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Yang C, Li T, Dong Q, Zhao Y. Chromosome classification via deep learning and its application to patients with structural abnormalities of chromosomes. Med Eng Phys 2023; 121:104064. [PMID: 37985030 DOI: 10.1016/j.medengphy.2023.104064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 09/18/2023] [Accepted: 10/16/2023] [Indexed: 11/22/2023]
Abstract
BACKGROUND AND OBJECTIVE Karyotyping is an important technique in cytogenetic practice for the early diagnosis of genetic diseases. Clinical karyotyping is tedious, time-consuming, and error-prone. The objective of our study was to develop a single-stage deep convolutional neural networks (DCNN)-based model to automatically classify normal and abnormal chromosomes in an end-to-end manner. METHODS We analyzed 2,424 normal chromosomes and 544 abnormal chromosomes. A preliminary support vector machine (SVM) model was developed to evaluate the basic recognition performance on the dataset. A DCNN-based model was then proposed to process the same dataset. RESULTS By utilizing the SVM model, the classification accuracy of 24 normal chromosomes was 86.01 %. The 32 types of normal and abnormal chromosomes got an accuracy of 85.37 %. The accuracy of the DCNN-based model performing the 24 normal chromosomal classification was 91.75 %. The accuracy of the 32 type classification was 87.76 %. To differentiate eight common structural abnormalities, we obtained accuracies that ranged from 90.84 % to 100 %, and the values of the AUC ranged from 91.81 % to 100 %. CONCLUSIONS Our proposed DCNN-based model effectively performed the karyotype classification in an end-to-end manner. It had the competence to be used as a prediction tool for abnormal karyotype detection and screening in genetic diagnosis without initial feature extraction. We believe our work is meaningful for genetic triage management to lower the cost in clinical practice.
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Affiliation(s)
- Chuan Yang
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang 110004, China; Department of Cardiology, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Tingting Li
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Qiulei Dong
- State Key Laboratory of Multimodal Artificial Intelligence Systems, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China; School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing 100049, China; Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Yanyan Zhao
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang 110004, China.
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Abstract
During the last few years a new generation of preimplantation genetic screening (PGS) has been introduced. In this paper, an overview of the different aspects of this so-called PGS 2.0 with respect to the why (what are the indications), the when (which developmental stage, i.e. which material should be studied) and the how (which molecular technique should be used) is given. With respect to the aims it is clear that PGS 2.0 can be used for a variety of indications. However, the beneficial effect of PGS 2.0 has not been proved yet in RCTs. It is clear that cleavage stage is not the optimal stage for biopsy. Almost all advocates of PGS 2.0 prefer trophectoderm biopsy. There are many new methods that allow the study of complete aneuploidy with respect to one or more of the 24 chromosomes. Because of the improved vitrification methods, selection of fresh embryos for transfer is more and more often replaced by frozen embryo transfer. The main goal of PGS has always been the improvement of IVF success. However, success is defined by different authors in many different ways. This makes it very difficult to compare the outcomes of different studies. In conclusion, the introduction of PGS 2.0 will depend on the success of the new biopsy strategies in combination with the analysis of all 24 chromosomes. It remains to be seen which approach will be the most successful and for which specific groups of patients.
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Affiliation(s)
- Joep Geraedts
- GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Karen Sermon
- Research Group Reproduction and Genetics, Vrije Universiteit Brussel, Laarbeeklaan 101, Brussels 1090, Belgium
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Ruttanajit T, Chanchamroen S, Cram DS, Sawakwongpra K, Suksalak W, Leng X, Fan J, Wang L, Yao Y, Quangkananurug W. Detection and quantitation of chromosomal mosaicism in human blastocysts using copy number variation sequencing. Prenat Diagn 2016; 36:154-62. [PMID: 26676536 DOI: 10.1002/pd.4759] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 10/30/2015] [Accepted: 12/10/2015] [Indexed: 12/27/2022]
Abstract
OBJECTIVE Currently, our understanding of the nature and reproductive potential of blastocysts associated with trophectoderm (TE) lineage chromosomal mosaicism is limited. The objective of this study was to first validate copy number variation sequencing (CNV-Seq) for measuring the level of mosaicism and second, examine the nature and level of mosaicism in TE biopsies of patient's blastocysts. METHOD TE biopy samples were analysed by array comparative genomic hybridization (CGH) and CNV-Seq to discriminate between euploid, aneuploid and mosaic blastocysts. RESULTS Using artificial models of TE mosaicism for five different chromosomes, CNV-Seq accurately and reproducibly quantitated mosaicism at levels of 50% and 20%. In a comparative 24-chromosome study of 49 blastocysts by array CGH and CNV-Seq, 43 blastocysts (87.8%) had a concordant diagnosis and 6 blastocysts (12.2%) were discordant. The discordance was attributed to low to medium levels of chromosomal mosaicism (30-70%) not detected by array CGH. In an expanded study of 399 blastocysts using CNV-Seq as the sole diagnostic method, the proportion of diploid-aneuploid mosaics (34, 8.5%) was significantly higher than aneuploid mosaics (18, 4.5%) (p < 0.02). CONCLUSION Mosaicism is a significant chromosomal abnormality associated with the TE lineage of human blastocysts that can be reliably and accurately detected by CNV-Seq.
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Affiliation(s)
| | | | - David S Cram
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Australia.,Berry Genomics, C., Limited, Beijing, China
| | | | | | - Xue Leng
- Berry Genomics, C., Limited, Beijing, China
| | - Junmei Fan
- Department of Obstetrics and Gynecology, PLA General Hospital, Beijing, China
| | - Li Wang
- Department of Obstetrics and Gynecology, PLA General Hospital, Beijing, China
| | - Yuanqing Yao
- Department of Obstetrics and Gynecology, PLA General Hospital, Beijing, China
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Sueoka K. Preimplantation genetic diagnosis: an update on current technologies and ethical considerations. Reprod Med Biol 2016; 15:69-75. [PMID: 29259423 DOI: 10.1007/s12522-015-0224-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 09/15/2015] [Indexed: 10/22/2022] Open
Abstract
The aim of reproductive medicine is to support the birth of healthy children. Advances in assisted reproductive technologies and genetic analysis have led to the introduction of preimplantation genetic diagnosis (PGD) for embryos. Indications for PGD have been a major topic in the fields of ethics and law. Concerns vary by nation, religion, population, and segment, and the continued rapid development of new technologies. In contrast to the ethical augment, technology has been developing at an excessively rapid speed. The most significant recent technological development provides the ability to perform whole genome amplification and sequencing of single embryonic cells by microarray or next-generation sequencing methods. As new affordable technologies are introduced, patients are presented with a growing variety of PGD options. Simultaneously, the ethical guidelines for the indications for testing and handling of genetic information must also rapidly correspond to the changes.
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Kaarouch I, Bouamoud N, Louanjli N, Madkour A, Copin H, Benkhalifa M, Sefrioui O. Impact of sperm genome decay on Day-3 embryo chromosomal abnormalities from advanced-maternal-age patients. Mol Reprod Dev 2015; 82:809-19. [PMID: 26191648 DOI: 10.1002/mrd.22526] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 07/17/2015] [Indexed: 01/06/2023]
Abstract
Infertile male patients often exhibit unconventional semen parameters, including DNA fragmentation, chromatin dispersion, and aneuploidy-collectively referred to as sperm genome decay (SGD). We investigated the correlation of SGD to embryo chromosomal abnormalities and its effect on clinical pregnancy rates in patients with advanced maternal age (AMA) (>40 years) who were undergoing intracytoplasmic sperm injection-preimplantation genetic screening (ICSI-PGS). Three groups were assessed: patients with AMA and male partners with normal sperm (AMA-N); AMA patients and male partners presenting with SGD (AMA-SGD); and young fertile female patients and male partners with SGD (Y-SGD). We found a significant increase in embryonic chromosomal abnormalities-polyploidy, nullisomy, mosaicism, and chaotic anomaly rates-when semen parameters are altered (76% vs. 67% and 66% in AMA-SGD vs. AMA-N and Y-SGD groups, respectively). Statistical analysis showed a correlation between SGD and aneuploidies of embryonic chromosomes 13, 16, 21, X, and Y, as well as negative clinical outcomes. Incorporation of molecular sperm analyses should therefore significantly minimize the risk of transmission of chromosomal anomalies from spermatozoa to embryos, and may provide better predictors of pregnancy than conventional sperm analyses. We also demonstrated that an ICSI-PGS program should be implemented for SGD patients in order to limit transmission of chromosomal paternal anomalies and to improve clinical outcome.
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Affiliation(s)
- Ismail Kaarouch
- Biochemistry and Immunology Laboratory, Mohammed V University, Faculty of Sciences, BP 1014, Avenue Ibn Batouta Agdal, Rabat, Morocco
| | - Nouzha Bouamoud
- Biochemistry and Immunology Laboratory, Mohammed V University, Faculty of Sciences, BP 1014, Avenue Ibn Batouta Agdal, Rabat, Morocco
| | - Noureddine Louanjli
- Labomac IVF Centers and Clinical Laboratory Medicine, Anfa Fertility Center, Privante Clinic of Human Reproduction and Endoscopic Surgery, Casablanca, Morocco
| | - Aicha Madkour
- Biochemistry and Immunology Laboratory, Mohammed V University, Faculty of Sciences, BP 1014, Avenue Ibn Batouta Agdal, Rabat, Morocco
| | - Henri Copin
- Reproductive Biology and Medical Cytogenetics Laboratory, Regional University Hospital & School of Medicine. Picardie University Jules Verne, Amiens, France
| | - Moncef Benkhalifa
- Reproductive Biology and Medical Cytogenetics Laboratory, Regional University Hospital & School of Medicine. Picardie University Jules Verne, Amiens, France
| | - Omar Sefrioui
- Anfa Fertility Center, Privante Clinic of Human Reproduction and Endoscopic Surgery, Casablanca, Morocco
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Abstract
Human reproduction is remarkably inefficient; nearly 70% of human conceptions do not survive to live birth. Spontaneous fetal aneuploidy is the most common cause for spontaneous loss, particularly in the first trimester of pregnancy. Although losses owing to de novo fetal aneuploidy occur at similar frequencies among women with sporadic and recurrent losses, some couples with recurrent pregnancy loss have additional associated genetic factors and some have nongenetic etiologies. Genetic testing of the products of conception from couples experiencing two or more losses may aid in defining the underlying etiology and in counseling patients about prognosis in a subsequent pregnancy. Parental karyotyping of couples who have experienced recurrent pregnancy loss (RPL) will detect some couples with an increased likelihood of recurrent fetal aneuploidy; this may direct interventions. The utility of preimplantation genetic analysis in couples with RPL is unproven, but new approaches to this testing show great promise.
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Affiliation(s)
- Kassie J Hyde
- University of Missouri School of Medicine, Columbia, Missouri 65201
| | - Danny J Schust
- Department of Obstetrics, Gynecology and Women's Health, University of Missouri School of Medicine, Columbia, Missouri 65201
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