1
|
Zhang S, Pei Z, Xiao M, Zhou J, Hu B, Zhu S, Sun X, Wu J, Lei C, Xu C. Comprehensive preimplantation genetic testing for balanced insertional translocation carriers. J Med Genet 2024; 61:794-802. [PMID: 38802138 DOI: 10.1136/jmg-2024-109851] [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: 01/03/2024] [Accepted: 05/12/2024] [Indexed: 05/29/2024]
Abstract
BACKGROUND Balanced insertional translocations (BITs) can increase the risk of infertility, recurrent miscarriages or neonatal birth defects due to chromosomal imbalances in gametes. However, studies on preimplantation genetic testing (PGT) for patients carrying BITs are inadequate. METHODS A preimplantation genetic genotyping and haplotype analysis approach was developed and implemented in this study. Genome-wide SNP genotyping was performed, followed by core family-based haplotype analysis. The balanced insertion segments in euploid embryos were inferred from the haplotypes inherited from the carrier parent. RESULTS A total of 10 BIT carrier couples were enrolled in our study. 15 in vitro fertilisation cycles were conducted, resulting in 73 blastocysts biopsied and subjected to PGT analysis. Among these, 20 blastocysts displayed rearrangement-related imbalances, 13 exhibited de novo aneuploidies, 15 presented a complex anomaly involving both imbalances and additional aneuploidies, while 25 were euploid. Within the euploid embryos, 12 were balanced carrier embryos and 13 were non-carrier embryos. To date, eight non-carrier and one carrier embryos have been transferred, resulting in seven clinical pregnancies. All pregnancies were recommended to perform prenatal diagnosis, our date revealed complete concordance between fetal genetic testing results and PGT results. Presently, five infants have been born from these pregnancies, and two pregnancies are still ongoing. CONCLUSION The proposed method facilitates comprehensive chromosome screening and the concurrent identification of balanced insertions or normal karyotypes in embryos. This study offers an effective and universally applicable strategy for BIT carriers to achieve a healthy pregnancy and prevent the transmission of BITs to their offspring.
Collapse
Affiliation(s)
- Shuo Zhang
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, Shanghai, China
| | - Zhenle Pei
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, Shanghai, China
| | - Min Xiao
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, Shanghai, China
| | - Jing Zhou
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, Shanghai, China
| | - Bin Hu
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, Shanghai, China
| | - Saijuan Zhu
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, Shanghai, China
| | - Xiaoxi Sun
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, Shanghai, China
- Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, Shanghai, China
| | - Junping Wu
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, Shanghai, China
| | - Caixia Lei
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, Shanghai, China
| | - Congjian Xu
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, Shanghai, China
- Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, Shanghai, China
| |
Collapse
|
2
|
Nakhod V, Krivenko A, Butkova T, Malsagova K, Kaysheva A. Advances in Molecular and Genetic Technologies and the Problems Related to Their Application in Personalized Medicine. J Pers Med 2024; 14:555. [PMID: 38929775 PMCID: PMC11204801 DOI: 10.3390/jpm14060555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/03/2024] [Accepted: 05/10/2024] [Indexed: 06/28/2024] Open
Abstract
Advances in the global personalized medicine market are directly related to innovations and developments in molecular and genetic technologies. This review focuses on the key trends in the development of these technologies in the healthcare sector. The existing global developments having an impact on the evolution of the personalized medicine market are reviewed. Efficient measures to support the development of molecular and genetic technologies are proposed.
Collapse
Affiliation(s)
- Valeriya Nakhod
- Institute of Biomedical Chemistry, 10 bld. 8, Pogodinskaya str., 119121 Moscow, Russia
| | | | | | | | | |
Collapse
|
3
|
Schrauwen I, Rajendran Y, Acharya A, Öhman S, Arvio M, Paetau R, Siren A, Avela K, Granvik J, Leal SM, Määttä T, Kokkonen H, Järvelä I. Optical genome mapping unveils hidden structural variants in neurodevelopmental disorders. Sci Rep 2024; 14:11239. [PMID: 38755281 PMCID: PMC11099145 DOI: 10.1038/s41598-024-62009-y] [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: 01/04/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024] Open
Abstract
While short-read sequencing currently dominates genetic research and diagnostics, it frequently falls short of capturing certain structural variants (SVs), which are often implicated in the etiology of neurodevelopmental disorders (NDDs). Optical genome mapping (OGM) is an innovative technique capable of capturing SVs that are undetectable or challenging-to-detect via short-read methods. This study aimed to investigate NDDs using OGM, specifically focusing on cases that remained unsolved after standard exome sequencing. OGM was performed in 47 families using ultra-high molecular weight DNA. Single-molecule maps were assembled de novo, followed by SV and copy number variant calling. We identified 7 variants of interest, of which 5 (10.6%) were classified as likely pathogenic or pathogenic, located in BCL11A, OPHN1, PHF8, SON, and NFIA. We also identified an inversion disrupting NAALADL2, a gene which previously was found to harbor complex rearrangements in two NDD cases. Variants in known NDD genes or candidate variants of interest missed by exome sequencing mainly consisted of larger insertions (> 1kbp), inversions, and deletions/duplications of a low number of exons (1-4 exons). In conclusion, in addition to improving molecular diagnosis in NDDs, this technique may also reveal novel NDD genes which may harbor complex SVs often missed by standard sequencing techniques.
Collapse
Affiliation(s)
- Isabelle Schrauwen
- Department of Neurology, Center for Statistical Genetics, Gertrude H. Sergievsky Center, Columbia University Medical Center, Columbia University, 630 W 168Th St, New York, NY, 10032, USA.
| | - Yasmin Rajendran
- Department of Neurology, Center for Statistical Genetics, Gertrude H. Sergievsky Center, Columbia University Medical Center, Columbia University, 630 W 168Th St, New York, NY, 10032, USA
| | - Anushree Acharya
- Department of Neurology, Center for Statistical Genetics, Gertrude H. Sergievsky Center, Columbia University Medical Center, Columbia University, 630 W 168Th St, New York, NY, 10032, USA
| | | | - Maria Arvio
- Päijät-Häme Wellbeing Services, Neurology, Lahti, Finland
| | - Ritva Paetau
- Department of Child Neurology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Auli Siren
- Kanta-Häme Central Hospital, Hämeenlinna, Finland
| | - Kristiina Avela
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Johanna Granvik
- The Wellbeing Services County of Ostrobothnia, Kokkola, Finland
| | - Suzanne M Leal
- Department of Neurology, Center for Statistical Genetics, Gertrude H. Sergievsky Center, Columbia University Medical Center, Columbia University, 630 W 168Th St, New York, NY, 10032, USA
- Taub Institute for Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA
| | - Tuomo Määttä
- The Wellbeing Services County of Kainuu, Kajaani, Finland
| | - Hannaleena Kokkonen
- Northern Finland Laboratory Centre NordLab and Medical Research Centre, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Irma Järvelä
- Department of Medical Genetics, University of Helsinki, Helsinki, Finland
| |
Collapse
|
4
|
Qin S, Zeng J, Wang J, Ye M, Deng Q, Wang X, Zhang Z, Yi D, Wu Y, Li-Ling J. Delineation of an inverted tandem Xq23-26.3 duplication in a female featuring extremely short stature and mild mental deficiency. Mol Cytogenet 2023; 16:33. [PMID: 38031145 PMCID: PMC10685508 DOI: 10.1186/s13039-023-00663-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/06/2023] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND Partial duplications involving the long arm of the X chromosome are associated with mental retardation, short stature, microcephaly, and a wide range of physical findings. Female carriers usually have no clinical phenotype. Occasionally, they may also have heterogeneous features due to non-random inactivation of the X chromosome. METHODS The peripheral blood sample was collected from the patient and subjected to a few genetic testing, including chromosomal karyotyping, Chromosomal microarray analysis (CMA), Optical genome mapping, short tandem repeat (STR) analysis for Determination of parental origin, and X chromosome inactivation (XCI) analysis. RESULTS We have identified a de novo Xq23-Xq26.3 duplication in an adult female featuring extremely short stature and mild mental deficiency. Chromosome analysis detected a duplication on Xq23-q26.3 with a size of approximately 20 Mb. The duplication region has encompassed a number of genes, among which ARHGEF6, PHF6, HPRT1 and SLC9A6 are associated with X-linked mental retardation. Further analysis suggested that the duplication has derived from her father, was of the inversion duplication type and involved various degrees of skewed X chromosome inactivation. CONCLUSION Correlation with her phenotypes might indicate new mechanisms by which the X chromosome may lead to short stature and mental retardation. Our findings thereby may shed more light on the phenotypic implication of functional disomy of X-chromosome genes.
Collapse
Affiliation(s)
- Shengfang Qin
- Department of Medical Genetics and Prenatal Diagnosis, Sichuan Provincial Maternity and Child Health Care Hospital, Chengdu, 610045, Sichuan, China.
| | - Jiuzhi Zeng
- West China Second University Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
- Department of Reproductive Medicine, Sichuan Provincial Maternity and Child Health Care Hospital, Chengdu, 610045, Sichuan, China
| | - Jin Wang
- Department of Medical Genetics and Prenatal Diagnosis, Sichuan Provincial Maternity and Child Health Care Hospital, Chengdu, 610045, Sichuan, China
| | - Mengling Ye
- Department of Medical Genetics and Prenatal Diagnosis, Sichuan Provincial Maternity and Child Health Care Hospital, Chengdu, 610045, Sichuan, China
| | - Qin Deng
- Department of Medical Genetics and Prenatal Diagnosis, Sichuan Provincial Maternity and Child Health Care Hospital, Chengdu, 610045, Sichuan, China
| | - Xueyan Wang
- Department of Medical Genetics and Prenatal Diagnosis, Sichuan Provincial Maternity and Child Health Care Hospital, Chengdu, 610045, Sichuan, China
| | - Zhuo Zhang
- Department of Medical Genetics and Prenatal Diagnosis, Sichuan Provincial Maternity and Child Health Care Hospital, Chengdu, 610045, Sichuan, China
| | - Dangying Yi
- Department of Medical Genetics and Prenatal Diagnosis, Sichuan Provincial Maternity and Child Health Care Hospital, Chengdu, 610045, Sichuan, China
| | - Yang Wu
- Department of Medical Genetics and Prenatal Diagnosis, Sichuan Provincial Maternity and Child Health Care Hospital, Chengdu, 610045, Sichuan, China
| | - Jesse Li-Ling
- West China Second University Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
- Department of Reproductive Medicine, Sichuan Provincial Maternity and Child Health Care Hospital, Chengdu, 610045, Sichuan, China.
| |
Collapse
|
5
|
Zhang Q, Wang Y, Xu Y, Zhou R, Huang M, Qiao F, Meng L, Liu A, Zhou J, Li L, Ji X, Xu Z, Hu P. Optical genome mapping for detection of chromosomal aberrations in prenatal diagnosis. Acta Obstet Gynecol Scand 2023. [PMID: 37366235 PMCID: PMC10378017 DOI: 10.1111/aogs.14613] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/23/2023] [Accepted: 06/08/2023] [Indexed: 06/28/2023]
Abstract
INTRODUCTION Chromosomal aberrations are the most important etiological factors for birth defects. Optical genome mapping is a novel cytogenetic tool for detecting a broad range of chromosomal aberrations in a single assay, but relevant clinical feasibility studies of optical genome mapping in prenatal diagnosis are limited. MATERIAL AND METHODS We retrospectively performed optical genome mapping analysis of amniotic fluid samples from 34 fetuses with various clinical indications and chromosomal aberrations detected through standard-of-care technologies, including karyotyping, fluorescence in situ hybridization, and/or chromosomal microarray analysis. RESULTS In total, we analyzed 46 chromosomal aberrations from 34 amniotic fluid samples, including 5 aneuploidies, 10 large copy number variations, 27 microdeletions/microduplications, 2 translocations, 1 isochromosome, and 1 region of homozygosity. Overall, 45 chromosomal aberrations could be confirmed by our customized analysis strategy. Optical genome mapping reached 97.8% concordant clinical diagnosis with standard-of-care methods for all chromosomal aberrations in a blinded fashion. Compared with the widely used chromosomal microarray analysis, optical genome mapping additionally determined the relative orientation and position of repetitive segments for seven cases with duplications or triplications. The additional information provided by optical genome mapping will be conducive to characterizing complex chromosomal rearrangements and allowing us to propose mechanisms to explain rearrangements and predict the genetic recurrence risk. CONCLUSIONS Our study highlights that optical genome mapping can provide comprehensive and accurate information on chromosomal aberrations in a single test, suggesting that optical genome mapping has the potential to become a promising cytogenetic tool for prenatal diagnosis.
Collapse
Affiliation(s)
- Qinxin Zhang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Yan Wang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Yiyun Xu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Ran Zhou
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Mingtao Huang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Fengchang Qiao
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Lulu Meng
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - An Liu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Jing Zhou
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Li Li
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Xiuqing Ji
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Zhengfeng Xu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Ping Hu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| |
Collapse
|
6
|
McNeill A. 2022: the year that was in the European Journal of Human Genetics. Eur J Hum Genet 2023; 31:131-133. [PMID: 36750730 PMCID: PMC9905485 DOI: 10.1038/s41431-023-01283-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Affiliation(s)
- Alisdair McNeill
- Department of Neuroscience, The University of Sheffield, Sheffield, UK.
- Sheffield Clinical Genetics Department, Sheffield Children's Hospital NHS Foundation Trust, Sheffield, UK.
| |
Collapse
|
7
|
Dai X, Shen L. Advances and Trends in Omics Technology Development. Front Med (Lausanne) 2022; 9:911861. [PMID: 35860739 PMCID: PMC9289742 DOI: 10.3389/fmed.2022.911861] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/09/2022] [Indexed: 12/11/2022] Open
Abstract
The human history has witnessed the rapid development of technologies such as high-throughput sequencing and mass spectrometry that led to the concept of “omics” and methodological advancement in systematically interrogating a cellular system. Yet, the ever-growing types of molecules and regulatory mechanisms being discovered have been persistently transforming our understandings on the cellular machinery. This renders cell omics seemingly, like the universe, expand with no limit and our goal toward the complete harness of the cellular system merely impossible. Therefore, it is imperative to review what has been done and is being done to predict what can be done toward the translation of omics information to disease control with minimal cell perturbation. With a focus on the “four big omics,” i.e., genomics, transcriptomics, proteomics, metabolomics, we delineate hierarchies of these omics together with their epiomics and interactomics, and review technologies developed for interrogation. We predict, among others, redoxomics as an emerging omics layer that views cell decision toward the physiological or pathological state as a fine-tuned redox balance.
Collapse
|
8
|
McNeill A. What's new in genetics in June 2022? Eur J Hum Genet 2022; 30:633-634. [PMID: 35676534 DOI: 10.1038/s41431-022-01122-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Alisdair McNeill
- Department of Neuroscience, The University of Sheffield, Sheffield, UK. .,Sheffield Clinical Genetics Department, Sheffield Children's Hospital NHS Foundation Trust, Sheffield, UK.
| |
Collapse
|