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Madritsch S, Arnold V, Haider M, Bosenge J, Pfeifer M, Weil B, Zechmeister M, Hengstschläger M, Neesen J, Laccone F. Aneuploidy detection in pooled polar bodies using rapid nanopore sequencing. J Assist Reprod Genet 2024; 41:1261-1271. [PMID: 38642269 PMCID: PMC11143085 DOI: 10.1007/s10815-024-03108-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 03/25/2024] [Indexed: 04/22/2024] Open
Abstract
PURPOSE Various screening techniques have been developed for preimplantation genetic testing for aneuploidy (PGT-A) to reduce implantation failure and miscarriages in women undergoing in vitro fertilisation (IVF) treatment. Among these methods, the Oxford nanopore technology (ONT) has already been tested in several tissues. However, no studies have applied ONT to polar bodies, a cellular material that is less restrictively regulated for PGT-A in some countries. METHODS We performed rapid short nanopore sequencing on pooled first and second polar bodies of 102 oocytes from women undergoing IVF treatment to screen for aneuploidy. An automated analysis pipeline was developed with the expectation of three chromatids per chromosome. The results were compared to those obtained by array-based comparative genomic hybridisation (aCGH). RESULTS ONT and aCGH were consistent for 96% (98/102) of sample ploidy classification. Of those samples, 36 were classified as euploid, while 62 were classified as aneuploid. The four discordant samples were assessed as euploid using aCGH but classified as aneuploid using ONT. The concordance of the ploidy classification (euploid, gain, or loss) per chromosome was 92.5% (2169 of 2346 of analysed chromosomes) using aCGH and ONT and increased to 97.7% (2113/2162) without the eight samples assessed as highly complex aneuploid using ONT. CONCLUSION The automated detection of the ploidy classification per chromosome and shorter duplications or deletions depending on the sequencing depth demonstrates an advantage of the ONT method over standard, commercial aCGH methods, which do not consider the presence of three chromatids in pooled polar bodies.
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Affiliation(s)
- Silvia Madritsch
- Institute of Medical Genetics, Medical University of Vienna, Währinger Straße 10, 1090, Vienna, Austria.
| | - Vivienne Arnold
- Institute of Medical Genetics, Medical University of Vienna, Währinger Straße 10, 1090, Vienna, Austria
- HLN-Genetik GmbH, Ortliebgasse 25/1, 1170, Vienna, Austria
| | - Martha Haider
- Institute of Medical Genetics, Medical University of Vienna, Währinger Straße 10, 1090, Vienna, Austria
- HLN-Genetik GmbH, Ortliebgasse 25/1, 1170, Vienna, Austria
| | - Julia Bosenge
- HLN-Genetik GmbH, Ortliebgasse 25/1, 1170, Vienna, Austria
| | - Mateja Pfeifer
- Institute of Medical Genetics, Medical University of Vienna, Währinger Straße 10, 1090, Vienna, Austria
| | - Beatrix Weil
- Institute of Medical Genetics, Medical University of Vienna, Währinger Straße 10, 1090, Vienna, Austria
- HLN-Genetik GmbH, Ortliebgasse 25/1, 1170, Vienna, Austria
| | | | - Markus Hengstschläger
- Institute of Medical Genetics, Medical University of Vienna, Währinger Straße 10, 1090, Vienna, Austria
- HLN-Genetik GmbH, Ortliebgasse 25/1, 1170, Vienna, Austria
| | - Jürgen Neesen
- Institute of Medical Genetics, Medical University of Vienna, Währinger Straße 10, 1090, Vienna, Austria
- HLN-Genetik GmbH, Ortliebgasse 25/1, 1170, Vienna, Austria
| | - Franco Laccone
- Institute of Medical Genetics, Medical University of Vienna, Währinger Straße 10, 1090, Vienna, Austria
- HLN-Genetik GmbH, Ortliebgasse 25/1, 1170, Vienna, Austria
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Liu Y, Shen J, Yang R, Zhang Y, Jia L, Guan Y. The Relationship between Human Embryo Parameters and De Novo Chromosomal Abnormalities in Preimplantation Genetic Testing Cycles. Int J Endocrinol 2022; 2022:9707081. [PMID: 35345425 PMCID: PMC8957472 DOI: 10.1155/2022/9707081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 12/17/2021] [Accepted: 02/24/2022] [Indexed: 11/17/2022] Open
Abstract
DESIGN In total, 456 PGT cycles, including 283 PGT-SR cycles and 173 PGT-A cycles, were assessed through comprehensive chromosome screening (CCS) from January 2017 to June 2020 at the Department of Reproductive Medicine of the Third Affiliated Hospital of Zhengzhou University. Trophectoderm (TE) biopsies were sequenced using next-generation sequencing (NGS). The incidence of de novo chromosome abnormalities was calculated, and the relationships between de novo chromosome abnormality rates and maternal age, number of oocytes retrieved, and parameters of cleavage-stage embryos and blastocyst-stage embryos were investigated. RESULTS The incidence of de novo chromosome abnormalities was 28.0% (318/1,135) in the PGT-SR cycles and 36.3% (214/590) in the PGT-A cycles, which increased with maternal age in both PGT-SR cycles (P = 0.018) and PGT-A cycles (P < 0.001). The incidence of de novo chromosome abnormalities was related to TE grade (P < 0.001), internal cell mass grade (P = 0.002), and development speed (day 5 vs. day 7: P < 0.001) of blastocyst-stage embryos. The incidence of de novo chromosomal abnormalities was irrelevant to the number of oocytes retrieved and the parameters of the embryo at the cleavage stage. CONCLUSION Blastocysts with higher morphology scores and faster progression had a lower incidence of de novo chromosome abnormalities, especially complex chromosome abnormalities. De novo chromosome abnormalities may negatively affect the morphological grading of blastocysts. Our findings will provide valuable information to the fertility doctor for embryo selection in non-PGT cycles.
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Affiliation(s)
- Yanli Liu
- Department of Reproductive Medicine, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Junhan Shen
- Department of Reproductive Medicine, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Rujing Yang
- Department of Reproductive Medicine, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yuchao Zhang
- Department of Reproductive Medicine, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Liting Jia
- Neonatal Screening Center, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yichun Guan
- Department of Reproductive Medicine, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
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Abstract
Over the past decade, genomic analyses of single cells-the fundamental units of life-have become possible. Single-cell DNA sequencing has shed light on biological questions that were previously inaccessible across diverse fields of research, including somatic mutagenesis, organismal development, genome function, and microbiology. Single-cell DNA sequencing also promises significant future biomedical and clinical impact, spanning oncology, fertility, and beyond. While single-cell approaches that profile RNA and protein have greatly expanded our understanding of cellular diversity, many fundamental questions in biology and important biomedical applications require analysis of the DNA of single cells. Here, we review the applications and biological questions for which single-cell DNA sequencing is uniquely suited or required. We include a discussion of the fields that will be impacted by single-cell DNA sequencing as the technology continues to advance.
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Affiliation(s)
- Gilad D Evrony
- Center for Human Genetics and Genomics, Grossman School of Medicine, New York University, New York, NY 10016, USA;
| | - Anjali Gupta Hinch
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom;
| | - Chongyuan Luo
- Department of Human Genetics, University of California, Los Angeles, California 90095, USA;
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Eggenhuizen GM, Go A, Koster MPH, Baart EB, Galjaard RJ. Confined placental mosaicism and the association with pregnancy outcome and fetal growth: a review of the literature. Hum Reprod Update 2021; 27:885-903. [PMID: 33984128 PMCID: PMC8382909 DOI: 10.1093/humupd/dmab009] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 01/30/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Chromosomal mosaicism can be detected in different stages of early life: in cleavage stage embryos, in blastocysts and biopsied cells from blastocysts during preimplantation genetic testing for aneuploidies (PGT-A) and later during prenatal testing, as well as after birth in cord blood. Mosaicism at all different stages can be associated with adverse pregnancy outcomes. There is an onward discussion about whether blastocysts diagnosed as chromosomally mosaic by PGT-A should be considered safe for transfer. An accurate diagnosis of mosaicism remains technically challenging and the fate of abnormal cells within an embryo remains largely unknown. However, if aneuploid cells persist in the extraembryonic tissues, they can give rise to confined placental mosaicism (CPM). Non-invasive prenatal testing (NIPT) uses cell-free (cf) DNA released from the placenta in maternal blood, facilitating the detection of CPM. In literature, conflicting evidence is found about whether CPM is associated with fetal growth restriction (FGR) and/or other pregnancy outcomes. This makes counselling for patients by clinicians challenging and more knowledge is needed for clinical decision and policy making. OBJECTIVE AND RATIONALE The objective of this review is to evaluate the association between CPM and prenatal growth and adverse pregnancy outcomes. All relevant literature has been reviewed in order to achieve an overview on merged results exploring the relation between CPM and FGR and other adverse pregnancy outcomes. SEARCH METHODS The following Medical Subject Headings (MESH) terms and all their synonyms were used: placental, trophoblast, cytotrophoblast, mosaicism, trisomy, fetal growth, birth weight, small for gestational age and fetal development. A search in Embase, PubMed, Medline Ovid, Web of Science, Cochrane Central Register of Controlled Trials (CENTRAL) and Google Scholar databases was conducted. Relevant articles published until 16 July 2020 were critically analyzed and discussed. OUTCOMES There were 823 articles found and screened based on their title/abstract. From these, 213 articles were selected and full text versions were obtained for a second selection, after which 70 publications were included and 328 cases (fetuses) were analyzed. For CPM in eight different chromosomes (of the total 14 analyzed), there was sufficient evidence that birth weight was often below the 5th percentile of fetal growth standards. FGR was reported in 71.7% of CPM cases and preterm birth (<37 weeks of delivery) was reported in 31.0% of cases. A high rate of structural fetal anomalies, 24.2%, in cases with CPM was also identified. High levels of mosaicism in CVS and presence of uniparental disomy (UPD) were significantly associated with adverse pregnancy outcomes. WIDER IMPLICATIONS Based on the literature, the advice to clinicians is to monitor fetal growth intensively from first trimester onwards in case of CPM, especially when chromosome 2, 3, 7, 13, 15, 16 and 22 are involved. In addition to this, it is advised to examine the fetuses thoroughly for structural fetal anomalies and raise awareness of a higher chance of (possibly extreme) premature birth. Despite prematurity in nearly a fifth of cases, the long-term follow-up of CPM life borns seems to be positive. More understanding of the biological mechanisms behind CPM will help in prioritizing embryos for transfer after the detection of mosaicism in embryos through PGT-A.
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Affiliation(s)
- Geerke M Eggenhuizen
- Department of Obstetrics and Gynaecology, Erasmus MC, University Medical Center, Rotterdam 3015CN, The Netherlands
| | - Attie Go
- Department of Obstetrics and Gynaecology, Erasmus MC, University Medical Center, Rotterdam 3015CN, The Netherlands
| | - Maria P H Koster
- Department of Obstetrics and Gynaecology, Erasmus MC, University Medical Center, Rotterdam 3015CN, The Netherlands
| | - Esther B Baart
- Department of Obstetrics and Gynaecology, Erasmus MC, University Medical Center, Rotterdam 3015CN, The Netherlands.,Department of Developmental Biology, Erasmus MC, University Medical Center, Rotterdam 3015CN, The Netherlands
| | - Robert Jan Galjaard
- Department of Clinical Genetics, Erasmus MC, University Medical Center, Rotterdam 3015CN, The Netherlands
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De Munck N, Bayram A, Elkhatib I, Liñán A, Arnanz A, Melado L, Lawrenz B, Fatemi MH. Segmental duplications and monosomies are linked to in vitro developmental arrest. J Assist Reprod Genet 2021; 38:2183-2192. [PMID: 33742344 DOI: 10.1007/s10815-021-02147-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/08/2021] [Indexed: 10/21/2022] Open
Abstract
PURPOSE To verify which genetic abnormalities prevent embryos to blastulate in a stage-specific time. METHODS A single center retrospective study was performed between April 2016 and January 2017. Patients requiring Preimplantation Genetic Testing for Aneuploidies (PGT-A) by Next Generation Sequencing (NGS) were included. All embryos were cultured in a time-lapse imaging system and single blastomere biopsy was performed on day 3 of development. Segmental duplications and deletions as well as whole chromosome monosomies and trisomies were registered. Embryo arrest was defined if the embryo failed to blastulate 118 h post-injection. A logistic regression model was applied using the time to blastulate as the response variable and the different mutations as explanatory variables. A p value < 0.05 was considered significant. RESULTS Of the 285 biopsied cleavage stage embryos, 103 (36.1%) were euploid, and 182 (63.9%) were aneuploid. There was a significant difference in the developmental arrest between euploid and aneuploid embryos (8.7% versus 42.9%; p = 0.0001). Segmental duplications and whole chromosome monosomies were found to have a significant effect on developmental arrest (p = 0.0163 and p = 0.0075), while trisomies and segmental deletions had no effect on developmental arrest. In case of segmental duplications, an increase of one extra segmental duplication increases the odd of arrest by 159%. For whole chromosome monosomies, the odd will only increase by 29% for every extra chromosomal monosomy. Both chromosomal abnormalities remained significant after adding age as an explanatory variable to the model (p = 0.014 and p = 0.009). CONCLUSION Day 3 cleavage stage embryos with segmental duplications or monosomies have a significantly decreased chance to reach the blastocyst stage.
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Affiliation(s)
- N De Munck
- ART Fertility Clinics, Abu Dhabi, United Arab Emirates.
| | - A Bayram
- ART Fertility Clinics, Abu Dhabi, United Arab Emirates
| | - I Elkhatib
- ART Fertility Clinics, Abu Dhabi, United Arab Emirates
| | - A Liñán
- ART Fertility Clinics, Abu Dhabi, United Arab Emirates
| | - A Arnanz
- ART Fertility Clinics, Abu Dhabi, United Arab Emirates
| | - L Melado
- ART Fertility Clinics, Abu Dhabi, United Arab Emirates
| | - B Lawrenz
- ART Fertility Clinics, Abu Dhabi, United Arab Emirates.,Obstetrical Department, Women´s University Hospital Tübingen, Tübingen, Germany
| | - M H Fatemi
- ART Fertility Clinics, Abu Dhabi, United Arab Emirates
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