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Sun F, Li H, Sun D, Fu S, Gu L, Shao X, Wang Q, Dong X, Duan B, Xing F, Wu J, Xiao M, Zhao F, Han JDJ, Liu Q, Fan X, Li C, Wang C, Shi T. Single-cell omics: experimental workflow, data analyses and applications. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2561-0. [PMID: 39060615 DOI: 10.1007/s11427-023-2561-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/18/2024] [Indexed: 07/28/2024]
Abstract
Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular features. Our exploration of how the genomes orchestrate the formation and maintenance of each cell, and control the cellular phenotypes of various organismsis, is both captivating and intricate. Since the inception of the first single-cell RNA technology, technologies related to single-cell sequencing have experienced rapid advancements in recent years. These technologies have expanded horizontally to include single-cell genome, epigenome, proteome, and metabolome, while vertically, they have progressed to integrate multiple omics data and incorporate additional information such as spatial scRNA-seq and CRISPR screening. Single-cell omics represent a groundbreaking advancement in the biomedical field, offering profound insights into the understanding of complex diseases, including cancers. Here, we comprehensively summarize recent advances in single-cell omics technologies, with a specific focus on the methodology section. This overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.
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Affiliation(s)
- Fengying Sun
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China
| | - Haoyan Li
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Dongqing Sun
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Shaliu Fu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China
| | - Lei Gu
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xin Shao
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314103, China
| | - Qinqin Wang
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xin Dong
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Bin Duan
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China
| | - Feiyang Xing
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jun Wu
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Minmin Xiao
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China.
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, 100871, China.
| | - Qi Liu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China.
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China.
| | - Xiaohui Fan
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314103, China.
- Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China.
| | - Chen Li
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Chenfei Wang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Tieliu Shi
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China.
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
- Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE, School of Statistics, East China Normal University, Shanghai, 200062, China.
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Tian Z, Lian W, Xu L, Long Y, Tang L, Wang H. Robust evidence reveals the reliable rate of normal/balanced embryos for identifying reciprocal translocation and Robertsonian translocation carriers. ZYGOTE 2024; 32:58-65. [PMID: 38083872 DOI: 10.1017/s0967199423000606] [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] [Indexed: 01/16/2024]
Abstract
We aimed to evaluate the reliable rate of normal/balanced embryos for reciprocal translocation and Robertsonian translocation carriers and to provide convincing evidence for clinical staff to conduct genetic counselling regarding common structural rearrangements to alleviate patient anxiety. The characteristics of 39,459 embryos that were sourced from unpublished data and literature were analyzed. The samples consisted of 17,536 embryo karyotypes that were not published and 21,923 embryo karyotypes obtained from the literature. Using the PubMed, Cochrane Library, Web of Science, and Embase databases, specific keywords were used to screen the literature for reciprocal translocation and Robertsonian translocation. The ratio of normal/balanced embryos in the overall data was calculated and analyzed, and we grouped the results according to gender to confirm if there were gender differences. We also divided the data into the cleavage stage and blastocyst stage according to the biopsy period to verify if there was a difference in the ratio of normal/balanced embryos. By combining the unpublished data and data derived from the literature, the average rates of normal/balanced embryos for reciprocal translocation and Robertsonian translocation carriers were observed to be 26.96% (7953/29,495) and 41.59% (4144/9964), respectively. Reciprocal translocation and Robertson translocation exhibited higher rates in male carriers than they did in female carriers (49.60% vs. 37.44%; 29.84% vs. 27.67%). Additionally, the data for both translocations exhibited differences in the normal/balanced embryo ratios between the cleavage and blastocyst stages of carriers for both Robertsonian translocation and reciprocal translocation (36.07% vs 43.43%; 24.88% vs 27.67%). The differences between the two location types were statistically significant (P < 0.05). The normal/balanced ratio of embryos in carriers of reciprocal and RobT was higher than the theoretical ratio, and the values ranged from 26.96% to 41.59%. Moreover, the male carriers possessed a higher number of embryos that were normal or balanced. The ratio of normal/balanced embryos in the blastocyst stage was higher than that in the cleavage stage. The results of this study provide a reliable suggestion for future clinic genetic consulting regarding the rate of normal/balanced embryos of reciprocal translocation and Robertsonian translocation carriers.
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Affiliation(s)
- Zhihua Tian
- Department of Reproduction and Genetics, the First Affiliated Hospital of Kunming Medical University, Kunming650032, China
| | - Wenchang Lian
- Department of Medical Genetics, Yikon Genomics Company, Ltd, Jiangsu Suzhou215021, China
| | - Li Xu
- Department of Reproduction and Genetics, the First Affiliated Hospital of Kunming Medical University, Kunming650032, China
| | - Yanxi Long
- Department of Reproduction and Genetics, the First Affiliated Hospital of Kunming Medical University, Kunming650032, China
| | - Li Tang
- Department of Reproduction and Genetics, the First Affiliated Hospital of Kunming Medical University, Kunming650032, China
| | - Huawei Wang
- Department of Reproduction and Genetics, the First Affiliated Hospital of Kunming Medical University, Kunming650032, China
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Latham KE. Preimplantation genetic testing: A remarkable history of pioneering, technical challenges, innovations, and ethical considerations. Mol Reprod Dev 2024; 91:e23727. [PMID: 38282313 DOI: 10.1002/mrd.23727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 12/15/2023] [Indexed: 01/30/2024]
Abstract
Preimplantation genetic testing (PGT) has emerged as a powerful companion to assisted reproduction technologies. The origins and history of PGT are reviewed here, along with descriptions of advances in molecular assays and sampling methods, their capabilities, and their applications in preventing genetic diseases and enhancing pregnancy outcomes. Additionally, the potential for increasing accuracy and genome coverage is considered, as well as some of the emerging ethical and legislative considerations related to the expanding capabilities of PGT.
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Affiliation(s)
- Keith E Latham
- Department of Animal Science, Michigan State University, East Lansing, Michigan, USA
- Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University, East Lansing, Michigan, USA
- Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, Michigan, USA
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Griffin DK, Brezina PR, Tobler K, Zhao Y, Silvestri G, Mccoy RC, Anchan R, Benner A, Cutting GR, Kearns WG. The human embryonic genome is karyotypically complex, with chromosomally abnormal cells preferentially located away from the developing fetus. Hum Reprod 2023; 38:180-188. [PMID: 36350568 PMCID: PMC10089293 DOI: 10.1093/humrep/deac238] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 09/26/2022] [Indexed: 11/11/2022] Open
Abstract
STUDY QUESTION Are chromosome abnormalities detected at Day 3 post-fertilization predominantly retained in structures of the blastocyst other than the inner cell mass (ICM), where chromosomally normal cells are preferentially retained? SUMMARY ANSWER In human embryos, aneuploid cells are sequestered away from the ICM, partly to the trophectoderm (TE) but more significantly to the blastocoel fluid within the blastocoel cavity (Bc) and to peripheral cells (PCs) surrounding the blastocyst during Day 3 to Day 5 progression. WHAT IS KNOWN ALREADY A commonly held dogma in all diploid eukaryotes is that two gametes, each with 'n' chromosomes (23 in humans), fuse to form a '2n' zygote (46 in humans); a state that remains in perpetuity for all somatic cell divisions. Human embryos, however, display high levels of chromosomal aneuploidy in early stages that reportedly declines from Day 3 (cleavage stage) to Day 5 (blastocyst) post-fertilization. While this observation may be partly because of aneuploid embryonic arrest before blastulation, it could also be due to embryo 'normalization' to a euploid state during blastulation. If and how this normalization occurs requires further investigation. STUDY DESIGN, SIZE, DURATION A total of 964 cleavage-stage (Day 3) embryos underwent single-cell biopsy and diagnosis for chromosome constitution. All were maintained in culture, assessing blastulation rate, both for those assessed euploid and aneuploid. Pregnancy rate was assessed for those determined euploid, blastulated and subsequently transferred. For those determined aneuploid and blastulated (174 embryos), ICM (all 174 embryos), TE (all 174), Bc (47 embryos) and PC (38 embryos) were analyzed for chromosome constitution. Specifically, concordance with the original Day 3 diagnosis and determination if any 'normalized' to euploid karyotypes within all four structures was assessed. PARTICIPANTS/MATERIALS, SETTING, METHODS All patients (144 couples) were undergoing routine preimplantation genetic testing for aneuploidy in three IVF clinical settings. Cleavage-stage biopsy preceded chromosome analysis by next-generation sequencing. All patients provided informed consent. Additional molecular testing was carried out on blastocyst embryos and was analyzed for up to four embryonic structures (ICM, TE, Bc and PC). MAIN RESULTS AND THE ROLE OF CHANCE Of 463/964 embryos (48%) diagnosed as euploid at Day 3, 70% blastulated (leading to a 59% pregnancy rate) and 30% degenerated. Conversely, of the 501 (52%) diagnosed as aneuploid, 65% degenerated and 35% (174) blastulated, a highly significant difference (P < 0.0001). Of the 174 that blastulated, the ratio of '(semi)concordant-aneuploid' versus 'normalized-euploid' versus 'other-aneuploid' embryos was, respectively, 39%/57%/3% in the ICM; 49%/48%/3% in the TE; 78%/21%/0% in the PC; and 83%/10%/5% in the Bc. The TE karyotype therefore has a positive predictive value of 86.7% in determining that of the ICM, albeit with marginally higher aneuploid rates of abnormalities (P = .071). Levels of abnormality in Bc/PC were significantly higher (P < 0.0001) versus the ploidy of the ICM and TE and nearly all chromosome abnormalities were (at least partially) concordant with Day 3 diagnoses. LIMITATIONS, REASONS FOR CAUTION The results only pertain to human IVF embryos so extrapolation to the in vivo situation and to other species is not certain. We acknowledge (rather than lineage-specific survival, as we suggest here) the possibility of other mechanisms, such as lineage-specific movement of cells, during blastulation. Ethical considerations, however, make investigating this mechanism difficult on human embryos. WIDER IMPLICATIONS OF THE FINDINGS Mosaic human cleavage-stage embryos can differentiate into a euploid ICM where euploid cell populations predominate. Sequestering of aneuploid cells/nuclei to structures no longer involved in fetal development has important implications for preimplantation and prenatal genetic testing. These results also challenge previous fundamental understandings of mitotic fidelity in early human development and indicate a complex and fluid nature of the human embryonic genome. STUDY FUNDING/COMPETING INTEREST(S) This research was funded by Organon Pharmaceuticals and Merck Serono by grants to W.G.K. W.G.K. is also an employee of AdvaGenix, who could, potentially, indirectly benefit financially from publication of this manuscript. R.C.M. is supported by the National Institute of General Medical Sciences of the National Institutes of Health under award number R35GM133747. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. D.K.G. provides paid consultancy services for Care Fertility. TRIAL REGISTRATION NUMBER : N/A.
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Affiliation(s)
- D K Griffin
- School of Biosciences, University of Kent, Canterbury, UK
| | - P R Brezina
- Jones Division of Reproductive Endocrinology, Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Fertility Associates of Memphis, Memphis, TN, USA
| | - K Tobler
- Jones Division of Reproductive Endocrinology, Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Idaho Center for Reproductive Medicine, Boise, ID, USA
| | - Yulian Zhao
- Jones Division of Reproductive Endocrinology, Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Mayo Clinic, Rochester, MN, USA
| | - G Silvestri
- School of Biosciences, University of Kent, Canterbury, UK
| | - R C Mccoy
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - R Anchan
- Department of Obstetrics and Gynecology, Harvard Medical School, Boston, MA, USA
| | | | - G R Cutting
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - W G Kearns
- Jones Division of Reproductive Endocrinology, Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,AdvaGenix, Rockville, MD, USA
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Zhang Z, Zhang L, Wang Y, Bi X, Liang L, Yuan Y, Su D, Wu X. Logistic regression analyses of factors affecting the euploidy of blastocysts undergoing in vitro fertilization and preimplantation genetic testing. Medicine (Baltimore) 2022; 101:e29774. [PMID: 35777007 PMCID: PMC9239646 DOI: 10.1097/md.0000000000029774] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Embryo chromosomal abnormalities are considered as the main cause of low pregnancy rate for in vitro fertilization (IVF). Recently, a new metric of success in assisted reproductive technology, that is, the ability to achieve at least 1 euploid blastocyst for transfer, has been brought into focus among clinicians. Our study aimed to investigate the effects of different factors on the euploidy of blastocysts undergoing IVF and preimplantation genetic testing (PGT). This retrospective observational study included 493 cycles underwent IVF/intracytroplasmatic sperm injection intended to obtain trophectoderm biopsy for PGT from June 2016 to December 2019 at a single academic fertility center. Logistic regression was adopted to analyze the clinical characteristics and embryonic data related to the ability to achieve at least 1 euploid blastocyst for transfer. The study took 1471 blastocysts from 493 cycles as samples for PGT. Among them, 149 cycles (30.22%) had no euploid blastocyst and 344 cycles (69.78%) had at least 1 euploid blastocyst. A multivariate logistic analysis suggested that maternal age >36, abnormal parental karyotype, nonfirst cycles and blastocysts number per cycle <3 were the risk factors for no euploid blastocyst. The parental karyotype, maternal age, number of cycles, and number of blastocysts per cycle were the dominant factors affecting the ability to achieve at least 1 euploid blastocyst for transfer and therefore could be regarded as potential predictors for genetic counseling.
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Affiliation(s)
- Zhiping Zhang
- Center of Reproductive Medicine, Affiliated Children’s Hospital of Shanxi & Women Health Center of Shanxi Medicine University, Taiyuan, Shanxi, China
| | - Lei Zhang
- Center of Reproductive Medicine, Affiliated Children’s Hospital of Shanxi & Women Health Center of Shanxi Medicine University, Taiyuan, Shanxi, China
| | - Yaoqin Wang
- Center of Reproductive Medicine, Affiliated Children’s Hospital of Shanxi & Women Health Center of Shanxi Medicine University, Taiyuan, Shanxi, China
| | - Xingyu Bi
- Center of Reproductive Medicine, Affiliated Children’s Hospital of Shanxi & Women Health Center of Shanxi Medicine University, Taiyuan, Shanxi, China
| | - Lixia Liang
- Center of Reproductive Medicine, Affiliated Children’s Hospital of Shanxi & Women Health Center of Shanxi Medicine University, Taiyuan, Shanxi, China
| | - Yuan Yuan
- Center of Reproductive Medicine, Affiliated Children’s Hospital of Shanxi & Women Health Center of Shanxi Medicine University, Taiyuan, Shanxi, China
| | - Dan Su
- Center of Reproductive Medicine, Affiliated Children’s Hospital of Shanxi & Women Health Center of Shanxi Medicine University, Taiyuan, Shanxi, China
| | - Xueqing Wu
- Center of Reproductive Medicine, Affiliated Children’s Hospital of Shanxi & Women Health Center of Shanxi Medicine University, Taiyuan, Shanxi, China
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Chen HF, Chen M, Ho HN. An overview of the current and emerging platforms for preimplantation genetic testing for aneuploidies (PGT-A) in in vitro fertilization programs. Taiwan J Obstet Gynecol 2021; 59:489-495. [PMID: 32653118 DOI: 10.1016/j.tjog.2020.05.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2020] [Indexed: 01/16/2023] Open
Abstract
Preimplantation genetic testing for aneuploidies (PGT-A) and PGT for monogenic disorders (PGT-M) have currently been used widely, aiming to improve IVF outcomes. Although with many years of unsatisfactory results, PGT-A has been revived because new technologies have been adopted, such as platforms to examine all 24 types of chromosomes in blastocysts. This report compiles current knowledge regarding the available PGT platforms, including quantitative PCR, array CGH, and next-generation sequencing. The diagnostic capabilities of are compared and respective advantages/disadvantages outlined. We also address the limitations of current technologies, such as assignment of embryos with balanced translocation. We also discuss the emerging novel PGT technologies that likely will change our future practice, such as non-invasive PGT examining spent culture medium. Current literature suggest that most platforms can effectively reach concordant results regarding whole-chromosome ploidy status of all 24 types of chromosomes. However, different platforms have different resolutions and experimental complexities; leading to different turnaround time, throughput and differential capabilities of detecting mosaicism, segmental mutations, unbalanced translocations, concurrent PGT-A and PGT-M etc. Based on these information, IVF staff can more appropriately interpret PGT data and counsel patients, and select suitable platforms to meet personalized needs. The present report also concisely discusses some crucial clinical outcomes by PGT, which can clarify the role of applying PGT in daily IVF programs. Finally the up-to-date information about the novel use of current technologies and the newly emerging technologies will also help identify the focus areas for the design of new platforms for PGT in the future.
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Affiliation(s)
- Hsin-Fu Chen
- Department of Obstetrics and Gynecology, College of Medicine and the Hospital, National Taiwan University, Taipei, Taiwan; Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.
| | - Ming Chen
- Department of Medical Genetics, College of Medicine and the Hospital, National Taiwan University, Taipei, Taiwan; Department of Obstetrics and Gynecology, Changhua Christian Hospital, Changhua, Taiwan; Department of Genomic Medicine and Center for Medical Genetics, Changhua Christian Hospital, Changhua, Taiwan.
| | - Hong-Nerng Ho
- Department of Obstetrics and Gynecology, College of Medicine and the Hospital, National Taiwan University, Taipei, Taiwan; Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan; Graduate Institute of Immunology, College of Medicine, National Taiwan University, Taiwan.
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Boynukalin FK, Gultomruk M, Turgut NE, Rubio C, Rodrigo L, Yarkiner Z, Ecemis S, Karlikaya G, Findikli N, Bahceci M. The impact of patient, embryo, and translocation characteristics on the ploidy status of young couples undergoing preimplantation genetic testing for structural rearrangements (PGT-SR) by next generation sequencing (NGS). J Assist Reprod Genet 2021; 38:387-396. [PMID: 33398513 PMCID: PMC7884505 DOI: 10.1007/s10815-020-02054-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 12/28/2020] [Indexed: 10/22/2022] Open
Abstract
PURPOSE To evaluate the factors that affect the incidence of euploid balanced embryos and interchromosomal effect (ICE) in carriers of different structural rearrangements. METHODS This retrospective study includes 95 couples with reciprocal translocations (RecT) and 36 couples with Robertsonian translocations (RobT) undergoing Preimplantation Genetic Testing for Structural Rearrangements (PGT-SR) between March 2016 and July 2019. Next-generation sequencing (NGS) was the technique used coupled with trophectoderm (TE) biopsy. Only cases with females under 38 years were included. A total of 532 blastocysts were evaluated. RESULTS The euploidy rate was similar in RobT when compared with RecT carriers [57/156 (36.5%) vs. 112/376 (29.8%), p = 0.127]. The pure ICE rate was significantly higher in RobT carriers [48/156 (30.8%) vs. 53/376 (14.1%), p < 0.001] than it was in RecT carriers. Female age was the independent factor for the probability of obtaining a euploid embryo in RecT and RobT carriers, and increasing female age decreases the probability of obtaining a euploid embryo. In RecT carriers, no significant differences were observed in euploidy rates, pure ICE, or combined ICE according to the length of the translocated fragment and the chromosome group. However, total ICE was significantly lower when there was a breakpoint in the short chromosome arm together with a breakpoint in the long arm [(44/158 (27.8%) for pq or qp, 51/155 (32.9%) for pp and 30/63 (47.6%) for qq; p = 0.02]. CONCLUSION The incidence of euploid/balanced blastocysts was similar in both types of translocations. However, there was a significant increase in pure ICE in RobT compared to RecT carriers. In RecT carriers, the presence of the breakpoints in the long arm of the chromosomes involved in the rearrangement resulted in a higher total ICE.
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Affiliation(s)
| | - Meral Gultomruk
- Bahceci Health Group, Hakki Yeten cad. No: 11 Terrace Fulya, Fulya, Istanbul, Turkey
| | - Niyazi Emre Turgut
- Bahceci Health Group, Hakki Yeten cad. No: 11 Terrace Fulya, Fulya, Istanbul, Turkey
| | - Carmen Rubio
- IGENOMIX, Calle Narcís Monturiol Estarriol no. 11 Parcela B, Edificio Europark, Parque Tecnológico de Paterna, 46980, Paterna, Valencia, Spain
| | - Lorena Rodrigo
- IGENOMIX, Calle Narcís Monturiol Estarriol no. 11 Parcela B, Edificio Europark, Parque Tecnológico de Paterna, 46980, Paterna, Valencia, Spain
| | - Zalihe Yarkiner
- Department of Statistics, Cyprus Science University, Dr. Fazil Kucuk Cad., 99320, Ozankoy, Cyprus
| | - Selen Ecemis
- Bahceci Health Group, Hakki Yeten cad. No: 11 Terrace Fulya, Fulya, Istanbul, Turkey
| | - Guvenc Karlikaya
- Bahceci Health Group, Hakki Yeten cad. No: 11 Terrace Fulya, Fulya, Istanbul, Turkey
| | - Necati Findikli
- Bahceci Health Group, Hakki Yeten cad. No: 11 Terrace Fulya, Fulya, Istanbul, Turkey
| | - Mustafa Bahceci
- Bahceci Health Group, Hakki Yeten cad. No: 11 Terrace Fulya, Fulya, Istanbul, Turkey
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Abstract
Despite the ever-increasing number of patients undergoing fertility treatments and the expanded use of genetic testing in this context, there has been limited focus in the literature on the involvement of genetics professionals in the assisted reproductive technology (ART) setting. Here we discuss the importance of genetic counseling within reproductive medicine. We review how genetic testing of embryos is performed, the process of gamete donation, the challenges associated with genetic testing, and the complexities of genetic test result interpretation.
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Affiliation(s)
- Debra Lilienthal
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, New York 10021, USA
| | - Michelle Cahr
- California Cryobank Life Sciences, Los Angeles, California 90025, USA
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Bunnell M, Esfandiari N. Preimplantation genetic testing as a component of root cause analysis of errors and reassignment of embryos in IVF. Reprod Biomed Online 2020; 41:975-977. [PMID: 32972874 DOI: 10.1016/j.rbmo.2020.08.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/10/2020] [Accepted: 08/24/2020] [Indexed: 11/28/2022]
Abstract
The risks of embryo/gamete mix-up are a threat to the integrity of the IVF process, with significant implications for affected families. The use of preimplantation genetic testing through single-nucleotide polymorphism array or next-generation sequencing technology can help to identify, characterize and ultimately help, in some cases, to find the root cause, and to mitigate the extent of these errors for a given patient or laboratory.
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Affiliation(s)
- Megan Bunnell
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA
| | - Navid Esfandiari
- Department of Obstetrics and Gynecology and Reproductive Sciences, University of Vermont Medical Center, Larner College of Medicine, Burlington, VT, USA.
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Flowers NJ, Burgess T, Giouzeppos O, Shi G, Love CJ, Hunt CE, Scarff KL, Archibald AD, Pertile MD. Genome-wide noninvasive prenatal screening for carriers of balanced reciprocal translocations. Genet Med 2020; 22:1944-1955. [PMID: 32807973 DOI: 10.1038/s41436-020-0930-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 07/26/2020] [Accepted: 07/27/2020] [Indexed: 12/27/2022] Open
Abstract
PURPOSE Balanced reciprocal translocation carriers are at increased risk of producing gametes with unbalanced forms of the translocation leading to miscarriage, fetal anomalies, and birth defects. We sought to determine if genome-wide cell-free DNA based noninvasive prenatal screening (gw-NIPS) could provide an alternative to prenatal diagnosis for carriers of these chromosomal rearrangements. METHODS This pilot series comprises a retrospective analysis of gw-NIPS and clinical outcome data from 42 singleton pregnancies where one parent carried a balanced reciprocal translocation. Gw-NIPS was performed between August 2015 and March 2018. Inclusion criteria required at least one translocation segment to be ≥15 Mb in size. RESULTS Forty samples (95%) returned an informative result; 7 pregnancies (17.5%) were high risk for an unbalanced translocation and confirmed after diagnostic testing. The remaining 33 informative samples were low risk and confirmed after diagnostic testing or normal newborn physical exam. Test sensitivity of 100% (95% confidence interval [CI]: 64.6-100%) and specificity of 100% (95% CI: 89.6-100%) were observed for this pilot series. CONCLUSION We demonstrate that gw-NIPS is a potential option for a majority of reciprocal translocation carriers. Further confirmation of this methodology could lead to adoption of this noninvasive alternative.
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Affiliation(s)
- Nicola Jane Flowers
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Trent Burgess
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Olivia Giouzeppos
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Grace Shi
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Clare Jane Love
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Clare Elizabeth Hunt
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Katrina Louise Scarff
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Alison Dalton Archibald
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Mark Domenic Pertile
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia. .,Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia.
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11
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Toft CLF, Ingerslev HJ, Kesmodel US, Diemer T, Degn B, Ernst A, Okkels H, Kjartansdóttir KR, Pedersen IS. A systematic review on concurrent aneuploidy screening and preimplantation genetic testing for hereditary disorders: What is the prevalence of aneuploidy and is there a clinical effect from aneuploidy screening? Acta Obstet Gynecol Scand 2020; 99:696-706. [PMID: 32039470 DOI: 10.1111/aogs.13823] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/23/2020] [Accepted: 02/05/2020] [Indexed: 11/29/2022]
Abstract
INTRODUCTION In assisted reproductive technology, aneuploidy is considered a primary cause of failed embryo implantation. This has led to the implementation of preimplantation genetic testing for aneuploidy in some clinics. The prevalence of aneuploidy and the use of aneuploidy screening during preimplantation genetic testing for inherited disorders has not previously been reviewed. Here, we systematically review the literature to investigate the prevalence of aneuploidy in blastocysts derived from patients carrying or affected by an inherited disorder, and whether screening for aneuploidy improves clinical outcomes. MATERIAL AND METHODS PubMed and Embase were searched for articles describing preimplantation genetic testing for monogenic disorders and/or structural rearrangements in combination with preimplantation genetic testing for aneuploidy. Original articles reporting aneuploidy rates at the blastocyst stage and/or clinical outcomes (positive human chorionic gonadotropin, gestational sacs/implantation rate, fetal heartbeat/clinical pregnancy, ongoing pregnancy, miscarriage, or live birth/delivery rate on a per transfer basis) were included. Case studies were excluded. RESULTS Of the 26 identified studies, none were randomized controlled trials, three were historical cohort studies with a reference group not receiving aneuploidy screening, and the remaining were case series. In weighted analysis, 34.1% of 7749 blastocysts were aneuploid. Screening for aneuploidy reduced the proportion of embryos suitable for transfer, thereby increasing the risk of experiencing a cycle without transferable embryos. In pooled analysis the percentage of embryos suitable for transfer was reduced from 57.5% to 37.2% following screening for aneuploidy. Among historical cohort studies, one reported significantly improved pregnancy and birth rates but did not control for confounding, one did not report any statistically significant difference between groups, and one properly designed study concluded that preimplantation genetic testing for aneuploidy enhanced the chance of achieving a pregnancy while simultaneously reducing the chance of miscarriage following single embryo transfer. CONCLUSIONS On average, aneuploidy is detected in 34% of embryos when performing a single blastocyst biopsy derived from patients carrying or affected by an inherited disorder. Accordingly, when screening for aneuploidy, the risk of experiencing a cycle with no transferable embryos increases. Current available data on the clinical effect of preimplantation genetic testing for aneuploidy performed concurrently with preimplantation genetic testing for inherited disorders are sparse, rendering the clinical effect from preimplantation genetic testing for aneuploidy difficult to access.
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Affiliation(s)
- Christian Liebst Frisk Toft
- Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | | | - Ulrik Schiøler Kesmodel
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.,Fertility Unit, Aalborg University Hospital, Aalborg, Denmark
| | - Tue Diemer
- Department of Clinical Genetics, Aalborg University Hospital, Aalborg, Denmark
| | - Birte Degn
- Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark
| | - Anja Ernst
- Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark
| | - Henrik Okkels
- Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark
| | | | - Inge Søkilde Pedersen
- Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
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12
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Shaulov T, Zhang L, Chung JT, Son WY, Buckett W, Ao A. Outcomes of Preimplantation Genetic Testing for Single Gene Defects in a Privately Funded Period and Publicly Funded Period: A North-American Single Center Experience. J Reprod Infertil 2020; 21:107-115. [PMID: 32500013 PMCID: PMC7253942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
BACKGROUND The purpose of this study was to assess whether the outcomes from IVF-preimplantation genetic testing (IVF-PGT) cycles for single gene defects (SGD) (PGT-M) differ between a privately funded period (PRP) and publicly funded period (PUP). METHODS A retrospective cohort study was conducted in a North-American single tertiary center. The PRP (March 1998 to July 2010) comprised 56 PGT-M cycles from 58 IVF cycles in 38 couples, and the PUP (August 2010 to May 2015) comprised 59 PGT-M cycles from 87 IVF cycles in 38 couples. One PGT-M cycle is defined as one biopsy procedure from one or serial IVF cycles. A p-value of 0.05 was considered statistically significant. RESULTS The clinical pregnancy rates (CPR) per PGT-M cycle were 30.4% and 52.5% in each period, respectively (p=0.021). The live birth rates (LBR) per PGT-M cycle were 21.5% versus 40.9% in each period, respectively (p=0.037). A sub-analysis within the PUP comparing 39 PGT-M cycles from 39 IVF cycles with 20 PGT-M cycles from 49 IVF cycles yielded CPRs per PGT-M cycle of 64.1% and 30.0% and LBRs per PGT-M cycle of 53.8% and 15.0%, in each group, respectively (p< 0.05 for both). CONCLUSION The transition from private to public funding and a single embryo transfer (ET) guideline has little impact on embryological and clinical outcomes of PGT-M cycles, and results in lower rates of multiple pregnancies. However, these two systems may serve different populations.
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Affiliation(s)
- Talya Shaulov
- MUHC Reproductive Centre, Department of Obstetrics and Gynecology, Montreal, Quebec, Canada
| | - Li Zhang
- MUHC Reproductive Centre, Department of Obstetrics and Gynecology, Montreal, Quebec, Canada
| | - Jin-Tae Chung
- MUHC Reproductive Centre, Department of Obstetrics and Gynecology, Montreal, Quebec, Canada
| | - Weon-Young Son
- MUHC Reproductive Centre, Department of Obstetrics and Gynecology, Montreal, Quebec, Canada
| | - William Buckett
- MUHC Reproductive Centre, Department of Obstetrics and Gynecology, Montreal, Quebec, Canada
| | - Asangla Ao
- MUHC Reproductive Centre, Department of Obstetrics and Gynecology, Montreal, Quebec, Canada,Department of Human Genetics, McGill University, Montreal, Quebec, Canada,McGill University Health Centre Research Institute, Montreal, Quebec, Canada,Corresponding Author: Asangla Ao, 888 De Maisonneuve E, Suite 200, Montreal, Quebec, Canada. H2L 4S8, 1-514-934-1934, Extension 34741, E-mail:
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13
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Less-invasive chromosome screening of embryos and embryo assessment by genetic studies of DNA in embryo culture medium. J Assist Reprod Genet 2019; 36:2505-2513. [PMID: 31728811 DOI: 10.1007/s10815-019-01603-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 10/04/2019] [Indexed: 10/25/2022] Open
Abstract
PURPOSE To perform a preliminary exploration of a new embryo rank in clinical practice by combining the embryo chromosome copy number and mitochondrial copy number analysis of DNA extracted from embryo culture medium and blastocoel fluid. METHOD Eighty-three ICSI embryos from day 2 or day 3 were cultured to day 5 or day 6. Thirty-two blastocysts of 3 cc or above were obtained. Culture medium and blastocoel fluid were collected at 24 h before blastocyst formation. The genomic DNA and mitochondrial DNA (mtDNA) from the culture medium combined with blastocoel fluid and the whole blastocyst were amplified and sequenced by MALBAC-NGS. We compared the chromosomal information generated by the new protocol from the culture medium and the information employed by the whole embryo method. A multivariable linear regression was performed to study the impact of the blastocyst morphological score, chromosomal abnormality, embryo mtDNA copy number, and female age on the culture medium mtDNA copy number. RESULTS (1) The DNA from 31 blastocysts was successfully amplified, and the successful amplification rate was 96.9% (31/32). The success rate of the amplification of genomic DNA extracted from the culture medium was 87.5% (28/32). (2) There were 18 blastocysts in which the less invasive method and the whole embryo method revealed the same results. The consistency rate was 66.7% (18/27). (3) The culture medium mitochondrial DNA copy number (MCN) had a significantly positive correlation with the blastocyst mitochondrial DNA copy number (P = 0.001), female age (P = 0.012), and blastocyst score (P = 0.014), but there was no obvious correlation with blastocyst chromosome (P = 0.138). CONCLUSIONS The preliminary exploration result of the less invasive approach for having an embryo rank was not satisfying, which still awaits further long-term evaluation.
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14
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Interchromosomal effect in carriers of translocations and inversions assessed by preimplantation genetic testing for structural rearrangements (PGT-SR). J Assist Reprod Genet 2019; 36:2547-2555. [PMID: 31696386 DOI: 10.1007/s10815-019-01593-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 09/24/2019] [Indexed: 02/06/2023] Open
Abstract
PURPOSE Balanced carriers of structural rearrangements have an increased risk of unbalanced embryos mainly due to the production of unbalanced gametes during meiosis. Aneuploidy for other chromosomes not involved in the rearrangements has also been described. The purpose of this work is to know if the incidence of unbalanced embryos, interchromosomal effect (ICE) and clinical outcomes differ in carriers of different structural rearrangements. METHODS Cohort retrospective study including 359 preimplantation genetic testing cycles for structural rearrangements from 304 couples was performed. Comparative genomic hybridisation arrays were used for chromosomal analysis. The results were stratified and compared according to female age and carrier sex. The impact of different cytogenetic features of chromosomal rearrangements was evaluated. RESULTS In carriers of translocations, we observed a higher percentage of abnormal embryos from day 3 biopsies compared with day 5/6 biopsies and for reciprocal translocations compared with other rearrangements. We observed a high percentage of embryos with aneuploidies for chromosomes not involved in the rearrangement that could be attributed to total ICE (aneuploid balanced and unbalanced embryos). No significant differences were observed in these percentages between types of rearrangements. Pure ICE (aneuploid balanced embyos) was independent of female age only for Robertsonian translocations, and significantly increased in day 3 biopsies for all types of abnormalities. Furthermore, total ICE for carriers of Robertsonian translocations and biopsy on day 3 was independent of female age too. High ongoing pregnancy rates were observed for all studied groups, with higher pregnancy rate for male carriers. CONCLUSION We observed a higher percentage of abnormal embryos for reciprocal translocations. No significant differences for total ICE was found among the different types of rearrangements, with higher pure ICE only for Robertsonian translocations. There was a sex effect for clinical outcome for carriers of translocations, with higher pregnancy rate for male carriers. The higher incidence of unbalanced and aneuploid embryos should be considered for reproductive counselling in carriers of structural rearrangements.
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15
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Khalife D, Ghazeeri G, Kutteh W. Review of current guidelines for recurrent pregnancy loss: new strategies for optimal evaluation of women who may be superfertile. Semin Perinatol 2019; 43:105-115. [PMID: 30642578 DOI: 10.1053/j.semperi.2018.12.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The current evidence-based guidelines for the evaluation of recurrent pregnancy loss recommended by the American Society for Reproductive Medicine and by the European Society of Human Reproduction and Embryology are compared and contrasted in this review. The clinical use of either of these guidelines will result in a probable diagnosis for only half of the affected patients. New strategies for a full evaluation of recurrent pregnancy loss incorporating 24- chromosome microarary on the products of conception offer more explanations for patients and caregivers. This new algorithm should decrease the use of empiric, unproven treatments. Combining the results of genetic testing on the miscarriage tissue with the conventional diagnostic tests has made it possible to explain the etiology of pregnancy loss in more than 90% of the cases. This cost-saving strategy can decrease the emotional distress and frustration for both couples and physicians when it comes to management of recurrent pregnancy loss.
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Affiliation(s)
- Dalia Khalife
- Reproductive Endocrinology and Infertility Division, Department of Obstetrics and Gynecology, American University of Beirut Medical Center P.O. Box: 113-6044. Beirut, Lebanon
| | - Ghina Ghazeeri
- Reproductive Endocrinology and Infertility Division, Department of Obstetrics and Gynecology, American University of Beirut Medical Center P.O. Box: 113-6044. Beirut, Lebanon
| | - William Kutteh
- Clinical Professor of Reproductive Endocrinology Vanderbilt University School of Medicine; Consulting Gynecologist, Department of Surgery Director of Fertility Preservation St. Jude Children's Research Hospital; Managing Partner, Director of Recurrent Pregnancy Loss Center Fertility Associates of Memphis 80 Humphreys Center, Suite 307 Memphis, TN 38120-2363 Phone: 901-747-2229 FAX: 901-747-4446.
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16
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Lammers J, Reignier A, Splingart C, Moradkhani K, Barrière P, Fréour T. Morphokinetic parameters in chromosomal translocation carriers undergoing preimplantation genetic testing. Reprod Biomed Online 2019; 38:177-183. [DOI: 10.1016/j.rbmo.2018.11.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 11/08/2018] [Accepted: 11/09/2018] [Indexed: 10/27/2022]
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17
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Cai Y, Ding M, Lin F, Diao Z, Zhang N, Sun H, Zhou J. Evaluation of preimplantation genetic testing based on next-generation sequencing for balanced reciprocal translocation carriers. Reprod Biomed Online 2019; 38:669-675. [PMID: 30885668 DOI: 10.1016/j.rbmo.2018.12.043] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 11/26/2018] [Accepted: 12/12/2018] [Indexed: 12/15/2022]
Abstract
RESEARCH QUESTION Can next-generation sequencing (NGS) based on copy number variation sequencing (CNV-Seq) identify normal/balanced embryos in balanced reciprocal translocation carriers and what are their reproductive outcomes? DESIGN One hundred couples with balanced reciprocal translocation who underwent a total of 134 preimplantation genetic testing (PGT) cycles between January 2015 and October 2017 were evaluated. Trophectoderm cells of blastocysts were biopsied for CNV-Seq-based NGS. All the balanced/normal blastocysts were vitrified and cryopreserved. Single balanced/normal blastocysts were warmed and transferred in the subsequent frozen embryo transfer (FET) cycle. RESULTS During the study period, 400 blastocysts were analysed by NGS-PGT, of which 109 (27.25%) were balanced and euploid. A total of 52 blastocysts were transferred in the FET cycle. Clinical pregnancy was confirmed in 34 women (65.38%), with a miscarriage rate of 2.94%; 26 healthy term babies were born, including 24 singletons and one set of twins, while eight couples had ongoing pregnancies. Amniocentesis revealed a fetal chromosome status that was consistent with the NGS-PGT results. Female carriers had a significantly higher blastocyst rate than did the male carriers (37.01% versus 31.27%, P = 0.04). The transferable blastocyst rate was higher in couples treated with gonadotrophin-releasing hormone (GnRH) antagonist than in those treated with GnRH agonist (38.20% versus 24.37%, P = 0.01). However, neither carrier sex nor ovarian stimulation protocol influenced the clinical pregnancy rate. CONCLUSIONS CNV-Seq-based NGS is an efficient and reliable PGT method for balanced reciprocal translocation.
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Affiliation(s)
- Yunni Cai
- Reproductive Medicine Centre, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing Jiangsu 210008, China
| | - Min Ding
- Reproductive Medicine Centre, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing Jiangsu 210008, China
| | - Fei Lin
- Reproductive Medicine Centre, Nanjing Drum Tower Hospital, The Affiliated Hospital to Nanjing University Medical School, Nanjing Jiangsu 210008, China
| | - Zhenyu Diao
- Reproductive Medicine Centre, Nanjing Drum Tower Hospital, The Affiliated Hospital to Nanjing University Medical School, Nanjing Jiangsu 210008, China
| | - Ningyuan Zhang
- Reproductive Medicine Centre, Nanjing Drum Tower Hospital, The Affiliated Hospital to Nanjing University Medical School, Nanjing Jiangsu 210008, China
| | - Haixiang Sun
- Reproductive Medicine Centre, Nanjing Drum Tower Hospital, The Affiliated Hospital to Nanjing University Medical School, Nanjing Jiangsu 210008, China
| | - Jianjun Zhou
- Reproductive Medicine Centre, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing Jiangsu 210008, China; Reproductive Medicine Centre, Nanjing Drum Tower Hospital, The Affiliated Hospital to Nanjing University Medical School, Nanjing Jiangsu 210008, China.
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18
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Mincarelli L, Lister A, Lipscombe J, Macaulay IC. Defining Cell Identity with Single-Cell Omics. Proteomics 2018; 18:e1700312. [PMID: 29644800 PMCID: PMC6175476 DOI: 10.1002/pmic.201700312] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 03/23/2018] [Indexed: 01/17/2023]
Abstract
Cells are a fundamental unit of life, and the ability to study the phenotypes and behaviors of individual cells is crucial to understanding the workings of complex biological systems. Cell phenotypes (epigenomic, transcriptomic, proteomic, and metabolomic) exhibit dramatic heterogeneity between and within the different cell types and states underlying cellular functional diversity. Cell genotypes can also display heterogeneity throughout an organism, in the form of somatic genetic variation-most notably in the emergence and evolution of tumors. Recent technical advances in single-cell isolation and the development of omics approaches sensitive enough to reveal these aspects of cell identity have enabled a revolution in the study of multicellular systems. In this review, we discuss the technologies available to resolve the genomes, epigenomes, transcriptomes, proteomes, and metabolomes of single cells from a wide variety of living systems.
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Affiliation(s)
- Laura Mincarelli
- Earlham InstituteNorwich Research ParkNorwichNR4 7UZUnited Kingdom
| | - Ashleigh Lister
- Earlham InstituteNorwich Research ParkNorwichNR4 7UZUnited Kingdom
| | - James Lipscombe
- Earlham InstituteNorwich Research ParkNorwichNR4 7UZUnited Kingdom
| | - Iain C. Macaulay
- Earlham InstituteNorwich Research ParkNorwichNR4 7UZUnited Kingdom
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19
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Ho JR, Arrach N, Rhodes-Long K, Ahmady A, Ingles S, Chung K, Bendikson KA, Paulson RJ, McGinnis LK. Pushing the limits of detection: investigation of cell-free DNA for aneuploidy screening in embryos. Fertil Steril 2018; 110:467-475.e2. [PMID: 29960707 DOI: 10.1016/j.fertnstert.2018.03.036] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 03/20/2018] [Accepted: 03/23/2018] [Indexed: 11/28/2022]
Abstract
OBJECTIVE To determine the accuracy of cell-free DNA (cfDNA) in spent embryo medium (SEM) for ploidy and sex detection at the cleavage and blastocyst stages. To determine if assisted hatching (AH) and morphologic grade influence cfDNA concentration and accuracy. DESIGN Prospective cohort. SETTING Academic fertility center. PATIENT(S) Nine patients undergoing IVF; 41 donated two-pronuclei embryos and 20 embryos from patients undergoing preimplantation genetic testing for aneuploidy (PGT-A). INTERVENTIONS(S) In a donated embryo arm, SEM was collected on days 3 and 5, with one-half of the embryos undergoing AH before and one-half after. In a clinical arm, SEM was collected on day 5 before trophectoderm (TE) biopsy. Samples underwent PGT-A with the use of next-generation sequencing. cfDNA results were compared with corresponding whole embryos and TE biopsies. MAIN OUTCOME MEASURE(S) Concordance rates, sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) for ploidy and sex detection with the use of cfDNA. RESULT(S) Of 141 samples, cfDNA was amplified in 39% and 80.4% of days 3 and 5 SEM, respectively. Concordances for ploidy and sex, respectively, were 56.3% and 81.3% between day 3 cfDNA and whole embryos, and 65% and 70% between day 5 cfDNA and TE biopsies. Day 5 cfDNA sensitivity and specificity for aneuploidy were 0.8 and 0.61, respectively. PPV and NPV were 0.47 and 0.88, respectively. Timing of AH and morphology did not influence cfDNA concentration or accuracy. CONCLUSION(S) cfDNA is detectable on days 3 and 5, but more accurate on day 5. Although our data suggest moderate concordance rates, PGT-A with the use of cfDNA must be further optimized before clinical implementation.
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Affiliation(s)
- Jacqueline R Ho
- Department of Obstetrics and Gynecology, University of Southern California, Los Angeles, California.
| | - Nabil Arrach
- Department of Microbiology and Molecular Genetics, University of California, Irvine, California; Progenesis, La Jolla, California
| | - Katherine Rhodes-Long
- Department of Obstetrics and Gynecology, University of Southern California, Los Angeles, California
| | - Ali Ahmady
- Department of Obstetrics and Gynecology, University of Southern California, Los Angeles, California
| | - Sue Ingles
- Department of Preventative Medicine, University of Southern California, Los Angeles, California
| | - Karine Chung
- Department of Obstetrics and Gynecology, University of Southern California, Los Angeles, California
| | - Kristin A Bendikson
- Department of Obstetrics and Gynecology, University of Southern California, Los Angeles, California
| | - Richard J Paulson
- Department of Obstetrics and Gynecology, University of Southern California, Los Angeles, California
| | - Lynda K McGinnis
- Department of Obstetrics and Gynecology, University of Southern California, Los Angeles, California
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20
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Wang J, Zeng Y, Ding C, Cai B, Lu B, Li R, Xu Y, Xu Y, Zhou C. Preimplantation genetic testing of Robertsonian translocation by SNP array-based preimplantation genetic haplotyping. Prenat Diagn 2018; 38:547-554. [PMID: 29799617 DOI: 10.1002/pd.5258] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 03/23/2018] [Accepted: 03/26/2018] [Indexed: 11/10/2022]
Abstract
OBJECTIVES The present study attempted to confirm a method that distinguishes a balanced Robertsonian translocation carrier embryo from a truly normal embryo in parallel with comprehensive chromosome screening (CCS). METHODS Comprehensive chromosome screening was performed in 107 embryos from 11 couples carrying Robertsonian translocations. Among them, embryos from 2 families had been transferred before the diagnosis of translocation, which resulted in successful pregnancies; embryos from the remaining families were transferred after the identification of translocations. The single nucleotide polymorphism (SNP) genotypes were acquired on a genome-wide basis, and breakpoint regions and flanking were assessed by establishing haplotypes. The predicted karyotypes from the transferred embryos were confirmed by prenatal diagnosis. RESULTS Among the 9 families finally undergoing translocation diagnosis, the amniotic cell karyotypes of 3 families were concordant with the results predicted by preimplantation genetic haplotyping, revealing a good consistency rate. After CCS, the euploid embryos from 2 other families could not be further detected because of the absence of abnormal embryos as probands. CONCLUSIONS Molecular karyotypes and haplotypes could be established with SNP microarray simultaneously in each embryo. SNP array-based PGT can simultaneously complete the CCS and identify Robertsonian translocation carriers, thus making it possible to prevent Robertsonian translocations from being passed to subsequent generations.
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Affiliation(s)
- Jing Wang
- Center for Reproductive Medicine and Department of Gynecology & Obstetrics, First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, China
| | - Yanhong Zeng
- Center for Reproductive Medicine and Department of Gynecology & Obstetrics, First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, China
| | - Chenhui Ding
- Center for Reproductive Medicine and Department of Gynecology & Obstetrics, First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, China
| | - Bin Cai
- Center for Reproductive Medicine and Department of Gynecology & Obstetrics, First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, China
| | - Baomin Lu
- Center for Reproductive Medicine and Department of Gynecology & Obstetrics, First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, China
| | - Rong Li
- Center for Reproductive Medicine and Department of Gynecology & Obstetrics, First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, China
| | - Yan Xu
- Center for Reproductive Medicine and Department of Gynecology & Obstetrics, First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, China
| | - Yanwen Xu
- Center for Reproductive Medicine and Department of Gynecology & Obstetrics, First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, China
| | - Canquan Zhou
- Center for Reproductive Medicine and Department of Gynecology & Obstetrics, First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, China
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Preliminary analysis of numerical chromosome abnormalities in reciprocal and Robertsonian translocation preimplantation genetic diagnosis cases with 24-chromosomal analysis with an aCGH/SNP microarray. J Assist Reprod Genet 2017; 35:177-186. [PMID: 28921398 DOI: 10.1007/s10815-017-1045-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 09/07/2017] [Indexed: 10/18/2022] Open
Abstract
PURPOSE The aim of this study was to determine whether an interchromosomal effect (ICE) occurred in embryos obtained from reciprocal translocation (rcp) and Robertsonian translocation (RT) carriers who were following a preimplantation genetic diagnosis (PGD) with whole chromosome screening with an aCGH and SNP microarray. We also analyzed the chromosomal numerical abnormalities in embryos with aneuploidy in parental chromosomes that were not involved with a translocation and balanced in involved parental translocation chromosomes. METHODS This retrospective study included 832 embryos obtained from rcp carriers and 382 embryos from RT carriers that were biopsied in 139 PGD cycles. The control group involved embryos obtained from age-matched patient karyotypes who were undergoing preimplantation genetic screening (PGS) with non-translocation, and 579 embryos were analyzed in the control group. A single blastomere at the cleavage stage or trophectoderm from a blastocyst was biopsied, and 24-chromosomal analysis with an aCGH/SNP microarray was conducted using the PGD/PGS protocols. Statistical analyses were implemented on the incidences of cumulative aneuploidy rates between the translocation carriers and the control group. RESULTS Reliable results were obtained from 138 couples, among whom only one patient was a balanced rcp or RT translocation carrier, undergoing PGD testing in our center from January 2012 to June 2014. For day 3 embryos, the aneuploidy rates were 50.7% for rcp carriers and 49.1% for RT carriers, compared with the control group, with 44.8% at a maternal age < 36 years. When the maternal age was ≥ 36 years, the aneuploidy rates were increased to 61.1% for rcp carriers, 56.7% for RT carriers, and 60.3% for the control group. There were no significant differences. In day 5 embryos, the aneuploidy rates were 24.5% for rcp carriers and 34.9% for RT carriers, compared with the control group with 53.6% at a maternal age < 36 years. When the maternal age was ≥ 36 years, the aneuploidy rates were 10.7% for rcp carriers, 26.3% for RT carriers, and 57.1% for the control group. The cumulative aneuploidy rates of chromosome translocation carriers were significantly lower than the control group. No ICE was observed in cleavage and blastocyst stage embryos obtained from these carriers. Additionally, the risk of chromosomal numerical abnormalities was observed in each of the 23 pairs of autosomes or sex chromosomes from day 3 and day 5 embryos. CONCLUSION There was not enough evidence to prove that ICE was present in embryos derived from both rcp and RT translocation carriers, regardless of the maternal age. However, chromosomal numerical abnormalities were noticed in 23 pairs of autosomes and sex chromosomes in parental structurally normal chromosomes. Thus, 24-chromosomal analysis with an aCGH/SNP microarray PGD protocol is required to decrease the risks of failure to diagnose aneuploidy in structurally normal chromosomes.
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Takyi A, Santolaya-Forgas J. Prenatal screening for chromosomal abnormalities in IVF patients that opted for preimplantation genetic screening/diagnosis (PGS/D): a need for revised algorithms in the era of personalized medicine. J Assist Reprod Genet 2017; 34:723-724. [PMID: 28357616 DOI: 10.1007/s10815-017-0907-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 03/07/2017] [Indexed: 02/06/2023] Open
Abstract
Obstetricians offer prenatal screening for most common chromosomal abnormalities to all pregnant women including those that had in vitro fertilization (IVF) and preimplantation genetic screening/diagnosis (PGS/D). We propose that free fetal DNA in maternal circulation together with the second trimester maternal serum alfa feto protein (MSAFP) and ultrasound imaging is the best prenatal screening test for chromosomal abnormalities and congenital anomalies in IVF-PGD/S patients because risk estimations from all other prenatal screening algorithms for chromosomal abnormalities depend heavily on maternal age which is irrelevant in PGS/D patients.
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Affiliation(s)
- Afua Takyi
- Rutgers Robert Wood Johnson Medical School, New Brunswick, USA
| | - Joaquin Santolaya-Forgas
- Perinatal Institute, Jersey Shore University Medical Center, 1944 Route 33, Suite 204, Neptune, NJ, 07753, USA.
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Number of blastocysts biopsied as a predictive indicator to obtain at least one normal/balanced embryo following preimplantation genetic diagnosis with single nucleotide polymorphism microarray in translocation cases. J Assist Reprod Genet 2016; 34:51-59. [PMID: 27822654 PMCID: PMC5330983 DOI: 10.1007/s10815-016-0831-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 10/23/2016] [Indexed: 11/12/2022] Open
Abstract
Purpose The aim of this study is to investigate the minimum number of blastocysts for biopsy to increase the likelihood of obtaining at least one normal/balanced embryo in preimplantation genetic diagnosis (PGD) for translocation carriers. Methods This blinded retrospective study included 55 PGD cycles for Robertsonian translocation (RT) and 181 cycles for reciprocal translocation (rcp) to indicate when only one of the couples carried a translocation. Single-nucleotide polymorphism microarray after trophectoderm biopsy was performed. Results Reliable results were obtained for 355/379 (93.7 %) biopsied blastocysts in RT group and 986/1053 (93.6 %) in rcp group. Mean numbers of biopsied embryos per patient, normal/balanced embryos per patient, and mean normal/balanced embryo rate per patient were 7.4, 3.1, and 40.7 % in RT group and 8.0, 2.1, and 27.3 %, respectively, in rcp group. In a regression model, three factors significantly affected the number of genetically transferrable embryos: number of biopsied embryos (P = 0.001), basal FSH level (P = 0.040), and maternal age (P = 0.027). ROC analysis with a cutoff of 1.5 was calculated for the number of biopsied embryos required to obtain at least one normal/balanced embryo for RT carriers. For rcp carriers, the cutoff was 3.5. The clinical pregnancy rate per embryo transfer was 44.2 and 42.6 % in RT and rcp groups (P = 0.836). Conclusions The minimum numbers of blastocysts to obtain at least one normal/balanced embryo for RT and rcp were 2 and 4 under the conditions of female age < 37 years with a basal FSH level < 11.4 IU/L.
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Novel embryo selection techniques to increase embryo implantation in IVF attempts. Arch Gynecol Obstet 2016; 294:1117-1124. [PMID: 27628754 DOI: 10.1007/s00404-016-4196-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 09/06/2016] [Indexed: 01/01/2023]
Abstract
PURPOSE The final success of an IVF attempt depends on several steps and decisions taken during the ovarian stimulation, the oocyte retrieval, the embryo culture and the embryo transfer. The final selection of the embryos most likely to implant is the final step in this process and the responsibility of the lab. Apart from strict morphologic criteria that historically have been used in embryo selection, additional information on genetic, metabolomic and morphokinetic characteristics of the embryo is recently combined to morphology to select the embryo most likely to produce a pregnancy. In this manuscript, we review the most recent information on the current methods used for embryo selection presenting the predictive capability of each one. METHODS A literature search was performed on Pubmed, Medline and Cochrane Database of Systematic Reviews for published studies using appropriate key words and phrases with no limits placed on time. RESULTS It seems that the combination of morphologic criteria in conjunction to embryo kinetics as documented by time-lapse technology provides the most reliable information on embryo quality. Blastocyst biopsy with subsequent comprehensive chromosome analysis allows the selection of the euploid embryos with the higher implantation potential. CONCLUSION Embryo time-lapse imaging and blastocyst biopsy combined to comprehensive chromosome analysis are the most promising technologies to increase pregnancy rates and reduce the possibility of multiple pregnancies. However, further studies will demonstrate the capability of routinely using these technologies to significantly improve IVF outcomes.
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Shamonki MI, Jin H, Haimowitz Z, Liu L. Proof of concept: preimplantation genetic screening without embryo biopsy through analysis of cell-free DNA in spent embryo culture media. Fertil Steril 2016; 106:1312-1318. [PMID: 27565258 DOI: 10.1016/j.fertnstert.2016.07.1112] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 07/05/2016] [Accepted: 07/21/2016] [Indexed: 11/29/2022]
Abstract
OBJECTIVE To assess whether preimplantation genetic screening (PGS) is possible by testing for free embryonic DNA in spent IVF media from embryos undergoing trophectoderm biopsy. DESIGN Prospective cohort analysis. SETTING Academic fertility center. PATIENT(S) Seven patients undergoing IVF and 57 embryos undergoing trophectoderm biopsy for PGS. INTERVENTION(S) On day 3 of development, each embryo was placed in a separate media droplet. All biopsied embryos received a PGS result by array comparative genomic hybridization. Preimplantation genetic screening was performed on amplified DNA extracted from media and results were compared with PGS results for the corresponding biopsy. MAIN OUTCOME MEASURE(S) [1] Presence of DNA in spent IVF culture media. [2] Correlation between genetic screening result from spent media and corresponding biopsy. RESULT(S) Fifty-five samples had detectable DNA ranging from 2-642 ng/μL after a 2-hour amplification. Six samples with the highest DNA levels underwent PGS, rendering one result with a derivative log ratio SD (DLRSD) of <0.85 (a quality control metric of oligonucleotide array comparative genomic hybridization). The fluid sample and trophectoderm results were identical demonstrating (45XY, -13). Three samples were reamplified 1 hour later and tested showing improving DLRSD. One of the three samples with a DLRSD of 0.85 demonstrated (46XY), consistent with the biopsy. Overnight DNA amplification showed DNA in all samples. CONCLUSION(S) We demonstrate two novel findings: the presence of free embryonic DNA in spent media and a result that is consistent with trophectoderm biopsy. Improvements in DNA collection, amplification, and testing may allow for PGS without biopsy in the future.
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Affiliation(s)
- Mousa I Shamonki
- Fertility and Surgical Associates of California, Thousand Oaks, California; University of California, Los Angeles, Fertility and Reproductive Health Center, Los Angeles, California.
| | - Helen Jin
- PacGenomics, Agoura Hills, California
| | | | - Lian Liu
- PacGenomics, Agoura Hills, California
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Murphy NM, Burton M, Powell DR, Rossello FJ, Cooper D, Chopra A, Hsieh MJ, Sayer DC, Gordon L, Pertile MD, Tait BD, Irving HR, Pouton CW. Haplotyping the human leukocyte antigen system from single chromosomes. Sci Rep 2016; 6:30381. [PMID: 27461731 PMCID: PMC4961964 DOI: 10.1038/srep30381] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 06/29/2016] [Indexed: 11/18/2022] Open
Abstract
We describe a method for determining the parental HLA haplotypes of a single individual without recourse to conventional segregation genetics. Blood samples were cultured to identify and sort chromosome 6 by bivariate flow cytometry. Single chromosome 6 amplification products were confirmed with a single nucleotide polymorphism (SNP) array and verified by deep sequencing to enable assignment of both alleles at the HLA loci, defining the two haplotypes. This study exemplifies a rapid and efficient method of haplotyping that can be applied to any chromosome pair, or indeed all chromosome pairs, using a single sorting operation. The method represents a cost-effective approach to complete phasing of SNPs, which will facilitate a deeper understanding of the links between SNPs, gene regulation and protein function.
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Affiliation(s)
- Nicholas M Murphy
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
- Preimplantation Genetic Diagnosis, Melbourne IVF, Melbourne, VIC, Australia
| | - Matthew Burton
- Flow Cytometry &Imaging, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - David R Powell
- Bioinformatics Platform, Monash University, Clayton, VIC, Australia
| | - Fernando J Rossello
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia
| | - Don Cooper
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, WA, Australia
| | - Abha Chopra
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, WA, Australia
| | - Ming Je Hsieh
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | | | - Lavinia Gordon
- Australian Genome Research Facility, The Walter and Eliza Hall Institute of Medical Research, Royal Parade, Parkville, VIC, Australia
| | - Mark D Pertile
- Victorian Clinical Genetics Services, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Brian D Tait
- Transplant Services, Australian Red Cross Blood Service, Parkville, VIC, Australia
| | - Helen R Irving
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Colin W Pouton
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
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Lu L, Lv B, Huang K, Xue Z, Zhu X, Fan G. Recent advances in preimplantation genetic diagnosis and screening. J Assist Reprod Genet 2016; 33:1129-34. [PMID: 27272212 DOI: 10.1007/s10815-016-0750-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 05/25/2016] [Indexed: 12/18/2022] Open
Abstract
Preimplantation genetic diagnosis/screening (PGD/PGS) aims to help couples lower the risks of transmitting genetic defects to their offspring, implantation failure, and/or miscarriage during in vitro fertilization (IVF) cycles. However, it is still being debated with regard to the practicality and diagnostic accuracy of PGD/PGS due to the concern of invasive biopsy and the potential mosaicism of embryos. Recently, several non-invasive and high-throughput assays have been developed to help overcome the challenges encountered in the conventional invasive biopsy and low-throughput analysis in PGD/PGS. In this mini-review, we will summarize the recent progresses of these new methods for PGD/PGS and discuss their potential applications in IVF clinics.
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Affiliation(s)
- Lina Lu
- Translational Center for Stem Cell Research, Tongji Hospital, Department of Regenerative Medicine, Tongji University School of Medicine, Shanghai, 200065, China.,School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Bo Lv
- Translational Center for Stem Cell Research, Tongji Hospital, Department of Regenerative Medicine, Tongji University School of Medicine, Shanghai, 200065, China
| | - Kevin Huang
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Zhigang Xue
- Translational Center for Stem Cell Research, Tongji Hospital, Department of Regenerative Medicine, Tongji University School of Medicine, Shanghai, 200065, China
| | - Xianmin Zhu
- School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Guoping Fan
- School of Life Sciences and Technology, Advanced Institute of Translational Medicine, Tongji University, 1239 Siping Road, Shanghai, 200092, China. .,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
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Validation of a next-generation sequencing–based protocol for 24-chromosome aneuploidy screening of blastocysts. Fertil Steril 2016; 105:1532-6. [DOI: 10.1016/j.fertnstert.2016.01.040] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 01/23/2016] [Accepted: 01/25/2016] [Indexed: 01/07/2023]
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Live births after simultaneous avoidance of monogenic diseases and chromosome abnormality by next-generation sequencing with linkage analyses. Proc Natl Acad Sci U S A 2015; 112:15964-9. [PMID: 26712022 DOI: 10.1073/pnas.1523297113] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In vitro fertilization (IVF), preimplantation genetic diagnosis (PGD), and preimplantation genetic screening (PGS) help patients to select embryos free of monogenic diseases and aneuploidy (chromosome abnormality). Next-generation sequencing (NGS) methods, while experiencing a rapid cost reduction, have improved the precision of PGD/PGS. However, the precision of PGD has been limited by the false-positive and false-negative single-nucleotide variations (SNVs), which are not acceptable in IVF and can be circumvented by linkage analyses, such as short tandem repeats or karyomapping. It is noteworthy that existing methods of detecting SNV/copy number variation (CNV) and linkage analysis often require separate procedures for the same embryo. Here we report an NGS-based PGD/PGS procedure that can simultaneously detect a single-gene disorder and aneuploidy and is capable of linkage analysis in a cost-effective way. This method, called "mutated allele revealed by sequencing with aneuploidy and linkage analyses" (MARSALA), involves multiple annealing and looping-based amplification cycles (MALBAC) for single-cell whole-genome amplification. Aneuploidy is determined by CNVs, whereas SNVs associated with the monogenic diseases are detected by PCR amplification of the MALBAC product. The false-positive and -negative SNVs are avoided by an NGS-based linkage analysis. Two healthy babies, free of the monogenic diseases of their parents, were born after such embryo selection. The monogenic diseases originated from a single base mutation on the autosome and the X-chromosome of the disease-carrying father and mother, respectively.
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Huang J, Li R, Lian Y, Chen L, Shi X, Qiao J, Liu P. Vitrified/warmed single blastocyst transfer in preimplantation genetic diagnosis/preimplantation genetic screening cycles. Int J Clin Exp Med 2015; 8:21605-21610. [PMID: 26885112 PMCID: PMC4723957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 10/31/2015] [Indexed: 06/05/2023]
Abstract
OBJECTIVE To investigate the single blastocyst transfer in preimplantation genetic diagnosis (PGD)/preimplantation genetic screening (PGS) cycles. METHODS 80 PGD/PGS cycles undergoing blastocyst biopsy were studied. There were 88 warming cycles during the study period. Only one warmed blastocyst was transferred per cycle. The outcomes were followed up to the infants were born. RESULTS The embryo implantation rate was 54.55% (48/88). The clinical pregnancy rate was 54.55% (48/88) per transfer cycle and 60% (48/80) per initial PGD/PGS cycle. There was no multi-pregnant in this study. The live birth rate was 42.05% (37/88) per transfer cycle and 46.25% (37/80) per initial PGD/PGS cycle. CONCLUSION In PGD/PGS cycles, single blastocyst transfer reduces the multiple pregnancy rate without affecting the clinical outcomes.
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Affiliation(s)
- Jin Huang
- Department of Obstetrics and Gynecology, Reproductive Medical Centre, Peking University Third HospitalBeijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education and Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive TechnologyBeijing 100191, China
| | - Rong Li
- Department of Obstetrics and Gynecology, Reproductive Medical Centre, Peking University Third HospitalBeijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education and Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive TechnologyBeijing 100191, China
| | - Ying Lian
- Department of Obstetrics and Gynecology, Reproductive Medical Centre, Peking University Third HospitalBeijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education and Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive TechnologyBeijing 100191, China
| | - Lixue Chen
- Department of Obstetrics and Gynecology, Reproductive Medical Centre, Peking University Third HospitalBeijing 100191, China
| | - Xiaodan Shi
- Department of Obstetrics and Gynecology, Reproductive Medical Centre, Peking University Third HospitalBeijing 100191, China
| | - Jie Qiao
- Department of Obstetrics and Gynecology, Reproductive Medical Centre, Peking University Third HospitalBeijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education and Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive TechnologyBeijing 100191, China
| | - Ping Liu
- Department of Obstetrics and Gynecology, Reproductive Medical Centre, Peking University Third HospitalBeijing 100191, China
- Key Laboratory of Assisted Reproduction, Ministry of Education and Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive TechnologyBeijing 100191, China
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Preimplantation genetic diagnosis: an update on current technologies and ethical considerations. Reprod Med Biol 2015; 15:69-75. [PMID: 29259423 DOI: 10.1007/s12522-015-0224-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 09/15/2015] [Indexed: 10/22/2022] Open
Abstract
The aim of reproductive medicine is to support the birth of healthy children. Advances in assisted reproductive technologies and genetic analysis have led to the introduction of preimplantation genetic diagnosis (PGD) for embryos. Indications for PGD have been a major topic in the fields of ethics and law. Concerns vary by nation, religion, population, and segment, and the continued rapid development of new technologies. In contrast to the ethical augment, technology has been developing at an excessively rapid speed. The most significant recent technological development provides the ability to perform whole genome amplification and sequencing of single embryonic cells by microarray or next-generation sequencing methods. As new affordable technologies are introduced, patients are presented with a growing variety of PGD options. Simultaneously, the ethical guidelines for the indications for testing and handling of genetic information must also rapidly correspond to the changes.
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Bono S, Biricik A, Spizzichino L, Nuccitelli A, Minasi MG, Greco E, Spinella F, Fiorentino F. Validation of a semiconductor next-generation sequencing-based protocol for preimplantation genetic diagnosis of reciprocal translocations. Prenat Diagn 2015; 35:938-44. [PMID: 26243475 DOI: 10.1002/pd.4665] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/30/2015] [Accepted: 07/31/2015] [Indexed: 11/07/2022]
Abstract
OBJECTIVE We aim to validate a semiconductor next-generation sequencing (NGS)-based method to detect unbalanced chromosome translocation in preimplantation embryos. METHODS The study consisted of a blinded retrospective evaluation with NGS of 145 whole-genome amplification products obtained from biopsy of cleavage-stage embryos or blastocysts, derived from 33 couples carrying different balanced translocations. Consistency of NGS-based copy number assignments was evaluated and compared with the results obtained by array-comparative genomic hybridization. RESULTS Reliably identified with the NGS-based protocol were 162 segmental imbalances derived from 33 different chromosomal translocations, with the smallest detectable chromosomal segment being 5 Mb in size. Of the 145 embryos analysed, 20 (13.8%) were balanced, 43 (29.6%) were unbalanced, 53 (36.5%) were unbalanced and aneuploid, and 29 (20%) were balanced but aneuploid. NGS sensitivity for unbalanced/aneuploid chromosomal call (consistency of chromosome copy number assignment) was 99.75% (402/403), with a specificity of 100% (3077/3077). NGS specificity and sensitivity for unbalanced/aneuploid embryo call were 100%. CONCLUSIONS Next-generation sequencing can detect chromosome imbalances in embryos with the added benefit of simultaneous comprehensive aneuploidy screening. Given the high level of consistency with array-comparative genomic hybridization, NGS has been demonstrated to be a robust high-throughput technique ready for clinical application in preimplantation genetic diagnosis for chromosomal translocations, with potential advantages of automation, increased throughput and reduced cost.
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Affiliation(s)
- S Bono
- GENOMA, Molecular Genetics Laboratory, Rome, Italy
| | - A Biricik
- GENOMA, Molecular Genetics Laboratory, Rome, Italy
| | | | - A Nuccitelli
- GENOMA, Molecular Genetics Laboratory, Rome, Italy
| | - M G Minasi
- Centre for Reproductive Medicine, European Hospital, Rome, Italy
| | - E Greco
- Centre for Reproductive Medicine, European Hospital, Rome, Italy
| | - F Spinella
- GENOMA, Molecular Genetics Laboratory, Rome, Italy
| | - F Fiorentino
- GENOMA, Molecular Genetics Laboratory, Rome, Italy
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Huang L, Ma F, Chapman A, Lu S, Xie XS. Single-Cell Whole-Genome Amplification and Sequencing: Methodology and Applications. Annu Rev Genomics Hum Genet 2015; 16:79-102. [PMID: 26077818 DOI: 10.1146/annurev-genom-090413-025352] [Citation(s) in RCA: 265] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We present a survey of single-cell whole-genome amplification (WGA) methods, including degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR), multiple displacement amplification (MDA), and multiple annealing and looping-based amplification cycles (MALBAC). The key parameters to characterize the performance of these methods are defined, including genome coverage, uniformity, reproducibility, unmappable rates, chimera rates, allele dropout rates, false positive rates for calling single-nucleotide variations, and ability to call copy-number variations. Using these parameters, we compare five commercial WGA kits by performing deep sequencing of multiple single cells. We also discuss several major applications of single-cell genomics, including studies of whole-genome de novo mutation rates, the early evolution of cancer genomes, circulating tumor cells (CTCs), meiotic recombination of germ cells, preimplantation genetic diagnosis (PGD), and preimplantation genomic screening (PGS) for in vitro-fertilized embryos.
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Affiliation(s)
- Lei Huang
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
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Huang J, Yan L, Fan W, Zhao N, Zhang Y, Tang F, Xie XS, Qiao J. Validation of multiple annealing and looping-based amplification cycle sequencing for 24-chromosome aneuploidy screening of cleavage-stage embryos. Fertil Steril 2014; 102:1685-91. [PMID: 25241375 DOI: 10.1016/j.fertnstert.2014.08.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Revised: 08/07/2014] [Accepted: 08/07/2014] [Indexed: 12/12/2022]
Abstract
OBJECTIVE To validate multiple annealing and looping-based amplification cycle (MALBAC) sequencing for 24-chromosome aneuploidy screening of cleavage embryos and to explore the chromosomal characteristics of embryos at the cleavage stage. DESIGN The 24-chromosome aneuploidy analyses of the blastomeres included comparative genomic hybridization (CGH), single nucleotide polymorphism (SNP), and MALBAC sequencing. SETTING University-affiliated IVF center. PATIENT(S) Three couples who delivered babies from the same IVF cycle, which included 23 donated, frozen cleavage embryos. INTERVENTION(S) None. MAIN OUTCOME MEASURE(S) Three blastomeres were selected from each single embryo and subject to CGH, SNP, and MALBAC sequencing for 24-chromosome aneuploidy, respectively. The results of MALBAC sequencing were compared with the results of CGH and SNP. The chromosomal status and occurrence of the abnormal chromosomes were investigated. The relationship between the embryos' morphology and the euploid state was analyzed. RESULT(S) Among the 23 donated embryos, the MALBAC sequencing results of 18 (78.26%) embryos were identical to those of CGH or SNP, including 8 embryos that had identical results by all three techniques. In terms of euploidy, only 6 of these 23 embryos (26.09%) were diploid. Blastomere abnormality was observed in all autosomes and sex chromosomes. In addition, the frequency of abnormality was different for certain chromosomes. CONCLUSION(S) With sequencing at 0.04× genome depth, MALBAC sequencing has been validated as a satisfactory method for 24-chromosome aneuploidy screening. The proportion of abnormal chromosomes was high in cleavage-stage embryos, and any chromosome could be abnormal.
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Affiliation(s)
- Jin Huang
- Department of Obstetrics and Gynecology, Reproductive Medical Centre, Peking University Third Hospital, Beijing, People's Republic of China; Key Laboratory of Assisted Reproduction, Ministry of Education and Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, People's Republic of China
| | - Liying Yan
- Department of Obstetrics and Gynecology, Reproductive Medical Centre, Peking University Third Hospital, Beijing, People's Republic of China; Key Laboratory of Assisted Reproduction, Ministry of Education and Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, People's Republic of China
| | - Wei Fan
- Biodynamic Optical Imaging Center, College of Life Sciences, Peking University, Beijing, People's Republic of China
| | - Nan Zhao
- Department of Obstetrics and Gynecology, Reproductive Medical Centre, Peking University Third Hospital, Beijing, People's Republic of China
| | - Yan Zhang
- Department of Obstetrics and Gynecology, Reproductive Medical Centre, Peking University Third Hospital, Beijing, People's Republic of China; Key Laboratory of Assisted Reproduction, Ministry of Education and Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, People's Republic of China
| | - Fuchou Tang
- Biodynamic Optical Imaging Center, College of Life Sciences, Peking University, Beijing, People's Republic of China
| | - X Sunney Xie
- Biodynamic Optical Imaging Center, College of Life Sciences, Peking University, Beijing, People's Republic of China; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
| | - Jie Qiao
- Department of Obstetrics and Gynecology, Reproductive Medical Centre, Peking University Third Hospital, Beijing, People's Republic of China; Key Laboratory of Assisted Reproduction, Ministry of Education and Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, People's Republic of China.
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