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Piyamongkol S, Mongkolchaipak S, Charoenkwan P, Sirapat R, Suriya W, Pantasri T, Tongsong T, Piyamongkol W. The successful strategy of comprehensive pre-implantation genetic testing for beta-thalassaemia-haemoglobin E disease and chromosome balance using karyomapping. J OBSTET GYNAECOL 2022; 42:2433-2441. [PMID: 35653778 DOI: 10.1080/01443615.2022.2070728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Thalassaemia is the commonest monogenic disease and causes a health and economic burden worldwide. Karyomapping can be used for pre-implantation genetic testing of monogenic disorders (PGT-M). This study applied karyomapping in two PGT-M cycles and made a comparison to polymerase chain reaction (PCR). Two families at risk of having beta-thalassaemia-haemoglobin E disease offspring decided to join the project and informed consent was obtained. Karyomapping results of family A (beta-thalassaemia (c.41_42delTCTT)-Hb E (c.26G>A) disease) revealed four normal, two beta-thalassaemia traits, one Hb E trait and six affected. Three embryos exhibited unbalanced chromosomes. One normal male embryo was transferred. Karyomapping results of family B (beta-thalassaemia (c.17A>T)-Hb E (c.26G>A) disease) revealed six Hb E traits and three affected. Three embryos were chromosomally unbalanced. One Hb E trait embryo was transferred. Two successful karyomapping PGT-M were performed, including deletion and single-base mutations. Karyomapping provides accuracy as regards the protocol and copy number variation which is common in pre-implantation embryos. Impact StatementWhat is already known on this subject? Thalassaemia syndrome is the commonest monogenic disease and causes a health and economic burden worldwide. Modern haplotyping using SNP array (aSNP) and karyomapping algorithms can be used for pre-implantation genetic testing of monogenic disorders (PGT-M). However, few clinical karyomapping PGT-M cycles have been done and validated so far.What do the results of this study add? Two successful clinical PGT-M cycles for beta-thalassaemia (c.41_42delTCTT and c.17A>T mutations)-haemoglobin E (c.26G>A) disease were performed using karyomapping. The outcome was two healthy babies. Multiplex fluorescent polymerase chain reaction (PCR) with mini-sequencing was also used for confirmation mutation analysis results. PCR confirmed haplotyping results in all embryos. Six embryos from both PGT-M cycles exhibited unbalanced chromosomes evidenced by aSNP.What are the implications of these findings for clinical practice and/or further research? Karyomapping provides accurate information quickly and the outcomes of the study will save time as regards protocol development, provide a usable universal PGT-M protocol and add additional copy number variation (CNV) information, chromosome number variation being a common issue in pre-implantation embryos.
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Affiliation(s)
- Sirivipa Piyamongkol
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Chiang Mai, Thailand
| | | | - Pimlak Charoenkwan
- Department of Pediatrics, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | | | - Wanwisa Suriya
- Department of Obstetrics and Gynaecology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Tawiwan Pantasri
- Department of Obstetrics and Gynaecology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Theera Tongsong
- Department of Obstetrics and Gynaecology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Wirawit Piyamongkol
- Department of Obstetrics and Gynaecology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
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Verdyck P, Berckmoes V, Van Laere S, Keymolen K, Olsen C, De Rycke M. Analysis of parental contribution for aneuploidy detection (APCAD): a novel method to detect aneuploidy and mosaicism in preimplantation embryos. Reprod Biomed Online 2021; 44:459-468. [PMID: 34930679 DOI: 10.1016/j.rbmo.2021.10.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 10/03/2021] [Accepted: 10/29/2021] [Indexed: 12/27/2022]
Abstract
RESEARCH QUESTION Can (mosaic) aneuploidy be reliably detected in preimplantation embryos after multiple displacement amplification and single nucleotide polymorphism detection, independent of haplotyping and copy number detection, with a new method 'analysis of parental contribution for aneuploidy detection' or 'APCAD'? DESIGN This method is based on the maternal contribution, a parameter that reflects the proportion of DNA that is of maternal origin for a given chromosome or chromosome segment. A maternal contribution deviating from 50% for autosomes is strongly indicative of a (mosaic) chromosomal anomaly. The method was optimized using cell mixtures with varying ratios of euploid and aneuploid (47,XY,+21) lymphocytes. Next, the maternal contribution was retrospectively measured for all chromosomes from 349 Karyomapping samples. RESULTS Retrospective analysis showed a skewed maternal contribution (<36.4 or >63.6%) in 57 out of 59 autosome meiotic trisomies and all autosome monosomies (n = 57), with values close to theoretical expectation. Thirty-two out of 7436 chromosomes, for which no anomalies had been observed with Karyomapping, showed a similarly skewed maternal contribution. CONCLUSIONS APCAD was used to measure the maternal contribution, which is an intuitive parameter independent of copy number detection. This method is useful for detecting copy number neutral anomalies and can confirm diagnosis of (mosaic) aneuploidy detected based on copy number. Mosaic and complete aneuploidy can be distinguished and the parent of origin for (mosaic) chromosome anomalies can be determined. Because of these benefits, the APCAD method has the potential to improve aneuploidy detection carried out by comprehensive preimplantation genetic testing methods.
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Affiliation(s)
- Pieter Verdyck
- Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Centrum Medische Genetica, Laarbeeklaan 101, Brussels 1090, Belgium.
| | - Veerle Berckmoes
- Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Centrum Medische Genetica, Laarbeeklaan 101, Brussels 1090, Belgium
| | - Sven Van Laere
- Vrije Universiteit Brussel (VUB), Interfaculty Center Data Processing and Statistics, Laarbeeklaan 103, Brussels 1090, Belgium
| | - Kathelijn Keymolen
- Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Centrum Medische Genetica, Laarbeeklaan 101, Brussels 1090, Belgium
| | - Catharina Olsen
- Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Centrum Medische Genetica, Laarbeeklaan 101, Brussels 1090, Belgium; Brussels Interuniversity Genomics High Throughput core (BRIGHTcore), VUB-ULB, Laarbeeklaan 101, Brussels 1090, Belgium
| | - Martine De Rycke
- Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Centrum Medische Genetica, Laarbeeklaan 101, Brussels 1090, Belgium
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Liu XY, Fan Q, Wang J, Li R, Xu Y, Guo J, Wang YZ, Zeng YH, Ding CH, Cai B, Zhou CQ, Xu YW. Higher chromosomal abnormality rate in blastocysts from young patients with idiopathic recurrent pregnancy loss. Fertil Steril 2020; 113:853-864. [PMID: 32228881 DOI: 10.1016/j.fertnstert.2019.11.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 11/10/2019] [Accepted: 11/12/2019] [Indexed: 12/21/2022]
Abstract
OBJECTIVE To determine whether the incidence of chromosomal abnormalities in blastocysts is higher in patients with idiopathic recurrent pregnancy loss (iRPL) who underwent preimplantation genetic testing for aneuploidy (PGT-A) than in those who underwent preimplantation genetic testing for monogenic defects (PGT-M). DESIGN Retrospective cohort study. SETTING University-affiliated reproductive center. PATIENT(S) A total of 62 patients with iRPL underwent 101 PGT-A cycles (iRPL group), and 212 patients underwent 311 PGT-M cycles (control group). INTERVENTIONS(S) Blastocyst biopsy and comprehensive chromosome screening technologies, including single-nucleotide polymorphism microarrays and next-generation sequencing. MAIN OUTCOME MEASURE(S) Incidence of chromosomal abnormalities in blastocysts and clinical miscarriage (CM) rate. RESULT(S) Stratification analysis by maternal age showed an increased incidence of chromosomal abnormalities in the iRPL group aged ≤35 years (48.9% vs. 36.9%), whereas no significant increase was found in the iRPL group aged >35 years (66.9% vs. 61.4%). After transfer of euploid embryos, women aged ≤35 years with iRPL exhibited an increased CM rate compared with the control group (26.1% vs. 3.1%). CONCLUSION(S) Young patients with iRPL have a significantly higher rate of chromosomal abnormalities in blastocysts compared with patients with no or sporadic CM. Although euploid embryos were transferred after PGT-A, young patients with iRPL had a higher CM rate, which may indicate that chromosomal abnormalities might not be the only causal factor for iRPL. Therefore, the role of PGT-A in iRPL still needs to be clarified.
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Affiliation(s)
- Xin-Yan Liu
- Guangdong Provincial Key Laboratory of Reproductive Medicine, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Qi Fan
- Guangdong Provincial Key Laboratory of Reproductive Medicine, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Jing Wang
- Guangdong Provincial Key Laboratory of Reproductive Medicine, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Rong Li
- Guangdong Provincial Key Laboratory of Reproductive Medicine, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Yan Xu
- Guangdong Provincial Key Laboratory of Reproductive Medicine, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Jing Guo
- Guangdong Provincial Key Laboratory of Reproductive Medicine, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Yi-Zi Wang
- Guangdong Provincial Key Laboratory of Reproductive Medicine, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Yan-Hong Zeng
- Guangdong Provincial Key Laboratory of Reproductive Medicine, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Chen-Hui Ding
- Guangdong Provincial Key Laboratory of Reproductive Medicine, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Bing Cai
- Guangdong Provincial Key Laboratory of Reproductive Medicine, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Can-Quan Zhou
- Guangdong Provincial Key Laboratory of Reproductive Medicine, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Yan-Wen Xu
- Guangdong Provincial Key Laboratory of Reproductive Medicine, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China.
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Preimplantation Genetic Testing for Chromosomal Abnormalities: Aneuploidy, Mosaicism, and Structural Rearrangements. Genes (Basel) 2020; 11:genes11060602. [PMID: 32485954 PMCID: PMC7349251 DOI: 10.3390/genes11060602] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 05/25/2020] [Accepted: 05/27/2020] [Indexed: 12/18/2022] Open
Abstract
There is a high incidence of chromosomal abnormalities in early human embryos, whether they are generated by natural conception or by assisted reproductive technologies (ART). Cells with chromosomal copy number deviations or chromosome structural rearrangements can compromise the viability of embryos; much of the naturally low human fecundity as well as low success rates of ART can be ascribed to these cytogenetic defects. Chromosomal anomalies are also responsible for a large proportion of miscarriages and congenital disorders. There is therefore tremendous value in methods that identify embryos containing chromosomal abnormalities before intrauterine transfer to a patient being treated for infertility—the goal being the exclusion of affected embryos in order to improve clinical outcomes. This is the rationale behind preimplantation genetic testing for aneuploidy (PGT-A) and structural rearrangements (-SR). Contemporary methods are capable of much more than detecting whole chromosome abnormalities (e.g., monosomy/trisomy). Technical enhancements and increased resolution and sensitivity permit the identification of chromosomal mosaicism (embryos containing a mix of normal and abnormal cells), as well as the detection of sub-chromosomal abnormalities such as segmental deletions and duplications. Earlier approaches to screening for chromosomal abnormalities yielded a binary result of normal versus abnormal, but the new refinements in the system call for new categories, each with specific clinical outcomes and nuances for clinical management. This review intends to give an overview of PGT-A and -SR, emphasizing recent advances and areas of active development.
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Shi D, Xu J, Niu W, Liu Y, Shi H, Yao G, Shi S, Li G, Song W, Jin H, Sun Y. Live births following preimplantation genetic testing for dynamic mutation diseases by karyomapping: a report of three cases. J Assist Reprod Genet 2020; 37:539-548. [PMID: 32124191 DOI: 10.1007/s10815-020-01718-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 02/13/2020] [Indexed: 02/07/2023] Open
Abstract
PURPOSE The preimplantation genetic testing for monogenic defects (PGT-M) is a beneficial strategy for the patients suffering from a Mendelian disease, which could protect their offspring from inheriting the disease. The purpose of this study is to report the effectiveness of PGT-M based on karyomapping for three cases of dynamic mutation diseases with trinucleotide repeat expansion. METHODS PGT-M was carried out on three couples, whose family members were diagnosed with Huntington's disease or spinocerebellar ataxias 2 or 12. The whole genome amplification was obtained using the multiple displacement amplification (MDA) method. Then, karyomapping was performed to detect the allele that is carrying the trinucleotide repeat expansion using single nucleotide polymorphism (SNP) linkage analyses, and the copy number variations (CNVs) of the embryos were also identified. Prenatal diagnosis was performed to validate the accuracy of PGT-M. RESULTS PGT-M was successfully performed on the three couples, and they accepted the transfers of euploid blastocysts without the relevant pathogenic allele. The clinical pregnancies were acquired and the prenatal diagnosis of the three families confirmed the effectiveness of karyomapping. The three born babies were healthy and free of the pathogenic alleles HTT, ATXN2, or PPP2R2B corresponding to Huntington's disease, spinocerebellar ataxias 2 or 12, respectively. CONCLUSION This study shows that karyomapping is a highly powerful and efficient approach for dynamic mutation detection in preimplantation embryos. In this work, we first report the birth of healthy babies that are free of the pathogenic gene for dynamic mutation diseases in patients receiving PGT-M by karyomapping.
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Affiliation(s)
- Dayuan Shi
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jiawei Xu
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China. .,Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China. .,Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China. .,Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
| | - Wenbin Niu
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yidong Liu
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hao Shi
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Guidong Yao
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Senlin Shi
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Gang Li
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wenyan Song
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Haixia Jin
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yingpu Sun
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China. .,Henan Key Laboratory of Reproduction and Genetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China. .,Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China. .,Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
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Konstantinidis M, Ravichandran K, Gunes Z, Prates R, Goodall NN, Roman B, Ribustello L, Shanmugam A, Colls P, Munné S, Wells D. Aneuploidy and recombination in the human preimplantation embryo. Copy number variation analysis and genome-wide polymorphism genotyping. Reprod Biomed Online 2019; 40:479-493. [PMID: 32147385 DOI: 10.1016/j.rbmo.2019.12.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 11/24/2019] [Accepted: 12/10/2019] [Indexed: 01/08/2023]
Abstract
RESEARCH QUESTION What are the incidence and patterns of meiotic trisomies and recombination separately and in relation to each other at the blastocyst stage via single nucleotide polymorphism genotyping combined with array comparative genomic hybridization. DESIGN Single nucleotide polymorphism microarrays were carried out on a total of 1442 blastocyst stage embryos derived from 268 fertile couples undergoing preimplantation genetic diagnosis for the purposes of avoiding transmittance of known single gene disorders to their offspring; 24-chromosome aneuploidy screening via array comparative genomic hybridization was carried out in parallel. RESULTS One hundred per cent of meiotic trisomies identified in these embryos were of maternal origin and their incidence increased significantly with advancing maternal age (P < 0.0001). A total of 55.8% of meiotic trisomies were meiosis I-type and 44.2% were meiosis II-type. Certain chromosomes were affected more by meiosis I-type errors, whereas others experienced more meiosis II-type errors. A detailed recombination analysis was carried out for 11,476 chromosomes and 17,763 recombination events were recorded. The average number of recombination sites was 24.0 ± 0.3 for male meiosis and 41.2 ± 0.6 for female meiosis (autosomes only). Sex-specific differences were observed in the locations of recombination sites. Comparative analysis conducted between 190 euploid embryos and 69 embryos presenting maternal meiotic trisomies showed similar recombination rates (P = 0.425) and non-recombinant chromatid rates (P = 0.435) between the two categories; differences, however, were observed when analysing embryos affected with specific maternal meiotic trisomies. CONCLUSIONS This study yielded unique data concerning recombination and the origin of aneuploidies observed during the first few days of life and provides a novel insight into these important biological processes.
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Affiliation(s)
| | | | - Zeynep Gunes
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford, UK
| | | | | | - Bo Roman
- CooperGenomics, Livingston New Jersey, USA
| | | | | | - Pere Colls
- CooperGenomics, Livingston New Jersey, USA
| | - Santiago Munné
- CooperGenomics, Livingston New Jersey, USA; Department of Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, Yale University, New Haven Connecticut, USA
| | - Dagan Wells
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford, UK; Juno Genetics, Oxford Science Park, Oxford, UK
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Baranov VS, Kogan IY, Kuznetzova TV. Advances in Developmental Genetics and Achievements in Assisted Reproductive Technology. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419100028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Cariati F, D'Argenio V, Tomaiuolo R. The evolving role of genetic tests in reproductive medicine. J Transl Med 2019; 17:267. [PMID: 31412890 PMCID: PMC6694655 DOI: 10.1186/s12967-019-2019-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 08/06/2019] [Indexed: 02/08/2023] Open
Abstract
Infertility is considered a major public health issue, and approximately 1 out of 6 people worldwide suffer from infertility during their reproductive lifespans. Thanks to technological advances, genetic tests are becoming increasingly relevant in reproductive medicine. More genetic tests are required to identify the cause of male and/or female infertility, identify carriers of inherited diseases and plan antenatal testing. Furthermore, genetic tests provide direction toward the most appropriate assisted reproductive techniques. Nevertheless, the use of molecular analysis in this field is still fragmented and cumbersome. The aim of this review is to highlight the conditions in which a genetic evaluation (counselling and testing) plays a role in improving the reproductive outcomes of infertile couples. We conducted a review of the literature, and starting from the observation of specific signs and symptoms, we describe the available molecular tests. To conceive a child, both partners' reproductive systems need to function in a precisely choreographed manner. Hence to treat infertility, it is key to assess both partners. Our results highlight the increasing importance of molecular testing in reproductive medicine.
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Affiliation(s)
| | - Valeria D'Argenio
- KronosDNA srl, Spinoff of Università Federico II, Naples, Italy.
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Via Sergio Pansini 5, 80131, Naples, Italy.
- CEINGE-Biotecnologie Avanzate scarl, Via Gaetano Salvatore 486, 80145, Naples, Italy.
| | - Rossella Tomaiuolo
- KronosDNA srl, Spinoff of Università Federico II, Naples, Italy
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Via Sergio Pansini 5, 80131, Naples, Italy
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Spindle and chromosome configuration analysis of human biopsied versus non-biopsied embryos by confocal laser scanning microscopy following vitrification. ZYGOTE 2019; 27:153-159. [PMID: 31060631 DOI: 10.1017/s0967199419000182] [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] [Indexed: 11/06/2022]
Abstract
SummaryThe aim of this study was to investigate the effects of zona drilling and biopsy on day 3 followed by vitrification on day 5 on the cytoskeleton and development of human embryos, by analysing survival rates and spindle and chromosome configurations by fluorescence and confocal laser scanning microscopy in human biopsied and non-biopsied embryos. In total, 98 human blastocysts (50 non-biopsied and 48 following biopsy on day 3) were vitrified on day 5 using either a commercial dimethyl sulphoxide (DMSO)-free vitrification kit or increasing concentrations of DMSO/EG (5%/5-10%/10-20%/20%). Following warming, the blastocysts were allowed to recover in culture for 24 h and were immunostained with α-tubulin, acetylated tubulin, and/or γ-tubulin antibodies in combination with 4',6-diamidino-2-phenylindole (DAPI). Labelled embryos were examined by both fluorescence and confocal laser scanning microscopy. The survival rates following warming (92% non-biopsied vs 83.3% biopsied) and the incidence of normal spindle chromosome configurations was not statistically different between the two groups (65.2% non-biopsied vs 59.2% biopsied, P>0.05). The incidence of spindle abnormalities including multipolarity, chromosome lagging, congression failure and chromosome bridging were also similar between the two groups (P>0.05). This study is the first to compare the incidence of cytoskeletal abnormalities in biopsied and non-biopsied human embryos following vitrification. We conclude that there was no significant difference in the survival rates and the incidence of spindle abnormalities between the two groups.
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Zeevi DA, Zahdeh F, Kling Y, Carmi S, Altarescu G. Off the street phasing (OTSP): no hassle haplotype phasing for molecular PGD applications. J Assist Reprod Genet 2019; 36:727-739. [PMID: 30617673 PMCID: PMC6504987 DOI: 10.1007/s10815-018-1392-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/18/2018] [Indexed: 11/28/2022] Open
Abstract
PURPOSE Pre-implantation genetic diagnosis (PGD) for molecular disorders requires the construction of parental haplotypes. Classically, haplotype resolution ("phasing") is obtained by genotyping multiple polymorphic markers in both parents and at least one additional relative. However, this process is time-consuming, and immediate family members are not always available. The recent availability of massive genomic data for many populations promises to eliminate the needs for developing family-specific assays and for recruiting additional family members. In this study, we aimed to validate population-assisted haplotype phasing for PGD. METHODS Targeted sequencing of CFTR gene variants and ~ 1700 flanking polymorphic SNPs (± 2 Mb) was performed on 54 individuals from 12 PGD families of (a) Full Ashkenazi (FA; n = 16), (b) mixed Ashkenazi (MA; n = 23 individuals with at least one Ashkenazi and one non-Ashkenazi grandparents), or (c) non-Ashkenazi (NA; n = 15) descent. Heterozygous genotype calls in each individual were phased using various whole genome reference panels and appropriate computational models. All computationally derived haplotype predictions were benchmarked against trio-based phasing. RESULTS Using the Ashkenazi reference panel, phasing of FA was highly accurate (99.4% ± 0.2% accuracy); phasing of MA was less accurate (95.4% ± 4.5% accuracy); and phasing of NA was predictably low (83.4% ± 6.6% accuracy). Strikingly, for founder mutation carriers, our haplotyping approach facilitated near perfect phasing accuracy (99.9% ± 0.1% and 98.2% ± 2.8% accuracy for W1282X and delF508 carriers, respectively). CONCLUSIONS Our results demonstrate the feasibility of replacing classical haplotype phasing with population-based phasing with uncompromised accuracy.
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Affiliation(s)
- David A Zeevi
- Medical Genetics Institute, Shaare Zedek Medical Center (SZMC), Bayit Str. 12, P.O.Box 3235, 91031, Jerusalem, Israel.
| | - Fouad Zahdeh
- Medical Genetics Institute, Shaare Zedek Medical Center (SZMC), Bayit Str. 12, P.O.Box 3235, 91031, Jerusalem, Israel
| | - Yehuda Kling
- Medical Genetics Institute, Shaare Zedek Medical Center (SZMC), Bayit Str. 12, P.O.Box 3235, 91031, Jerusalem, Israel
| | - Shai Carmi
- Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gheona Altarescu
- Medical Genetics Institute, Shaare Zedek Medical Center (SZMC), Bayit Str. 12, P.O.Box 3235, 91031, Jerusalem, Israel
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11
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Beyer CE, Lewis A, Willats E, Mullen J. Preimplantation genetic testing using Karyomapping for a paternally inherited reciprocal translocation: a case study. J Assist Reprod Genet 2019; 36:951-963. [PMID: 30756205 DOI: 10.1007/s10815-019-01413-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 01/28/2019] [Indexed: 12/30/2022] Open
Abstract
PURPOSE Preimplantation genetic testing (PGT) using Karyomapping is used to screen embryos for single gene disorders prior to implantation. While Karyomapping is not designed to screen for abnormalities in chromosome copy number, this testing is based upon a genome-wide analysis of single nucleotide polymorphisms (SNP) and, as such, some chromosome abnormalities are detected. The aim of this study was to validate whether Karyomapping could provide reliable and accurate PGT for a paternal 46,XY,t(10;19)(p15;p13.3) reciprocal translocation. METHODS Feasibility/validation for PGT was performed using DNA from the couple, as well as DNA from the paternal parents and from a previous unbalanced pregnancy. Karyomapping was performed using Illumina's HumanKaryomap-12 BeadChip microarray technology. SNP analysis was performed using BlueFuse Multi software (Illumina). Transmission of the translocation was assessed through the analysis of SNP markers on the chromosome regions of interest. RESULTS PGT-SR was determined to be feasible as chromosomal SNP analysis could reliably distinguish normal/balanced outcomes from all unbalanced outcomes. The couple transferred a normal/balanced embryo in an elective single embryo transfer procedure following 2 IVF/PGT-SR cycles. A clinical pregnancy was achieved. CONCLUSION This is the first report of PGT-SR test validation using Karyomapping for a 46,XY,t(10;19)(p15;p13.3) reciprocal translocation. Karyomapping may offer a means of detecting unbalanced forms of chromosome rearrangements when other PGT platforms fail.
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Affiliation(s)
- C E Beyer
- Monash IVF, Suite 1, 252 Clayton Rd, Clayton, Victoria, 3168, Australia.
| | - A Lewis
- Monash IVF, Suite 1, 252 Clayton Rd, Clayton, Victoria, 3168, Australia
| | - E Willats
- Monash IVF, Suite 1, 252 Clayton Rd, Clayton, Victoria, 3168, Australia
| | - J Mullen
- Monash IVF, Suite 1, 252 Clayton Rd, Clayton, Victoria, 3168, Australia
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12
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Karyomapping in Preimplantation Genetic Testing of Patients with Beta-thalassemia and Sickle Cell Anemia. ANADOLU KLINIĞI TIP BILIMLERI DERGISI 2019. [DOI: 10.21673/anadoluklin.438117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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13
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Kubicek D, Hornak M, Horak J, Navratil R, Tauwinklova G, Rubes J, Vesela K. Incidence and origin of meiotic whole and segmental chromosomal aneuploidies detected by karyomapping. Reprod Biomed Online 2018; 38:330-339. [PMID: 30639160 DOI: 10.1016/j.rbmo.2018.11.023] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 11/14/2018] [Accepted: 11/15/2018] [Indexed: 10/27/2022]
Abstract
RESEARCH QUESTION What is the incidence and origin of meiotic whole and segmental aneuploidies detected by karyomapping at a blastocyst stage in human-derived IVF embryos? What is the distribution of various types of errors, including rare chromosomal abnormalities? DESIGN The incidence of chromosomal aneuploidies was assessed in 967 trophectoderm biopsies from 180 couples who underwent 215 cycles of IVF with preimplantation genetic testing for monogenetic disease with a known causal mutation with a mean maternal age of 32.7 years. DNA from both parents and a reference sample was genotyped together with the analysed trophectoderm samples by karyomapping (single-nucleotide-polymorphism-based array). RESULTS Chromosomal abnormalities were detected in 31% of the analysed samples. At least one whole chromosomal aneuploidy was detected in 27.1% of the trophectoderm biopsies, whereas a segmental aneuploidy was detected in 5.1% of the trophectoderm biopsies. Our results reveal that segmental aneuploidies predominantly affect paternally derived chromosomes (70.4%; P < 0.01) compared with whole chromosomal aneuploidies that more frequently affect maternally derived chromosomes (90.1%; P < 0.0001). Also, the frequency of meiosis I (MI) and meiosis II (MII) errors was established in meiotic trisomies; MI errors were observed to be more frequent (n = 102/147 [69.4%]) than MII errors (n = 45/147 [30.6%]). CONCLUSIONS Karyomapping is a robust method that is suitable for preimplantation genetic testing for monogenetic disease and for detecting meiotic aneuploidies, including meiotic segmental aneuploidies, and provides complex information about their parental origin. Our results revealed that segmental aneuploidy more frequently affects paternal chromosomes compared with whole chromosomal aneuploidy in human IVF embryos at the blastocyst stage.
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Affiliation(s)
- David Kubicek
- Repromeda, Clinic for Reproductive Medicine and Preimplantation Genetic Diagnosis, Biology Park, Studentská 812/6, 625 00 Brno, Czech Republic; Central European Institute of Technology - Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic.
| | - Miroslav Hornak
- Repromeda, Clinic for Reproductive Medicine and Preimplantation Genetic Diagnosis, Biology Park, Studentská 812/6, 625 00 Brno, Czech Republic; Central European Institute of Technology - Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic
| | - Jakub Horak
- Repromeda, Clinic for Reproductive Medicine and Preimplantation Genetic Diagnosis, Biology Park, Studentská 812/6, 625 00 Brno, Czech Republic
| | - Rostislav Navratil
- Repromeda, Clinic for Reproductive Medicine and Preimplantation Genetic Diagnosis, Biology Park, Studentská 812/6, 625 00 Brno, Czech Republic
| | - Gabriela Tauwinklova
- Repromeda, Clinic for Reproductive Medicine and Preimplantation Genetic Diagnosis, Biology Park, Studentská 812/6, 625 00 Brno, Czech Republic
| | - Jiri Rubes
- Central European Institute of Technology - Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic
| | - Katerina Vesela
- Repromeda, Clinic for Reproductive Medicine and Preimplantation Genetic Diagnosis, Biology Park, Studentská 812/6, 625 00 Brno, Czech Republic
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14
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Backenroth D, Zahdeh F, Kling Y, Peretz A, Rosen T, Kort D, Zeligson S, Dror T, Kirshberg S, Burak E, Segel R, Levy-Lahad E, Zangen D, Altarescu G, Carmi S, Zeevi DA. Haploseek: a 24-hour all-in-one method for preimplantation genetic diagnosis (PGD) of monogenic disease and aneuploidy. Genet Med 2018; 21:1390-1399. [DOI: 10.1038/s41436-018-0351-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 10/25/2018] [Indexed: 11/09/2022] Open
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15
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Griffin DK, Ogur C. Chromosomal analysis in IVF: just how useful is it? Reproduction 2018; 156:F29-F50. [PMID: 29945889 DOI: 10.1530/rep-17-0683] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 03/23/2018] [Indexed: 12/11/2022]
Abstract
Designed to minimize chances of genetically abnormal embryos, preimplantation genetic diagnosis (PGD) involves in vitro fertilization (IVF), embryo biopsy, diagnosis and selective embryo transfer. Preimplantation genetic testing for aneuploidy (PGT-A) aims to avoid miscarriage and live born trisomic offspring and to improve IVF success. Diagnostic approaches include fluorescence in situ hybridization (FISH) and more contemporary comprehensive chromosome screening (CCS) including array comparative genomic hybridization (aCGH), quantitative polymerase chain reaction (PCR), next-generation sequencing (NGS) and karyomapping. NGS has an improved dynamic range, and karyomapping can detect chromosomal and monogenic disorders simultaneously. Mosaicism (commonplace in human embryos) can arise by several mechanisms; those arising initially meiotically (but with a subsequent post-zygotic 'trisomy rescue' event) usually lead to adverse outcomes, whereas the extent to which mosaics that are initially chromosomally normal (but then arise purely post-zygotically) can lead to unaffected live births is uncertain. Polar body (PB) biopsy is the least common sampling method, having drawbacks including cost and inability to detect any paternal contribution. Historically, cleavage-stage (blastomere) biopsy has been the most popular; however, higher abnormality levels, mosaicism and potential for embryo damage have led to it being superseded by blastocyst (trophectoderm - TE) biopsy, which provides more cells for analysis. Improved biopsy, diagnosis and freeze-all strategies collectively have the potential to revolutionize PGT-A, and there is increasing evidence of their combined efficacy. Nonetheless, PGT-A continues to attract criticism, prompting questions of when we consider the evidence base sufficient to justify routine PGT-A? Basic biological research is essential to address unanswered questions concerning the chromosome complement of human embryos, and we thus entreat companies, governments and charities to fund more. This will benefit both IVF patients and prospective parents at risk of aneuploid offspring following natural conception. The aim of this review is to appraise the 'state of the art' in terms of PGT-A, including the controversial areas, and to suggest a practical 'way forward' in terms of future diagnosis and applied research.
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Affiliation(s)
- Darren K Griffin
- School of BiosciencesCentre for Interdisciplinary Studies of Reproduction, University of Kent, Canterbury, UK
| | - Cagri Ogur
- Bahceci Genetic Diagnosis Centerİstanbul, Turkey.,Department of BioengineeringYildiz Technical University, İstanbul, Turkey
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16
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Novel Double Factor PGT strategy analyzing blastocyst stage embryos in a single NGS procedure. PLoS One 2018; 13:e0205692. [PMID: 30332465 PMCID: PMC6192598 DOI: 10.1371/journal.pone.0205692] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 09/28/2018] [Indexed: 12/16/2022] Open
Abstract
In families at risk from monogenic diseases affected offspring, it is fundamental the development of a suitable Double Factor Preimplantation Genetic Testing (DF-PGT) method for both single-gene analysis and chromosome complement screening. Aneuploidy is not only a major issue in advanced-maternal-age patients and balanced translocation carriers, but also the aneuploidy rate is extremely high in patients undergoing in vitro fertilization (IVF), even in young donors. To adequate NGS technology to the DF-PGT strategy four different whole genome amplification systems (Sureplex, MALBAC, and two multiple displacement amplification systems-MDA) were tested using TruSight One panel on cell lines and blastocyst trophectoderm biopsies-TE. Embryo cytogenetic status was analyzed by Nexus software. Sureplex and MALBAC DNA products were considered not suitable for PGT diagnosis due to inconsistent and poor results on Trusight one (TSO) panel. Results obtained with both MDA based methods (GEH-MDA and RG-MDA) were appropriate for direct mutation detection by TSO NGS platform. Nevertheless, RG-MDA amplification products showed better coverage and lower ADO rates than GEH-MDA. The present work also demonstrates that the same TSO sequencing data is suitable not only for the direct mutation detection, but also for the indirect mutation detection by linkage analysis of informative SNPs. The present work also demonstrates that Nexus software is competent for the detection of CNV by using with TSO sequencing data from RG-MDA products, allowing for the whole cytogenetic characterization of the embryos. In conclusion, successfully development of an innovative and promising DF-PGT strategy using TSO-NGS technology in TE biopsies, performed in-house in a single laboratory experience, has been done in the present work. Additional studies should be performed before it could be used as a diagnostic alternative in order to validate this approach for the detection of chromosomal aneuploidies.
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17
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Romanelli V, Poli M, Capalbo A. Preimplantation genetic testing in assisted reproductive technology. Panminerva Med 2018; 61:30-41. [PMID: 29962185 DOI: 10.23736/s0031-0808.18.03506-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Preimplantation genetic testing is a methodology aimed at the assessment of the genetic composition of an embryo. This diagnostic approach has been used in assisted reproduction for almost thirty years. During these years, the technologies used for embryo's genetic analysis have been continuously improved allowing the development of more precise, comprehensive and robust strategies that are clinically employed nowadays. In this review, the main diagnostic approaches used for embryo genetic and chromosomal assessment are described and discussed both from an embryological and genetic standpoint.
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Affiliation(s)
| | - Maurizio Poli
- Igenomix, Marostica, Vicenza, Italy.,Reproomics, Amsterdam, The Netherlands
| | - Antonio Capalbo
- Igenomix, Marostica, Vicenza, Italy - .,Section of Histology and Embryology, Department of Musculoskeletal Anatomy, Histology, and Legal Medicine, Sapienza University, Rome, Italy
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18
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Wu H, Shen X, Huang L, Zeng Y, Gao Y, Shao L, Lu B, Zhong Y, Miao B, Xu Y, Wang Y, Li Y, Xiong L, Lu S, Xie XS, Zhou C. Genotyping single-sperm cells by universal MARSALA enables the acquisition of linkage information for combined pre-implantation genetic diagnosis and genome screening. J Assist Reprod Genet 2018; 35:1071-1078. [PMID: 29790070 DOI: 10.1007/s10815-018-1158-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 03/08/2018] [Indexed: 12/29/2022] Open
Abstract
PURPOSE This paper aims to investigate the feasibility of performing pre-implantation genetic diagnosis (PGD) and pre-implantation genetic screening (PGS) simultaneously by a universal strategy without the requirement of genotyping relevant affected family members or lengthy preliminary work on linkage analysis. METHODS By utilizing a universal Mutated Allele Revealed by Sequencing with Aneuploidy and Linkage Analyses (MARSALA) strategy based on low depth whole genome sequencing (~3x), not involving specific primers' design nor the enrichment of SNP markers for haplotype construction. Single-sperm cells and trephectoderm cells from in vitro fertilized embryos from a couple carrying HBB mutations were genotyped. Haplotypes of paternal alleles were constructed and investigated in embryos, and the chromosome copy number profiles were simultaneously analyzed. RESULTS The universal MARSALA strategy allows the selection of a euploid embryo free of disease mutations for in uterus transfer and successful pregnancy. A follow-up amniocentesis was performed at 17 weeks of gestation to confirm the PGD/PGS results. CONCLUSION We present the first successful PGD procedure based on genotyping multiple single-sperm cells to obtain SNP linkage information. Our improved PGD/PGS procedure does not require genotyping the proband or relevant family members and therefore can be applicable to a wider population of patients when conducting PGD for monogenic disorders.
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Affiliation(s)
- Haitao Wu
- Reproductive Medicine Center, Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-Sen University, Jiangmen, Guangdong, 529030, China.,Reproductive Medicine Center, First Affiliated Hospital of Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, Guangdong, 510080, China
| | - Xiaoting Shen
- Reproductive Medicine Center, First Affiliated Hospital of Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, Guangdong, 510080, China
| | - Lei Huang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 01238, USA.,Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Yanhong Zeng
- Reproductive Medicine Center, First Affiliated Hospital of Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, Guangdong, 510080, China
| | - Yumei Gao
- Yikon Genomics Co., Ltd., 1698 Wangyuan Road, Building #26, Fengxian District, Shanghai, 201400, China
| | - Lin Shao
- Yikon Genomics Co., Ltd., 1698 Wangyuan Road, Building #26, Fengxian District, Shanghai, 201400, China
| | - Baomin Lu
- Reproductive Medicine Center, First Affiliated Hospital of Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, Guangdong, 510080, China
| | - Yiping Zhong
- Reproductive Medicine Center, First Affiliated Hospital of Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, Guangdong, 510080, China
| | - Benyu Miao
- Reproductive Medicine Center, First Affiliated Hospital of Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, Guangdong, 510080, China
| | - Yanwen Xu
- Reproductive Medicine Center, First Affiliated Hospital of Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, Guangdong, 510080, China
| | - Yali Wang
- Reproductive Medicine Center, First Affiliated Hospital of Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, Guangdong, 510080, China
| | - Yubin Li
- Reproductive Medicine Center, First Affiliated Hospital of Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, Guangdong, 510080, China
| | - Luoxing Xiong
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, 100871, China.,Peking-Tsinghua Center for Life Sciences (CLS), Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Sijia Lu
- Yikon Genomics Co., Ltd., 1698 Wangyuan Road, Building #26, Fengxian District, Shanghai, 201400, China
| | - X Sunney Xie
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 01238, USA.,Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, 100871, China
| | - Canquan Zhou
- Reproductive Medicine Center, First Affiliated Hospital of Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, Guangdong, 510080, China.
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19
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Kubikova N, Babariya D, Sarasa J, Spath K, Alfarawati S, Wells D. Clinical application of a protocol based on universal next-generation sequencing for the diagnosis of beta-thalassaemia and sickle cell anaemia in preimplantation embryos. Reprod Biomed Online 2018; 37:136-144. [PMID: 29853423 DOI: 10.1016/j.rbmo.2018.05.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 04/30/2018] [Accepted: 05/02/2018] [Indexed: 10/16/2022]
Abstract
RESEARCH QUESTION Mutations of the beta-globin gene (HBB) cause beta-thalassaemia and sickle cell anaemia. These are the most common cause of severe inherited disease in humans. Traditional preimplantation genetic testing protocols for detecting HBB mutations frequently involve labour intensive, patient-specific test designs owing to the wide diversity of disease-associated HBB mutations. We, therefore, asked the question whether a universally applicable preimplantation genetic testing method can be developed to test for HBB gene mutations. DESIGN A multiplex polymerase chain reaction protocol was designed, allowing simultaneous amplification of multiple overlapping DNA fragments encompassing the entire HBB gene sequence in addition to 17 characterized, closely linked single nucleotide polymorphisms (SNP). Amplicons were then analysed using a next-generation sequencing method, revealing mutations and SNP genotypes. The protocol was extensively validated, optimized and eventually clinically applied on whole-genome amplified DNA derived from embryos of three couples carrying different combinations of beta-thalassaemia mutations. RESULTS The HBB mutation status and associated SNP haplotypes were successfully determined in all 21 embryos. Analysis of 141 heterozygous sites showed no instances of allele dropout and the test displayed 100% concordance compared with the results obtained from karyomapping. This suggests that the combination of trophectoderm biopsy and highly sensitive next-generation sequencing may provide superior accuracy than typically achieved using traditional preimplantation genetic testing methods. Importantly, no patient-specific test design or optimization was needed. CONCLUSIONS It is hoped that protocols that deliver almost universally applicable low-cost tests, without compromising diagnostic accuracy, will improve patient access to preimplantation genetic testing, especially in less affluent parts of the world.
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Affiliation(s)
- Nada Kubikova
- University of Oxford, Nuffield Department of Women's and Reproductive Health, John Radcliffe Hospital, Level 3, Women's Centre, Oxford, OX3 9DU, UK.
| | - Dhruti Babariya
- CooperGenomics, Institute of Reproductive Sciences, Oxford Business Park North, Alec Issigonis Way, Oxford OX4 2HW, UK
| | | | - Katharina Spath
- CooperGenomics, Institute of Reproductive Sciences, Oxford Business Park North, Alec Issigonis Way, Oxford OX4 2HW, UK
| | - Samer Alfarawati
- CooperGenomics, Institute of Reproductive Sciences, Oxford Business Park North, Alec Issigonis Way, Oxford OX4 2HW, UK
| | - Dagan Wells
- University of Oxford, Nuffield Department of Women's and Reproductive Health, John Radcliffe Hospital, Level 3, Women's Centre, Oxford, OX3 9DU, UK
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20
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Hao Y, Chen D, Zhang Z, Zhou P, Cao Y, Wei Z, Xu X, Chen B, Zou W, Lv M, Ji D, He X. Successful preimplantation genetic diagnosis by targeted next-generation sequencing on an ion torrent personal genome machine platform. Oncol Lett 2018. [PMID: 29541197 PMCID: PMC5835955 DOI: 10.3892/ol.2018.7876] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Hearing loss may place a heavy burden on the patient and patient's family. Given the high incidence of hearing loss among newborns and the huge cost of treatment and care (including cochlear implantation), prenatal diagnosis is strongly recommended. Termination of the fetus may be considered as an extreme outcome to the discovery of a potential deaf fetus, and therefore preimplantation genetic diagnosis has become an important option for avoiding the birth of affected children without facing the risk of abortion following prenatal diagnosis. In one case, a couple had a 7-year-old daughter affected by non-syndromic sensorineural hearing loss. The affected fetus carried a causative compound heterozygous mutation c.919-2 A>G (IVS7-2 A>G) and c.1707+5 G>A (IVS15+5 G>A) of the solute carrier family 26 member 4 gene inherited from maternal and paternal sides, respectively. The present study applied multiple displacement amplification for whole genome amplification of biopsied trophectoderm cells and next-generation sequencing (NGS)-based single nucleotide polymorphism haplotyping on an Ion Torrent Personal Genome Machine. One unaffected embryo was transferred in a frozen-thawed embryo transfer cycle and the patient was impregnated. To conclude, to the best of our knowledge, this may be the first report of NGS-based preimplantation genetic diagnosis (PGD) for non-syndromic hearing loss caused by a compound heterozygous mutation using an Ion Torrent Personal Genome Machine. NGS provides unprecedented high-throughput, highly parallel and base-pair resolution data for genetic analysis. The method meets the requirements of medium-sized diagnostics laboratories. With decreased costs compared with previous techniques (such as Sanger sequencing), this technique may have potential widespread clinical application in PGD of other types of monogenic disease.
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Affiliation(s)
- Yan Hao
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Institute of Reproductive Genetics, Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Anhui Province Key Laboratory of Reproductive Health and Genetics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Dawei Chen
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Institute of Reproductive Genetics, Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Anhui Province Key Laboratory of Reproductive Health and Genetics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Zhiguo Zhang
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Institute of Reproductive Genetics, Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Anhui Province Key Laboratory of Reproductive Health and Genetics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Ping Zhou
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Institute of Reproductive Genetics, Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Anhui Province Key Laboratory of Reproductive Health and Genetics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Yunxia Cao
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Institute of Reproductive Genetics, Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Anhui Province Key Laboratory of Reproductive Health and Genetics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Zhaolian Wei
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Institute of Reproductive Genetics, Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Anhui Province Key Laboratory of Reproductive Health and Genetics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Xiaofeng Xu
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Institute of Reproductive Genetics, Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Anhui Province Key Laboratory of Reproductive Health and Genetics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Beili Chen
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Institute of Reproductive Genetics, Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Anhui Province Key Laboratory of Reproductive Health and Genetics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Weiwei Zou
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Institute of Reproductive Genetics, Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Anhui Province Key Laboratory of Reproductive Health and Genetics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Mingrong Lv
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Institute of Reproductive Genetics, Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Anhui Province Key Laboratory of Reproductive Health and Genetics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Dongmei Ji
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Institute of Reproductive Genetics, Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Anhui Province Key Laboratory of Reproductive Health and Genetics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Xiaojin He
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Institute of Reproductive Genetics, Anhui Medical University, Hefei, Anhui 230022, P.R. China.,Anhui Province Key Laboratory of Reproductive Health and Genetics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
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21
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Li G, Niu W, Jin H, Xu J, Song W, Guo Y, Su Y, Sun Y. Importance of embryo aneuploidy screening in preimplantation genetic diagnosis for monogenic diseases using the karyomap gene chip. Sci Rep 2018; 8:3139. [PMID: 29453426 PMCID: PMC5816636 DOI: 10.1038/s41598-018-21094-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 01/29/2018] [Indexed: 12/16/2022] Open
Abstract
We investigated the incidence of aneuploidy in embryos from couples carrying monogenic diseases and the effect of embryo aneuploidy screening on the monogenic disease preimplantation genetic diagnosis (PGD). From November 2014 to April 2017, 36 couples carrying monogenic diseases were enrolled. The karyomap gene chip technique was used to analyze the blastocysts from the subjects and select normal embryos for transfer. A total of 43 single-gene PGD cycles were performed. A total of 687 eggs were obtained and 186 blastocysts were biopsed. After analysis via karyomap chip, 175 blastocysts received diagnostic results. In our monogenic disease PGD, 66.8% (117/175) of the embryos were diagnosed as normal or non-pathogenic (silent carriers), and 33.2% (58/175) of the embryos were diagnosed as abnormal or pathogenic. For preimplantation genetic screening (PGS), the aneuploidy rate of embryos was 22.9% (40/175). Among embryos diagnosed as normal for monogenic diseases, 26.5% (31/117) of the embryos were aneuploid and could not be transferred. Thus, approximately 1/4 of normal or non-pathogenic blastocysts diagnosed based on monogenic disease PGD were aneuploid, indicating the necessity and importance of embryo aneuploidy screening during PGD for monogenic diseases.
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Affiliation(s)
- Gang Li
- Reproductive Medical Center, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wenbin Niu
- Reproductive Medical Center, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Haixia Jin
- Reproductive Medical Center, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jiawei Xu
- Reproductive Medical Center, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wenyan Song
- Reproductive Medical Center, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yihong Guo
- Reproductive Medical Center, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yingchun Su
- Reproductive Medical Center, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yingpu Sun
- Reproductive Medical Center, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
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22
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Harper JC, Aittomäki K, Borry P, Cornel MC, de Wert G, Dondorp W, Geraedts J, Gianaroli L, Ketterson K, Liebaers I, Lundin K, Mertes H, Morris M, Pennings G, Sermon K, Spits C, Soini S, van Montfoort APA, Veiga A, Vermeesch JR, Viville S, Macek M. Recent developments in genetics and medically assisted reproduction: from research to clinical applications. Eur J Hum Genet 2018; 26:12-33. [PMID: 29199274 PMCID: PMC5839000 DOI: 10.1038/s41431-017-0016-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Accepted: 09/14/2017] [Indexed: 12/15/2022] Open
Abstract
Two leading European professional societies, the European Society of Human Genetics and the European Society for Human Reproduction and Embryology, have worked together since 2004 to evaluate the impact of fast research advances at the interface of assisted reproduction and genetics, including their application into clinical practice. In September 2016, the expert panel met for the third time. The topics discussed highlighted important issues covering the impacts of expanded carrier screening, direct-to-consumer genetic testing, voiding of the presumed anonymity of gamete donors by advanced genetic testing, advances in the research of genetic causes underlying male and female infertility, utilisation of massively parallel sequencing in preimplantation genetic testing and non-invasive prenatal screening, mitochondrial replacement in human oocytes, and additionally, issues related to cross-generational epigenetic inheritance following IVF and germline genome editing. The resulting paper represents a consensus of both professional societies involved.
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Affiliation(s)
- J C Harper
- Institute for Women's Health, University College London, London, UK
| | - K Aittomäki
- Laboratory of Genetics, Helsinki University Hospital, Helsinki, Finland
| | - P Borry
- Department of Public Health and Primary Care, Centre for Biomedical Ethics and Law, KU Leuven, Leuven, Belgium
| | - M C Cornel
- Department of Clinical Genetics, Section Community Genetics, Amsterdam Public Health Research Institute, VU University Medical Center, Amsterdam, The Netherlands
| | - G de Wert
- Department of Health, Ethics and Society, Research Schools CAPHRI and GROW, Maastricht University, Maastricht, The Netherlands
| | - W Dondorp
- Department of Health, Ethics and Society, Research Schools CAPHRI and GROW, Maastricht University, Maastricht, The Netherlands
| | - J Geraedts
- Department Genetics and Cell Biology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - L Gianaroli
- S.I.S.Me.R. Reproductive Medicine Unit, Bologna, Italy
| | | | - I Liebaers
- Center for Medical Genetics, UZ Brussels, Brussels, Belgium
- Research Group Reproduction and Genetics, Vrije Universiteit Brussel, Brussels, Belgium
| | - K Lundin
- Reproductive Medicine, Sahlgrenska University Hospital, Göteborg, Sweden
| | - H Mertes
- Bioethics Institute Ghent, Department of Philosophy and Moral Science, Ghent University, Ghent, Belgium
| | - M Morris
- Synlab Genetics, Lausanne, Switzerland
| | - G Pennings
- Bioethics Institute Ghent, Department of Philosophy and Moral Science, Ghent University, Ghent, Belgium
| | - K Sermon
- Research Group Reproduction and Genetics, Vrije Universiteit Brussel, Brussels, Belgium
| | - C Spits
- Research Group Reproduction and Genetics, Vrije Universiteit Brussel, Brussels, Belgium
| | - S Soini
- Helsinki Biobank, Helsinki University Central Hospital, Helsinki, Finland
| | - A P A van Montfoort
- IVF Laboratory, Department of Obstetrics & Gynaecology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - A Veiga
- Barcelona Stem Cell Bank, Centre of Regenerative Medicine in Barcelona, Hospital Duran i Reynals, Barcelona, Spain
- Reproductive Medicine Service of Dexeus Woman Health, Barcelona, Spain
| | - J R Vermeesch
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - S Viville
- Institute of Parasitology and Pathology, University of Strasbourg, Strasbourg, France
- Laboratory of Genetic Diagnostics, UF3472-Genetics of Infertility, Nouvel Hôpital Civil, Strasbourg, France
| | - M Macek
- Department of Biology and Medical Genetics, Charles University-2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic.
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23
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Harper JC, Aittomäki K, Borry P, Cornel MC, de Wert G, Dondorp W, Geraedts J, Gianaroli L, Ketterson K, Liebaers I, Lundin K, Mertes H, Morris M, Pennings G, Sermon K, Spits C, Soini S, van Montfoort APA, Veiga A, Vermeesch JR, Viville S, Macek M. Recent developments in genetics and medically-assisted reproduction: from research to clinical applications †‡. Hum Reprod Open 2017; 2017:hox015. [PMID: 31486804 PMCID: PMC6276693 DOI: 10.1093/hropen/hox015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 11/14/2017] [Indexed: 12/13/2022] Open
Abstract
Two leading European professional societies, the European Society of Human Genetics and the European Society for Human Reproduction and Embryology, have worked together since 2004 to evaluate the impact of fast research advances at the interface of assisted reproduction and genetics, including their application into clinical practice. In September 2016, the expert panel met for the third time. The topics discussed highlighted important issues covering the impacts of expanded carrier screening, direct-to-consumer genetic testing, voiding of the presumed anonymity of gamete donors by advanced genetic testing, advances in the research of genetic causes underlying male and female infertility, utilisation of massively-parallel sequencing in preimplantation genetic testing and non-invasive prenatal screening, mitochondrial replacement in human oocytes, and additionally, issues related to cross-generational epigenetic inheritance following IVF and germline genome editing. The resulting paper represents a consensus of both professional societies involved.
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Affiliation(s)
- J C Harper
- Institute for Women's Health, University College London, 86-96 Chenies Mews, London WC1E 6HX, UK
| | - K Aittomäki
- Laboratory of Genetics, Helsinki University Hospital, PO Box 720, FI-00029, Helsinki, Finland
| | - P Borry
- Department of Public Health and Primary Care, Centre for Biomedical Ethics and Law, KU Leuven, Kapucijnenvoer 35 - Box 7001. B-3000, Leuven Belgium
| | - M C Cornel
- Department of Clinical Genetics, Amsterdam Public Health Research Institute, VU University Medical Center, PO Box 7057, 1007 MB, Amsterdam, The Netherlands
| | - G de Wert
- Department of Health, Ethics and Society, Research Schools CAPHRI and GROW, Maastricht University, De Byeplein 1, 6229 HA Maastricht, The Netherlands
| | - W Dondorp
- Department of Health, Ethics and Society, Research Schools CAPHRI and GROW, Maastricht University, De Byeplein 1, 6229 HA Maastricht, The Netherlands
| | - J Geraedts
- Department Genetics and Cell Biology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, P.O. Box 616, 6200 MD Maastricht, The Netherlands
| | - L Gianaroli
- S.I.S.Me.R. Reproductive Medicine Unit, Via Mazzini 12, 40138 Bologna, Italy
| | - K Ketterson
- Althea Science, Inc., 3 Regent St #301, Livingston, NJ 07039, USA
| | - I Liebaers
- Centre for Medical Genetics, UZ Brussel, Laarbeeklaan 101, B-1090 Brussels, Belgium
- Research Group Reproduction and Genetics, Vrije Universiteit Brussel, Laarbeeklaan 101, B-1090, Brussels, Belgium
| | - K Lundin
- Reproductive Medicine, Sahlgrenska University Hospital, Blå Stråket 6, 413 45, Göteborg, Sweden
| | - H Mertes
- Bioethics Institute Ghent, Department of Philosophy and Moral Science, Ghent University, Belgium
| | - M Morris
- Synlab Genetics, chemin d'Entre-Bois 21, CH-1018, Lausanne, Switzerland
| | - G Pennings
- Bioethics Institute Ghent, Department of Philosophy and Moral Science, Ghent University, Belgium
| | - K Sermon
- Research Group Reproduction and Genetics, Vrije Universiteit Brussel, Laarbeeklaan 101, B-1090, Brussels, Belgium
| | - C Spits
- Research Group Reproduction and Genetics, Vrije Universiteit Brussel, Laarbeeklaan 101, B-1090, Brussels, Belgium
| | - S Soini
- Helsinki Biobank, Helsinki University Central Hospital, Haartmaninkatu 3, PO Box 400, 00029 HUS, Helsinki, Finland
| | - A P A van Montfoort
- IVF laboratory, Department of Obstetrics and Gynaecology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
| | - A Veiga
- Barcelona Stem Cell Bank, Centre of Regenerative Medicine in Barcelona, Hospital Duran i Reynals, Gran Via de l' Hospitalet 199, 08908, Hospitalet de Llobregat, Barcelona, Spain
- Reproductive Medicine Service of Dexeus Woman Health, Gran Via Carles III, 71-75 - 08028 Barcelona, Spain
| | - J R Vermeesch
- Department of Human Genetics, KU Leuven, O&N I Herestraat 49 - Box 602, B-3000 Leuven, Belgium
| | - S Viville
- Institute of Parasitology and Pathology, University of Strasbourg, 3 rue Koberlé, 67000 Strasbourg, France
- Laboratory of Genetic Diagnostics, UF3472-Genetics of Infertility, Nouvel Hôpital Civil, 1 place de l'Hôpital, 67091 Strasbourg cedex, France
| | - M Macek
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and Motol University Hospital, V Úvalu 84, Prague CZ-15006, Czech Republic
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Abstract
INTRODUCTION Preimplantation genetic diagnosis and screening (PGD/PGS) has been applied clinically for >25 years however inherent drawbacks include the necessity to tailor each case to the trait in question, and that technology to detect monogenic and chromosomal disorders respectively is fundamentally different. Areas covered: The area of preimplantation genetics has evolved over the last 25 years, adapting to changes in technology and the need for more efficient, streamlined diagnoses. Karyomapping allows the determination of inheritance from the (grand)parental haplobocks through assembly of inherited chromosomal segments. The output displays homologous chromosomes, crossovers and the genetic status of the embryos by linkage comparison, as well as chromosomal disorders. It also allows for determination of heterozygous SNP calls, avoiding the risks of allele dropout, a common problem with other PGD techniques. Manuscripts documenting the evolution of preimplantation genetics, especially those investigating technologies that would simultaneously detect monogenic and chromosomal disorders, were selected for review. Expert commentary: Karyomapping is currently available for detection of single gene disorders; ~1000 clinics worldwide offer it (via ~20 diagnostic laboratories) and ~2500 cases have been performed. Due an inability to detect post-zygotic trisomy reliably however and confounding problems of embryo mosaicism, karyomapping has yet to be applied clinically for detection of chromosome disorders.
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Affiliation(s)
- Rebecca L Gould
- a The Bridge Centre , London , UK.,b School of Biological Sciences , University of Kent , Canterbury , UK
| | - Darren K Griffin
- b School of Biological Sciences , University of Kent , Canterbury , UK
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25
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Sanders KD, Griffin DK. Chromosomal Preimplantation Genetic Diagnosis: 25 Years and Counting. JOURNAL OF FETAL MEDICINE 2017. [DOI: 10.1007/s40556-017-0123-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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26
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Christodoulou C, Dheedene A, Heindryckx B, van Nieuwerburgh F, Deforce D, De Sutter P, Menten B, Van den Abbeel E. Preimplantation genetic diagnosis for chromosomal rearrangements with the use of array comparative genomic hybridization at the blastocyst stage. Fertil Steril 2017; 107:212-219.e3. [PMID: 27793373 DOI: 10.1016/j.fertnstert.2016.09.045] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 09/09/2016] [Accepted: 09/27/2016] [Indexed: 02/02/2023]
Affiliation(s)
- Christodoulos Christodoulou
- Ghent Fertility and Stem Cell Team, Department for Reproductive Medicine, Ghent University Hospital, Ghent, Belgium.
| | - Annelies Dheedene
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Björn Heindryckx
- Ghent Fertility and Stem Cell Team, Department for Reproductive Medicine, Ghent University Hospital, Ghent, Belgium
| | - Filip van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Petra De Sutter
- Ghent Fertility and Stem Cell Team, Department for Reproductive Medicine, Ghent University Hospital, Ghent, Belgium
| | - Björn Menten
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Etienne Van den Abbeel
- Ghent Fertility and Stem Cell Team, Department for Reproductive Medicine, Ghent University Hospital, Ghent, Belgium
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27
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Noninvasive chromosome screening of human embryos by genome sequencing of embryo culture medium for in vitro fertilization. Proc Natl Acad Sci U S A 2016; 113:11907-11912. [PMID: 27688762 DOI: 10.1073/pnas.1613294113] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Preimplantation genetic screening (PGS) is widely used to select in vitro-fertilized embryos free of chromosomal abnormalities and to improve the clinical outcome of in vitro fertilization (IVF). A disadvantage of PGS is that it requires biopsy of the preimplantation human embryo, which can limit the clinical applicability of PGS due to the invasiveness and complexity of the process. Here, we present and validate a noninvasive chromosome screening (NICS) method based on sequencing the genomic DNA secreted into the culture medium from the human blastocyst. By using multiple annealing and looping-based amplification cycles (MALBAC) for whole-genome amplification (WGA), we performed next-generation sequencing (NGS) on the spent culture medium used to culture human blastocysts (n = 42) and obtained the ploidy information of all 24 chromosomes. We validated these results by comparing each with their corresponding whole donated embryo and obtained a high correlation for identification of chromosomal abnormalities (sensitivity, 0.882, and specificity, 0.840). With this validated NICS method, we performed chromosome screening on IVF embryos from seven couples with balanced translocation, azoospermia, or recurrent pregnancy loss. Six of them achieved successful clinical pregnancies, and five have already achieved healthy live births thus far. The NICS method avoids the need for embryo biopsy and therefore substantially increases the safety of its use. The method has the potential of much wider chromosome screening applicability in clinical IVF, due to its high accuracy and noninvasiveness.
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28
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Zhao M, Chen M, Lee CG, Chong SS. Identification of Novel Microsatellite Markers <1 Mb from the HTT CAG Repeat and Development of a Single-Tube Tridecaplex PCR Panel of Highly Polymorphic Markers for Preimplantation Genetic Diagnosis of Huntington Disease. Clin Chem 2016; 62:1096-105. [PMID: 27335079 DOI: 10.1373/clinchem.2016.255711] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 05/11/2016] [Indexed: 12/11/2022]
Abstract
BACKGROUND Preimplantation genetic diagnosis (PGD) of Huntington disease (HD) generally employs linkage analysis of flanking microsatellite markers to complement direct mutation testing, as well as for exclusion testing. Thus far, only 10 linked markers have been developed for use in HD PGD, with a maximum of 3 markers coamplified successfully. We aimed to develop a single-tube multiplex PCR panel of highly polymorphic markers to simplify HD PGD. METHODS An in silico search was performed to identify all markers within 1 Mb flanking the huntingtin (HTT) gene. Selected markers were optimized in a single-tube PCR panel, and their polymorphism indices were determined in 2 populations. The panel was tested on 63 single cells to validate its utility in PGD. RESULTS We identified 102 markers in silico, of which 56 satisfied the selection criteria. After initial testing, 12 markers with potentially high heterozygosity were optimized into a single-tube PCR panel together with a 13th more distally located marker. Analysis of DNA from 183 Chinese and Caucasian individuals revealed high polymorphism indices for all markers (polymorphism information content >0.5), with observed heterozygosities ranging from 0.5-0.92. All individuals were heterozygous for at least 5 markers, with 99.5% of individuals heterozygous for at least 2 markers upstream and downstream of the HTT CAG repeat. CONCLUSIONS The tridecaplex marker assay amplified reliably from single cells either directly or after whole genome amplification, thus validating its standalone use in HD exclusion PGD or as a complement to HTT CAG repeat expansion-mutation detection.
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Affiliation(s)
| | | | - Caroline G Lee
- Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Division of Medical Sciences, National Cancer Center, Singapore; Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School, Singapore
| | - Samuel S Chong
- Departments of Pediatrics and Preimplantation Genetic Diagnosis Center, Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore; Molecular Diagnosis Center and Clinical Cytogenetics Service, Department of Laboratory Medicine, National University Hospital, National University Health System, Singapore.
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29
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Handyside AH. Live births following karyomapping - a "key" milestone in the development of preimplantation genetic diagnosis. Reprod Biomed Online 2016; 31:307-8. [PMID: 26353913 DOI: 10.1016/j.rbmo.2015.07.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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30
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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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31
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Clinical applications of MARSALA for preimplantation genetic diagnosis of spinal muscular atrophy. J Genet Genomics 2016; 43:541-547. [PMID: 27599922 DOI: 10.1016/j.jgg.2016.03.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 03/11/2016] [Accepted: 03/14/2016] [Indexed: 11/22/2022]
Abstract
Conventional PCR methods combined with linkage analysis based on short tandem repeats (STRs) or Karyomapping with single nucleotide polymorphism (SNP) arrays, have been applied to preimplantation genetic diagnosis (PGD) for spinal muscular atrophy (SMA), an autosome recessive disorder. However, it has limitations in SMA diagnosis by Karyomapping, and these methods are unable to distinguish wild-type embryos with carriers effectively. Mutated allele revealed by sequencing with aneuploidy and linkage analyses (MARSALA) is a new method allowing embryo selection by a one-step next-generation sequencing (NGS) procedure, which has been applied in PGD for both autosome dominant and X-linked diseases in our group previously. In this study, we carried out PGD based on MARSALA for two carrier families with SMA affected children. As a result, one of the couples has given birth to a healthy baby free of mutations in SMA-causing gene. It is the first time that MARSALA was applied to PGD for SMA, and we can distinguish the embryos with heterozygous deletion (carriers) from the wild-type (normal) ones accurately through this NGS-based method. In addition, direct mutation detection allows us to identify the affected embryos (homozygous deletion), which can be regarded as probands for linkage analysis, in case that the affected family member is absent. In the future, the NGS-based MARSALA method is expected to be used in PGD for all monogenetic disorders with known pathogenic gene mutation.
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32
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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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Kakourou G, Vrettou C, Kattamis A, Destouni A, Poulou M, Moutafi M, Kokkali G, Pantos K, Davies S, Kitsiou-Tzeli S, Kanavakis E, Traeger-Synodinos J. Complex preimplantation genetic diagnosis for beta-thalassaemia, sideroblastic anaemia, and human leukocyte antigen (HLA)-typing. Syst Biol Reprod Med 2015; 62:69-76. [DOI: 10.3109/19396368.2015.1100692] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Coates A, Hesla JS, Hurliman A, Coate B, Holmes E, Matthews R, Mounts EL, Turner KJ, Thornhill AR, Griffin DK. Use of suboptimal sperm increases the risk of aneuploidy of the sex chromosomes in preimplantation blastocyst embryos. Fertil Steril 2015; 104:866-872. [DOI: 10.1016/j.fertnstert.2015.06.033] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 06/24/2015] [Accepted: 06/24/2015] [Indexed: 01/15/2023]
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35
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Qin Y, Gao WQ. Concise Review: Patient-Derived Stem Cell Research for Monogenic Disorders. Stem Cells 2015; 34:44-54. [DOI: 10.1002/stem.2112] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 06/05/2015] [Accepted: 06/20/2015] [Indexed: 12/24/2022]
Affiliation(s)
- Yiren Qin
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med-X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine; hanghai Jiao Tong University; Shanghai People's Republic of China
| | - Wei-Qiang Gao
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med-X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine; hanghai Jiao Tong University; Shanghai People's Republic of China
- School of Biomedical Engineering & Med-X Research Institute; Shanghai Jiao Tong University; Shanghai People's Republic of China
- Collaborative Innovation Center of Systems Biomedicine; Shanghai Jiao Tong University; Shanghai People's Republic of China
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Kumar A, Ryan A, Kitzman JO, Wemmer N, Snyder MW, Sigurjonsson S, Lee C, Banjevic M, Zarutskie PW, Lewis AP, Shendure J, Rabinowitz M. Whole genome prediction for preimplantation genetic diagnosis. Genome Med 2015; 7:35. [PMID: 26019723 PMCID: PMC4445980 DOI: 10.1186/s13073-015-0160-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 03/24/2015] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Preimplantation genetic diagnosis (PGD) enables profiling of embryos for genetic disorders prior to implantation. The majority of PGD testing is restricted in the scope of variants assayed or by the availability of extended family members. While recent advances in single cell sequencing show promise, they remain limited by bias in DNA amplification and the rapid turnaround time (<36 h) required for fresh embryo transfer. Here, we describe and validate a method for inferring the inherited whole genome sequence of an embryo for preimplantation genetic diagnosis (PGD). METHODS We combine haplotype-resolved, parental genome sequencing with rapid embryo genotyping to predict the whole genome sequence of a day-5 human embryo in a couple at risk of transmitting alpha-thalassemia. RESULTS Inheritance was predicted at approximately 3 million paternally and/or maternally heterozygous sites with greater than 99% accuracy. Furthermore, we successfully phase and predict the transmission of an HBA1/HBA2 deletion from each parent. CONCLUSIONS Our results suggest that preimplantation whole genome prediction may facilitate the comprehensive diagnosis of diseases with a known genetic basis in embryos.
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Affiliation(s)
- Akash Kumar
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195 USA
| | | | - Jacob O Kitzman
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195 USA
| | | | - Matthew W Snyder
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195 USA
| | | | - Choli Lee
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195 USA
| | | | - Paul W Zarutskie
- Department of Obstetrics and Gynecology, University of Washington School of Medicine, Seattle, WA 98195 USA
| | - Alexandra P Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195 USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195 USA
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Thornhill AR, Handyside AH, Ottolini C, Natesan SA, Taylor J, Sage K, Harton G, Cliffe K, Affara N, Konstantinidis M, Wells D, Griffin DK. Karyomapping-a comprehensive means of simultaneous monogenic and cytogenetic PGD: comparison with standard approaches in real time for Marfan syndrome. J Assist Reprod Genet 2015; 32:347-56. [PMID: 25561157 PMCID: PMC4363232 DOI: 10.1007/s10815-014-0405-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 12/11/2014] [Indexed: 11/25/2022] Open
Affiliation(s)
- Alan R Thornhill
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
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