10.1159/000518253] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 06/28/2021] [Indexed: 01/16/2023]
Abstract
INTRODUCTION Recent literature highlights the clinical utility of genetic testing for patients with kidney disease. Genetic testing provides significant benefits for reproductive risk counseling, including the option of in vitro fertilization with preimplantation genetic testing for monogenic disease (PGT-M). PGT-M allows for a significant reduction in risk for a pregnancy affected with the familial disease. We aim to summarize our experience with PGT-M for genes with kidney involvement as either a primary or secondary feature of the disease. METHODS All PGT-M tests performed by the reference laboratory between September 2010 and July 2020 were reviewed for clinical indication and cases for which the disease tested included a renal component. Each patient referred for PGT-M had an existing molecular genetic diagnosis themselves or in their family. Frequency of each condition, gene, inheritance pattern, and year over year increase in referral cases was analyzed. RESULTS In the study cohort, the most common disease targeted was autosomal dominant polycystic kidney disease, caused by pathogenic variants in the PKD1 or PKD2 genes, which accounted for 16.5% (64/389) of cases. The 5 most common referral indications accounted for 51.9% (202/389) of the cases. Autosomal recessive inheritance accounted for 52.0% (26/50) of conditions for which PGT-M was performed. The number of PGT-M tests performed for conditions that included either primary or secondary kidney disease increased from 5 cases in 2010 to 47 cases in the 2020 study period. DISCUSSION/CONCLUSION These data suggest that the pursuit of PGT-M by couples at risk for passing on conditions with a kidney component is common and has significantly increased since 2010. With this rising trend of patients undergoing PGT-M and the prerequisite of molecular genetic confirmation in the PGT-M process, this study underscores the importance of the reproductive component to a molecular genetic diagnosis for patients with kidney disease, especially as the accessibility of genetic testing and utilization by nephrologists grows.
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Affiliation(s)
| | | | | | | | | | | | - Yan Bai
- Natera, Inc., San Carlos, California, USA
| | - Jessica M Coleman
- Nephrology and Hypertension Medical Associates, P.C., Beaufort, South Carolina, USA
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16
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Xiao M, Lei CX, Xi YP, Lu YL, Wu JP, Li XY, Zhang S, Zhu SJ, Zhou J, Li X, Zhang YP, Sun XX. Next-Generation Sequencing Is More Efficient at Detecting Mosaic Embryos and Improving Pregnancy Outcomes than Single-Nucleotide Polymorphism Array Analysis. J Mol Diagn 2021; 23:710-718. [PMID: 33781963 DOI: 10.1016/j.jmoldx.2021.02.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 01/27/2021] [Accepted: 02/25/2021] [Indexed: 11/26/2022] Open
Abstract
We compared chromosomal mosaicism, detected by next-generation sequencing (NGS), during preimplantation genetic testing (PGT) with that detected by single-nucleotide polymorphism (SNP) array-based PGT to assess the pregnancy outcomes associated with both platforms in a retrospective cohort study of patients undergoing in vitro fertilization in a single university-based assisted reproduction center. In total, 6427 blastocysts biopsied from 1513 patients who underwent 2833 oocyte retrievals from January 2017 to February 2019 were identified. The incidence of mosaicism was significantly higher in the NGS-based PGT group than in the SNP array-based PGT group. Furthermore, some aneuploid specimens were affected by mosaicism. The total mosaicism detection rate with NGS-based PGT (23.3%) was significantly higher than that with SNP array-based PGT (7.7%). Mosaicism rates were similar when stratified by maternal age or PGT type. The SNP array cohort showed a significantly higher spontaneous abortion rate than the NGS cohort (10.07% versus 6.33%; P = 0.0403). The ongoing pregnancy/live birth rate was higher in the NGS cohort (44.1%) than in the SNP array cohort (42.28%). Our results confirm that NGS-based PGT can detect mosaicism more frequently than SNP array-based PGT in trophectoderm specimens. Therefore, clinical application of NGS for PGT may improve pregnancy outcomes compared with that of SNP array-based PGT. More detailed blastocyst detection and classification is necessary to prioritize embryo transfers.
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Affiliation(s)
- Min Xiao
- Shanghai Ji Ai Genetics and In Vitro Fertilization Institute, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China; Genetics Center of Obstetrics and Gynecology of Fudan University, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Cai-Xia Lei
- Shanghai Ji Ai Genetics and In Vitro Fertilization Institute, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Yan-Ping Xi
- Shanghai Ji Ai Genetics and In Vitro Fertilization Institute, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Yu-Lin Lu
- Berry Genomics Corp., Beijing, China
| | - Jun-Ping Wu
- Shanghai Ji Ai Genetics and In Vitro Fertilization Institute, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | | | - Shuo Zhang
- Shanghai Ji Ai Genetics and In Vitro Fertilization Institute, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China; Genetics Center of Obstetrics and Gynecology of Fudan University, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Sai-Juan Zhu
- Shanghai Ji Ai Genetics and In Vitro Fertilization Institute, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Jing Zhou
- Shanghai Ji Ai Genetics and In Vitro Fertilization Institute, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Xiong Li
- Shanghai Ji Ai Genetics and In Vitro Fertilization Institute, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Yue-Ping Zhang
- Shanghai Ji Ai Genetics and In Vitro Fertilization Institute, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Xiao-Xi Sun
- Shanghai Ji Ai Genetics and In Vitro Fertilization Institute, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China; Berry Genomics Corp., Beijing, China; Key Laboratory of Female Reproductive Endocrine-Related Diseases, The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China.
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17
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Masset H, Tšuiko O, Vermeesch JR. Genome-wide abnormalities in embryos: Origins and clinical consequences. Prenat Diagn 2021; 41:554-563. [PMID: 33524193 DOI: 10.1002/pd.5895] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 12/03/2020] [Accepted: 12/30/2020] [Indexed: 12/25/2022]
Abstract
Ploidy or genome-wide chromosomal anomalies such as triploidy, diploid/triploid mixoploidy, chimerism, and genome-wide uniparental disomy are the cause of molar pregnancies, embryonic lethality, and developmental disorders. While triploidy and genome-wide uniparental disomy can be ascribed to fertilization or meiotic errors, the mechanisms causing mixoploidy and chimerism remain shrouded in mystery. Different models have been proposed, but all remain hypothetical and controversial, are deduced from the developmental persistent genomic constitutions present in the sample studied and lack direct evidence. New single-cell genomic methodologies, such as single-cell genome-wide haplotyping, provide an extended view of the constitution of normal and abnormal embryos and have further pinpointed the existence of mixoploidy in cleavage-stage embryos. Based on those recent findings, we suggest that genome-wide anomalies, which persist in fetuses and patients, can for a large majority be explained by a noncanonical first zygotic cleavage event, during which maternal and paternal genomes in a single zygote, segregate to different blastomeres. This process, termed heterogoneic division, provides an overarching theoretical basis for the different presentations of mixoploidy and chimerism.
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Affiliation(s)
- Heleen Masset
- Department of Human Genetics, Laboratory for Cytogenetics and Genome Research, KU Leuven, Leuven, Belgium
| | - Olga Tšuiko
- Department of Human Genetics, Laboratory for Cytogenetics and Genome Research, KU Leuven, Leuven, Belgium
| | - Joris R Vermeesch
- Department of Human Genetics, Laboratory for Cytogenetics and Genome Research, KU Leuven, Leuven, Belgium.,Center of Human Genetics, University Hospitals of Leuven, Leuven, Belgium
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18
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Can embryo morphokinetic parameters predict euploid pregnancy loss? Fertil Steril 2020; 115:382-388. [PMID: 33059893 DOI: 10.1016/j.fertnstert.2020.08.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/20/2020] [Accepted: 08/11/2020] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To use time-lapse imaging to compare embryo morphokinetic parameters between embryos resulting in euploid pregnancy loss and euploid embryos resulting in live birth. DESIGN Retrospective cohort study. SETTING Single academic fertility center. PATIENT(S) All euploid single embryo transfers between October 2015 and January 2018. INTERVENTION(S) Collection and analysis of baseline characteristics, cycle parameters, and outcomes. MAIN OUTCOME MEASURE(S) Embryo morphokinetic measurements assessed with time-lapse imaging for time to syngamy (TPNf), time to two cells, time to three cells, time to four cells, time to eight cells, time to morula, and time to blastocyst. RESULT(S) The study included 192 euploid single-embryo transfers. Of these, the pregnancy rate was 78% (150 of 193) and the live-birth rate was 63% (121 of 193). There were 43 transfers that did not result in pregnancy, 15 biochemical pregnancy losses, 13 clinical losses, and 121 live births. There was no statistically significant difference in age, body mass index, or number of oocytes retrieved between the groups. Unadjusted and adjusted models revealed no differences in the morphokinetics of embryos resulting in euploid miscarriage compared with those resulting in live birth. CONCLUSION(S) Embryos that resulted in a euploid miscarriage did not display evidence of abnormal morphokinetics on time-lapse imaging. Euploid pregnancy loss is likely multifactorial, including both embryo and endometrial factors. Further research is needed to identify factors that can predict and prevent euploid loss.
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Masset H, Zamani Esteki M, Dimitriadou E, Dreesen J, Debrock S, Derhaag J, Derks K, Destouni A, Drüsedau M, Meekels J, Melotte C, Peeraer K, Tšuiko O, van Uum C, Allemeersch J, Devogelaere B, François KO, Happe S, Lorson D, Richards RL, Theuns J, Brunner H, de Die-Smulders C, Voet T, Paulussen A, Coonen E, Vermeesch JR. Multi-centre evaluation of a comprehensive preimplantation genetic test through haplotyping-by-sequencing. Hum Reprod 2020; 34:1608-1619. [PMID: 31348829 DOI: 10.1093/humrep/dez106] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/16/2019] [Indexed: 12/14/2022] Open
Abstract
STUDY QUESTION Can reduced representation genome sequencing offer an alternative to single nucleotide polymorphism (SNP) arrays as a generic and genome-wide approach for comprehensive preimplantation genetic testing for monogenic disorders (PGT-M), aneuploidy (PGT-A) and structural rearrangements (PGT-SR) in human embryo biopsy samples? SUMMARY ANSWER Reduced representation genome sequencing, with OnePGT, offers a generic, next-generation sequencing-based approach for automated haplotyping and copy-number assessment, both combined or independently, in human single blastomere and trophectoderm samples. WHAT IS KNOWN ALREADY Genome-wide haplotyping strategies, such as karyomapping and haplarithmisis, have paved the way for comprehensive PGT, i.e. leveraging PGT-M, PGT-A and PGT-SR in a single workflow. These methods are based upon SNP array technology. STUDY DESIGN, SIZE, DURATION This multi-centre verification study evaluated the concordance of PGT results for a total of 225 embryos, including 189 originally tested for a monogenic disorder and 36 tested for a translocation. Concordance for whole chromosome aneuploidies was also evaluated where whole genome copy-number reference data were available. Data analysts were kept blind to the results from the reference PGT method. PARTICIPANTS/MATERIALS, SETTING, METHODS Leftover blastomere/trophectoderm whole genome amplified (WGA) material was used, or secondary trophectoderm biopsies were WGA. A reduced representation library from WGA DNA together with bulk DNA from phasing references was processed across two study sites with the Agilent OnePGT solution. Libraries were sequenced on an Illumina NextSeq500 system, and data were analysed with Agilent Alissa OnePGT software. The embedded PGT-M pipeline utilises the principles of haplarithmisis to deduce haplotype inheritance whereas both the PGT-A and PGT-SR pipelines are based upon read-count analysis in order to evaluate embryonic ploidy. Concordance analysis was performed for both analysis strategies against the reference PGT method. MAIN RESULTS AND THE ROLE OF CHANCE PGT-M analysis was performed on 189 samples. For nine samples, the data quality was too poor to analyse further, and for 20 samples, no result could be obtained mainly due to biological limitations of the haplotyping approach, such as co-localisation of meiotic crossover events and nullisomy for the chromosome of interest. For the remaining 160 samples, 100% concordance was obtained between OnePGT and the reference PGT-M method. Equally for PGT-SR, 100% concordance for all 36 embryos tested was demonstrated. Moreover, with embryos originally analysed for PGT-M or PGT-SR for which genome-wide copy-number reference data were available, 100% concordance was shown for whole chromosome copy-number calls (PGT-A). LIMITATIONS, REASONS FOR CAUTION Inherent to haplotyping methodologies, processing of additional family members is still required. Biological limitations caused inconclusive results in 10% of cases. WIDER IMPLICATIONS OF THE FINDINGS Employment of OnePGT for PGT-M, PGT-SR, PGT-A or combined as comprehensive PGT offers a scalable platform, which is inherently generic and thereby, eliminates the need for family-specific design and optimisation. It can be considered as both an improvement and complement to the current methodologies for PGT. STUDY FUNDING/COMPETING INTEREST(S) Agilent Technologies, the KU Leuven (C1/018 to J.R.V. and T.V.) and the Horizon 2020 WIDENLIFE (692065 to J.R.V. and T.V). H.M. is supported by the Research Foundation Flanders (FWO, 11A7119N). M.Z.E, J.R.V. and T.V. are co-inventors on patent applications: ZL910050-PCT/EP2011/060211- WO/2011/157846 'Methods for haplotyping single cells' and ZL913096-PCT/EP2014/068315 'Haplotyping and copy-number typing using polymorphic variant allelic frequencies'. T.V. and J.R.V. are co-inventors on patent application: ZL912076-PCT/EP2013/070858 'High-throughput genotyping by sequencing'. Haplarithmisis ('Haplotyping and copy-number typing using polymorphic variant allelic frequencies') has been licensed to Agilent Technologies. The following patents are pending for OnePGT: US2016275239, AU2014345516, CA2928013, CN105874081, EP3066213 and WO2015067796. OnePGT is a registered trademark. D.L., J.T. and R.L.R. report personal fees during the conduct of the study and outside the submitted work from Agilent Technologies. S.H. and K.O.F. report personal fees and other during the conduct of the study and outside the submitted work from Agilent Technologies. J.A. reports personal fees and other during the conduct of the study from Agilent Technologies and personal fees from Agilent Technologies and UZ Leuven outside the submitted work. B.D. reports grants from IWT/VLAIO, personal fees during the conduct of the study from Agilent Technologies and personal fees and other outside the submitted work from Agilent Technologies. In addition, B.D. has a patent 20160275239 - Genetic Analysis Method pending. The remaining authors have no conflicts of interest.
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Affiliation(s)
- Heleen Masset
- Laboratory for Cytogenetics and Genome Research, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Masoud Zamani Esteki
- Laboratory for Cytogenetics and Genome Research, Department of Human Genetics, KU Leuven, Leuven, Belgium.,Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands.,Research Institute GROW, Maastricht University Medical Centre, Maastricht, The Netherlands
| | | | - Jos Dreesen
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands.,Research Institute GROW, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Sophie Debrock
- Leuven University Fertility Center, University Hospitals Leuven, Leuven, Belgium
| | - Josien Derhaag
- Research Institute GROW, Maastricht University Medical Centre, Maastricht, The Netherlands.,Department of Obstetrics and Gynaecology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Kasper Derks
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Aspasia Destouni
- Laboratory for Cytogenetics and Genome Research, Department of Human Genetics, KU Leuven, Leuven, Belgium.,Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA.,Department of Comparative Biomedical Sciences, Louisiana State University School of Veterinary Medicine, Baton Rouge, LA, USA
| | - Marion Drüsedau
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Jeroen Meekels
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Cindy Melotte
- Center for Human Genetics, University Hospitals of Leuven, Leuven, Belgium
| | - Karen Peeraer
- Leuven University Fertility Center, University Hospitals Leuven, Leuven, Belgium
| | - Olga Tšuiko
- Laboratory for Cytogenetics and Genome Research, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Chris van Uum
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Joke Allemeersch
- Diagnostics and Genomics Group, Agilent Technologies, Heverlee, Belgium
| | | | | | - Scott Happe
- Diagnostics and Genomics Group, Agilent Technologies, Cedar Creek, TX, USA
| | - Dennis Lorson
- Diagnostics and Genomics Group, Agilent Technologies, Heverlee, Belgium
| | - Rebecca Louise Richards
- Diagnostics and Genomics Group, Agilent Technologies, Heverlee, Belgium.,Diagnostics and Genomics Group, Agilent Technologies, Niel, Belgium
| | - Jessie Theuns
- Diagnostics and Genomics Group, Agilent Technologies, Niel, Belgium
| | - Han Brunner
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands.,Research Institute GROW, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Christine de Die-Smulders
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands.,Research Institute GROW, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Thierry Voet
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Aimée Paulussen
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands.,Research Institute GROW, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Edith Coonen
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands.,Research Institute GROW, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Joris Robert Vermeesch
- Laboratory for Cytogenetics and Genome Research, Department of Human Genetics, KU Leuven, Leuven, Belgium.,Center for Human Genetics, University Hospitals of Leuven, Leuven, Belgium
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Next-generation sequencing analysis of each blastomere in good-quality embryos: insights into the origins and mechanisms of embryonic aneuploidy in cleavage-stage embryos. J Assist Reprod Genet 2020; 37:1711-1718. [PMID: 32445153 DOI: 10.1007/s10815-020-01803-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 04/28/2020] [Indexed: 01/06/2023] Open
Abstract
PURPOSE To explore the whole-chromosome status, origins, and mechanisms of chromosomal abnormalities in good-quality cleavage embryos using multiple annealing and looping-based amplification cycle (MALBAC) sequencing. METHODS The embryos studied came from7 patients (maternal aged 26-35) who had healthy birth from the same IVF cycles. These 21 frozen day 3 good-quality embryos were thawed and disaggregated into individual blastomere. Each blastomere was collected and analyzed by MALBAC sequencing. RESULTS Conclusive results were obtained from a high percentage of blastomeres (95.3%). A total of 46.6% of blastomeres were diploid, 53.4% were abnormal, and 28.0% had complex aneuploidy. Out of 21 embryos, 3 (14.3%) were normal and 18 (85.7%) were mosaics, showing the occurrence of mitotic errors; aneuploidy was confirmed in all cells of 4 of the 18 embryos, which showed the coexistence of meiotic errors. Conclusive results were obtained from all blastomeres of 15 embryos (71.4%, 15/21), which enabled us to reconstruct the cell lineage on the basis of the chromosomal content of the blastomeres in each division. There were 9 mitotic errors (8.7%, 9/103): nondisjunction accounted for 88.9% (8/9), and endoreplication accounted for 11.1% (1/9). CONCLUSIONS In good-quality embryos, there was a high rate and diverse array of chromosomal abnormalities. Morphological evaluation does not appear to assist in the reduction in meiotic errors from parental origins. Mitotic errors were common, and nondisjunction was found to be the main mechanism causing malsegregation during the cleavage divisions.
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21
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Tyc KM, McCoy RC, Schindler K, Xing J. Mathematical modeling of human oocyte aneuploidy. Proc Natl Acad Sci U S A 2020; 117:10455-10464. [PMID: 32350135 PMCID: PMC7229693 DOI: 10.1073/pnas.1912853117] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Aneuploidy is the leading contributor to pregnancy loss, congenital anomalies, and in vitro fertilization (IVF) failure in humans. Although most aneuploid conceptions are thought to originate from meiotic division errors in the female germline, quantitative studies that link the observed phenotypes to underlying error mechanisms are lacking. In this study, we developed a mathematical modeling framework to quantify the contribution of different mechanisms of erroneous chromosome segregation to the production of aneuploid eggs. Our model considers the probabilities of all possible chromosome gain/loss outcomes that arise from meiotic errors, such as nondisjunction (NDJ) in meiosis I and meiosis II, and premature separation of sister chromatids (PSSC) and reverse segregation (RS) in meiosis I. To understand the contributions of different meiotic errors, we fit our model to aneuploidy data from 11,157 blastocyst-stage embryos. Our best-fitting model captures several known features of female meiosis, for instance, the maternal age effect on PSSC. More importantly, our model reveals previously undescribed patterns, including an increased frequency of meiosis II errors among eggs affected by errors in meiosis I. This observation suggests that the occurrence of NDJ in meiosis II is associated with the ploidy status of an egg. We further demonstrate that the model can be used to identify IVF patients who produce an extreme number of aneuploid embryos. The dynamic nature of our mathematical model makes it a powerful tool both for understanding the relative contributions of mechanisms of chromosome missegregation in human female meiosis and for predicting the outcomes of assisted reproduction.
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Affiliation(s)
- Katarzyna M Tyc
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, NJ 08854
- Human Genetic Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ 08854
| | - Rajiv C McCoy
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
| | - Karen Schindler
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, NJ 08854
- Human Genetic Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ 08854
| | - Jinchuan Xing
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, NJ 08854;
- Human Genetic Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ 08854
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22
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The mechanisms and clinical application of mosaicism in preimplantation embryos. J Assist Reprod Genet 2019; 37:497-508. [PMID: 31838629 DOI: 10.1007/s10815-019-01656-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 12/05/2019] [Indexed: 02/08/2023] Open
Abstract
Embryos containing distinct cell lines are referred to as mosaic embryos, which are considered to be caused by mitotic errors in chromosome segregation during preimplantation development. As the accuracy and resolution of detection techniques improve, more and more mosaic embryos were identified recently. The impacts of mosaic embryos on survival and potential pregnancy outcome have been reported to be diverse in different studies. Because of the universality and clinical significance of mosaicism, it is essential to unravel the mechanisms and consequences with regard to this phenomenon in human pre- and post-implantation embryos. The purpose of this review is to explore the mechanisms, causes of mosaicism, and the development of pre- and post-implantation mosaic embryos in the light of recent emerging data, with the aim of providing new references for clinical applications.
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23
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Pericentric inversion (Inv) 9 variant-reproductive risk factor or benign finding? J Assist Reprod Genet 2019; 36:2557-2561. [PMID: 31734857 PMCID: PMC6910900 DOI: 10.1007/s10815-019-01601-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 10/09/2019] [Indexed: 11/24/2022] Open
Abstract
Purpose To report the unbalanced chromosome rearrangement rate and overall aneuploidy rate in day 5/6 embryos from a series of patients who underwent in vitro fertilization (IVF) with preimplantation genetic testing for structural rearrangements (PGT-SR) for the pericentric inversion 9 variant, inv(9)(p11q13) or inv(9)(p12q13), with concurrent 24 chromosome preimplantation genetic testing for aneuploidy (PGT-A). Methods This was a retrospective cohort analysis. IVF cycles and embryo biopsies were performed by referring clinics. Fifty-two trophectoderm biopsy samples from seven couples were sent to a single lab for PGT-SR for an inversion 9 variant with concurrent 24 chromosome PGT-A using single-nucleotide polymorphism (SNP) microarrays with bioinformatics. Results The unbalanced rearrangement rate for this embryo cohort was 0/52 (0.0%); mean maternal age per embryo was 33.3 years (range 21–39 years). The overall euploid rate was 61.5% and aneuploidy rate was 38.5%. Conclusions Chromosome 9 pericentric inversions did not result in unbalanced structural rearrangements in day 5/6 embryo samples, supporting that this population variant is not associated with increased reproductive risks.
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24
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Maisenbacher MK, Merrion K, Kutteh WH. Single-nucleotide polymorphism microarray detects molar pregnancies in 3% of miscarriages. Fertil Steril 2019; 112:700-706. [DOI: 10.1016/j.fertnstert.2019.06.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/24/2019] [Accepted: 06/10/2019] [Indexed: 11/16/2022]
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25
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Escribà MJ, Vendrell X, Peinado V. Segmental aneuploidy in human blastocysts: a qualitative and quantitative overview. Reprod Biol Endocrinol 2019; 17:76. [PMID: 31526391 PMCID: PMC6745804 DOI: 10.1186/s12958-019-0515-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 08/19/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Microarray-based and next generation sequencing (NGS) technologies have revealed that segmental aneuploidy is frequently present in human oocytes, cleavage-stage embryos and blastocysts. However, very little research has analyzed the type, size, chromosomal distribution and topography of the chromosomal segments at the different stages of development. METHODS This is a retrospective study of 822 PGT-A (preimplantation genetic test for aneuploidies) performed on trophectoderm samples from 3565 blastocysts biopsied between January 2016 and April 2017. The cycles in question had been initiated for varying clinical indications. Samples were analyzed by next generation sequencing-based technology. Segmental aneuploidies were evaluated when fragment size was > 5 Mb. Blastocysts presenting a single segmental aneuploidy (SSA), without any additional whole-chromosome gain/loss, were statistically analyzed for incidence, type, size and chromosomal emplacement. Segment sizes relative to the whole chromosome or arm (chromosome- and arm-ratios) were also studied. RESULTS 8.4% (299/3565) of blastocysts exhibited segmental aneuploidy for one or more chromosomes, some of which were associated with whole-chromosome aneuploidy while others were not. Nearly half of them (4.5%: 159/3565 of blastocysts) exhibited pure-SSA, meaning that a single chromosome was affected by a SSA. Segments were more frequent in medium-sized metacentric or submetacentric chromosomes and particularly in q-chrmosome arms, variables that were related to trophectoderm quality. SSA size was related to a greater extent to chromosome number and the arm affected than it was to SSA type. In absolute values (Mb), SSA size was larger in large chromosomes. However, the SSA:chromosome ratio was constant across all chromosomes and never exceeded 50% of the chromosome. CONCLUSIONS SSA frequency is chromosome- and topographically dependent, and its incidence is not related to clinical or embryological factors, but rather to trophectoderm quality. SSA might be originated by chromosome instability in response to chromothripsis, bias introduced by the biopsy and/or iatrogenic effects. TRIAL REGISTRATION Retrospectively registered.
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Affiliation(s)
| | - Xavier Vendrell
- Reproductive Genetics Unit, Sistemas Genómicos, Parque Tecnológico Paterna, 46980, Valencia, Spain
| | - Vanessa Peinado
- Igenomix, Parque Tecnológico Paterna, 46980, Valencia, Spain
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26
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Simpson JL, Kuliev A, Rechitsky S. Overview of Preimplantation Genetic Diagnosis (PGD): Historical Perspective and Future Direction. Methods Mol Biol 2019; 1885:23-43. [PMID: 30506188 DOI: 10.1007/978-1-4939-8889-1_2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Preimplantation genetic diagnosis (PGD) can be considered the earliest form of prenatal testing. It was first used in humans over 26 years ago. At its inception, PGD could only be performed for a limited number of genetic disorders. Technological advances in molecular biology and cytogenomics have been utilized in the field of PGD to greatly expand the spectrum of genetic disorders that can now be detected in early human embryos.
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Affiliation(s)
- Joe Leigh Simpson
- March of Dimes Foundation, White Plains, NY, USA. .,Florida International University, Miami, FL, USA. .,Reproductive Genetics Institute, Inc. (RGI), Northbrook, IL, USA.
| | - Anver Kuliev
- Florida International University, Miami, FL, USA.,Reproductive Genetics Institute, Inc. (RGI), Northbrook, IL, USA
| | - Svetlana Rechitsky
- Florida International University, Miami, FL, USA.,Reproductive Genetics Institute, Inc. (RGI), Northbrook, IL, USA
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27
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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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28
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Daughtry BL, Rosenkrantz JL, Lazar NH, Fei SS, Redmayne N, Torkenczy KA, Adey A, Yan M, Gao L, Park B, Nevonen KA, Carbone L, Chavez SL. Single-cell sequencing of primate preimplantation embryos reveals chromosome elimination via cellular fragmentation and blastomere exclusion. Genome Res 2019; 29:367-382. [PMID: 30683754 PMCID: PMC6396419 DOI: 10.1101/gr.239830.118] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 01/22/2019] [Indexed: 12/12/2022]
Abstract
Aneuploidy that arises during meiosis and/or mitosis is a major contributor to early embryo loss. We previously showed that human preimplantation embryos encapsulate missegregated chromosomes into micronuclei while undergoing cellular fragmentation and that fragments can contain chromosomal material, but the source of this DNA was unknown. Here, we leveraged the use of a nonhuman primate model and single-cell DNA-sequencing (scDNA-seq) to examine the chromosomal content of 471 individual samples comprising 254 blastomeres, 42 polar bodies, and 175 cellular fragments from a large number (N = 50) of disassembled rhesus cleavage-stage embryos. Our analysis revealed that the aneuploidy and micronucleation frequency is conserved between humans and macaques, and that fragments encapsulate whole and/or partial chromosomes lost from blastomeres. Single-cell/fragment genotyping showed that these chromosome-containing cellular fragments (CCFs) can be maternally or paternally derived and display double-stranded DNA breaks. DNA breakage was further indicated by reciprocal subchromosomal losses/gains between blastomeres and large segmental errors primarily detected at the terminal ends of chromosomes. By combining time-lapse imaging with scDNA-seq, we determined that multipolar divisions at the zygote or two-cell stage were associated with CCFs and generated a random mixture of chromosomally normal and abnormal blastomeres with uniparental or biparental origins. Despite frequent chromosome missegregation at the cleavage-stage, we show that CCFs and nondividing aneuploid blastomeres showing extensive DNA damage are prevented from incorporation into blastocysts. These findings suggest that embryos respond to chromosomal errors by encapsulation into micronuclei, elimination via cellular fragmentation, and selection against highly aneuploid blastomeres to overcome chromosome instability during preimplantation development.
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Affiliation(s)
- Brittany L Daughtry
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University School of Medicine, Portland, Oregon 97239, USA.,Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Beaverton, Oregon 97006, USA
| | - Jimi L Rosenkrantz
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Beaverton, Oregon 97006, USA.,Department of Molecular and Medical Genetics, Oregon Health and Science University School of Medicine, Portland, Oregon 97239, USA
| | - Nathan H Lazar
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University School of Medicine, Portland, Oregon 97239, USA
| | - Suzanne S Fei
- Bioinformatics and Biostatistics Core, Oregon National Primate Research Center, Beaverton, Oregon 97006, USA
| | - Nash Redmayne
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Beaverton, Oregon 97006, USA
| | - Kristof A Torkenczy
- Department of Molecular and Medical Genetics, Oregon Health and Science University School of Medicine, Portland, Oregon 97239, USA
| | - Andrew Adey
- Department of Molecular and Medical Genetics, Oregon Health and Science University School of Medicine, Portland, Oregon 97239, USA.,Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University School of Medicine, Portland, Oregon 97239, USA
| | - Melissa Yan
- Bioinformatics and Biostatistics Core, Oregon National Primate Research Center, Beaverton, Oregon 97006, USA
| | - Lina Gao
- Bioinformatics and Biostatistics Core, Oregon National Primate Research Center, Beaverton, Oregon 97006, USA
| | - Byung Park
- Bioinformatics and Biostatistics Core, Oregon National Primate Research Center, Beaverton, Oregon 97006, USA
| | - Kimberly A Nevonen
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University School of Medicine, Portland, Oregon 97239, USA
| | - Lucia Carbone
- Department of Molecular and Medical Genetics, Oregon Health and Science University School of Medicine, Portland, Oregon 97239, USA.,Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University School of Medicine, Portland, Oregon 97239, USA.,Bioinformatics and Biostatistics Core, Oregon National Primate Research Center, Beaverton, Oregon 97006, USA.,Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University School of Medicine, Portland, Oregon 97239, USA.,Division of Primate Genetics, Oregon National Primate Research Center, Beaverton, Oregon 97006, USA
| | - Shawn L Chavez
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Beaverton, Oregon 97006, USA.,Department and Physiology and Pharmacology, Oregon Health and Science University School of Medicine, Portland, Oregon 97239, USA.,Department of Obstetrics and Gynecology, Oregon Health and Science University School of Medicine, Portland, Oregon 97239, USA.,Department of Biomedical Engineering, Oregon Health and Science University School of Medicine, Portland, Oregon 97239, USA
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29
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Griffin DK, Ogur C. Chromosomal analysis in IVF: just how useful is it? Reproduction 2018; 156:F29-F50. [PMID: 29945889 DOI: 10.1530/rep-17-0683] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 03/23/2018] [Indexed: 12/11/2022]
Abstract
Designed to minimize chances of genetically abnormal embryos, preimplantation genetic diagnosis (PGD) involves in vitro fertilization (IVF), embryo biopsy, diagnosis and selective embryo transfer. Preimplantation genetic testing for aneuploidy (PGT-A) aims to avoid miscarriage and live born trisomic offspring and to improve IVF success. Diagnostic approaches include fluorescence in situ hybridization (FISH) and more contemporary comprehensive chromosome screening (CCS) including array comparative genomic hybridization (aCGH), quantitative polymerase chain reaction (PCR), next-generation sequencing (NGS) and karyomapping. NGS has an improved dynamic range, and karyomapping can detect chromosomal and monogenic disorders simultaneously. Mosaicism (commonplace in human embryos) can arise by several mechanisms; those arising initially meiotically (but with a subsequent post-zygotic 'trisomy rescue' event) usually lead to adverse outcomes, whereas the extent to which mosaics that are initially chromosomally normal (but then arise purely post-zygotically) can lead to unaffected live births is uncertain. Polar body (PB) biopsy is the least common sampling method, having drawbacks including cost and inability to detect any paternal contribution. Historically, cleavage-stage (blastomere) biopsy has been the most popular; however, higher abnormality levels, mosaicism and potential for embryo damage have led to it being superseded by blastocyst (trophectoderm - TE) biopsy, which provides more cells for analysis. Improved biopsy, diagnosis and freeze-all strategies collectively have the potential to revolutionize PGT-A, and there is increasing evidence of their combined efficacy. Nonetheless, PGT-A continues to attract criticism, prompting questions of when we consider the evidence base sufficient to justify routine PGT-A? Basic biological research is essential to address unanswered questions concerning the chromosome complement of human embryos, and we thus entreat companies, governments and charities to fund more. This will benefit both IVF patients and prospective parents at risk of aneuploid offspring following natural conception. The aim of this review is to appraise the 'state of the art' in terms of PGT-A, including the controversial areas, and to suggest a practical 'way forward' in terms of future diagnosis and applied research.
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Affiliation(s)
- Darren K Griffin
- School of BiosciencesCentre for Interdisciplinary Studies of Reproduction, University of Kent, Canterbury, UK
| | - Cagri Ogur
- Bahceci Genetic Diagnosis Centerİstanbul, Turkey.,Department of BioengineeringYildiz Technical University, İstanbul, Turkey
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30
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Guzman L, Nuñez D, López R, Inoue N, Portella J, Vizcarra F, Noriega-Portella L, Noriega-Hoces L, Munné S. The number of biopsied trophectoderm cells may affect pregnancy outcomes. J Assist Reprod Genet 2018; 36:145-151. [PMID: 30328573 DOI: 10.1007/s10815-018-1331-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 10/03/2018] [Indexed: 01/02/2023] Open
Abstract
OBJECTIVE To study if the number of trophectoderm (TE) biopsied cells has an impact on implantation rates. DESIGN A retrospective cohort study in a single-center study. SETTING In vitro fertilization center. PATIENTS Patients who underwent PGT-A from January 2013 to March 2016. In total, 482 vitrified/warmed single embryo transfers were included. INTERVENTIONS None. MAIN OUTCOME MEASURES Clinical pregnancies rate, implantation rate. RESULTS Overall, clinical pregnancies per embryo transfer were higher when a regular TE were biopsied compared to larger size biopsy cells (66% (175/267) vs 53% (115/215) (p < 0.005) respectively). Pregnancy rates were also analyzed according to embryo morphology at the moment of embryo biopsy, when a good-quality embryo was transferred the clinical outcome was 75% (81/108) in group 1 and 61% (60/99) in group 2 (p < 0.05). Data was also stratified by age in patients ≤ 35 years and > 35 years. The clinical pregnancy was 67% (51/76) in women ≤ 35 years and 65% (124/191) in women > 35 years when a regular size biopsy was performed. These results significantly reduced when a larger size biopsy was performed 54% (49/91) and 53% (66/124), respectively (p < 0.05). Further investigation indicated that miscarriage rate was similar between these groups (4% (7/182) in group 1 and 5% (6/121) in group 2). CONCLUSIONS These findings underscore that when a large amount of TE cells are biopsied, it may negatively affect implantation rates, but once implanted, the embryos have the same chance to miscarry or reach term.
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Affiliation(s)
- Luis Guzman
- PRANOR Laboratorio, Grupo de Reproducción Asistida, Av. Monterrico 1045, Urb El Derby de Monterrico, 33, Lima, Peru. .,ADN Diagnostico, Calle Los Olivos 364. San Isidro, 33, Lima, Peru.
| | - D Nuñez
- PRANOR Laboratorio, Grupo de Reproducción Asistida, Av. Monterrico 1045, Urb El Derby de Monterrico, 33, Lima, Peru
| | - R López
- ADN Diagnostico, Calle Los Olivos 364. San Isidro, 33, Lima, Peru
| | - N Inoue
- PRANOR Laboratorio, Grupo de Reproducción Asistida, Av. Monterrico 1045, Urb El Derby de Monterrico, 33, Lima, Peru
| | - J Portella
- PRANOR Laboratorio, Grupo de Reproducción Asistida, Av. Monterrico 1045, Urb El Derby de Monterrico, 33, Lima, Peru
| | - F Vizcarra
- Clínica Monterrico, Av. Monterrico 1045. Urb El Derby de Monterrico, 33, Lima, Peru
| | - L Noriega-Portella
- PRANOR Laboratorio, Grupo de Reproducción Asistida, Av. Monterrico 1045, Urb El Derby de Monterrico, 33, Lima, Peru.,Clínica Monterrico, Av. Monterrico 1045. Urb El Derby de Monterrico, 33, Lima, Peru
| | - L Noriega-Hoces
- PRANOR Laboratorio, Grupo de Reproducción Asistida, Av. Monterrico 1045, Urb El Derby de Monterrico, 33, Lima, Peru.,Clínica Monterrico, Av. Monterrico 1045. Urb El Derby de Monterrico, 33, Lima, Peru
| | - S Munné
- CooperGenomics, Livingston, NJ, 0703, USA
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31
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Pregnancy outcomes from more than 1,800 in vitro fertilization cycles with the use of 24-chromosome single-nucleotide polymorphism–based preimplantation genetic testing for aneuploidy. Fertil Steril 2018; 110:113-121. [DOI: 10.1016/j.fertnstert.2018.03.026] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 03/15/2018] [Accepted: 03/19/2018] [Indexed: 11/20/2022]
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32
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Handyside AH. ‘Designer babies’ almost thirty years on. Reproduction 2018; 156:F75-F79. [DOI: 10.1530/rep-18-0157] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 06/12/2018] [Indexed: 11/08/2022]
Abstract
The first pregnancies and live births following in vitro fertilisation (IVF) and preimplantation genetic testing (PGT), formerly known as preimplantation genetic diagnosis, were reported in 1990, almost 30 years ago, in several couples at risk of X-linked inherited conditions, which typically only affect boys inheriting the X chromosome with the affected gene from their carrier mothers. At that time, it was only possible to identify the sex of the embryo by amplifying a Y-linked repeat sequence in single cells biopsied at cleavage stages and avoid the transfer of males, half of which would be affected. The extensive publicity surrounding these cases and the perceived risk of using IVF and PGT for desirable characteristics not related to health, such as sex selection, led to the epithet of ‘designer babies’ which continues to resonate to this day. Here, I briefly reflect on how the technology of PGT has evolved over the decades and whether it deserves this reputation. With efficient methods for whole genome amplification and the genomic revolution, we now have highly accurate universal tests that combine marker-based diagnosis of almost any monogenic disorder with the detection of aneuploidy. PGT is now clinically well established and is likely to remain a valuable alternative for couples at risk of having affected children.
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Glinsky G, Durruthy-Durruthy J, Wossidlo M, Grow EJ, Weirather JL, Au KF, Wysocka J, Sebastiano V. Single cell expression analysis of primate-specific retroviruses-derived HPAT lincRNAs in viable human blastocysts identifies embryonic cells co-expressing genetic markers of multiple lineages. Heliyon 2018; 4:e00667. [PMID: 30003161 PMCID: PMC6039856 DOI: 10.1016/j.heliyon.2018.e00667] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 02/01/2018] [Accepted: 06/21/2018] [Indexed: 12/03/2022] Open
Abstract
Chromosome instability and aneuploidies occur very frequently in human embryos, impairing proper embryogenesis and leading to cell cycle arrest, loss of cell viability, and developmental failures in 50–80% of cleavage-stage embryos. This high frequency of cellular extinction events represents a significant experimental obstacle challenging analyses of individual cells isolated from human preimplantation embryos. We carried out single cell expression profiling of 241 individual cells recovered from 32 human embryos during the early and late stages of viable human blastocyst (VHB) differentiation. Classification of embryonic cells was performed solely based on expression patterns of human pluripotency-associated transcripts (HPAT), which represent a family of primate-specific transposable element-derived lincRNAs highly expressed in human embryonic stem cells and regulating nuclear reprogramming and pluripotency induction. We then validated our findings by analyzing transcriptomes of 1,708 individual cells recovered from more than 100 human embryos and 259 mouse cells from more than 40 mouse embryos at different stages of preimplantation embryogenesis. HPAT's expression-guided spatiotemporal reconstruction of human embryonic development inferred from single-cell expression analysis of VHB differentiation enabled identification of telomerase-positive embryonic cells co-expressing key pluripotency regulatory genes and genetic markers of three major lineages. Follow-up validation analyses confirmed the emergence in human embryos prior to lineage segregation of telomerase-positive cells co-expressing genetic markers of multiple lineages. Observations reported in this contribution support the hypothesis of a developmental pathway of creation embryonic lineages and extraembryonic tissues from telomerase-positive pre-lineage cells manifesting multi-lineage precursor phenotype.
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Affiliation(s)
- Gennadi Glinsky
- Institute of Engineering in Medicine, University of California, San Diego, 9500 Gilman Dr. MC 0435, La Jolla, CA 92093-0435, USA
| | - Jens Durruthy-Durruthy
- Department of Obstetrics and Gynecology, Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Mark Wossidlo
- Department of Cell- and Developmental Biology, Center of Anatomy and Cell Biology, Schwarzspanierstrasse 17, 1090 Vienna, Austria
| | - Edward J Grow
- Department of Chemical and Systems Biology, Stanford University, Stanford, California, USA
| | - Jason L Weirather
- Department of Internal Medicine, University of Iowa, Iowa City, IA, USA.,Department of Biostatistics, University of Iowa, Iowa City, IA, USA
| | - Kin Fai Au
- Department of Internal Medicine, University of Iowa, Iowa City, IA, USA.,Department of Biostatistics, University of Iowa, Iowa City, IA, USA
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University, Stanford, California, USA
| | - Vittorio Sebastiano
- Department of Obstetrics and Gynecology, Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
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Li P, Song Z, Yao Y, Huang T, Mao R, Huang J, Ma Y, Dong X, Huang W, Huang J, Chen T, Qu T, Li L, Zhong Y, Gu J. Preimplantation Genetic Screening with Spent Culture Medium/Blastocoel Fluid for in Vitro Fertilization. Sci Rep 2018; 8:9275. [PMID: 29915225 PMCID: PMC6006313 DOI: 10.1038/s41598-018-27367-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 05/18/2018] [Indexed: 02/05/2023] Open
Abstract
Preimplantation genetic screening (PGS) detects chromosomal aneuploidy from DNA extracted from trophectodermal biopsy of the embryos before implantation. Although a controlled study showed no difference in pregnancy rates between this invasive cell biopsy technique and a non-biopsied control group, the potential long-term damage by the current PGS method has not be completely ruled out. We therefore tested a less-invasive protocol which utilizes spent culture medium combining with blastocoel fluid (ECB) to assess chromosomal aneuploidy. We compared the new protocol with the currently employed trophectodermal biopsy method against chromosomal information obtained from the remaining embryo. We found that the new technique generated information about aneuploidy that was not entirely identical to obtained from the biopsied trophectoderm or the remaining embryo. As the origins of the DNA extracted from the three sample types were not the same, the significance and interpretation of each result would have its own meaning. The possible implications derived from the ECB results as well as those from cell biopsy were discussed. The effectiveness of this new approach in selecting the best embryo for uterine implantation awaits further long term evaluation.
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Affiliation(s)
- Penghao Li
- Jinxin Research Institute for Reproductive Medicine and Genetics, Chengdu Jinjiang Hospital for Maternal and Child Health Care, 66 Jingxiu Road, Chengdu, 610066, China
| | - Zhe Song
- Laboratory of Molecular Pathology, Center of Molecular Diagnosis and Personalized Medicine, Provincial Key Laboratory of Infectious Diseases and Molecular Pathology, Shantou University Medical College, Shantou, China
| | - Yaxin Yao
- Department of Clinical Research, Yikon Genomics Co. Ltd., Building 26, 1698 Wangyuan Road, Fengxian District, Shanghai, 201499, China
| | - Tianhua Huang
- Jinxin Research Institute for Reproductive Medicine and Genetics, Chengdu Jinjiang Hospital for Maternal and Child Health Care, 66 Jingxiu Road, Chengdu, 610066, China
| | - Rurong Mao
- Jinxin Research Institute for Reproductive Medicine and Genetics, Chengdu Jinjiang Hospital for Maternal and Child Health Care, 66 Jingxiu Road, Chengdu, 610066, China
| | - Jun Huang
- Jinxin Research Institute for Reproductive Medicine and Genetics, Chengdu Jinjiang Hospital for Maternal and Child Health Care, 66 Jingxiu Road, Chengdu, 610066, China
| | - Yongyi Ma
- Jinxin Research Institute for Reproductive Medicine and Genetics, Chengdu Jinjiang Hospital for Maternal and Child Health Care, 66 Jingxiu Road, Chengdu, 610066, China
| | - Xin Dong
- Jinxin Research Institute for Reproductive Medicine and Genetics, Chengdu Jinjiang Hospital for Maternal and Child Health Care, 66 Jingxiu Road, Chengdu, 610066, China
| | - Wenlong Huang
- Laboratory of Molecular Pathology, Center of Molecular Diagnosis and Personalized Medicine, Provincial Key Laboratory of Infectious Diseases and Molecular Pathology, Shantou University Medical College, Shantou, China
| | - Jihua Huang
- Jinxin Research Institute for Reproductive Medicine and Genetics, Chengdu Jinjiang Hospital for Maternal and Child Health Care, 66 Jingxiu Road, Chengdu, 610066, China
| | - Tianjian Chen
- Hayward Genetics Center, Department of Pediatrics, Tulane University School of Medicine, New Orleans, LA, USA
| | - Ting Qu
- Jinxin Research Institute for Reproductive Medicine and Genetics, Chengdu Jinjiang Hospital for Maternal and Child Health Care, 66 Jingxiu Road, Chengdu, 610066, China
| | - Lingxiao Li
- Jinxin Research Institute for Reproductive Medicine and Genetics, Chengdu Jinjiang Hospital for Maternal and Child Health Care, 66 Jingxiu Road, Chengdu, 610066, China
| | - Ying Zhong
- Jinxin Research Institute for Reproductive Medicine and Genetics, Chengdu Jinjiang Hospital for Maternal and Child Health Care, 66 Jingxiu Road, Chengdu, 610066, China.
| | - Jiang Gu
- Jinxin Research Institute for Reproductive Medicine and Genetics, Chengdu Jinjiang Hospital for Maternal and Child Health Care, 66 Jingxiu Road, Chengdu, 610066, China.
- Laboratory of Molecular Pathology, Center of Molecular Diagnosis and Personalized Medicine, Provincial Key Laboratory of Infectious Diseases and Molecular Pathology, Shantou University Medical College, Shantou, China.
- Department of Pathology, Beijing University Health Science Center, Beijing, China.
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Friedenthal J, Maxwell SM, Munné S, Kramer Y, McCulloh DH, McCaffrey C, Grifo JA. Next generation sequencing for preimplantation genetic screening improves pregnancy outcomes compared with array comparative genomic hybridization in single thawed euploid embryo transfer cycles. Fertil Steril 2018; 109:627-632. [DOI: 10.1016/j.fertnstert.2017.12.017] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 11/30/2017] [Accepted: 12/15/2017] [Indexed: 10/17/2022]
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36
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Popescu F, Jaslow CR, Kutteh WH. Recurrent pregnancy loss evaluation combined with 24-chromosome microarray of miscarriage tissue provides a probable or definite cause of pregnancy loss in over 90% of patients. Hum Reprod 2018. [DOI: 10.1093/humrep/dey021] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- F Popescu
- Department of Biology, Rhodes College, Memphis, TN 38112, USA
| | - C R Jaslow
- Department of Biology, Rhodes College, Memphis, TN 38112, USA
| | - W H Kutteh
- Division of Reproductive Endocrinology, Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Memphis, TN 38120, USA
- Director of Fertility Preservation, Department of Gynecology, St. Jude Children’s Research Center, Memphis, TN 38105, USA
- Director of Recurrent Pregnancy Loss Center, Fertility Associates of Memphis, Memphis, TN 38120, USA
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Sullivan-Pyke C, Dokras A. Preimplantation Genetic Screening and Preimplantation Genetic Diagnosis. Obstet Gynecol Clin North Am 2018; 45:113-125. [DOI: 10.1016/j.ogc.2017.10.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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38
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Gat I, Li N, Yasovich N, Antes R, Kuznyetsov V, Zohni K, Weizman NF, Librach C. Sperm DNA fragmentation index does not correlate with blastocyst euploidy rate in egg donor cycles. Gynecol Endocrinol 2018; 34:212-216. [PMID: 28972428 DOI: 10.1080/09513590.2017.1379500] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
Sperm DNA fragmentation is a known etiology for male infertility. We evaluated the impact of sperm DNA fragmentation index (DFI) on blastocyst euploidy in IVF cycles with egg donors. This observational retrospective study, which was conducted in a university affiliated fertility clinic, included IVF-ICSI-pre-implantation Genetic Screening (PGS) egg donor cycles in which DFI was tested prior to IVF, between January 1st, 2014 and July 31st, 2016. Twenty-seven cycles with DFI > 15% were included in the study group and compared with 18 cycles of DFI < 15% within control group. Research group participants had significantly lower sperm count and motility (55.4*106/ml and 37.4%, respectively) compared with controls (92.5*106/ml and 55.7%, respectively, p < .05). The groups were similar in terms of donors' demography (age, BMI), ovarian reserve (AMH, AFC) and response to hormonal stimulation (E2 level on triggering day and number of retrieved eggs). Embryo development (from 2PN through day 3 embryos to blastocysts) was similar as well. The number of biopsied blastocysts from study and control groups was 171 and 87, respectively. PGS with array comprehensive genomic hybridization revealed comparable euploidy rates of 69.3% and 67.3%, respectively (p > .05). DFI did not have an impact on the blastocyst euploidy rate in IVF cycles with egg donors.
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Affiliation(s)
- Itai Gat
- a CReATe Fertility Centre , Toronto , Canada
- b Pinchas Borenstein Talpiot Medical Leadership Program, Sheba Medical Centre , Tel Hashomer, Israel, affiliated to Sackler Medical School, Tel Aviv University , Tel Aviv , Israel
| | - Nancy Li
- a CReATe Fertility Centre , Toronto , Canada
| | | | - Ran Antes
- a CReATe Fertility Centre , Toronto , Canada
| | | | | | | | - Clifford Librach
- a CReATe Fertility Centre , Toronto , Canada
- c Department of Obstetrics and Gynecology , University of Toronto , Toronto , Canada
- d Department of Physiology , University of Toronto , Toronto , Canada
- e Department of Gynecology , Women's College Hospital , Toronto , Canada
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Abstract
PURPOSE OF REVIEW Aneuploidy is a leading cause of pregnancy failure. Although initial attempts to perform preimplantation genetic screening did not improve outcomes, validated techniques were developed to safely and effectively increase pregnancy rates. Still, many embryos designated as euploid do not implant. Current approaches are being refined to provide additional biologic insight into why this is the case. At present, the diagnosis and clinical relevance of segmental aneuploidy and mosaicism are amongst the more heavily investigated. RECENT FINDINGS Class I data have proven the safety of trophectoderm biopsy and validation studies have shown single nucleotide polymorphism array and quantitative PCR can accurately detect whole chromosome aneuploidy. Similar studies to validate next generation sequencing are underway. Although randomized control trials have demonstrated the clinical utility of preimplantation genetic screening, recent data on the impact of mosaicism and segmental aneuploidy require clarification. SUMMARY Several well powered randomized control trials have shown preimplantation genetic screening improves implantation rate. Plausible explanations for euploid failures include undetected mosaicism and segmental aneuploidy. However, the true incidence and dispersion of mosaicism within the embryo is unknown. Likewise, the resolution of detection and clinical significance of segmental aneuploidy is unclear. Further research to validate proposed detection algorithms and class I data to determine if detection impacts outcomes is needed.
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Spinella F, Fiorentino F, Biricik A, Bono S, Ruberti A, Cotroneo E, Baldi M, Cursio E, Minasi MG, Greco E. Extent of chromosomal mosaicism influences the clinical outcome of in vitro fertilization treatments. Fertil Steril 2018; 109:77-83. [DOI: 10.1016/j.fertnstert.2017.09.025] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/05/2017] [Accepted: 09/21/2017] [Indexed: 11/29/2022]
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Are blastocyst aneuploidy rates different between fertile and infertile populations? J Assist Reprod Genet 2017; 35:403-408. [PMID: 29063503 DOI: 10.1007/s10815-017-1060-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 10/05/2017] [Indexed: 10/18/2022] Open
Abstract
PURPOSE This study aimed to determine if patients with infertility or recurrent pregnancy loss have higher rates of embryo aneuploidy than fertile controls. METHODS This was a retrospective review of all pre-implantation genetic screening (PGS) cases processed by a single reference lab prior to March 2014 after a blastocyst biopsy. Cases were excluded if no indication for PGS was designated or patients were translocation carriers. The fertile control group consisted of patients undergoing IVF with PGS for sex selection only. The comparison cohorts included those with recurrent pregnancy loss, male factor infertility, unexplained infertility, prior failed IVF, or previous aneuploid conceptions. A quasi-binomial regression model was used to assess the relationship between the dependent variable, aneuploidy rate and the independent variables, maternal age and reason for PGS. A quasi-Poisson regression model was used to evaluate the relationship between similar independent variables and the number of blastocyst biopsies per case. RESULTS The initial study population consisted of 3378 IVF-PGS cycles and 18,387 analyzed trophectoderm samples. Controlling for maternal age, we observed an increased rate of aneuploidy among patients with recurrent pregnancy loss (OR 1.330, p < 0.001), prior aneuploid pregnancy (OR 1.439, p < 0.001), or previous failed IVF cycles (OR 1.356, p = 0.0012) compared to fertile controls. Patients with unexplained and male factor infertility did not have a significantly different aneuploidy rate than controls (p > 0.05). The increase in aneuploidy in patients with RPL and prior IVF failure was driven by both an increase in meiotic (OR 1.488 and 1.508, p < 0.05) and mitotic errors (1.269 and 1.393, p < 0.05) relative to fertile controls, while patients with prior aneuploid pregnancies had only an increased risk of meiotic error aneuploidies (OR 1.650, p < 0.05). CONCLUSIONS Patients with recurrent pregnancy loss, previous IVF failures, and prior aneuploid pregnancies have a significantly higher, age-independent, aneuploidy rate compared to patients without infertility.
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Zhang J, Tao W, Liu H, Yu G, Li M, Ma S, Wu K. Morphokinetic parameters from a time-lapse monitoring system cannot accurately predict the ploidy of embryos. J Assist Reprod Genet 2017; 34:1173-1178. [PMID: 28676910 DOI: 10.1007/s10815-017-0965-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 05/25/2017] [Indexed: 10/19/2022] Open
Abstract
PURPOSE This study aimed to test whether there is an association between embryo morphokinetic parameters and ploidy status. METHODS Patients with high risk of aneuploidy were analyzed by time-lapse microscopy combined with preimplantation genetic screening (PGS). Accordingly, 256 blastocysts from 75 patients were subjected to trophectoderm biopsy and microarray comparative genomic hybridization (array-CGH). Blastocyst development process was analyzed using time-lapse images. RESULTS Morphokinetic parameters: tPNf, t2, t3, t4, t5, t8, t9, tcom, tM, tSB, tB, tEB, CC1, CC2, CC3, S2, S3, t5-t2, and tB-tSB showed no significant difference in euploid embryos compared to aneuploid counterparts. In addition, two risk models based on previously published morphokinetic parameters failed to segregate euploid from aneuploid embryos. CONCLUSIONS Morphokinetic parameters subjected to investigation in the present study failed to improve the chance of selecting euploid embryos.
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Affiliation(s)
- Jingye Zhang
- Center for Reproductive Medicine, Shandong University, 157 Jingliu Road, Jinan, 250021, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, China.,The Key laboratory for Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, China
| | - Wenrong Tao
- Center for Reproductive Medicine, Shandong University, 157 Jingliu Road, Jinan, 250021, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, China.,The Key laboratory for Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, China
| | - Hui Liu
- Center for Reproductive Medicine, Shandong University, 157 Jingliu Road, Jinan, 250021, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, China.,The Key laboratory for Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, China
| | - Guanling Yu
- Center for Reproductive Medicine, Shandong University, 157 Jingliu Road, Jinan, 250021, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, China.,The Key laboratory for Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, China
| | - Mei Li
- Center for Reproductive Medicine, Shandong University, 157 Jingliu Road, Jinan, 250021, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, China.,The Key laboratory for Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, China
| | - Shuiying Ma
- Center for Reproductive Medicine, Shandong University, 157 Jingliu Road, Jinan, 250021, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, China.,The Key laboratory for Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, China
| | - Keliang Wu
- Center for Reproductive Medicine, Shandong University, 157 Jingliu Road, Jinan, 250021, China. .,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, China. .,The Key laboratory for Reproductive Endocrinology (Shandong University), Ministry of Education, Jinan, China.
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43
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Replacing single frozen-thawed euploid embryos in a natural cycle in ovulatory women may increase live birth rates compared to medicated cycles in anovulatory women. J Assist Reprod Genet 2017. [PMID: 28647784 DOI: 10.1007/s10815-017-0983-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
PURPOSE The goal of this study was to compare pregnancy outcomes between natural frozen embryo transfer (FET) cycles in ovulatory women and programmed FET cycles in anovulatory women after undergoing in vitro fertilization with preimplantation genetic screening (IVF-PGS). METHODS This was a retrospective cohort study performed at an academic medical center. Patients undergoing single FET IVF-PGS cycles between October 2011 and December 2014 were included. Patients were stratified by type of endometrial replacement: programmed cycles with estrogen/progesterone replacement and natural cycles. IVF-PGS with 24-chromosome screening was performed on all included patients. Those patients with euploid embryos had single embryo transfer in a subsequent FET. The primary study outcome was live birth/ongoing pregnancy rate. Secondary outcomes included implantation, biochemical pregnancy, and miscarriage rates. RESULTS One hundred thirteen cycles met inclusion criteria: 65 natural cycles and 48 programmed cycles. The programmed FET group was younger (35.9 ± 4.5 vs. 37.5 ± 3.7, P = 0.03) and had a higher AMH (3.95 ± 4.2 vs. 2.37 ± 2.4, P = 0.045). The groups were similar for BMI, gravidity, parity, history of uterine surgery, and incidence of Asherman's syndrome. There was also no difference in embryo grade at biopsy or transfer, and proportion of day 5 and day 6 transfers. Implantation rates were higher in the natural FET group (0.66 ± 0.48 vs. 0.44 ± 0.50, P = 0.02). There was no difference in the rates of biochemical pregnancy or miscarriage. After controlling for age, live birth/ongoing pregnancy rate was higher in natural FETs with an adjusted odds ratio of 2.68 (95% CI 1.22-5.87). CONCLUSIONS Natural FET in ovulatory women after IVF-PGS is associated with increased implantation and live birth rates compared to programmed FET in anovulatory women. Further investigation is needed to determine whether these findings hold true in other patient cohorts.
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Vermeesch JR, Voet T, Devriendt K. Prenatal and pre-implantation genetic diagnosis. Nat Rev Genet 2017; 17:643-56. [PMID: 27629932 DOI: 10.1038/nrg.2016.97] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The past decade has seen the development of technologies that have revolutionized prenatal genetic testing; that is, genetic testing from conception until birth. Genome-wide single-cell arrays and high-throughput sequencing analyses are dramatically increasing our ability to detect embryonic and fetal genetic lesions, and have substantially improved embryo selection for in vitro fertilization (IVF). Moreover, both invasive and non-invasive mutation scanning of the genome are helping to identify the genetic causes of prenatal developmental disorders. These advances are changing clinical practice and pose novel challenges for genetic counselling and prenatal care.
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Affiliation(s)
- Joris Robert Vermeesch
- Centre for Human Genetics, Department of Human Genetics, University of Leuven, 49 Herestraat, Leuven 3000, Belgium
| | - Thierry Voet
- Centre for Human Genetics, Department of Human Genetics, University of Leuven, 49 Herestraat, Leuven 3000, Belgium
| | - Koenraad Devriendt
- Centre for Human Genetics, Department of Human Genetics, University of Leuven, 49 Herestraat, Leuven 3000, Belgium
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Aleksandrova NV, Shubina ES, Ekimov AN, Kodyleva TA, Mukosey IS, Makarova NP, Kulakova EV, Levkov LA, Barkov IY, Trofimov DY, Sukhikh GT. Comparative results of preimplantation genetic screening by array comparative genomic hybridization and new-generation sequencing. Mol Biol 2017. [DOI: 10.1134/s0026893317010022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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46
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Current experience concerning mosaic embryos diagnosed during preimplantation genetic screening. Fertil Steril 2017; 107:1113-1119. [DOI: 10.1016/j.fertnstert.2017.03.016] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 03/15/2017] [Accepted: 03/15/2017] [Indexed: 11/19/2022]
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47
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McCoy RC. Mosaicism in Preimplantation Human Embryos: When Chromosomal Abnormalities Are the Norm. Trends Genet 2017; 33:448-463. [PMID: 28457629 DOI: 10.1016/j.tig.2017.04.001] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 03/31/2017] [Accepted: 04/03/2017] [Indexed: 11/15/2022]
Abstract
Along with errors in meiosis, mitotic errors during post-zygotic cell division contribute to pervasive aneuploidy in human embryos. Relatively little is known, however, about the genesis of these errors or their fitness consequences. Rapid technological advances are helping to close this gap, revealing diverse molecular mechanisms contributing to mitotic error. These include altered cell cycle checkpoints, aberrations of the centrosome, and failed chromatid cohesion, mirroring findings from cancer biology. Recent studies are challenging the idea that mitotic error is abnormal, emphasizing that the fitness impacts of mosaicism depend on its scope and severity. In light of these findings, technical and philosophical limitations of various screening approaches are discussed, along with avenues for future research.
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Affiliation(s)
- Rajiv C McCoy
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
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Vera-Rodriguez M, Rubio C. Assessing the true incidence of mosaicism in preimplantation embryos. Fertil Steril 2017; 107:1107-1112. [PMID: 28433370 DOI: 10.1016/j.fertnstert.2017.03.019] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 03/21/2017] [Indexed: 10/19/2022]
Abstract
Modern technologies applied to the field of preimplantation genetic diagnosis for aneuploidy screening (PGD-A) have improved the ability to identify the presence of mosaicism. Consequently, new questions can now be addressed regarding the potential impact of embryo mosaicism on diagnosis accuracy and the feasibility of considering mosaic embryos for transfer. The frequency of chromosomal mosaicism in products of conception (POCs) of early miscarriages has been reported to be low. Mosaic embryos with an aneuploid inner cell mass are typically lost during the first trimester owing to spontaneous miscarriages. Most of the mosaics in established pregnancies would derive from placental mosaicism or placental aneuploidy, and mosaic embryos with aneuploid inner cell mass should be lost mainly due to first-trimester spontaneous miscarriages. The well described clinical outcomes of live births from mosaic embryos suggest a wide spectrum of phenotypes, from healthy to severely impaired. Therefore, there is a need to balance the risks of discarding a possibly viable embryo with that of transferring an embryo that may ultimately have a lower implantation potential.
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Affiliation(s)
| | - Carmen Rubio
- Igenomix and Igenomix Foundation, Valencia, Spain.
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49
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Vendrell X, Fernández-Pedrosa V, Triviño JC, Bautista-Llácer R, Collado C, Rodríguez O, García-Mengual E, Ferrer E, Calatayud C, Ruiz-Jorro M. New protocol based on massive parallel sequencing for aneuploidy screening of preimplantation human embryos. Syst Biol Reprod Med 2017; 63:162-178. [PMID: 28394645 DOI: 10.1080/19396368.2017.1312633] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Novel next-generation sequencing procedures have rapidly emerged into the preimplantation genetic screening framework. This work presents the design and validation of a new low-coverage whole-genome sequencing assay for aneuploidy detection in single blastomeres and trophectodermal samples from preimplantation embryos. The validation ensures analytical sensitivity, specificity, robustness, precision, limit of detection, resolution, and reproducibility. Specific parameters to measure the performance are defined, and the results are compared with a standardized array-based method to stablish the concordance. From the single cell genomics point of view, the main novelties are the length of reads of the libraries (150 nucleotides) together with a paired-end strategy and the design of an original algorithm and copy number viewer. A total of 129 samples were included in six experimental runs using a MiSeq Illumina platform. Samples included: single amniocytes, single blastomeres (cleavage-stage embryos), trophectoderm samples (blastocyst), and diluted DNA. Sensitivity and specificity were calculated per chromosome yielding 96% and 99%, respectively. The percentage of concordant samples was 98.2% and all of the aneuploid samples were confirmed. In conclusion, the validation yields highly reliable and reproducible results, representing an accurate and cost-effective strategy for the routine detection of aneuploidy in human embryos.
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Affiliation(s)
- Xavier Vendrell
- a Reproductive Genetics Unit , Sistemas Genómicos Ltd. , Paterna , Valencia , Spain
| | | | - Juan Carlos Triviño
- c Bioinformatics Department , Sistemas Genómicos Ltd. , Paterna , Valencia , Spain
| | - Rosa Bautista-Llácer
- a Reproductive Genetics Unit , Sistemas Genómicos Ltd. , Paterna , Valencia , Spain
| | - Carmen Collado
- b Next-Generation Sequencing Laboratory , Sistemas Genómicos Ltd. , Paterna , Valencia , Spain
| | - Oscar Rodríguez
- c Bioinformatics Department , Sistemas Genómicos Ltd. , Paterna , Valencia , Spain
| | - Elena García-Mengual
- a Reproductive Genetics Unit , Sistemas Genómicos Ltd. , Paterna , Valencia , Spain
| | - Empar Ferrer
- d CREA Reproductive Medicine Center , Valencia , Spain
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Maisenbacher MK, Merrion K, Pettersen B, Young M, Paik K, Iyengar S, Kareht S, Sigurjonsson S, Demko ZP, Martin KA. Incidence of the 22q11.2 deletion in a large cohort of miscarriage samples. Mol Cytogenet 2017; 10:6. [PMID: 28293297 PMCID: PMC5345148 DOI: 10.1186/s13039-017-0308-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 02/22/2017] [Indexed: 03/16/2023] Open
Abstract
Background The 22q11.2 deletion syndrome is the most common microdeletion syndrome in livebirths, but data regarding its incidence in other populations is limited and also include ascertainment bias. This study was designed to determine the incidence of the 22q11.2 deletion in miscarriage samples sent for clinical molecular cytogenetic testing. Results Twenty-six thousand one hundred one fresh product of conception (POC) samples were sent to a CLIA- certified, CAP-accredited laboratory from April 2010–-May 2016 for molecular cytogenetic miscarriage testing using a single-nucleotide polymorphism (SNP)-based microarray platform. A retrospective review determined the incidence of the 22q11.2 deletion in this sample set. Fetal results were obtained in 22,451 (86%) cases, of which, 15 (0.07%) had a microdeletion in the 22q11.2 region (incidence, 1/1497). Of those, 12 (80%) cases were found in samples that were normal at the resolution of traditional karyotyping (i.e., had no chromosome abnormalities above 10 Mb in size) and three (20%) cases had additional findings (Trisomy 15, Trisomy 16, XXY). Ten (67%) cases with a 22q11.2 deletion had the common ~3 Mb deletion; the remaining 5 cases had deletions ranging in size from 0.65 to 1.5 Mb. A majority (12/15) of cases had a deletion on the maternally inherited chromosome. No significant relationship between maternal age and presence of a fetal 22q11.2 deletion was observed. Conclusions The observed incidence of 1/1497 for the 22q11.2 deletion in miscarriage samples is higher than the reported general population prevalence (1/4000–1/6000). Further research is needed to determine whether the 22q11.2 deletion is a causal factor for miscarriage.
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Affiliation(s)
| | | | | | - Michael Young
- Natera, Inc., 201 Industrial Road, San Carlos, 94070 CA USA
| | - Kiyoung Paik
- Natera, Inc., 201 Industrial Road, San Carlos, 94070 CA USA
| | - Sushma Iyengar
- Natera, Inc., 201 Industrial Road, San Carlos, 94070 CA USA
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