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Xu H, Pu J, Wu Z, Huang Y, Han C, Li X. A healthy live birth after mosaic blastocyst transfer in preimplantation genetic testing for GATA1-related cytopenia combined with HLA matching. BMC Med Genomics 2024; 17:177. [PMID: 38961467 PMCID: PMC11221145 DOI: 10.1186/s12920-024-01951-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 06/27/2024] [Indexed: 07/05/2024] Open
Abstract
BACKGROUND GATA1-related cytopenia (GRC) is characterized by thrombocytopaenia and/or anaemia ranging from mild to severe. Haematopoietic stem cell transplantation (HSCT) is a healing therapeutic choice for GRC patients. We identified a novel pathogenic variant (GATA1: c.1019delG) in a boy with GATA1-related cytopenia. Then we performed preimplantation genetic testing (PGT) in this GRC family. After a mosaic embryo transfered, a healthy and HLA-compatible with the proband baby was delivered. CASE PRESENTATION The proband is a 6-year-old boy who was diagnosed to have transfusion-dependent anaemia since 3 year old. Whole-exome sequencing (WES) showed that the proband has a hemizygous variant c.1019delG in GATA1, which is inherited from his mother. His parents decided to undergo PGT to have a health and HLA-compatible offspring. After whole genome amplification (WGA) of biopsied trophectoderm (TE) cells, next generation sequencing (NGS)-based PGT was preformed to analyse embryos on chromosomal aneuploidy, target mutation and HLA typing. There were 3 embryos HLA-matched to the proband. The genotypes of the 3 embryos were heterozygous variant, hemizygous variant, normal respectively. After a heterozygous, mosaic partial trisomy (chr)16, and HLA-matched embryo transfer, a healthy baby was delivered and whose HSCT is compatible with the proband. CONCLUSIONS NGS-based PGT-HLA is a valuable procedure for the treatment of GATA1-related cytopenia caused by GATA1 variants, or other haematological disorders, oncological and immunological diseases. Furthermore, our study reconfirms that mosaic embryos transfer would bring healthy offspring.
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Affiliation(s)
- Huiling Xu
- Department of Reproductive Medicine, Affiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical University (Shenzhen Maternity & Child Healthcare Hospital), Shenzhen, Guangdong, China
| | - Jiajie Pu
- Department of Bioinformatics, 01life Institute, Shenzhen, 518000, Guangdong, China
| | - Zhengzhong Wu
- Department of Reproductive Medicine, Affiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical University (Shenzhen Maternity & Child Healthcare Hospital), Shenzhen, Guangdong, China
| | - Yulong Huang
- Department of Reproductive Medicine, Affiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical University (Shenzhen Maternity & Child Healthcare Hospital), Shenzhen, Guangdong, China
| | - Chanlin Han
- Department of Reproductive Medicine, Affiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical University (Shenzhen Maternity & Child Healthcare Hospital), Shenzhen, Guangdong, China
| | - Xuemei Li
- Department of Reproductive Medicine, Affiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical University (Shenzhen Maternity & Child Healthcare Hospital), Shenzhen, Guangdong, China.
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Mattar CN, Chew WL, Lai PS. Embryo and fetal gene editing: Technical challenges and progress toward clinical applications. Mol Ther Methods Clin Dev 2024; 32:101229. [PMID: 38533521 PMCID: PMC10963250 DOI: 10.1016/j.omtm.2024.101229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
Gene modification therapies (GMTs) are slowly but steadily making progress toward clinical application. As the majority of rare diseases have an identified genetic cause, and as rare diseases collectively affect 5% of the global population, it is increasingly important to devise gene correction strategies to address the root causes of the most devastating of these diseases and to provide access to these novel therapies to the most affected populations. The main barriers to providing greater access to GMTs continue to be the prohibitive cost of developing these novel drugs at clinically relevant doses, subtherapeutic effects, and toxicity related to the specific agents or high doses required. In vivo strategy and treating younger patients at an earlier course of their disease could lower these barriers. Although currently regarded as niche specialties, prenatal and preconception GMTs offer a robust solution to some of these barriers. Indeed, treating either the fetus or embryo benefits from economy of scale, targeting pre-pathological tissues in the fetus prior to full pathogenesis, or increasing the likelihood of complete tissue targeting by correcting pluripotent embryonic cells. Here, we review advances in embryo and fetal GMTs and discuss requirements for clinical application.
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Affiliation(s)
- Citra N.Z. Mattar
- Experimental Fetal Medicine Group, Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, Level 12, Singapore, Singapore 119228
- Department of Obstetrics and Gynaecology, National University Health System, Singapore, 1E Kent Ridge Road, NUHS Tower Block, Level 12, Singapore, Singapore 119228
| | - Wei Leong Chew
- Genome Institute of Singapore, Agency for Science, Technology and Research (A∗STAR), Singapore, 60 Biopolis St, Singapore, Singapore 138672
| | - Poh San Lai
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, Level 12, Singapore, Singapore 119228
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Sakkas D, Gulliford C, Ardestani G, Ocali O, Martins M, Talasila N, Shah JS, Penzias AS, Seidler EA, Sanchez T. Metabolic imaging of human embryos is predictive of ploidy status but is not associated with clinical pregnancy outcomes: a pilot trial. Hum Reprod 2024; 39:516-525. [PMID: 38195766 DOI: 10.1093/humrep/dead268] [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: 07/24/2023] [Revised: 11/28/2023] [Indexed: 01/11/2024] Open
Abstract
STUDY QUESTION Does fluorescence lifetime imaging microscopy (FLIM)-based metabolic imaging assessment of human blastocysts prior to frozen transfer correlate with pregnancy outcomes? SUMMARY ANSWER FLIM failed to distinguish consistent patterns in mitochondrial metabolism between blastocysts leading to pregnancy compared to those that did not. WHAT IS KNOWN ALREADY FLIM measurements provide quantitative information on NAD(P)H and flavin adenine dinucleotide (FAD+) concentrations. The metabolism of embryos has long been linked to their viability, suggesting the potential utility of metabolic measurements to aid in selection. STUDY DESIGN, SIZE, DURATION This was a pilot trial enrolling 121 IVF couples who consented to have their frozen blastocyst measured using non-invasive metabolic imaging. After being warmed, 105 couples' good-quality blastocysts underwent a 6-min scan in a controlled temperature and gas environment. FLIM-assessed blastocysts were then transferred without any intervention in management. PARTICIPANTS/MATERIALS, SETTING, METHODS Eight metabolic parameters were obtained from each blastocyst (4 for NAD(P)H and 4 for FAD): short and long fluorescence lifetime, fluorescence intensity, and fraction of the molecule engaged with enzyme. The redox ratio (intensity of NAD(P)H)/(intensity of FAD) was also calculated. FLIM data were combined with known metadata and analyzed to quantify the ability of metabolic imaging to differentiate embryos that resulted in pregnancy from embryos that did not. De-identified discarded aneuploid human embryos (n = 158) were also measured to quantify correlations with ploidy status and other factors. Statistical comparisons were performed using logistic regression and receiver operating characteristic (ROC) curves with 5-fold cross-validation averaged over 100 repeats with random sampling. AUC values were used to quantify the ability to distinguish between classes. MAIN RESULTS AND THE ROLE OF CHANCE No metabolic imaging parameters showed significant differences between good-quality blastocysts resulting in pregnancy versus those that did not. A logistic regression using metabolic data and metadata produced an ROC AUC of 0.58. In contrast, robust AUCs were obtained when classifying other factors such as comparison of Day 5 (n = 64) versus Day 6 (n = 41) blastocysts (AUC = 0.78), inner cell mass versus trophectoderm (n = 105: AUC = 0.88) and aneuploid (n = 158) versus euploid and positive pregnancy embryos (n = 108) (AUC = 0.82). LIMITATIONS, REASONS FOR CAUTION The study protocol did not select which embryo to transfer and the cohort of 105 included blastocysts were all high quality. The study was also limited in number of participants and study sites. Increased power and performing the trial in more sites may have provided a stronger conclusion regarding the merits of the use of FLIM clinically. WIDER IMPLICATIONS OF THE FINDINGS FLIM failed to distinguish consistent patterns in mitochondrial metabolism between good-quality blastocysts leading to pregnancy compared to those that did not. Blastocyst ploidy status was, however, highly distinguishable. In addition, embryo regions and embryo day were consistently revealed by FLIM. While metabolic imaging detects mitochondrial metabolic features in human blastocysts, this pilot trial indicates it does not have the potential to serve as an effective embryo viability detection tool. This may be because mitochondrial metabolism plays an alternative role post-implantation. STUDY FUNDING/COMPETING INTEREST(S) This study was sponsored by Optiva Fertility, Inc. Boston IVF contributed to the clinical site and services. Becker Hickl, GmbH, provided the FLIM system on loan. T.S. was the founder and held stock in Optiva Fertility, Inc., and D.S. and E.S. had options with Optiva Fertility, Inc., during this study. TRIAL REGISTRATION NUMBER The study was approved by WCG Connexus IRB (Study Number 1298156).
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Affiliation(s)
- Denny Sakkas
- Boston IVF, Research Department, Waltham, MA, USA
| | | | | | - Olcay Ocali
- Boston IVF, Research Department, Waltham, MA, USA
| | | | | | - Jaimin S Shah
- Boston IVF, Research Department, Waltham, MA, USA
- Department of Obstetrics and Gynecology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Obstetrics, Gynecology and Reproductive Biology, Harvard Medical School, Boston, MA, USA
| | - Alan S Penzias
- Boston IVF, Research Department, Waltham, MA, USA
- Department of Obstetrics and Gynecology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Obstetrics, Gynecology and Reproductive Biology, Harvard Medical School, Boston, MA, USA
| | - Emily A Seidler
- Boston IVF, Research Department, Waltham, MA, USA
- Department of Obstetrics and Gynecology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Obstetrics, Gynecology and Reproductive Biology, Harvard Medical School, Boston, MA, USA
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De Coster T, Zhao Y, Tšuiko O, Demyda-Peyrás S, Van Soom A, Vermeesch JR, Smits K. Genome-wide equine preimplantation genetic testing enabled by simultaneous haplotyping and copy number detection. Sci Rep 2024; 14:2003. [PMID: 38263320 PMCID: PMC10805710 DOI: 10.1038/s41598-023-48103-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 11/22/2023] [Indexed: 01/25/2024] Open
Abstract
In different species, embryonic aneuploidies and genome-wide errors are a major cause of developmental failure. The increasing number of equine embryos being produced worldwide provides the opportunity to characterize and rank or select embryos based on their genetic profile prior to transfer. Here, we explored the possibility of generic, genome-wide preimplantation genetic testing concurrently for aneuploidies (PGT-A) and monogenic (PGT-M) traits and diseases in the horse, meanwhile assessing the incidence and spectrum of chromosomal and genome-wide errors in in vitro-produced equine embryos. To this end, over 70,000 single nucleotide polymorphism (SNP) positions were genotyped in 14 trophectoderm biopsies and corresponding biopsied blastocysts, and in 26 individual blastomeres from six arrested cleavage-stage embryos. Subsequently, concurrent genome-wide copy number detection and haplotyping by haplarithmisis was performed and the presence of aneuploidies and genome-wide errors and the inherited parental haplotypes for four common disease-associated genes with high carrier frequency in different horse breeds (GBE1, PLOD1, B3GALNT2, MUTYH), and for one color coat-associated gene (STX17) were compared in biopsy-blastocyst combinations. The euploid (n = 12) or fully aneuploid (n = 2) state and the inherited parental haplotypes for 42/45 loci of interest of the biopsied blastocysts were predicted by the biopsy samples in all successfully analyzed biopsy-blastocyst combinations (n = 9). Two biopsies showed a loss of maternal chromosome 28 and 31, respectively, which were confirmed in the corresponding blastocysts. In one of those biopsies, additional complex aneuploidies not present in the blastocyst were found. Five out of six arrested embryos contained chromosomal and/or genome-wide errors in most of their blastomeres, demonstrating their contribution to equine embryonic arrest in vitro. The application of the described PGT strategy would allow to select equine embryos devoid of genetic errors and pathogenetic variants, and with the variants of interest, which will improve foaling rate and horse quality. We believe this approach will be a gamechanger in horse breeding.
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Affiliation(s)
- T De Coster
- Department of Internal Medicine, Reproduction and Population Medicine, Ghent University, Merelbeke, Belgium.
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
| | - Y Zhao
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - O Tšuiko
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - S Demyda-Peyrás
- Department of Genetics, University of Córdoba, Córdoba, Spain
- Department of Animal Production, Veterinary School, National University of La Plata, La Plata, Argentina
| | - A Van Soom
- Department of Internal Medicine, Reproduction and Population Medicine, Ghent University, Merelbeke, Belgium
| | - J R Vermeesch
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - K Smits
- Department of Internal Medicine, Reproduction and Population Medicine, Ghent University, Merelbeke, Belgium.
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Wirleitner B, Hrubá M, Schuff M, Hradecký L, Stecher A, Damko A, Stadler J, Spitzer D, Obkircher M, Murtinger M. Embryo drop-out rates in preimplantation genetic testing for aneuploidy (PGT-A): a retrospective data analysis from the DoLoRes study. J Assist Reprod Genet 2024; 41:193-203. [PMID: 37878220 PMCID: PMC10789689 DOI: 10.1007/s10815-023-02976-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 10/16/2023] [Indexed: 10/26/2023] Open
Abstract
PURPOSE To evaluate the decline in transferable embryos in preimplantation genetic testing for aneuploidy (PGT-A) cycles due to (a) non-biopsable blastocyst quality, (b) failure of genetic analysis, (c) diagnosis of uniform numerical or structural chromosomal aberrations, and/or (d) chromosomal aberrations in mosaic constitution. METHODS This retrospective multicenter study comprised outcomes of 1562 blastocysts originating from 363 controlled ovarian stimulation cycles, respectively, 226 IVF couples in the period between January 2016 and December 2018. Inclusion criteria were PGT-A cycles with trophectoderm biopsy (TB) and next generation sequencing (NGS). RESULTS Out of 1562 blastocysts, 25.8% were lost due to non-biopsable and/or non-freezable embryo quality. In 10.3% of all biopsied blastocysts, genetic analysis failed. After exclusion of embryos with uniform or chromosomal aberrations in mosaic, only 18.1% of those originally yielded remained as diagnosed euploid embryos suitable for transfer. This translates into 50.4% of patients and 57.6% of stimulated cycles with no euploid embryo left for transfer. The risk that no transfer can take place rose significantly with a lower number of oocytes and with increasing maternal age. The chance for at least one euploid blastocyst/cycle in advanced maternal age (AMA)-patients was 33.3% compared to 52.1% in recurrent miscarriage (RM), 59.8% in recurrent implantation failure (RIF), and 60.0% in severe male factor (SMF). CONCLUSIONS The present study demonstrates that PGT-A is accompanied by high embryo drop-out rates. IVF-practitioners should be aware that their patients run a high risk of ending up without any embryo suitable for transfer after (several) stimulation cycles, especially in AMA patients. Patients should be informed in detail about the frequency of inconclusive or mosaic results, with the associated risk of not having an euploid embryo available for transfer after PGT-A, as well as the high cost involved in this type of testing.
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Affiliation(s)
| | - Martina Hrubá
- Next Fertility IVF Prof. Zech, Smetany 2, 30100, Pilsen, Czech Republic
- Next Lab Genetika, Parková 11a, 32600, Pilsen, Czech Republic
| | - Maximilian Schuff
- Next Fertility IVF Prof. Zech, Roemerstrasse 2, 6900, Bregenz, Austria
| | - Libor Hradecký
- Next Fertility IVF Prof. Zech, Smetany 2, 30100, Pilsen, Czech Republic
| | - Astrid Stecher
- Next Fertility IVF Prof. Zech, Roemerstrasse 2, 6900, Bregenz, Austria
| | - Adriane Damko
- Next Fertility IVF Prof. Zech, Roemerstrasse 2, 6900, Bregenz, Austria
| | - Jürgen Stadler
- Next Fertility IVF Prof. Zech, Innsbrucker Bundesstrasse 35, 5020, Salzburg, Austria
| | - Dietmar Spitzer
- Next Fertility IVF Prof. Zech, Innsbrucker Bundesstrasse 35, 5020, Salzburg, Austria
| | | | - Maximilian Murtinger
- Next Fertility IVF Prof. Zech, Roemerstrasse 2, 6900, Bregenz, Austria
- Next Fertility St. Gallen, Kürsteinerstrasse 2, 9015, St. Gallen, Switzerland
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Campos G. PGT-A mosaicism based on NGS intermediate copy numbers: is it time to stop reporting them? J Assist Reprod Genet 2023; 40:2925-2932. [PMID: 37735311 PMCID: PMC10656405 DOI: 10.1007/s10815-023-02936-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/06/2023] [Indexed: 09/23/2023] Open
Abstract
Mosaicism represents a genuine real phenomenon, but its high prevalence and undisclosed clinical significance, stress the burden on genetic counseling and the management of PGT-A results. Even though the assumption of mosaicism from NGS intermediate chromosome copy number profiles may represent a reasonable interpretation, other potential technical reasons, including amplification bias, contamination, biopsy technique, or the analysis algorithms, may constitute alternative explanations. Thresholds confining mosaicism ranges are established according to models employing mixtures of normal and abnormal cells with steady conditions of quantity and quality which are unable to reflect the full extent of variability present in a trophectoderm (TE) biopsy specimen. When the concordance of TE with the ICM is considered, mosaic TE biopsies poorly correlate with the chromosomal status of the remaining embryo, displaying mostly ICM aneuploidy in cases of TE high-range mosaics diagnosis and euploidy when mosaicism grade in TE is less than 50% (low-mid range mosaicism), which implies an evident overestimation of mosaicism results. Indeed, a binary classification of NGS profiles that excludes mosaic ranges, including only euploid and aneuploid diagnosis, provides higher specificity and accuracy in identifying abnormal embryos and discarding them. As intermediate copy number profiles do not represent strong evidence of mosaicism but only an inaccurate and misleading assumption, and considering that no increased risk has been reported in the offspring, until diagnosis specificity is improved and its clinical implications are determined, laboratories should consider limiting predictions to euploid and aneuploid and stop reporting mosaicism.
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Affiliation(s)
- Gerard Campos
- Geisinger Medical Center, Women's Health Fertility Clinic, Danville, PA, USA.
- GIREXX Fertility Clinics, Barcelona, Spain.
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Rajendran S, Brendel M, Barnes J, Zhan Q, Malmsten JE, Zisimopoulos P, Sigaras A, Ofori-Atta K, Meseguer M, Miller KA, Hoffman D, Rosenwaks Z, Elemento O, Zaninovic N, Hajirasouliha I. Automatic Ploidy Prediction and Quality Assessment of Human Blastocyst Using Time-Lapse Imaging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.31.555741. [PMID: 37693566 PMCID: PMC10491146 DOI: 10.1101/2023.08.31.555741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Assessing fertilized human embryos is crucial for in vitro-fertilization (IVF), a task being revolutionized by artificial intelligence and deep learning. Existing models used for embryo quality assessment and chromosomal abnormality (ploidy) detection could be significantly improved by effectively utilizing time-lapse imaging to identify critical developmental time points for maximizing prediction accuracy. Addressing this, we developed and compared various embryo ploidy status prediction models across distinct embryo development stages. We present BELA (Blastocyst Evaluation Learning Algorithm), a state-of-the-art ploidy prediction model surpassing previous image- and video-based models, without necessitating subjective input from embryologists. BELA uses multitask learning to predict quality scores that are used downstream to predict ploidy status. By achieving an AUC of 0.76 for discriminating between euploidy and aneuploidy embryos on the Weill Cornell dataset, BELA matches the performance of models trained on embryologists' manual scores. While not a replacement for preimplantation genetic testing for aneuploidy (PGT-A), BELA exemplifies how such models can streamline the embryo evaluation process, reducing time and effort required by embryologists.
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