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Yang L, Xu Y, Xia J, Yan H, Ding C, Shi Q, Wu Y, Liu P, Pan J, Zeng Y, Zhang Y, Chen F, Jiang H, Xu Y, Li W, Zhou C, Gao Y. Simultaneous detection of genomic imbalance in patients receiving preimplantation genetic testing for monogenic diseases (PGT-M). Front Genet 2022; 13:976131. [PMID: 36246639 PMCID: PMC9559864 DOI: 10.3389/fgene.2022.976131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/31/2022] [Indexed: 11/23/2022] Open
Abstract
Background: Preimplantation genetic test for monogenic disorders (PGT-M) has been used to select genetic disease-free embryos for implantation during in vitro fertilization (IVF) treatment. However, embryos tested by PGT-M have risks of harboring chromosomal aneuploidy. Hence, a universal method to detect monogenic diseases and genomic imbalances is required. Methods: Here, we report a novel PGT-A/M procedure allowing simultaneous detection of monogenic diseases and genomic imbalances in one experiment. Library was prepared in a special way that multiplex polymerase chain reaction (PCR) was integrated into the process of whole genome amplification. The resulting library was used for one-step low-pass whole genome sequencing (WGS) and high-depth target enrichment sequencing (TES). Results: The TAGs-seq PGT-A/M was first validated with genomic DNA (gDNA) and the multiple displacement amplification (MDA) products of a cell line. Over 90% of sequencing reads covered the whole-genome region with around 0.3–0.4 × depth, while around 5.4%–7.3% of reads covered target genes with >10000 × depth. Then, for clinical validation, 54 embryos from 8 women receiving PGT-M of β-thalassemia were tested by the TAGs-seq PGT-A/M. In each embryo, an average of 20.0 million reads with 0.3 × depth of the whole-genome region was analyzed for genomic imbalance, while an average of 0.9 million reads with 11260.0 × depth of the target gene HBB were analyzed for β-thalassemia. Eventually, 18 embryos were identified with genomic imbalance with 81.1% consistency to karyomapping results. 10 embryos contained β-thalassemia with 100% consistency to conventional PGT-M method. Conclusion: TAGs-seq PGT-A/M simultaneously detected genomic imbalance and monogenic disease in embryos without dramatic increase of sequencing data output.
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Affiliation(s)
- Lin Yang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Yan Xu
- Reproductive Medicine Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Reproductive Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jun Xia
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | | | - Chenhui Ding
- Reproductive Medicine Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Reproductive Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | | | | | | | - Jiafu Pan
- Reproductive Medicine Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Reproductive Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yanhong Zeng
- Reproductive Medicine Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Reproductive Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | | | | | | | - Yanwen Xu
- Reproductive Medicine Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Reproductive Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Yanwen Xu, ; Wei Li, ; Canquan Zhou, ; Ya Gao,
| | - Wei Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- Hebei Industrial Technology Research Institute of Genomics in Maternal and Child Health, Shijiazhuang, China
- *Correspondence: Yanwen Xu, ; Wei Li, ; Canquan Zhou, ; Ya Gao,
| | - Canquan Zhou
- Reproductive Medicine Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Reproductive Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Yanwen Xu, ; Wei Li, ; Canquan Zhou, ; Ya Gao,
| | - Ya Gao
- BGI-Shenzhen, Shenzhen, China
- Shenzhen Engineering Laboratory for Birth Defects Screening, Shenzhen, China
- *Correspondence: Yanwen Xu, ; Wei Li, ; Canquan Zhou, ; Ya Gao,
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2
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Stocker E, Johal S, Rippel L, Darrah R. Frequency of embryos appropriate for transfer following preimplantation genetic testing for monogenic disease. J Assist Reprod Genet 2022; 39:2043-2050. [PMID: 35920991 PMCID: PMC9474744 DOI: 10.1007/s10815-022-02571-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 07/08/2022] [Indexed: 11/26/2022] Open
Abstract
PURPOSE To identify specific likelihoods that an embryo will be classified as appropriate for transfer after preimplantation genetic testing for detection of a monogenic disorder (PGT-M), with or without preimplantation genetic testing for aneuploidy (PGT-A), separated by inheritance pattern. METHODS Retrospective chart review of 181 selected PGT-M cycles performed at CooperGenomics in 2018 or 2019. For each cycle, the following main outcome data was collected: the number of embryos classified as affected with monogenic disease, the number detected to be chromosomally abnormal, the number that were recombinant, the number that had no result, and if applicable, the number which were aneuploid. RESULTS There were significantly fewer embryos appropriate to consider for transfer when PGT-A was included for autosomal recessive and X-linked disorders. There were also fewer for autosomal dominant disorders, though this was not statistically significant. When PGT-A was not included, 45.8% of autosomal dominant, 69% of autosomal recessive, and 47.8% of X-linked embryos were appropriate to consider for transfer. When PGT-A analysis was included, 29% of autosomal dominant, 41% of autosomal recessive, and 22% of X-linked embryos were appropriate to consider for transfer. 96.8% of women elect to include PGT-A when pursuing PGT-M. CONCLUSION This study resulted in specific likelihoods that an embryo would be found appropriate for clinicians and patients to consider for transfer based on the inheritance pattern of the monogenic disease being tested for and whether aneuploidy analysis was included.
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Affiliation(s)
- Emma Stocker
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA.
| | | | - Larisa Rippel
- Center for Human Genetics, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Rebecca Darrah
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
- Frances Payne Bolton School of Nursing, Case Western Reserve University, Cleveland, OH, USA
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3
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Courage C, Koehler U, Kleinle S, Neuhann T, Holinski-Feder E, Abicht A. Präkonzeptionsscreening. GYNAKOLOGISCHE ENDOKRINOLOGIE 2022. [DOI: 10.1007/s10304-021-00434-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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4
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Porto A, Gaber Caffrey R, Crowley-Matoka M, Spencer S, Li M, Propst L. Offering preimplantation genetic testing for monogenic disorders (PGT-M) for conditions with reduced penetrance or variants of uncertain significance: Ethical insight from U.S. laboratory genetic counselors. J Genet Couns 2021; 31:261-268. [PMID: 34347921 DOI: 10.1002/jgc4.1482] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 06/27/2021] [Accepted: 07/04/2021] [Indexed: 11/10/2022]
Abstract
Preimplantation genetic testing for monogenic disorders (PGT-M) was originally developed to identify embryos affected with serious childhood-onset disorders, but its use has recently broadened. Guidance on the use of PGT-M in the United States (U.S.) is currently limited, with no formal laws or guidelines established on its use. The goals of this study were to determine for which types of conditions U.S. laboratories currently do not offer PGT-M, to explore ethical considerations U.S. laboratory genetic counselors (GCs) take into consideration when deciding to accept or reject a PGT-M request, and to explore whether U.S. laboratory GCs believe PGT-M should be offered for conditions with reduced penetrance or for variants of uncertain significance (VUS). Qualitative analysis of semi-structured interviews with nine genetic counselors, from five different PGT-M laboratories, was conducted. Participants were required to be GCs working at a PGT-M laboratory in the U.S. and either actively counsel patients on PGT-M or determine a patient's eligibility for PGT-M. Two participants reported their separate laboratories have no limitations for allowable PGT-M testing, while the other seven participants representing three other laboratories reported having limitations. The main ethical consideration GCs reported considering when deciding to accept or reject a PGT-M request was patient autonomy, with a focus on the patient understanding risks of the testing. All participants reported believing PGT-M should be allowable for conditions with reduced penetrance and VUS, with all participants stating their respective laboratories allow for this currently. However, all participants reported a lack of sufficient guidelines and that having guidelines from a professional organization would be beneficial to their practice. In conclusion, lack of current guidelines in the United States has created discrepancies between PGT-M laboratories. PGT-M laboratory GCs support the use of PGT-M for conditions with reduced penetrance and VUS with informed consent. The need for guidelines is supported.
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Affiliation(s)
- Anthony Porto
- Center for Genetic Medicine, Northwestern University, Chicago, IL, USA.,Reproductive Medicine Associates of Connecticut, Norwalk, CT, USA
| | | | - Megan Crowley-Matoka
- Departments of Medical Education/Anthropology, Northwestern University, Chicago, IL, USA
| | - Sara Spencer
- Department of Ob/Gyn, Northwestern Medical Group, Chicago, IL, USA
| | - Mindy Li
- Division of Genetics, Department of Pediatrics, Rush University Medical Center, Chicago, IL, USA
| | - Lauren Propst
- Igenomix USA, Torrance, CA, USA.,BillionToOne Inc, Menlo Park, CA, USA
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5
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Payne MR, Skytte AB, Harper JC. The use of expanded carrier screening of gamete donors. Hum Reprod 2021; 36:1702-1710. [PMID: 33842976 PMCID: PMC8129592 DOI: 10.1093/humrep/deab067] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 01/15/2021] [Indexed: 12/14/2022] Open
Abstract
STUDY QUESTION What are the sperm and egg donor rejection rates after expanded carrier screening (ECS)? SUMMARY ANSWER Using an ECS panel looking at 46/47 genes, 17.6% of donors were rejected. WHAT IS KNOWN ALREADY The use of ECS is becoming commonplace in assisted reproductive technology, including testing of egg and sperm donors. Most national guidelines recommend rejection of donors if they are carriers of a genetic disease. If the use of ECS increases, there will be a decline in the number of donors available. STUDY DESIGN, SIZE, DURATION A review of the current preconception ECS panels available to donors was carried out through an online search. The genetic testing results of donors from Cryos International were analysed to determine how many were rejected on the basis of the ECS. PARTICIPANTS/MATERIALS, SETTING, METHODS Data on gamete donors and their carrier status was provided by Cryos International, who screen donors using their own bespoke ECS panel. The ECS panels identified through the review were compared to the Cryos International panel and data. MAIN RESULTS AND THE ROLE OF CHANCE A total of 16 companies and 42 associated ECS panels were reviewed. There were a total of 2673 unique disorders covered by the panels examined, with a mean of 329 disorders screened. None of these disorders were common to all panels. Cryos International screen 46 disorders in males and 47 in females. From 883 candidate donors, 17.6% (155/883) were rejected based on their ECS result. Carriers of alpha-thalassaemia represented the largest proportion of those rejected (19.4%, 30/155), then spinal muscular atrophy (15.5%, 24/155) and cystic fibrosis (14.8%, 23/155). LIMITATIONS, REASONS FOR CAUTION Panel information was found on company websites and may not have been accurate. WIDER IMPLICATIONS OF THE FINDINGS This study highlights the need for consistent EU regulations and guidelines that allow genetic matching of gamete donors to their recipients, preventing the need to reject donors who are known carriers. A larger ECS panel would be most beneficial; however, this would not be viable without matching of donors and recipients. STUDY FUNDING/COMPETING INTEREST(S) No specific funding was obtained. J.C.H. is the founder of Global Women Connected, a platform to discuss women's health issues and the Embryology and PGD Academy, who deliver education in clinical embryology. She has been paid to give a lecture by Cryos in 2019. A-B.S. is an employee of Cryos International. TRIAL REGISTRATION NUMBER N/A.
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Affiliation(s)
- Molly R Payne
- Institute for Women’s Health, University College London, London, UK
| | | | - Joyce C Harper
- Institute for Women’s Health, University College London, London, UK
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6
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Pennings G. Expanded carrier screening should not be mandatory for gamete donors. Hum Reprod 2021; 35:1256-1261. [PMID: 32369167 DOI: 10.1093/humrep/deaa088] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 03/27/2020] [Accepted: 04/06/2020] [Indexed: 12/31/2022] Open
Abstract
More and more centers are imposing expanded carrier screening (ECS) on their gamete donors. In some clinics and gamete banks, gamete donors are not given this right, contrary to the freedom to decline genetic screening in the general population. The possible social and psychological burdens that are recognized for infertility patients and the general population are downplayed for gamete donors. The procedure of imposing ECS on gamete donors shows that the interests of the recipients are valued higher than those of the donors. The general ethical argument defended here is the principle of proportionality: the burdens imposed on donors have to be balanced against the potential benefits for the offspring and the recipients. The risk reduction of ECS is below 1% and is too small to outweigh the potential dangers and disadvantages for donors. The conclusion is that clinics may ask, but not compel, donors to submit to ECS provided that they offer appropriate genetic and psychological counseling.
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Affiliation(s)
- Guido Pennings
- Department of Philosophy and Moral Science, Bioethics Institute Ghent (BIG), Ghent University, Gent, Belgium
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7
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Sallevelt SCEH, Stegmann APA, de Koning B, Velter C, Steyls A, van Esch M, Lakeman P, Yntema H, Esteki MZ, de Die-Smulders CEM, Gilissen C, van den Wijngaard A, Brunner HG, Paulussen ADC. Diagnostic exome-based preconception carrier testing in consanguineous couples: results from the first 100 couples in clinical practice. Genet Med 2021; 23:1125-1136. [PMID: 33742171 PMCID: PMC8187149 DOI: 10.1038/s41436-021-01116-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 01/31/2021] [Accepted: 02/02/2021] [Indexed: 01/20/2023] Open
Abstract
Purpose Consanguineous couples are at increased risk of being heterozygous for the same autosomal recessive (AR) disorder(s), with a 25% risk of affected offspring as a consequence. Until recently, comprehensive preconception carrier testing (PCT) for AR disorders was unavailable in routine diagnostics. Here we developed and implemented such a test in routine clinical care. Methods We performed exome sequencing (ES) for 100 consanguineous couples. For each couple, rare variants that could give rise to biallelic variants in offspring were selected. These variants were subsequently filtered against a gene panel consisting of ~2,000 genes associated with known AR disorders (OMIM-based). Remaining variants were classified according to American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) guidelines, after which only likely pathogenic and pathogenic (class IV/V) variants, present in both partners, were reported. Results In 28 of 100 tested consanguineous couples (28%), likely pathogenic and pathogenic variants not previously known in the couple or their family were reported conferring 25% risk of affected offspring. Conclusion ES-based PCT provides a powerful diagnostic tool to identify AR disease carrier status in consanguineous couples. Outcomes provided significant reproductive choices for a higher proportion of these couples than previous tests.
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Affiliation(s)
- Suzanne C E H Sallevelt
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands
| | - Alexander P A Stegmann
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands.,Research School for Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands
| | - Bart de Koning
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands
| | - Crool Velter
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands
| | - Anja Steyls
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands
| | - Melanie van Esch
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands
| | - Phillis Lakeman
- Amsterdam UMC, Department of Clinical Genetics, Amsterdam Reproduction and Development Research Institute, University of Amsterdam, Amsterdam, The Netherlands
| | - Helger Yntema
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Masoud Zamani Esteki
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands.,Research School for Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands
| | - Christine E M de Die-Smulders
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands.,Research School for Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Arthur van den Wijngaard
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands.,Research School for Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands
| | - Han G Brunner
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands.,Research School for Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands.,Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.,Donders center for Neuroscience, Radboudumc, Nijmegen, The Netherlands.,MHENS school of Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Aimée D C Paulussen
- Department of Clinical Genetics, Maastricht University Medical Center+ (MUMC+), Maastricht, The Netherlands. .,Research School for Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands.
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8
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de Wert G, van der Hout S, Goddijn M, Vassena R, Frith L, Vermeulen N, Eichenlaub-Ritter U. The ethics of preconception expanded carrier screening in patients seeking assisted reproduction. Hum Reprod Open 2021; 2021:hoaa063. [PMID: 33604456 PMCID: PMC7880037 DOI: 10.1093/hropen/hoaa063] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 10/30/2020] [Indexed: 02/02/2023] Open
Abstract
Expanded carrier screening (ECS) entails a screening offer for carrier status for multiple recessive disorders simultaneously and allows testing of couples or individuals regardless of ancestry or geographic origin. Although universal ECS—referring to a screening offer for the general population—has generated considerable ethical debate, little attention has been given to the ethics of preconception ECS for patients applying for assisted reproduction using their own gametes. There are several reasons why it is time for a systematic reflection on this practice. Firstly, various European fertility clinics already offer preconception ECS on a routine basis, and others are considering such a screening offer. Professionals involved in assisted reproduction have indicated a need for ethical guidance for ECS. Secondly, it is expected that patients seeking assisted reproduction will be particularly interested in preconception ECS, as they are already undertaking the physical, emotional and economic burdens of such reproduction. Thirdly, an offer of preconception ECS to patients seeking assisted reproduction raises particular ethical questions that do not arise in the context of universal ECS: the professional’s involvement in the conception implies that both parental and professional responsibilities should be taken into account. This paper reflects on and provides ethical guidance for a responsible implementation of preconception ECS to patients seeking assisted reproduction using their own gametes by assessing the proportionality of such a screening offer: do the possible benefits clearly outweigh the possible harms and disadvantages? If so, for what kinds of disorders and under what conditions?
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Affiliation(s)
- Guido de Wert
- Department of Health, Ethics and Society; CAPHRI School for Public Health and Primary Care, Maastricht University; and GROW School for Oncology and Developmental Biology, Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Sanne van der Hout
- Department of Health, Ethics and Society; CAPHRI School for Public Health and Primary Care, Maastricht University; and GROW School for Oncology and Developmental Biology, Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Mariëtte Goddijn
- Centre for Reproductive Medicine, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Rita Vassena
- Clinica EUGIN, Carrer de Balmes 236, Barcelona 08006, Spain
| | - Lucy Frith
- Department of Public Health, Policy & Systems, Institute of Population Health, University of Liverpool, Liverpool L69 3BX, UK
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Capalbo A, Poli M, Riera-Escamilla A, Shukla V, Kudo Høffding M, Krausz C, Hoffmann ER, Simon C. Preconception genome medicine: current state and future perspectives to improve infertility diagnosis and reproductive and health outcomes based on individual genomic data. Hum Reprod Update 2020; 27:254-279. [PMID: 33197264 DOI: 10.1093/humupd/dmaa044] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 08/13/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Our genetic code is now readable, writable and hackable. The recent escalation of genome-wide sequencing (GS) applications in population diagnostics will not only enable the assessment of risks of transmitting well-defined monogenic disorders at preconceptional stages (i.e. carrier screening), but also facilitate identification of multifactorial genetic predispositions to sub-lethal pathologies, including those affecting reproductive fitness. Through GS, the acquisition and curation of reproductive-related findings will warrant the expansion of genetic assessment to new areas of genomic prediction of reproductive phenotypes, pharmacogenomics and molecular embryology, further boosting our knowledge and therapeutic tools for treating infertility and improving women's health. OBJECTIVE AND RATIONALE In this article, we review current knowledge and potential development of preconception genome analysis aimed at detecting reproductive and individual health risks (recessive genetic disease and medically actionable secondary findings) as well as anticipating specific reproductive outcomes, particularly in the context of IVF. The extension of reproductive genetic risk assessment to the general population and IVF couples will lead to the identification of couples who carry recessive mutations, as well as sub-lethal conditions prior to conception. This approach will provide increased reproductive autonomy to couples, particularly in those cases where preimplantation genetic testing is an available option to avoid the transmission of undesirable conditions. In addition, GS on prospective infertility patients will enable genome-wide association studies specific for infertility phenotypes such as predisposition to premature ovarian failure, increased risk of aneuploidies, complete oocyte immaturity or blastocyst development failure, thus empowering the development of true reproductive precision medicine. SEARCH METHODS Searches of the literature on PubMed Central included combinations of the following MeSH terms: human, genetics, genomics, variants, male, female, fertility, next generation sequencing, genome exome sequencing, expanded carrier screening, secondary findings, pharmacogenomics, controlled ovarian stimulation, preconception, genetics, genome-wide association studies, GWAS. OUTCOMES Through PubMed Central queries, we identified a total of 1409 articles. The full list of articles was assessed for date of publication, limiting the search to studies published within the last 15 years (2004 onwards due to escalating research output of next-generation sequencing studies from that date). The remaining articles' titles were assessed for pertinence to the topic, leaving a total of 644 articles. The use of preconception GS has the potential to identify inheritable genetic conditions concealed in the genome of around 4% of couples looking to conceive. Genomic information during reproductive age will also be useful to anticipate late-onset medically actionable conditions with strong genetic background in around 2-4% of all individuals. Genetic variants correlated with differential response to pharmaceutical treatment in IVF, and clear genotype-phenotype associations are found for aberrant sperm types, oocyte maturation, fertilization or pre- and post-implantation embryonic development. All currently known capabilities of GS at the preconception stage are reviewed along with persisting and forthcoming barriers for the implementation of precise reproductive medicine. WIDER IMPLICATIONS The expansion of sequencing analysis to additional monogenic and polygenic traits may enable the development of cost-effective preconception tests capable of identifying underlying genetic causes of infertility, which have been defined as 'unexplained' until now, thus leading to the development of a true personalized genomic medicine framework in reproductive health.
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Affiliation(s)
- Antonio Capalbo
- Igenomix Italy, Marostica, Italy.,Igenomix Foundation, INCLIVA, Valencia, Spain
| | | | - Antoni Riera-Escamilla
- Andrology Department, Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Barcelona, Spain
| | - Vallari Shukla
- Department of Cellular and Molecular Medicine, DRNF Center for Chromosome Stability, University of Copenhagen, Copenhagen, Denmark
| | - Miya Kudo Høffding
- Department of Cellular and Molecular Medicine, DRNF Center for Chromosome Stability, University of Copenhagen, Copenhagen, Denmark
| | - Csilla Krausz
- Andrology Department, Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Barcelona, Spain.,Department of Experimental and Clinical Biomedical Sciences "Mario Serio", Centre of Excellence DeNothe, University of Florence, Florence, Italy
| | - Eva R Hoffmann
- Department of Cellular and Molecular Medicine, DRNF Center for Chromosome Stability, University of Copenhagen, Copenhagen, Denmark
| | - Carlos Simon
- Igenomix Foundation, INCLIVA, Valencia, Spain.,Department of Obstetrics and Gynecology, University of Valencia, Valencia, Spain.,Department of Obstetrics and Gynecology BIDMC, Harvard University, Cambridge, MA, USA
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10
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Hudson N, Culley L, Herbrand C, Pavone V, Pennings G, Provoost V, Coveney C, Funes SL. Reframing egg donation in Europe: new regulatory challenges for a shifting landscape. HEALTH POLICY AND TECHNOLOGY 2020. [DOI: 10.1016/j.hlpt.2020.04.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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11
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Rothwell E, Lamb B, Johnson E, Gurtcheff S, Riches N, Fagan M, Sabatello M, Johnstone E. Patient perspectives and experiences with in vitro fertilization and genetic testing options. Ther Adv Reprod Health 2020; 14:2633494119899942. [PMID: 32518912 PMCID: PMC7254585 DOI: 10.1177/2633494119899942] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 12/18/2019] [Indexed: 12/31/2022] Open
Abstract
Objective: Decision-making and patient experiences with embryo selection during in vitro fertilization often include genetic testing options. The purpose of this study was to gain insight about the experiences and perspectives of women using in vitro fertilization and genetic technologies. Methods: Interviews (n = 37) were conducted among female patients who had undergone in vitro fertilization, underwent expanded carrier screening, and were offered pre-implantation genetic testing for aneuploidy between July 2016 and July 2017. The interviews were transcribed and a content analysis was conducted on the transcripts. Results: Categories that emerged from the data analysis included unexpected outcomes, uncertainty, unanticipated emotional consequences, too much emphasis on the woman’s contributions and questions about embryo viability. Patient experiences with genetic technologies during in vitro fertilization played a significant role within these results. Conclusion: The emotional and psychological impacts of infertility during in vitro fertilization were the primary concerns discussed by participants. Future research is needed to identify ways to help manage unexpected outcomes and continuous uncertainty, including the increasing use of genetic technologies, to not add to the psychological burden of infertility. There is a need to explore more support options or counseling services for patients struggling with infertility during in vitro fertilization treatment.
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Affiliation(s)
- Erin Rothwell
- Associate Vice President for Research, Integrity and Compliance, The University of Utah, 75 South 2000 East, Salt Lake City, UT 84112, USA
| | - Brandy Lamb
- Department of Obstetrics and Gynecology, The University of Utah, Salt Lake City, UT, USA
| | - Erin Johnson
- Department of Obstetrics and Gynecology, The University of Utah, Salt Lake City, UT, USA
| | | | - Naomi Riches
- Department of Obstetrics and Gynecology, The University of Utah, Salt Lake City, UT, USA
| | - Melinda Fagan
- Department of Philosophy, The University of Utah, Salt Lake City, UT, USA
| | - Maya Sabatello
- Department of Psychiatry, Columbia University, New York, NY, USA
| | - Erica Johnstone
- Department of Obstetrics and Gynecology, The University of Utah, Salt Lake City, UT, USA
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12
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Hreinsson J, Iwarsson E, Hanson C, Grøndahl ML, Løssl K, Hydén‐Granskog C, Ingerslev HJ, Petersen MR, Bredbacka P, Nøhr B, Savolainen L, Hnida C, Toft CLF, Hindkjær J, Aagaard J, Lundin K, Roos LKS. Preimplantation genetic testing practices in the Nordic countries. Acta Obstet Gynecol Scand 2020; 99:707-715. [DOI: 10.1111/aogs.13821] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 01/27/2020] [Accepted: 02/02/2020] [Indexed: 11/29/2022]
Affiliation(s)
| | - Erik Iwarsson
- Department of Molecular Medicine and Surgery Karolinska Institutet and Clinical Genetics Karolinska University Laboratory Karolinska University Hospital Stockholm Sweden
| | - Charles Hanson
- Reproductive Medicine Sahlgrenska University Hospital Gothenburg Sweden
| | - Marie Louise Grøndahl
- Department of Obstetrics and Gynecology Department of Reproductive Medicine Copenhagen University Hospital Herlev Herlev Denmark
| | - Kristine Løssl
- The Fertility Clinic – Section 4071 Copenhagen University Hospital Rigshospitalet Copenhagen Denmark
| | | | - Hans Jakob Ingerslev
- Fertility Unit and Center for Preimplantation Genetic Testing Aalborg University Hospital Aalborg Denmark
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13
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Murphy NM, Samarasekera TS, Macaskill L, Mullen J, Rombauts LJF. Genome sequencing of human in vitro fertilisation embryos for pathogenic variation screening. Sci Rep 2020; 10:3795. [PMID: 32123222 PMCID: PMC7052235 DOI: 10.1038/s41598-020-60704-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 02/13/2020] [Indexed: 12/22/2022] Open
Abstract
Whole-genome sequencing of preimplantation human embryos to detect and screen for genetic diseases is a technically challenging extension to preconception screening. Combining preconception genetic screening with preimplantation testing of human embryos facilitates the detection of de novo mutations and self-validates transmitted variant detection in both the reproductive couple and the embryo’s samples. Here we describe a trio testing workflow that involves whole-genome sequencing of amplified DNA from biopsied embryo trophectoderm cells and genomic DNA from both parents. Variant prediction software and annotation databases were used to assess variants of unknown significance and previously not described de novo variants in five single-gene preimplantation genetic testing couples and eleven of their embryos. Pathogenic variation, tandem repeat, copy number and structural variations were examined against variant calls for compound heterozygosity and predicted disease status was ascertained. Multiple trio testing showed complete concordance with known variants ascertained by single-nucleotide polymorphism array and uncovered de novo and transmitted pathogenic variants. This pilot study describes a method of whole-genome sequencing and analysis for embryo selection in high-risk couples to prevent early life fatal genetic conditions that adversely affect the quality of life of the individual and families.
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Affiliation(s)
- Nicholas M Murphy
- Genetic Technologies Ltd., Victoria, Australia. .,Monash IVF, Clayton, Victoria, Australia. .,GenEmbryomics Pty. Ltd., Victoria, Australia. .,Drug Delivery Disposition and Dynamics, Faculty of Pharmacy and Pharmaceutical Sciences, Parkville, Melbourne, Victoria, Australia.
| | | | | | | | - Luk J F Rombauts
- Monash IVF, Clayton, Victoria, Australia.,Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, Victoria, Australia.,Department of Obstetrics and Gynaecology, Monash University, Clayton, Victoria, Australia.,Monash Women's & Newborn Program, Monash Health, Victoria, Australia
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14
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Capalbo A, Valero RA, Jimenez-Almazan J, Pardo PM, Fabiani M, Jiménez D, Simon C, Rodriguez JM. Optimizing clinical exome design and parallel gene-testing for recessive genetic conditions in preconception carrier screening: Translational research genomic data from 14,125 exomes. PLoS Genet 2019; 15:e1008409. [PMID: 31589614 PMCID: PMC6797235 DOI: 10.1371/journal.pgen.1008409] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 10/17/2019] [Accepted: 09/10/2019] [Indexed: 12/20/2022] Open
Abstract
Limited translational genomic research data have been reported on the application of exome sequencing and parallel gene testing for preconception carrier screening (PCS). Here, we present individual-level data from a large PCS program in which exome sequencing was routinely performed on either gamete donors (5,845) or infertile patients (8,280) undergoing in vitro fertilization (IVF) treatment without any known family history of inheritable genetic conditions. Individual-level data on pathogenic variants were used to define conditions for PCS based on criteria for severity, penetrance, inheritance pattern, and age of onset. Fetal risk was defined based on actual carrier frequency data accounting for the specific inheritance pattern (fetal disease risk, FDR). In addition, large-scale application of exome sequencing for PCS allowed a deep investigation of the incidence of medically actionable secondary findings in this population. Exome sequencing achieved remarkable clinical sensitivity for reproductive risk of highly penetrant childhood-onset disorders (1/337 conceptions) through analysis of 114 selected gene-condition pairs. A significant contribution to fetal disease risk was observed for rare (carrier rate < 1:100) and X-linked conditions (16.7% and 41.2% of total FDR, respectively). Subgroup analysis of 776 IVF couples identified 37 at increased reproductive risk (4.8%; 95% CI = 3.4–6.5). Further, two additional couples had increased risk for very rare conditions when both members of a parental pair were treated as a unit and the search was extended to the entire exome. About 2.3% of participants showed at least one pathogenic variant for genes included in the updated American College of Medical Genetics and Genomics v2.0 list of secondary findings. Gamete donors and IVF couples showed similar carrier burden for both carrier screening and secondary findings, indicating no causal relationship to fertility. These translational research data will facilitate development of more effective PCS strategies that maximize clinical sensitivity with minimal counterproductive effects. We provide here crucial information for optimizing the gene-panel design for preconception carrier screening based on the analysis of a large exome sequencing dataset from infertile individuals and gamete donors. Sequencing the entire coding portion of the human genome combined with separate analysis for few relevant genes offers the possibility to detect most of the pathogenetic variants associated with recessive Mendelian diseases and to develop preconception screening strategies that maximise clinical sensitivity with minimal counterproductive effects. Using a large dataset of individual-level exome sequencing data, we have defined gene specific and aggregate fetal risk detectable for conditions selected on discrete criteria of severity, penetrance, inheritance pattern, and age of onset. About 1 out of 300 affected pregnancies can be detected based on a gene-panel of 114 conditions and ~5% of the couples analysed showed an increased risk that warrant consideration from a reproductive viewpoint. These results suggest the use of exome sequencing and parallel gene testing is clinically effective and feasible for preconception carrier screening after proper validation and translational research has been carried out. However, further studies are necessary to define the best framework for clinical implementation and the actual detection rate of at risk couples.
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Affiliation(s)
- Antonio Capalbo
- Igenomix Reproductive Genetic Laboratory, Marostica, Italy
- DAHFMO Unit of Histology and Medical Embryology, Sapienza University of Rome, Italy
- Igenomix, Valencia, Spain
- * E-mail: (AC); (JM)
| | | | | | | | - Marco Fabiani
- Igenomix Reproductive Genetic Laboratory, Marostica, Italy
| | | | - Carlos Simon
- Igenomix, Valencia, Spain
- Department of Obstetrics and Gynecology, Valencia University; and INCLIVA, Valencia, Spain
- Department of Obstetrics and Gynecology, School of Medicine, Stanford University, Stanford, California, United States of America
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15
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Capalbo A, Chokoshvili D, Dugoff L, Franasiak J, Gleicher N, Pennings G, Simon C. Should the reproductive risk of a couple aiming to conceive be tested in the contemporary clinical context? Fertil Steril 2019; 111:229-238. [PMID: 30642571 DOI: 10.1016/j.fertnstert.2018.11.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 11/30/2018] [Indexed: 11/27/2022]
Affiliation(s)
| | - Davit Chokoshvili
- Centre for Biomedical Ethics and Law, Department of Public Health and Primary Care, University of Leuven, Leuven, Belgium
| | - Lorraine Dugoff
- Maternal Fetal Medicine and Reproductive Genetics, Department of Obstetrics and Gynecology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania
| | - Jason Franasiak
- IVI-RMA America, Reproductive Medicine Associates of New Jersey, Basking Ridge, New Jersey; Department of Obstetrics and Gynecology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Norbert Gleicher
- Center for Human Reproduction, New York, New York; Foundation for Reproductive Medicine, New York, New York; Stem Cell Biology and Molecular Embryology Laboratory, Rockefeller University, New York, New York; Department of Obstetrics and Gynecology, Vienna University of Medicine, Vienna, Austria
| | - Guido Pennings
- Bioethics Institute Ghent (BIG), Department of Philosophy and Moral Science, Ghent University, Ghent, Belgium
| | - Carlos Simon
- Department of Obstetrics and Gynecology, Valencia University, and INCLIVA, Valencia, Spain; Department of Obstetrics and Gynecology, Stanford University, Stanford, California; Igenomix, Valencia, Spain.
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16
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Clarke EV, Schneider JL, Lynch F, Kauffman TL, Leo MC, Rosales AG, Dickerson JF, Shuster E, Wilfond BS, Goddard KAB. Assessment of willingness to pay for expanded carrier screening among women and couples undergoing preconception carrier screening. PLoS One 2018; 13:e0200139. [PMID: 30020962 PMCID: PMC6051630 DOI: 10.1371/journal.pone.0200139] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 06/20/2018] [Indexed: 12/21/2022] Open
Abstract
Background Expanded carrier screening can provide risk information for numerous conditions. Understanding how individuals undergoing preconception expanded carrier screening value this information is important. The NextGen study evaluated the use of genome sequencing for expanded carrier screening and reporting secondary findings, and we measured participants’ willingness to pay for this approach to understand how it is valued by women and couples planning a pregnancy. Methods We assessed 277 participants’ willingness to pay for genome sequencing reporting carrier results for 728 gene/condition pairs and results for 121 secondary findings. We explored the association between attitudes and demographic factors and willingness to pay for expanded carrier screening using genome sequencing and conducted interviews with 58 of these participants to probe the reasoning behind their preferences. Results Most participants were willing to pay for expanded carrier screening using genome sequencing. Willingness to pay was associated with income level and religiosity, but not risk status for a condition in the carrier panel. Participants willing to pay nothing or a small amount cited issues around financial resources, whereas those willing to pay higher amounts were motivated by “peace of mind” from carrier results. Conclusion Women and couples planning a pregnancy value genome sequencing. The potentially high out-of-pocket cost of this service could result in healthcare disparities, since maximum amounts that participants were willing to pay were higher than a typical copay and related to income.
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Affiliation(s)
- Elizabeth V. Clarke
- Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, United States of America
- * E-mail:
| | - Jennifer L. Schneider
- Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, United States of America
| | - Frances Lynch
- Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, United States of America
| | - Tia L. Kauffman
- Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, United States of America
| | - Michael C. Leo
- Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, United States of America
| | - Ana G. Rosales
- Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, United States of America
| | - John F. Dickerson
- Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, United States of America
| | - Elizabeth Shuster
- Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, United States of America
| | - Benjamin S. Wilfond
- Seattle Children’s Hospital and Research Institute, Trueman Katz Center for Pediatric Bioethics, Seattle, Washington, United States of America
| | - Katrina A. B. Goddard
- Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, United States of America
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