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Ren J, Peng C, Chen H, Zhou F, Keqie Y, Li Y, Yang H, Zhang H, Du Z, Hu T, Zhang X, Luo S, Fan W, Wang Y, Wang H, Chen X, Liu S. Asian Screening Array and Next-Generation Sequencing Based Panels Applied to Preimplantation Genetic Testing for Monogenic Disorders Preclinical Workup in 294 Families: A Retrospective Analysis. Prenat Diagn 2024. [PMID: 39072792 DOI: 10.1002/pd.6639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 07/07/2024] [Accepted: 07/16/2024] [Indexed: 07/30/2024]
Abstract
OBJECTIVE Currently, the most commonly used methods for linkage analysis of pre-implantation genetic testing for monogenic disorders (PGT-M) are next generation sequencing (NGS) and SNP array. We aim to investigate whether the application efficacy of Asian screening array (ASA) in PGT-M preclinical workup for the Chinese population is superior to NGS based single nucleotide polymorphism (SNP) panels. METHODS We conducted a retrospective analysis by reviewing 294 couples from a single center over the past 4 years and compared the detection results between NGS-based SNP panels and ASA. Using the numbers of informative SNPs upstream and downstream flanking of variants, we assessed the detection efficiency of both methods in monogenic diseases, chromosomal microdeletion syndrome and males with de novo variants, among other scenarios. RESULTS Results indicate that ASA offers a greater number of informative SNPs compared with NGS-based SNP panels. Additionally, data analysis for ASA is generally more straightforward and may require less computational resources. While ASA can address most PGT-M challenges, we have also identified certain genes in previous tests that are not suitable for PGT-M using ASA. CONCLUSION The application of ASA in PGT-M preclinical workup for Chinese populations has good practical value as it can perform linkage analysis for most genetic variants. However, for certain variants, NGS or other testing methods, such as mutated allele revealed by sequencing with aneuploidy and linkage analysis (MARSALA), may still be necessary for completion.
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Affiliation(s)
- Jun Ren
- Department of Medical Genetics, Center for Prenatal Diagnosis, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Cuiting Peng
- Department of Medical Genetics, Center for Prenatal Diagnosis, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Han Chen
- Department of Medical Genetics, Center for Prenatal Diagnosis, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Fan Zhou
- Department of Medical Genetics, Center for Prenatal Diagnosis, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Yuezhi Keqie
- Department of Medical Genetics, Center for Prenatal Diagnosis, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Yutong Li
- Department of Medical Genetics, Center for Prenatal Diagnosis, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Hong Yang
- Department of Medical Genetics, Center for Prenatal Diagnosis, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Haixia Zhang
- Department of Medical Genetics, Center for Prenatal Diagnosis, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Ze Du
- Department of Medical Genetics, Center for Prenatal Diagnosis, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Ting Hu
- Department of Medical Genetics, Center for Prenatal Diagnosis, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Xuemei Zhang
- Department of Medical Genetics, Center for Prenatal Diagnosis, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Shan Luo
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
- Department of Obstetrics and Gynecology, Center of Reproductive Medicine, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Wei Fan
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
- Department of Obstetrics and Gynecology, Center of Reproductive Medicine, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Yan Wang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
- Department of Obstetrics and Gynecology, Center of Reproductive Medicine, West China Second University Hospital, Sichuan University, Chengdu, China
| | - He Wang
- Department of Medical Genetics, Center for Prenatal Diagnosis, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Xinlian Chen
- Department of Medical Genetics, Center for Prenatal Diagnosis, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Shanling Liu
- Department of Medical Genetics, Center for Prenatal Diagnosis, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
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Rogers A, Menezes M, Kane SC, Zander-Fox D, Hardy T. Preimplantation Genetic Testing for Monogenic Conditions: Is Cell-Free DNA Testing the Next Step? Mol Diagn Ther 2021; 25:683-690. [PMID: 34495483 DOI: 10.1007/s40291-021-00556-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2021] [Indexed: 11/25/2022]
Abstract
Genetic assessment of an embryo via preimplantation genetic testing (PGT) represents an important reproductive option for couples wanting to try and improve success rates from in vitro fertilisation (IVF) cycles, as well as reduce their risk of having a child born with a genetic condition. Currently, biopsy of the developing embryo prior to transfer allows genetic assessment of an embryo for either chromosome copy number (aneuploidy [PGT-A] or segmental rearrangement [PGT-SR]) or to avoid the transmission of a single gene condition (monogenic conditions [PGT-M]). However, this technology is invasive and commands considerable resources. Non-invasive PGT (niPGT) offers a potential alternate mode of embryonic analysis. Whilst the utility of niPGT-A has been recently explored, there has been limited consideration of niPGT-M as an option for couples at risk of passing on a single gene or chromosomal condition. This review examines the historical and current clinical context of preimplantation embryonic analysis for monogenic conditions, in addition to important considerations surrounding the origin and analysis of cell-free deoxyribose nucleic acid (cfDNA), whether it is sourced via blastocentesis or spent embryonic culture medium (SCM). Future capabilities of this testing modality will almost certainly be enhanced by integration of whole genome sequencing into everyday practice. In addition, the increased utilisation of reproductive carrier screening as part of standard reproductive healthcare will likely result in the identification of a larger high-risk population. As a result, stratification of limited and highly specialised reproductive genetic resources will be required. Prospective parents should continue to be made aware of the limitations of this technology, with prenatal confirmatory testing remaining an essential part of antenatal care in these patients. However, niPGT-M poses an important alternate testing modality for high-risk couples, particularly in the setting of embryos that cannot be biopsied for traditional PGT-M and as demand for this treatment continues to grow.
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Affiliation(s)
- Alice Rogers
- Genetics, Repromed, Monash IVF, 180 Fullarton Road, Dulwich, SA, 5065, Australia
| | - Melody Menezes
- Monash Ultrasound for Women, Richmond, VIC, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Stefan C Kane
- Monash Ultrasound for Women, Richmond, VIC, Australia
- Department of Obstetrics and Gynaecology, The University of Melbourne, Parkville, VIC, Australia
- Department of Maternal Fetal Medicine, The Royal Women's Hospital, Parkville, VIC, Australia
| | - Deirdre Zander-Fox
- Monash IVF Group, Clayton, VIC, Australia
- Monash University, Clayton, VIC, Australia
- The University of Adelaide, Adelaide, SA, Australia
- University of South Australia, Adelaide, SA, Australia
| | - Tristan Hardy
- Genetics, Repromed, Monash IVF, 180 Fullarton Road, Dulwich, SA, 5065, Australia.
- Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia.
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Expanded clinical validation of Haploseek for comprehensive preimplantation genetic testing. Genet Med 2021; 23:1334-1340. [PMID: 33772222 DOI: 10.1038/s41436-021-01145-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 11/08/2022] Open
Abstract
PURPOSE We previously developed Haploseek, a method for comprehensive preimplantation genetic testing (PGT). However, some key features were missing, and the method has not yet been systematically validated. METHODS We extended Haploseek to incorporate DNA from embryo grandparents and to allow testing of variants on chromosome X or in regions where parents share common haplotypes. We then validated Haploseek on 151 embryo biopsies from 27 clinical PGT cases. We sequenced all biopsies to low coverage (0.2×), and performed single-nucleotide polymorphism (SNP) microarray genotyping on the embryos' parents and siblings/grandparents. We used the extended Haploseek to predict chromosome copy-number variants (CNVs) and relevant variant-flanking haplotypes in each embryo. We validated haplotype predictions for each clinical sample against polymerase chain reaction (PCR)-based PGT case results, and CNV predictions against established commercial kits. RESULTS For each of the 151 embryo biopsies, all Haploseek-derived haplotypes and CNVs were concordant with clinical PGT results. The cases included 17 autosomal dominant, 5 autosomal recessive, and 3 X-linked monogenic disorders. In addition, we evaluated 1 Robertsonian and 2 reciprocal translocations, and 17 cases of chromosome copy-number counting were performed. CONCLUSION Our results demonstrate that Haploseek is clinically accurate and fit for all standard clinical PGT applications.
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Xi Y, Chen G, Lei C, Wu J, Zhang S, Xiao M, Zhang W, Zhang Y, Sun X. Expanded carrier screening in Chinese patients seeking the help of assisted reproductive technology. Mol Genet Genomic Med 2020; 8:e1340. [PMID: 32573981 PMCID: PMC7507411 DOI: 10.1002/mgg3.1340] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 04/27/2020] [Accepted: 05/12/2020] [Indexed: 01/05/2023] Open
Abstract
Background Expanded carrier screening (ECS) has emerged as an effective approach to identify at‐risk couples (ARCs)—before they initiate attempts at reproduction—who possess a high probability of having a child affected by severe recessive diseases. The objective of this study was to evaluate the clinical utility of ECS in Chinese patients seeking the help of assisted reproductive technology (ART). Methods An ECS test, which covers 201 genes implicated in 135 recessive (autosomal or X‐linked) diseases, was routinely offered to all ART patients in a single genetics and in vitro fertilization clinic. Additional options for preimplantation or prenatal genetic diagnosis were discussed and offered to all ARCs. All ECS results were aggregated and the clinical decisions of the ARCs were surveyed. Results A total of 2,923 ART patients, representing 1,462 couples, were screened. Overall, 46.73% of the individuals were found to be the carriers for at least 1 of the 135 diseases. Of the tested couples, 2.26% (n = 33) were identified as ARCs. As of the completion of this study, 21 (63.6%) ARCs have decided to avert an affected pregnancy with the help of preimplantation genetic testing for monogenetic conditions. The cumulative carrier rate of the 187 autosomal recessive genes in the ECS panel for the 2,836 Han Chinese individuals without a family history was estimated to be 45.91%. The estimated at‐risk couple rate indicates that the screening for only the top 31 genes with gene carrier rates >0.5% would identify more than 94% of the ARCs identified by screening all 187 genes. Conclusion Our study demonstrates that ESC yields a significant clinical value for ART patients in China. In addition, by estimating the yields of the ECS panel, we identify genes that are appropriate for screening the Han population.
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Affiliation(s)
- Yanping Xi
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Guangquan Chen
- WuXi NextCODE Genomics (Shanghai) Co., Ltd., Shanghai, China
| | - Caixia Lei
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Junping Wu
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Shuo Zhang
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Min Xiao
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Wenbi Zhang
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Yueping Zhang
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Xiaoxi Sun
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China.,Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics, and Gynecology Hospital of Fudan University, Shanghai, China
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Hardy T. The role of prenatal diagnosis following preimplantation genetic testing for single-gene conditions: A historical overview of evolving technologies and clinical practice. Prenat Diagn 2020; 40:647-651. [PMID: 32037566 DOI: 10.1002/pd.5662] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 12/11/2019] [Accepted: 01/26/2020] [Indexed: 11/12/2022]
Abstract
Preimplantation genetic testing for monogenic conditions (PGT-M) has become a valued reproductive option for couples at risk of having a child with a single gene condition. In line with developments in molecular genetics, there has been an overall trend toward laboratory techniques with higher accuracy in comparison to earlier PGT-M techniques. The recommendation for confirmatory prenatal diagnostic testing has remained a standard component of PGT-M counseling, reflecting the inherent difficulties of testing the limited number of cells obtained from embryo biopsy, as well as recognition of the biological and human factors that may lead to misdiagnosis in a PGT-M cycle. Reported misdiagnosis rates are less than 1 in 200 pregnancies following PGT-M, although updated data regarding newer methods of PGT-M are required. There is limited evidence available regarding clinician and patient behavior in pregnancies resulting from PGT-M cycles. It remains essential that clinicians involved in the care of patients undergoing PGT-M provide appropriate counseling regarding the risks of misdiagnosis and the importance of confirmatory prenatal diagnosis. The nature of PGT-M test design lends itself to cell-free DNA-based noninvasive prenatal testing for monogenic conditions (NIPT-M), which is likely to become a popular method in the near future.
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Affiliation(s)
- Tristan Hardy
- Repromed, Adelaide, Australia.,Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia
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Karyomapping in preimplantation genetic testing for β-thalassemia combined with HLA matching: a systematic summary. J Assist Reprod Genet 2019; 36:2515-2523. [PMID: 31758512 DOI: 10.1007/s10815-019-01595-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 09/24/2019] [Indexed: 12/11/2022] Open
Abstract
PURPOSE To investigate the validity, accuracy, and clinical outcomes of Karyomapping in preimplantation genetic testing (PGT) for β-thalassemia combined with human leukocyte antigen (HLA) matching. METHODS A total of 128 cycles from January 2014 to December 2017 were identified, and 1205 embryos were biopsied. The case group included 88 cycles using Karyomapping for PGT-HLA, compared with 40 cycles using polymerase chain reaction-short tandem repeat (PCR-STR) as the control group. RESULTS There were significant differences in the HLA matching rate (21.34 vs. 14.37%), the matched transferable embryo rate (9.79 vs. 14.07%), the clinical pregnancy rate (65.08 vs. 41.86%), and the spontaneous miscarriage rate (2.44 vs. 22.22%) between the case and control groups. In the case group, nearly 1/3 (33.37%) of the embryos showed aneuploidy. According to the results of single nucleotide polymorphism (SNP) haplotype analysis, the recombination rates of HBB (hemoglobin subunit beta) and HLA were 11.46% and 5.61% respectively. HLA gene recombination was mostly distributed between HLA-A and HLA-B and the downstream region of HLA-DQB1. In addition, STR analysis could be considered in the case of copy-neutral loss of heterozygosity (LOH) in the region where the HLA gene is located. CONCLUSION Karyomapping contributes to accurate selection of matched embryos, along with aneuploidy screening. However, STRs assist identification in cases of LOH in the target region.
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Satirapod C, Sukprasert M, Panthan B, Charoenyingwattana A, Chitayanan P, Chantratita W, Choktanasiri W, Trachoo O, Hongeng S. Clinical utility of combined preimplantation genetic testing methods in couples at risk of passing on beta thalassemia/hemoglobin E disease: A retrospective review from a single center. PLoS One 2019; 14:e0225457. [PMID: 31751397 PMCID: PMC6872132 DOI: 10.1371/journal.pone.0225457] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 11/05/2019] [Indexed: 12/11/2022] Open
Abstract
Thalassemia and hemoglobinopathy is a group of hereditary blood disorder with diverse clinical manifestation inherited by autosomal recessive manner. The Beta thalassemia/Hemoglobin E disease (HbE/βthal) causes a variable degree of hemolysis and the most severe form of HbE/βthal disease develop a lifelong transfusion-dependent anemia. Preimplantation genetic testing (PGT) is an established procedure of embryo genetic analysis to avoid the risk of passing on this particular condition from the carrier parents to their offspring. Preimplantation genetic testing for chromosomal aneuploidy (PGT-A) also facilitates the selection of embryos without chromosomal aberration resulting in the successful embryo implantation rate. Herein, we study the clinical outcome of using combined PGT-M and PGT-A in couples at risk of passing on HbE/βthal disease. The study was performed from January 2016 to December 2017. PGT-M was developed using short tandem repeat linkage analysis around the beta globin gene cluster and direct mutation testing using primer extension-based mini-sequencing. Thereafter, we recruited 15 couples at risk of passing on HbE/βthal disease who underwent a combined total of 22 IVF cycles. PGT was performed in 106 embryos with a 3.89% allele drop-out rate. Using combined PGT-M and PGT-A methods, 80% of women obtained satisfactory genetic testing results and were able to undergo embryo transfer within the first two cycles. The successful implantation rate was 64.29%. PGT accuracy was evaluated by prenatal and postnatal genetic confirmation and 100% had a genetic status consistent with PGT results. The overall clinical outcome of successful live birth for couples at risk of producing offspring with HbE/βthal was 53.33%. Conclusively, combined PGT-M and PGT-A is a useful technology to prevent HbE/βthal disease in the offspring of recessive carriers.
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Affiliation(s)
- Chonthicha Satirapod
- Department of Obstetrics and Gynecology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Matchuporn Sukprasert
- Department of Obstetrics and Gynecology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Bhakbhoom Panthan
- Center for Medical Genomics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Angkana Charoenyingwattana
- Center for Medical Genomics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | | | - Wasun Chantratita
- Center for Medical Genomics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Wicharn Choktanasiri
- Department of Obstetrics and Gynecology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Objoon Trachoo
- Center for Medical Genomics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
- Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
- * E-mail:
| | - Suradej Hongeng
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
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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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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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10
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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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