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Lan Y, Zhou H, He S, Shu J, Liang L, Wei H, Luo J, Wang C, Zhao X, Qiu Q, Huang P. Appropriate whole genome amplification and pathogenic loci detection can improve the accuracy of preimplantation genetic diagnosis for deletional α-thalassemia. Front Endocrinol (Lausanne) 2024; 14:1176063. [PMID: 38523870 PMCID: PMC10957767 DOI: 10.3389/fendo.2023.1176063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 11/13/2023] [Indexed: 03/26/2024] Open
Abstract
Objective To improve the accuracy of preimplantation genetic testing (PGT) in deletional α-thalassemia patients. Design Article. Patients fifty-two deletional α-thalassemia couples. Interventions Whole genome amplification (WGA), Next-generation sequencing (NGS) and PCR mutation loci detection. Main outcome measures WGA, Single nucleotide polymorphism (SNP) and PCR mutation loci detection results; Analysis of embryo chromosome copy number variation (CNV). Results Multiple Displacement Amplification (MDA) and Multiple Annealing and Looping-Based Amplification Cycles (MALBAC) methods for PGT for deletional α-thalassemia. Blastocyst biopsy samples (n = 253) were obtained from 52 deletional α-thalassemia couples. The results of the comparison of experimental data between groups MALBAC and MDA are as follows: (i) The average allele drop-out (ADO) rate, MALBAC vs. MDA = 2.27% ± 3.57% vs. 0.97% ± 1.4%, P=0.451); (ii) WGA success rate, MALBAC vs. MDA = 98.61% vs. 98.89%, P=0.851; (iii) SNP haplotype success rate, MALBAC vs. MDA = 94.44% vs. 96.68%, P=0.409; (iv) The result of SNP haplotype analysis is consistent with that of Gap-PCR/Sanger sequencing results, MALBAC vs. MDA = 36(36/72, 50%) vs. 151(151/181, 83.43%), P=0; (v) Valid SNP loci, MALBAC vs. MDA = 30 ± 9 vs. 34 ± 10, P=0.02; (vi) The mean CV values, MALBAC vs. MDA = 0.12 ± 0.263 vs. 0.09 ± 0.40, P=0.916; (vii) The average number of raw reads, MALBAC vs. MDA =3244259 ± 999124 vs. 3713146 ± 1028721, P=0; (viii) The coverage of genome (%), MALBAC vs. MDA = 5.02 ± 1.09 vs. 5.55 ± 1.49, P=0.008. Conclusions Our findings indicate that MDA is superior to MALBAC for PGT of deletional α-thalassemia. Furthermore, SNP haplotype analysis combined with PCR loci detection can improve the accuracy and detection rate of deletional α-thalassemia.
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Affiliation(s)
- Yueyun Lan
- Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Key Laboratory of Reproductive Health and Birth Defect Prevention, Nanning, China
- Genetic and Metabolic Central Laboratory of Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Hong Zhou
- Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Key Laboratory of Reproductive Health and Birth Defect Prevention, Nanning, China
| | - Sheng He
- Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Key Laboratory of Reproductive Health and Birth Defect Prevention, Nanning, China
- Genetic and Metabolic Central Laboratory of Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Nanning, China
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Nanning, China
| | - Jinhui Shu
- Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Key Laboratory of Reproductive Health and Birth Defect Prevention, Nanning, China
| | - Lifang Liang
- Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Key Laboratory of Reproductive Health and Birth Defect Prevention, Nanning, China
- Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Nanning, China
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Nanning, China
| | - Hongwei Wei
- Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Key Laboratory of Reproductive Health and Birth Defect Prevention, Nanning, China
- Genetic and Metabolic Central Laboratory of Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Nanning, China
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Nanning, China
| | - Jingsi Luo
- Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Key Laboratory of Reproductive Health and Birth Defect Prevention, Nanning, China
- Genetic and Metabolic Central Laboratory of Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Caizhu Wang
- Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Key Laboratory of Reproductive Health and Birth Defect Prevention, Nanning, China
| | - Xin Zhao
- Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Key Laboratory of Reproductive Health and Birth Defect Prevention, Nanning, China
| | - Qingming Qiu
- Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Key Laboratory of Reproductive Health and Birth Defect Prevention, Nanning, China
- Genetic and Metabolic Central Laboratory of Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Nanning, China
| | - Peng Huang
- Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Key Laboratory of Reproductive Health and Birth Defect Prevention, Nanning, China
- Genetic and Metabolic Central Laboratory of Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Guangxi Key Laboratory of Precision Medicine for Genetic Diseases, Nanning, China
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Zhang P, Zhao X, Li Q, Xu Y, Cheng Z, Yang L, Wang H, Tao Y, Huang G, Wu R, Zhou H, Zhao S. Proband-independent haplotyping based on NGS-based long-read sequencing for detecting pathogenic variant carrier status in preimplantation genetic testing for monogenic diseases. Front Mol Biosci 2024; 11:1329580. [PMID: 38516188 PMCID: PMC10955336 DOI: 10.3389/fmolb.2024.1329580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 02/12/2024] [Indexed: 03/23/2024] Open
Abstract
Preimplantation genetic testing for monogenic diseases (PGT-M) can be used to select embryos that do not develop disease phenotypes or carry disease-causing genes for implantation into the mother's uterus, to block disease transmission to the offspring, and to increase the birth rate of healthy newborns. However, the traditional PGT-M technique has some limitations, such as its time consumption, experimental procedural complexity, and the need for a complete family or reference embryo to construct the haplotype. In this study, proband-independent haplotyping based on NGS-based long-read sequencing (Phbol-seq) was used to effectively construct haplotypes. By targeting the mutation sites of single gene disease point mutations and small fragment deletion carriers, embryos carrying parental disease-causing mutations were successfully identified by linkage analysis. The efficiency of embryo resolution was then verified by classical Sanger sequencing, and it was confirmed that the construction of haplotype and SNP linkage analysis by Phbol-seq could accurately and effectively detect whether embryos carried parental pathogenic mutations. After the embryos confirmed to be nonpathogenic by Phbol-seq-based PGT-M and confirmed to have normal copy number variation by Phbol-seq-based PGT-A were transplanted into the uterus, gene detection in amniotic fluid of the implanted embryos was performed, and the results confirmed that Phbol-seq technology could accurately distinguish normal genotype embryos from genetically modified carrier embryos. Our results suggest that Phbol-seq is an effective strategy for accurately locating mutation sites and accurately distinguishing between embryos that inherit disease-causing genes and normal embryos that do not. This is critical for Phbol-seq-based PGT-M and could help more single-gene disease carriers with incomplete families, de novo mutations or suspected germline mosaicism to have healthy babies with normal phenotypes. It also helps to reduce the transmission of monogenic genetic diseases in the population.
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Affiliation(s)
- Peiyu Zhang
- Department of Obstetrics and Gynecology, Guizhou Medical University, Guiyang, China
| | - Xiaomei Zhao
- Reproductive Medicine Center, Department of Obstetrics and Gynecology of the Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Qinshan Li
- Department of Obstetrics and Gynecology, Affiliated Hospital of Guizhou Medical University, Guiyang, China
- Prenatal Diagnosis Center, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Yaqiong Xu
- Department of Obstetrics and Gynecology, Guizhou Medical University, Guiyang, China
| | - Zengmei Cheng
- Department of Obstetrics and Gynecology, Guizhou Medical University, Guiyang, China
| | - Lu Yang
- Department of Obstetrics and Gynecology, Guizhou Medical University, Guiyang, China
| | - Houmei Wang
- Department of Obstetrics and Gynecology, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Yang Tao
- Reproductive Medicine Center, Department of Obstetrics and Gynecology of The First People’s Hospital of Bijie, Bijie, China
| | - Guanyou Huang
- Reproductive Medicine Center, Department of Obstetrics and Gynecology of the Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Rui Wu
- Reproductive Medicine Center, Department of Obstetrics and Gynecology of the Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Hua Zhou
- Reproductive Medicine Center, Department of Obstetrics and Gynecology of the Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Shuyun Zhao
- Reproductive Medicine Center, Department of Obstetrics and Gynecology of the Affiliated Hospital of Guizhou Medical University, Guiyang, China
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Liang Y, Li M, Fei J, Chen Z. Should non-invasive prenatal testing be recommended for patients who achieve pregnancy with PGT? BMC Pregnancy Childbirth 2024; 24:100. [PMID: 38302865 PMCID: PMC10832195 DOI: 10.1186/s12884-024-06284-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/21/2024] [Indexed: 02/03/2024] Open
Abstract
OBJECTIVE To determine whether non-invasive prenatal testing is an alternative testing option to preimplantation genetic testing (PGT) in pregnant patients. METHODS This was a retrospective study of the clinical outcomes of patients who underwent PGT and invasive or non-invasive pregnancy testing after euploid blastocyst transfer at our IVF centre between January 2017 and December 2022. RESULTS In total, 321 patients were enrolled in this study, 138 (43.0%) received invasive pregnancy testing, and 183 (57.0%) patients underwent non-invasive testing. The mean age of the patients in Group 2 was higher than that of the patients in Group 1 (35.64 ± 4.74 vs. 31.04 ± 4.15 years, P < 0.001). The basal LH and AMH levels were higher in Group 1 than in Group 2 (4.30 ± 2.68 vs. 3.40 ± 1.88, P = 0.003; 5.55 ± 11.22 vs. 4.09 ± 3.55, P = 0.012), but the clinical outcomes were not significantly different. Furthermore, the clinical outcomes of patients undergoing invasive testing were similar to those of patients undergoing non-invasive testing with the same PGT indication. CONCLUSION Our results suggest that non-invasive pregnancy testing is a suitable alternative option for detecting the foetal chromosomal status in a PGT cycle. However, the usefulness of non-invasive testing in PGT-M patients is still limited.
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Affiliation(s)
- Yunhao Liang
- Center of Reproductive Medicine, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, CN, China
| | - Meiyi Li
- Center of Reproductive Medicine, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, CN, China
| | - Jia Fei
- Peking Jabrehoo Med Tech Co., Ltd, Beijing, CN, China
| | - Zhiheng Chen
- Center of Reproductive Medicine, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, CN, China.
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Wen X, Du J, Li Z, Liu N, Huo J, Li J, Ke W, Wu J, Fang X, Lin X. Establishment of linkage phase, using Oxford Nanopore Technologies, for preimplantation genetic testing of Coffin-Lowry syndrome with a de novo RPS6KA3 mutation. Front Genet 2023; 14:1169868. [PMID: 37779904 PMCID: PMC10538565 DOI: 10.3389/fgene.2023.1169868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 08/30/2023] [Indexed: 10/03/2023] Open
Abstract
Background: This study aimed to perform preimplantation genetic testing (PGT) for a female Coffin-Lowry Syndrome (CLS) patient with a de novo mutation (DNM) in RPS6KA3. It was challenging to establish the haplotype in this family because of the lack of information from affected family members. Hence, we explored a new and reliable strategy for the detection of the DNM in PGT, using Oxford Nanopore Technologies (ONT) and the MARSALA platform. Methods: We performed whole-exome sequencing (WES) on the proband and confirmed the pathogenic mutation by Sanger sequencing. The proband then underwent PGT to prevent the transmission of the pathogenic mutation to her offspring. We diverged from the conventional methods and used long-read sequencing (LRS) on the ONT platform to directly detect the mutation and nearby SNPs, for construction of the haplotype in the preclinical phase of PGT. In the clinical phase of embryo diagnosis, the MARSALA method was used to detect both the SNP-based haplotype and chromosome copy number variations (CNVs), in each blastocyst. Finally, a normal embryo was selected by comparison to the haplotype of the proband and transferred into the uterus. Sanger sequencing and karyotyping were performed by amniocentesis, at 17 weeks of gestation, to confirm the accuracy of PGT. Results: Using WES, we found the novel, heterozygous, pathogenic c.1496delG (p.Gly499Valfs*25) mutation of RPS6KA3 in the proband. The SNP-based haplotype that was linked to the pathogenic mutation site was successfully established in the proband, without the need for other family members to be tested with ONT. Eight blastocysts were biopsied to perform PGT and were assessed with a haplotype linkage analysis (30 SNP sites selected), to give results that were consistent with direct mutation detection using Sanger sequencing. The results of PGT showed that three of the eight blastocysts were normal, without the DNM. Moreover, the patient had a successful pregnancy, after transfer of a normal blastocyst into the uterus, and delivered a healthy baby. Conclusion: The ONT platform, combined with the MARSALA method, can be used to perform PGT for DNM patients without the need for other samples as a reference.
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Affiliation(s)
- Xiaojun Wen
- Reproductive Medicine Center, Boai Hospital of Zhongshan Affiliated to Southern Medical University, Zhongshan, China
| | - Jing Du
- Reproductive Medicine Center, Boai Hospital of Zhongshan Affiliated to Southern Medical University, Zhongshan, China
| | - Zhiming Li
- Reproductive Medicine Center, Boai Hospital of Zhongshan Affiliated to Southern Medical University, Zhongshan, China
| | - Nengqing Liu
- Reproductive Medicine Center, Boai Hospital of Zhongshan Affiliated to Southern Medical University, Zhongshan, China
| | - Junye Huo
- Reproductive Medicine Center, Boai Hospital of Zhongshan Affiliated to Southern Medical University, Zhongshan, China
| | - Jieliang Li
- Reproductive Medicine Center, Boai Hospital of Zhongshan Affiliated to Southern Medical University, Zhongshan, China
| | - Wanna Ke
- Reproductive Medicine Center, Boai Hospital of Zhongshan Affiliated to Southern Medical University, Zhongshan, China
| | - Jiaqi Wu
- Reproductive Medicine Center, Boai Hospital of Zhongshan Affiliated to Southern Medical University, Zhongshan, China
| | - Xiaowu Fang
- Reproductive Medicine Center, Boai Hospital of Zhongshan Affiliated to Southern Medical University, Zhongshan, China
| | - Xiufeng Lin
- Reproductive Medicine Center, Boai Hospital of Zhongshan Affiliated to Southern Medical University, Zhongshan, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, China
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