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Fu X, Shi Y, Ma J, Zhang K, Wang G, Li G, Xiao L, Wang H. Advances of multiplex ligation-dependent probe amplification technology in molecular diagnostics. Biotechniques 2022; 73:205-213. [PMID: 36309987 DOI: 10.2144/btn-2022-0017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Multiplex ligation-dependent probe amplification (MLPA) is a multiplex copy number analysis tool which is routinely used to detect large mutations in genetic diseases. With continuous modifications, MLPA has been extended for the detection of DNA methylation variation, single nucleotide polymorphisms, chromosome abnormalities and other forms of genomic variation. The combination with other techniques has even enlarged the application of MLPA in molecular diagnostics of various human diseases. In this review, the principle of MLPA-based techniques as well as their main and latest applications in clinical detection are described. It is believed that with improved automation, increased multiplexing, lower cost and the combination with other technologies, MLPA will play an increasingly important role in molecular diagnosis of human disease.
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Affiliation(s)
- Xiaoni Fu
- The National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Yinmin Shi
- The National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Jiying Ma
- The National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Kaiqian Zhang
- The National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Guowei Wang
- The National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Gang Li
- The National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Lei Xiao
- The National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Huijuan Wang
- The National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University, Xi'an, Shaanxi, 710069, China
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Zhang S, Xu L, Yu M, Zhang J. Hypomethylation of the DAZ3 promoter in idiopathic asthenospermia: a screening tool for liquid biopsy. Sci Rep 2020; 10:17996. [PMID: 33093613 PMCID: PMC7581813 DOI: 10.1038/s41598-020-75110-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 10/08/2020] [Indexed: 11/27/2022] Open
Abstract
Given the role of the deleted in azoospermia gene in male infertility, whether the somatic deleted in azoospermia methylation status is associated with idiopathic asthenospermia should be determined. To investigate the methylation levels of the deleted in azoospermia promoter in peripheral white blood cells from idiopathic asthenospermia patients relative to those in normozoospermia controls, 61 ethylene diamine tetraacetic acid anticoagulant blood samples were drawn from all participants for DNA isolation. The deleted in azoospermia promoter methylation ratio was detected by MassARRAY-based methylation quantification and confirmed by quantitative methylation-specific polymerase chain reaction. A MassARRAY-based methylation analysis showed that the deleted in azoospermia 3 promoter (0 to − 2 kbp) was significantly hypomethylated in peripheral white blood cells from idiopathic asthenospermia males, specifically one CpG site (− 246 to − 247). Quantitative methylation-specific polymerase chain reaction data further confirmed that the methylation level of the deleted in azoospermia 3 promoter region in idiopathic asthenospermia patients was significantly lower than that in normozoospermia males. The area under the receiver operating characteristic curve determined by quantitative methylation-specific polymerase chain reaction was 0.737 (95% confidence interval: 0.552 to 0.924), with a sensitivity of 53.9% and a specificity of 88.2% at a cut-off level of 74.7%. Therefore, our results suggested that methylation ratio detection of the deleted in azoospermia 3 promoter region by real-time polymerase chain reaction assay is a promising and feasible tool for liquid biopsy in the clinical laboratories. The methylation status of other reported infertility-related genes should also be investigated in peripheral white blood cells.
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Affiliation(s)
- Shichang Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Li Xu
- Department of Clinical Nutrition, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Mengyao Yu
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Jiexin Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China.
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Wen L, Liu Q, Xu J, Liu X, Shi C, Yang Z, Zhang Y, Xu H, Liu J, Yang H, Huang H, Qiao J, Tang F, Chen ZJ. Recent advances in mammalian reproductive biology. SCIENCE CHINA. LIFE SCIENCES 2020; 63:18-58. [PMID: 31813094 DOI: 10.1007/s11427-019-1572-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 10/22/2019] [Indexed: 01/05/2023]
Abstract
Reproductive biology is a uniquely important topic since it is about germ cells, which are central for transmitting genetic information from generation to generation. In this review, we discuss recent advances in mammalian germ cell development, including preimplantation development, fetal germ cell development and postnatal development of oocytes and sperm. We also discuss the etiologies of female and male infertility and describe the emerging technologies for studying reproductive biology such as gene editing and single-cell technologies.
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Affiliation(s)
- Lu Wen
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology Third Hospital, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Qiang Liu
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology Third Hospital, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Jingjing Xu
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China
| | - Xixi Liu
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology Third Hospital, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Chaoyi Shi
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China
| | - Zuwei Yang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China
| | - Yili Zhang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China
| | - Hong Xu
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China
| | - Jiang Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Hui Yang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Hefeng Huang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China.
| | - Jie Qiao
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology Third Hospital, College of Life Sciences, Peking University, Beijing, 100871, China.
| | - Fuchou Tang
- Beijing Advanced Innovation Center for Genomics, Department of Obstetrics and Gynecology Third Hospital, College of Life Sciences, Peking University, Beijing, 100871, China.
| | - Zi-Jiang Chen
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Jinan, 250021, China.
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Netherton J, Ogle R, Hetherington L, Velkov T, Rose R, Baker M. DNA variants are an unlikely explanation for the changing quality of spermatozoa within the same individual. HUM FERTIL 2019; 24:376-388. [PMID: 31642381 DOI: 10.1080/14647273.2019.1679397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
It has recently been suggested that the human sperm genome is highly unstable, which may be a reasonable explanation as to why men, even fertile men, produce defective spermatozoa. Furthermore, an unstable genome may also explain why the semen profile of the same man changes from one ejaculate to the next. As such, we took multiple ejaculates (between 3 and 6) from 7 individuals over a 6-month period and isolated sperm through density gradients. We then compared the DNA of: (i) good and poor-quality spermatozoa within the same ejaculate; and (ii) from multiple ejaculates from the same individual. Our results suggest that on a global level, DNA present within spermatozoa is actually quite stable and similar between both good and poor sperm. This is important information for the assisted reproductive community when it comes to sperm selection.
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Affiliation(s)
- Jacob Netherton
- Department of Environmental and Life Sciences, University of Newcastle , Callaghan , New South Wales , Australia
| | - Rachel Ogle
- Department of Environmental and Life Sciences, University of Newcastle , Callaghan , New South Wales , Australia
| | - Louise Hetherington
- Department of Environmental and Life Sciences, University of Newcastle , Callaghan , New South Wales , Australia
| | - Tony Velkov
- Department of Pharmacology & Therapeutics, School of Biomedical Sciences, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne , Victoria , Australia
| | - Ryan Rose
- Fertility SA, St. Andrews Hospital , Adelaide , South Australia , Australia.,Adelaide Health and Medical Sciences, Robinson Research Institute, The University of Adelaide , Adelaide , South Australia , Australia
| | - Mark Baker
- Department of Environmental and Life Sciences, University of Newcastle , Callaghan , New South Wales , Australia
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New insights into the genetics of spermatogenic failure: a review of the literature. Hum Genet 2019; 138:125-140. [PMID: 30656449 DOI: 10.1007/s00439-019-01974-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 01/09/2019] [Indexed: 12/23/2022]
Abstract
Genetic anomalies are known to affect about 15% of infertile patients with azoospermia or severe oligozoospermia. Despite a throughout diagnostic work-up, in up to the 72% of the male partners of infertile couples, no etiological factor can be found; hence, the cause of infertility remains unclear. Recently, several novel genetic causes of spermatogenic failure (SPGF) have been described. The aim of this review was to collect all the available evidence of SPGF genetics, matching data from in-vitro and animal models with those in human beings to provide a comprehensive and updated overview of the genes capable of affecting spermatogenesis. By reviewing the literature, we provided a list of 60 candidate genes for SPGF. Their investigation by Next Generation Sequencing in large cohorts of patients with apparently idiopathic infertility would provide new interesting data about their racial- and ethnic-related prevalence in infertile patients, likely raising the diagnostic yields. We propose a phenotype-based approach to identify the genes to look for.
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Colaco S, Modi D. Genetics of the human Y chromosome and its association with male infertility. Reprod Biol Endocrinol 2018; 16:14. [PMID: 29454353 PMCID: PMC5816366 DOI: 10.1186/s12958-018-0330-5] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 02/06/2018] [Indexed: 12/12/2022] Open
Abstract
The human Y chromosome harbors genes that are responsible for testis development and also for initiation and maintenance of spermatogenesis in adulthood. The long arm of the Y chromosome (Yq) contains many ampliconic and palindromic sequences making it predisposed to self-recombination during spermatogenesis and hence susceptible to intra-chromosomal deletions. Such deletions lead to copy number variation in genes of the Y chromosome resulting in male infertility. Three common Yq deletions that recur in infertile males are termed as AZF (Azoospermia Factor) microdeletions viz. AZFa, AZFb and AZFc. As estimated from data of nearly 40,000 Y chromosomes, the global prevalence of Yq microdeletions is 7.5% in infertile males; however the European infertile men are less susceptible to Yq microdeletions, the highest prevalence is in Americans and East Asian infertile men. In addition, partial deletions of the AZFc locus have been associated with infertility but the effect seems to be ethnicity dependent. Analysis of > 17,000 Y chromosomes from fertile and infertile men has revealed an association of gr/gr deletion with male infertility in Caucasians and Mongolian men, while the b2/b3 deletion is associated with male infertility in African and Dravidian men. Clinically, the screening for Yq microdeletions would aid the clinician in determining the cause of male infertility and decide a rational management strategy for the patient. As these deletions are transmitted to 100% of male offspring born through assisted reproduction, testing of Yq deletions will allow the couples to make an informed choice regarding the perpetuation of male infertility in future generations. With the emerging data on association of Yq deletions with testicular cancers and neuropsychiatric conditions long term follow-up data is urgently needed for infertile men harboring Yq deletions. If found so, the information will change the current the perspective of androgenetics from infertility and might have broad implication in men health.
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Affiliation(s)
- Stacy Colaco
- Department of Molecular and Cellular Biology, ICMR-National Institute for Research in Reproductive Health, JM Street, Parel, Mumbai, Maharashtra, 400012, India
| | - Deepak Modi
- Department of Molecular and Cellular Biology, ICMR-National Institute for Research in Reproductive Health, JM Street, Parel, Mumbai, Maharashtra, 400012, India.
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Zonozi F, Mozdarani H, Salimi M, Mozdarani S, Fallahi P, Mozdarani S, Heidari Z. High frequency of microdeletion in TTY2 gene family in peripheral blood leukocytes of non-obstructive azoospermia patients. AIMS GENETICS 2017; 4:202-212. [PMID: 31435509 PMCID: PMC6690235 DOI: 10.3934/genet.2017.4.202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Accepted: 11/22/2017] [Indexed: 11/18/2022]
Abstract
About 10-15% of non-obstructive azoospermia (NOA) patients show AZFc microdeletion in their blood leukocytes. However, if AZF genes were involved in impaired spermatogenesis, a higher frequency of chromosomal microdeletions was expected. In this study the frequency of AZFc microdeletion was compared with TTY2 gene family, i.e., TTY2A2A and TTY2A12A in blood leukocytes of NOA patients and normal fertile control. In the present study 30 normal fertile individuals with mean age of 35.0 ± 6.0 and 30 NOA patients with mean age of 34.0 ± 7.0 were screened for microdeletion of TTY2L2A and TTY2L12A at Yq11 and Yp11 respectively and sequence-tagged site (STS) markers for AZFc gene using multiplex PCR technique. At the first step karyotyping was done for all subjects using standard G-banding technique to identify patients with normal karyotype as well as non-affected normal controls for molecular analysis. Results showed no AZFc microdeletion in normal and NAO patients whereas one TTY2L2A microdeletion in normal control (3.3%) and 4 in NOA (13.3%) was observed (p < 0.05). However our data indicated that 6 of 30 NOA patients (20%) showed TTY2L12A microdeletion whereas there was no observed microdeletion in normal control (p < 0.01). Results indicate that the studied genes might be involved in impaired spermatogenesis more effective than the routinely screened AZF genes in infertile men. Therefore, screening these genes along with AZF genes might be valuable for infertile patients. The reason why these genes are deleted from Y chromosome is not known but might be associated with genomic instability induced by environmental physico-chemical genotoxic agents.
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Affiliation(s)
- Farideh Zonozi
- Department of Genetics, Islamic Azad University, Damghan Branch, Damghan, Iran
| | - Hossein Mozdarani
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mahdieh Salimi
- Department of Medical Genetics, Medical Biotechnology Institute, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Sohail Mozdarani
- Cytogenome Medical Genetics Laboratory, Chamran Medical Building, Ale-Ahmad Highway, Tehran, Iran
| | | | - Sahar Mozdarani
- Cytogenome Medical Genetics Laboratory, Chamran Medical Building, Ale-Ahmad Highway, Tehran, Iran
| | - Zahra Heidari
- Cytogenome Medical Genetics Laboratory, Chamran Medical Building, Ale-Ahmad Highway, Tehran, Iran
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