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He Q, Zhang Y, Song M, Zhou Y, Lin D, Ma Y, Sun F, Li Q. Detection of AZF microdeletions and analysis of reproductive hormonal profiles in Hainan men undergoing assisted reproductive technology. BMC Urol 2024; 24:123. [PMID: 38867229 PMCID: PMC11167749 DOI: 10.1186/s12894-024-01503-x] [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: 11/21/2023] [Accepted: 05/28/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND Male infertility has become a global health problem, and genetic factors are one of the essential causes. Y chromosome microdeletion is the leading genetic factor cause of male infertility. The objective of this study is to investigate the correlation between male infertility and Y chromosome microdeletions in Hainan, the sole tropical island province of China. METHODS We analyzed the semen of 897 infertile men from Hainan in this study. Semen analysis was measured according to WHO criteria by professionals at the Department of Reproductive Medicine, the First Affiliated Hospital of Hainan Medical University, where samples were collected. Y chromosome AZF microdeletions were confirmed by detecting six STS markers using multiple polymerase chain reactions on peripheral blood DNA. The levels of reproductive hormones, including FSH, LH, PRL, T, and E2, were quantified using the enzyme-linked immunosorbent assay (ELISA). RESULTS The incidence of Y chromosome microdeletion in Hainan infertile men was 7.13%. The occurrence rate of Y chromosome microdeletion was 6.69% (34/508) in the oligozoospermia group and 7.71% (30/389) in the azoospermia group. The deletion of various types in the AZF subregion was observed in the group with azoospermia, whereas no AZFb deletion was detected in the oligozoospermia group. Among all patients with microdeletions, the deletion rate of the AZFc region was the higher at 68.75% (44 out of 64), followed by a deletion rate of 6.25% (4 out of 64) for the AZFa region and a deletion rate of 4.69% (3 out of 64) for the AZFb region. The deletion rate of the AZFa region was significantly higher in patients with azoospermia than in patients with oligozoospermia (0.51% vs. 0.39%, p < 0.001). In comparison, the deletion rate of the AZFc region was significantly higher in patients with oligozoospermia (3.08% vs. 6.30%, p < 0.001). Additionally, the AZFb + c subregion association deletion was observed in the highest proportion among all patients (0.89%, 8/897), followed by AZFa + b + c deletion (0.56%, 5/897), and exclusively occurred in patients with azoospermia. Hormone analysis revealed FSH (21.63 ± 2.01 U/L vs. 10.15 ± 0.96 U/L, p = 0.001), LH (8.96 ± 0.90 U/L vs. 4.58 ± 0.42 U/L, p < 0.001) and PRL (263.45 ± 21.84 mIU/L vs. 170.76 ± 17.10 mIU/L, p = 0.002) were significantly increased in azoospermia patients with microdeletions. Still, P and E2 levels were not significantly different between the two groups. CONCLUSIONS The incidence of AZF microdeletion can reach 7.13% in infertile men in Hainan province, and the deletion of the AZFc subregion is the highest. Although the Y chromosome microdeletion rate is distinct in different regions or populations, the regions mentioned above of the Y chromosome may serve an indispensable role in regulating spermatogenesis. The analysis of Y chromosome microdeletion plays a crucial role in the clinical assessment and diagnosis of male infertility.
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Affiliation(s)
- Qina He
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Hainan Provincial Clinical Research Center for Thalassemia, the Key Laboratory of Tropical Translational Medicine of Ministry of Education, Department of Reproductive Medicine, the First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, Hainan, 571101, China
- Haikou Key Laboratory for Preservation of Human Genetic Resource, the First Affiliated Hospital of Hainan Medical University, Haikou, Hainan, 571101, China
| | - Yongle Zhang
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Hainan Provincial Clinical Research Center for Thalassemia, the Key Laboratory of Tropical Translational Medicine of Ministry of Education, Department of Reproductive Medicine, the First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, Hainan, 571101, China
- Haikou Key Laboratory for Preservation of Human Genetic Resource, the First Affiliated Hospital of Hainan Medical University, Haikou, Hainan, 571101, China
| | - Mengyi Song
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Hainan Provincial Clinical Research Center for Thalassemia, the Key Laboratory of Tropical Translational Medicine of Ministry of Education, Department of Reproductive Medicine, the First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, Hainan, 571101, China
- Haikou Key Laboratory for Preservation of Human Genetic Resource, the First Affiliated Hospital of Hainan Medical University, Haikou, Hainan, 571101, China
| | - Yao Zhou
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Hainan Provincial Clinical Research Center for Thalassemia, the Key Laboratory of Tropical Translational Medicine of Ministry of Education, Department of Reproductive Medicine, the First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, Hainan, 571101, China
- Haikou Key Laboratory for Preservation of Human Genetic Resource, the First Affiliated Hospital of Hainan Medical University, Haikou, Hainan, 571101, China
| | - Dan Lin
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Hainan Provincial Clinical Research Center for Thalassemia, the Key Laboratory of Tropical Translational Medicine of Ministry of Education, Department of Reproductive Medicine, the First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, Hainan, 571101, China
- Haikou Key Laboratory for Preservation of Human Genetic Resource, the First Affiliated Hospital of Hainan Medical University, Haikou, Hainan, 571101, China
| | - Yanlin Ma
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Hainan Provincial Clinical Research Center for Thalassemia, the Key Laboratory of Tropical Translational Medicine of Ministry of Education, Department of Reproductive Medicine, the First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, Hainan, 571101, China.
- Haikou Key Laboratory for Preservation of Human Genetic Resource, the First Affiliated Hospital of Hainan Medical University, Haikou, Hainan, 571101, China.
| | - Fei Sun
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Hainan Provincial Clinical Research Center for Thalassemia, the Key Laboratory of Tropical Translational Medicine of Ministry of Education, Department of Reproductive Medicine, the First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, Hainan, 571101, China.
- Haikou Key Laboratory for Preservation of Human Genetic Resource, the First Affiliated Hospital of Hainan Medical University, Haikou, Hainan, 571101, China.
- Department of Obstetrics and Gynecology, Reproductive Medicine, Nanfang Hospital, Southern Medical University, Guangdong, 510515, China.
| | - Qi Li
- Hainan Provincial Key Laboratory for Human Reproductive Medicine and Genetic Research, Hainan Provincial Clinical Research Center for Thalassemia, the Key Laboratory of Tropical Translational Medicine of Ministry of Education, Department of Reproductive Medicine, the First Affiliated Hospital of Hainan Medical University, Hainan Medical University, Haikou, Hainan, 571101, China.
- Haikou Key Laboratory for Preservation of Human Genetic Resource, the First Affiliated Hospital of Hainan Medical University, Haikou, Hainan, 571101, China.
- Hainan Modern Women and Children's Hospital, Reproductive Medicine, Haikou, Hainan, 571101, China.
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Xu Y, Pang Q. Repetitive DNA Sequences in the Human Y Chromosome and Male Infertility. Front Cell Dev Biol 2022; 10:831338. [PMID: 35912115 PMCID: PMC9326358 DOI: 10.3389/fcell.2022.831338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/24/2022] [Indexed: 11/13/2022] Open
Abstract
The male-specific Y chromosome, which is well known for its diverse and complex repetitive sequences, has different sizes, genome structures, contents and evolutionary trajectories from other chromosomes and is of great significance for testis development and function. The large number of repetitive sequences and palindrome structure of the Y chromosome play an important role in maintaining the stability of male sex determining genes, although they can also cause non-allelic homologous recombination within the chromosome. Deletion of certain Y chromosome sequences will lead to spermatogenesis disorders and male infertility. And Y chromosome genes are also involved in the occurrence of reproductive system cancers and can increase the susceptibility of other tumors. In addition, the Y chromosome has very special value in the personal identification and parentage testing of male-related cases in forensic medicine because of its unique paternal genetic characteristics. In view of the extremely high frequency and complexity of gene rearrangements and the limitations of sequencing technology, the analysis of Y chromosome sequences and the study of Y-gene function still have many unsolved problems. This article will introduce the structure and repetitive sequence of the Y chromosome, summarize the correlation between Y chromosome various sequence deletions and male infertility for understanding the repetitive sequence of Y chromosome more systematically, in order to provide research motivation for further explore of the molecules mechanism of Y-deletion and male infertility and theoretical foundations for the transformation of basic research into applications in clinical medicine and forensic medicine.
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Affiliation(s)
- Yong Xu
- Department of Emergency Surgery, Jining NO 1 People’s Hospital, Jining, China
| | - Qianqian Pang
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Jining, China
- *Correspondence: Qianqian Pang,
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S Al-Ouqaili MT, Al-Ani SK, Alaany R, Al-Qaisi MN. Detection of partial and/or complete Y chromosome microdeletions of azoospermia factor a (AZFa) sub-region in infertile Iraqi patients with azoospermia and severe oligozoospermia. J Clin Lab Anal 2022; 36:e24272. [PMID: 35122324 PMCID: PMC8906023 DOI: 10.1002/jcla.24272] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/23/2022] [Accepted: 01/24/2022] [Indexed: 12/08/2022] Open
Abstract
BACKGROUND This study aimed to analyze the incidence of azoospermia factor a (AZFa) microdeletions in the Y chromosome and their association with male infertility in a population with azoospermia and severe oligozoospermia from Iraq. METHODS A total of 75 infertile Iraqi males and 25 healthy controls were included in this study. The semen analysis was performed to determine the azoospermia, severe oligozoospermia, or normal cases. The AZFa microdeletions were investigated using the real-time polymerase chain reaction (real-time PCR). Then, AZFa sub-region deletions were investigated by a conventional PCR. RESULTS In total, 40 men with azoospermia and 35 men with severe oligozoospermia were selected. Out of 75 infertile males, 46 (61.3%) individuals had AZFa microdeletions, of whom 32 (69.6%) had partial deletion, while 14 (30.4%) males had complete deletion using real-time PCR. The frequency of microdeletions was significantly different between the infertile and control group (p-value < 0.00001). The proportion of AZFa microdeletions appeared higher in azoospermia men (72.5%, n = 29/40) than severe oligozoospermia men (48.6%, n = 17/35), but based on the conventional PCR results, only one azoospermia patient (2.2%) was shown to have complete AZFa deletion, while the other 45 patients (97.8%) had partial AZFa deletions. CONCLUSION In this study, the partial AZFa microdeletions were more numerous than complete AZFa deletion. According to our results, the AZFa microdeletions might be associated with male infertility and spermatogenic failure. It is recommended to investigate the AZFa sub-region microdeletions in patients that shown AZFa microdeletions in primary screening.
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Affiliation(s)
- Mushtak T S Al-Ouqaili
- Department of Microbiology, College of Medicine, University of Anbar, Al-Anbar Governorate, Ramadi, Iraq
| | - Sahar K Al-Ani
- Ministry of Health, Al-Anbar Health Office, Al-Anbar Governorate, Ramadi, Iraq
| | - Rehab Alaany
- Ministry of Health, Al-Anbar Health Office, Al-Anbar Governorate, Ramadi, Iraq
| | - Mohammed N Al-Qaisi
- Ministry of Health, Al-Anbar Health Office, Al-Anbar Governorate, Ramadi, Iraq
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Rogers MJ. Y chromosome copy number variation and its effects on fertility and other health factors: a review. Transl Androl Urol 2021; 10:1373-1382. [PMID: 33850773 PMCID: PMC8039628 DOI: 10.21037/tau.2020.04.06] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The Y chromosome is essential for testis development and spermatogenesis. It is a chromosome with the lowest gene density owing to its medium size but paucity of coding genes. The Y chromosome is unique in that the majority of its structure is highly repetitive sequences, with the majority of these limited genes occurring in 9 amplionic sequences throughout the chromosome. The repetitive nature has its benefits as it can be protective against gene loss over many generations, but it can also predispose the Y chromosome to having wide variations of the number of gene copies present in these repeated sequences. This is known as copy number variation. Copy number variation is not unique to the Y chromosome but copy number variation is a well-known cause of male infertility and having effects on spermatogenesis. This is most commonly seen as deletions of the AZF sequences on the Y chromosome. However, there are other implications for copy number variation beyond just the AZF deletions that can affect spermatogenesis and potentially have other health implications. Copy number variations of TSPY1, DAZ, CDY1, RBMY1, the DYZ1 array, along with minor deletions of gr/gr, b1/b3, and b2/b3 have all be implicated in affecting spermatogenesis. UTY copy number variations have been implicated in risk for cardiovascular disease, and other deletions within gr/gr and the AZF sequences have been implicated in cancer and neuropsychiatric diseases. This review sets out to describe the Y chromosome and unique susceptibility to copy number variation and then to examine how this growing body of research impacts spermatogenesis and other health factors.
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Affiliation(s)
- Marc J Rogers
- Department of Urology, Medical University of South Carolina, Charleston, SC, USA
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Y chromosome structural variation in infertile men detected by targeted next-generation sequencing. J Assist Reprod Genet 2021; 38:941-948. [PMID: 33454900 DOI: 10.1007/s10815-020-02031-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 12/08/2020] [Indexed: 01/21/2023] Open
Abstract
PURPOSE To provide a validated method to identify copy number variation (CNV) in regions of the Y chromosome of infertile men by next-generation sequencing (NGS). METHODS Semen analysis was used to determine the quality of semen and diagnose infertility. Deletion of the azoospermia factor (AZF) region in the Y chromosome was detected by a routine sequence-tagged-site PCR (STS-PCR) method. We then used the NGS method to detect CNV in the AZF region, including deletions and duplications. RESULTS A total of 326 samples from male infertility patients, family members, and sperm donors were studied between January 2011 and May 2017. AZF microdeletions were detected in 120 patients by STS-PCR, and these results were consistent with the results from NGS. In addition, of the 160 patients and male family members who had no microdeletions detected by STS-PCR, 51 cases were found to exhibit Y chromosome structural variations by the NGS method (31.88%, 51/160). No microdeletions were found in 46 donors by STS-PCR, but the NGS method revealed 11 of these donors (23.91%, 11/46) carried structural variations, which were mainly in the AZFc region, including partial deletions and duplications. CONCLUSION The established NGS method can replace the conventional STS-PCR method to detect Y chromosome microdeletions. The NGS method can detect CNV, such as partial deletion or duplication, and provide details of the abnormal range and size of variations.
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Punjani N, Kang C, Schlegel PN. Clinical implications of Y chromosome microdeletions among infertile men. Best Pract Res Clin Endocrinol Metab 2020; 34:101471. [PMID: 33214080 DOI: 10.1016/j.beem.2020.101471] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Male factor infertility contributes significantly to couples facing difficulty achieving a pregnancy. Genetic factors, and specifically those related to the Y chromosome, may occur in up to 15% of men with oligozoospermia or azoospermia. A subset of loci within the Y chromosome, known as the azoospermia factors (AZFa, AZFb, and AZFc), have been associated with male infertility. Emerging evidence has demonstrated that microdeletions of at least a subset of these regions may also have impacts on systemic conditions. This review provides a brief review of male infertility and the structure of the Y chromosome, and further highlights the role of Y chromosome microdeletions in male infertility and other systemic disease.
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Affiliation(s)
- Nahid Punjani
- Division of Urology, Weill Cornell Medical College, New York, NY, USA
| | - Caroline Kang
- Division of Urology, Weill Cornell Medical College, New York, NY, USA.
| | - Peter N Schlegel
- Division of Urology, Weill Cornell Medical College, New York, NY, USA.
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7
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Andreassi MG, Borghini A, Vecoli C, Piccaluga E, Guagliumi G, Del Greco M, Gaita F, Picano E. Reproductive outcomes and Y chromosome instability in radiation-exposed male workers in cardiac catheterization laboratory. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:361-368. [PMID: 31605552 DOI: 10.1002/em.22341] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 09/10/2019] [Accepted: 09/18/2019] [Indexed: 06/10/2023]
Abstract
Occupational radiation exposure may impact the reproductive outcome of male workers in the cardiac catheterization laboratory (cath Lab) who receive a dose of ~1-10 mSv/year. An increased copy number variation (CNV) in azoospermia factor region c (AZFc) of the Y chromosome is a marker of spermatogenic failure, previously associated with radiation exposure. This study sought to investigate the association between paternal exposure in the Cath Lab and adverse reproductive outcomes as well as to assess the induction of CNV in the AZFc region. In a case-control study, we enrolled 193 catheterization lab workers (Group I) and 164 age-matched unexposed controls (Group II). Reproductive outcomes were assessed through a structured questionnaire. Two sequence-tagged sites (SY1197 and SY579) in AZFc region were evaluated by qRT-PCR in 83 exposed and 47 unexposed subjects. Exposed workers had a higher prevalence of low birth weight in offspring (Group I = 13% vs. II = 5.3%, P = 0.02; ORadjusted = 2.7; 95% CI: 1.1-6.3; P = 0.02). The mean of CNV (microdeletion and microduplication) for SY1197 was significantly higher in the exposed workers (Group I = 1.53 ± 0.85 vs. Group II = 1.02 ± 0.41; P = 0.0005). Despite the study design limitations, our findings show that chronic occupational radiation exposure of male workers is correlated with higher prevalence of low birth weight in offspring and instability in the Y chromosome AZFc region. Environ. Mol. Mutagen. 61:361-368, 2020. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
| | | | | | | | - Giulio Guagliumi
- Cardiovascular Department, Papa Giovanni XXIII Hospital, Bergamo, Italy
| | | | - Fiorenzo Gaita
- Division of Cardiology, Department of Medical Science, University of Turin, Turin, Italy
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Shi W, Louzada S, Grigorova M, Massaia A, Arciero E, Kibena L, Ge XJ, Chen Y, Ayub Q, Poolamets O, Tyler-Smith C, Punab M, Laan M, Yang F, Hallast P, Xue Y. Evolutionary and functional analysis of RBMY1 gene copy number variation on the human Y chromosome. Hum Mol Genet 2019; 28:2785-2798. [PMID: 31108506 PMCID: PMC6687947 DOI: 10.1093/hmg/ddz101] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/10/2019] [Accepted: 05/11/2019] [Indexed: 01/17/2023] Open
Abstract
Human RBMY1 genes are located in four variable-sized clusters on the Y chromosome, expressed in male germ cells and possibly associated with sperm motility. We have re-investigated the mutational background and evolutionary history of the RBMY1 copy number distribution in worldwide samples and its relevance to sperm parameters in an Estonian cohort of idiopathic male factor infertility subjects. We estimated approximate RBMY1 copy numbers in 1218 1000 Genomes Project phase 3 males from sequencing read-depth, then chose 14 for valid ation by multicolour fibre-FISH. These fibre-FISH samples provided accurate calibration standards for the entire panel and led to detailed insights into population variation and mutational mechanisms. RBMY1 copy number worldwide ranged from 3 to 13 with a mode of 8. The two larger proximal clusters were the most variable, and additional duplications, deletions and inversions were detected. Placing the copy number estimates onto the published Y-SNP-based phylogeny of the same samples suggested a minimum of 562 mutational changes, translating to a mutation rate of 2.20 × 10-3 (95% CI 1.94 × 10-3 to 2.48 × 10-3) per father-to-son Y-transmission, higher than many short tandem repeat (Y-STRs), and showed no evidence for selection for increased or decreased copy number, but possible copy number stabilizing selection. An analysis of RBMY1 copy numbers among 376 infertility subjects failed to replicate a previously reported association with sperm motility and showed no significant effect on sperm count and concentration, serum follicle stimulating hormone (FSH), luteinizing hormone (LH) and testosterone levels or testicular and semen volume. These results provide the first in-depth insights into the structural rearrangements underlying RBMY1 copy number variation across diverse human lineages.
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Affiliation(s)
- Wentao Shi
- Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- Department of Genetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Sandra Louzada
- Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Marina Grigorova
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu 50411, Estonia
| | - Andrea Massaia
- Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- National Heart and Lung Institute, Imperial College London, London SW7 2AZ, UK
| | - Elena Arciero
- Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Laura Kibena
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu 50411, Estonia
| | - Xiangyu Jack Ge
- Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- Faculty of Biology, Medicine and Health, School of Biological Science, Division of Musculoskeletal and Dermatological Science, University of Manchester, Manchester M13 9PL, UK
| | - Yuan Chen
- Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Qasim Ayub
- Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- Monash University Malaysia Genomics Facility, Tropical Medicine and Biology Multidisciplinary Platform, Bandar Sunway, Selangor Darul Ehsan 47500, Malaysia
- School of Science, Monash University Malaysia, Bandar Sunway, Selangor Darul Ehsan 47500, Malaysia
| | - Olev Poolamets
- Andrology Unit, Tartu University Hospital, Tartu 50406, Estonia
| | - Chris Tyler-Smith
- Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Margus Punab
- Andrology Unit, Tartu University Hospital, Tartu 50406, Estonia
| | - Maris Laan
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu 50411, Estonia
| | - Fengtang Yang
- Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Pille Hallast
- Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu 50411, Estonia
| | - Yali Xue
- Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
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Colaco S, Modi D. Consequences of Y chromosome microdeletions beyond male infertility. J Assist Reprod Genet 2019; 36:1329-1337. [PMID: 31214882 DOI: 10.1007/s10815-019-01492-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 05/16/2019] [Indexed: 12/14/2022] Open
Abstract
PURPOSE The human Y chromosome plays a central role in sex determination and spermatogenesis. The azoospermia factor (AZF) loci on the Y chromosome contain genes that were thought to be testis specific with their deletions leading to spermatogenic failure. However, beyond the testis, the AZF genes (mainly those in AZFa and AZFb loci) are widely expressed in multiple tissues. Further, these genes are predicted to play roles in processes such as gene regulation and protein synthesis. These observations suggest that the AZF genes may have functions beyond regulation of fertility. RESULTS Three major areas have emerged where alternations in AZF genes have effects beyond infertility. (1) Poor-quality embryos are generated in assisted reproduction when sperm from men harboring Y chromosome microdeletions are used, (2) a higher preponderance of neuropsychiatry disorders is observed in men with deletions in AZF genes, and (3) copy number variations and altered expression of AZF genes are found in several cancers. CONCLUSION While our data is preliminary and observational in nature, systematic studies are required to address how genetic alterations in the Y chromosome can affect the health of men beyond infertility. This information will provide a different perspective in the area of androgenetics and have implications in devising strategies for maintaining the overall well-being of infertile males.
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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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Teitz LS, Pyntikova T, Skaletsky H, Page DC. Selection Has Countered High Mutability to Preserve the Ancestral Copy Number of Y Chromosome Amplicons in Diverse Human Lineages. Am J Hum Genet 2018; 103:261-275. [PMID: 30075113 DOI: 10.1016/j.ajhg.2018.07.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/10/2018] [Indexed: 02/07/2023] Open
Abstract
Amplicons-large, highly identical segmental duplications-are a prominent feature of mammalian Y chromosomes. Although they encode genes essential for fertility, these amplicons differ vastly between species, and little is known about the selective constraints acting on them. Here, we develop computational tools to detect amplicon copy number with unprecedented accuracy from high-throughput sequencing data. We find that one-sixth (16.9%) of 1,216 males from the 1000 Genomes Project have at least one deleted or duplicated amplicon. However, each amplicon's reference copy number is scrupulously maintained among divergent branches of the Y chromosome phylogeny, including the ancient branch A00, indicating that the reference copy number is ancestral to all modern human Y chromosomes. Using phylogenetic analyses and simulations, we demonstrate that this pattern of variation is incompatible with neutral evolution and instead displays hallmarks of mutation-selection balance. We also observe cases of amplicon rescue, in which deleted amplicons are restored through subsequent duplications. These results indicate that, contrary to the lack of constraint suggested by the differences between species, natural selection has suppressed amplicon copy number variation in diverse human lineages.
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Han H, Zhang X, Zhao X, Xia X, Lei C, Dang R. Eight Y chromosome genes show copy number variations in horses. Arch Anim Breed 2018. [DOI: 10.5194/aab-61-263-2018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract. Copy number variations (CNVs), which represent a significant source of genetic diversity on the Y chromosome in mammals, have been shown to be associated with the development of many complex phenotypes, such as reproduction and male fertility. The occurrence of CNVs has been confirmed on the Y chromosome in horses. However, the copy numbers (CNs) of Equus caballus Y chromosome (ECAY) genes are largely unknown. To demonstrate the copy number variations of Y chromosome genes in horses, the quantitative real-time polymerase chain reaction (qPCR) method was applied to measure the CNVs of the eukaryotic translation initiation factor 1A Y (EIF1AY), equine testis-specific transcript on Y 1 (ETSTY1), equine testis-specific transcript on Y 4 (ETSTY4), equine testis-specific transcript on Y 5 (ETSTY5), equine transcript Y4 (ETY4), ubiquitin activating enzyme Y (UBE1Y), sex determining region Y (SRY), and inverted repeat 2 Y (YIR2) across 14 Chinese domestic horse breeds in this study. Our results revealed that these eight genes were multi-copy; furthermore, some of the well acknowledged single-copy genes such as SRY and EIF1AY were found to be multi-copy in this research. The median copy numbers (MCNs) varied among different breeds for the same gene. The CNVs of Y chromosome genes showed different distribution patterns among Chinese horse breeds, indicating the impact of natural selection on copy numbers. Our results will provide fundamental information for future functional studies.
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Yan Y, Yang X, Liu Y, Shen Y, Tu W, Dong Q, Yang D, Ma Y, Yang Y. Copy number variation of functional RBMY1 is associated with sperm motility: an azoospermia factor-linked candidate for asthenozoospermia. Hum Reprod 2018; 32:1521-1531. [PMID: 28498920 DOI: 10.1093/humrep/dex100] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 04/28/2017] [Indexed: 02/05/2023] Open
Abstract
STUDY QUESTION What is the influence of copy number variation (CNV) in functional RNA binding motif protein Y-linked family 1 (RBMY1) on spermatogenic phenotypes? SUMMARY ANSWER The RBMY1 functional copy dosage is positively correlated with sperm motility, and dosage insufficiency is an independent risk factor for asthenozoospermia. WHAT IS KNOWN ALREADY RBMY1, a multi-copy gene expressed exclusively in the adult testis, is one of the most important candidates for male infertility in the azoospermia factor (AZF) region of the Y-chromosome. RBMY1 encodes an RNA-binding protein that serves as a pre-mRNA splicing regulator during spermatogenesis, and male mice deficient in Rbmy are sterile. STUDY DESIGN, SIZE, DURATION A total of 3127 adult males were recruited from 2009 to 2016; of this group, the dosage of RBMY1 functional copy were investigated in 486 fertile males. In the remaining 2641 males with known spermatogenesis status, 1070 Y-chromosome haplogroup (Y-hg) O3* or O3e carriers without chromosomal aberration or known AZF structure mutations responsible for spermatogenic impairment, including 506 men with normozoospermia and 564 men with oligozoospermia or/and asthenozoospermia, were screened, and the RBMY1 functional copy dosage and copy conversion were determined to explore their associations with sperm phenotypes. The correlation between RBMY1 dosage and its mRNA level or RBMY1 protein level and the correlation between sperm RBMY1 level and motility were analysed in 15 testis tissue samples and eight semen samples. Ten additional semen samples were used to confirm the subcellular localization of RBMY1 in individual sperm. PARTICIPANTS/MATERIALS, SETTING, METHODS All the Han volunteers donating whole blood, semen and testis tissue were from southwest China. RBMY1 copy number, copy conversion, mRNA/protein amount and protein location in sperm were detected using the AccuCopy® assay method, paralog ratio test, quantitative PCR, western blotting and immunofluorescence staining methods, respectively. MAIN RESULTS AND THE ROLE OF CHANCE This study identified Y-hg-independent CNV of functional RBMY1 in the enrolled population. A difference in the distribution of RBMY1 copy number was observed between the group with normal sperm motility and the group with asthenozoospermia. A positive correlation between the RBMY1 copy dosage and sperm motility was identified, and the males with fewer than six copies of RBMY1 showed an elevated risk for asthenozoospermia relative to those with six RBMY1 copies, the most common dosage in the population. The RBMY1 copy dosage was positively correlated with its mRNA and protein level in the testis. Sperm with high motility were found to carry more RBMY1 protein than those with relatively low motility. The RBMY1 protein was confirmed to predominantly localize in the neck and mid-piece region of sperm as well as the principal piece of the sperm tail. Our population study completes a chain of evidence suggesting that RBMY1 influences the susceptibility of males to asthenozoospermia by modulating sperm motility. LIMITATIONS REASONS FOR CAUTION High sequence similarity between the RBMY1 functional copies and a large number of pseudogenes potentially reduces the accuracy of the copy number detection. The mechanism underlying the CNV in RBMY1 is still unclear, and the effect of the structural variations in the RBMY1 copy cluster on the copy dosage of other protein-coding genes located in the region cannot be excluded, which may potentially bias our observations. WIDER IMPLICATIONS OF THE FINDINGS Asthenozoospermia is a multi-factor complex disease with a limited number of proven susceptibility genes. This study identified a novel genomic candidate independently contributing to the condition, enriching our understanding of the role of AZF-linked genes in male reproduction. Our finding provides insight into the physiological and pathological characteristics of RBMY1 in terms of sperm motility, supplies persuasive evidence of the significance of RBMY1 copy number analysis in the clinical counselling of male infertility resulting from asthenozoospermia. STUDY FUNDING/COMPETING INTEREST(S) This work was funded by the National Natural Science Foundation of China (Nos. 81370748 and 30971598). The authors have no conflicts of interest.
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Affiliation(s)
- Yuanlong Yan
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, No. 1, Keyuan Road 4, Gaopeng Street, Chengdu, Sichuan 610041, China
| | - Xiling Yang
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, No. 1, Keyuan Road 4, Gaopeng Street, Chengdu, Sichuan 610041, China
| | - Yunqiang Liu
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, No. 1, Keyuan Road 4, Gaopeng Street, Chengdu, Sichuan 610041, China
| | - Ying Shen
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, No. 1, Keyuan Road 4, Gaopeng Street, Chengdu, Sichuan 610041, China
| | - Wenling Tu
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, No. 1, Keyuan Road 4, Gaopeng Street, Chengdu, Sichuan 610041, China
| | - Qiang Dong
- Department of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Dong Yang
- Reproductive Medicine Institute, Chengdu Women's and Children's Central Hospital, Chengdu, Sichuan 610031, China
| | - Yongyi Ma
- Jinjiang Maternal and Child Health Hospital, Chengdu, Sichuan 610016, China
| | - Yuan Yang
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, No. 1, Keyuan Road 4, Gaopeng Street, Chengdu, Sichuan 610041, China
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Dynamic Copy Number Evolution of X- and Y-Linked Ampliconic Genes in Human Populations. Genetics 2018; 209:907-920. [PMID: 29769284 PMCID: PMC6028258 DOI: 10.1534/genetics.118.300826] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 05/15/2018] [Indexed: 11/18/2022] Open
Abstract
Ampliconic genes are multicopy genes often located on sex chromosomes and enriched for testis-expressed genes. Here, Lucotte et al. developed new bioinformatic approaches to investigate the ampliconic gene copy number and their coding... Ampliconic genes are multicopy, with the majority found on sex chromosomes and enriched for testis-expressed genes. While ampliconic genes have been associated with the emergence of hybrid incompatibilities, we know little about their copy number distribution and their turnover in human populations. Here, we explore the evolution of human X- and Y-linked ampliconic genes by investigating copy number variation (CNV) and coding variation between populations using the Simons Genome Diversity Project. We develop a method to assess CNVs using the read depth on modified X and Y chromosome targets containing only one repetition of each ampliconic gene. Our results reveal extensive standing variation in copy number both within and between human populations for several ampliconic genes. For the Y chromosome, we can infer multiple independent amplifications and losses of these gene copies even within closely related Y haplogroups, that diversified < 50,000 years ago. Moreover, X- and Y-linked ampliconic genes seem to have a faster amplification dynamic than autosomal multicopy genes. Looking at expression data from another study, we also find that X- and Y-linked ampliconic genes with extensive CNV are significantly more expressed than genes with no CNV during meiotic sex chromosome inactivation (for both X and Y) and postmeiotic sex chromosome repression (for the Y chromosome only). While we cannot rule out that the XY-linked ampliconic genes are evolving neutrally, this study gives insights into the distribution of copy number within human populations and demonstrates an extremely fast turnover in copy number of these regions.
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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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Analysis of 62 hybrid assembled human Y chromosomes exposes rapid structural changes and high rates of gene conversion. PLoS Genet 2017; 13:e1006834. [PMID: 28846694 PMCID: PMC5591018 DOI: 10.1371/journal.pgen.1006834] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 09/08/2017] [Accepted: 05/22/2017] [Indexed: 11/21/2022] Open
Abstract
The human Y-chromosome does not recombine across its male-specific part and is therefore an excellent marker of human migrations. It also plays an important role in male fertility. However, its evolution is difficult to fully understand because of repetitive sequences, inverted repeats and the potentially large role of gene conversion. Here we perform an evolutionary analysis of 62 Y-chromosomes of Danish descent sequenced using a wide range of library insert sizes and high coverage, thus allowing large regions of these chromosomes to be well assembled. These include 17 father-son pairs, which we use to validate variation calling. Using a recent method that can integrate variants based on both mapping and de novo assembly, we genotype 10898 SNVs and 2903 indels (max length of 27241 bp) in our sample and show by father-son concordance and experimental validation that the non-recurrent SNP and indel variation on the Y chromosome tree is called very accurately. This includes variation called in a 0.9 Mb centromeric heterochromatic region, which is by far the most variable in the Y chromosome. Among the variation is also longer sequence-stretches not present in the reference genome but shared with the chimpanzee Y chromosome. We analyzed 2.7 Mb of large inverted repeats (palindromes) for variation patterns among the two palindrome arms and identified 603 mutation and 416 gene conversions events. We find clear evidence for GC-biased gene conversion in the palindromes (and a balancing AT mutation bias), but irrespective of this, also a strong bias towards gene conversion towards the ancestral state, suggesting that palindromic gene conversion may alleviate Muller’s ratchet. Finally, we also find a large number of large-scale gene duplications and deletions in the palindromic regions (at least 24) and find that such events can consist of complex combinations of simultaneous insertions and deletions of long stretches of the Y chromosome. The Y chromosome is extraordinary in many respects; it is non-recombining along most of its length, it carries many testis-expressed genes that are often found in palindromes and thus in several copies, and it is generally highly repetitive with very few unique genes. Its evolutionary process is not well understood in general because short-read mapping in such complex sequence is difficult. We combine de novo assembly and mapping to investigate evolution in more than 60% of the length of 62 Y chromosomes of Danish descent. We find that Y chromosome evolution is very dynamic even among the set of closely related Y chromosomes in Denmark with many cases of complex duplications and deletions of large regions including whole genes, clear evidence of GC-biased gene conversion in the palindromes and a tendency for gene conversion to revert mutations to their ancestral state.
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Abstract
The properties of the human Y chromosome - namely, male specificity, haploidy and escape from crossing over - make it an unusual component of the genome, and have led to its genetic variation becoming a key part of studies of human evolution, population history, genealogy, forensics and male medical genetics. Next-generation sequencing (NGS) technologies have driven recent progress in these areas. In particular, NGS has yielded direct estimates of mutation rates, and an unbiased and calibrated molecular phylogeny that has unprecedented detail. Moreover, the availability of direct-to-consumer NGS services is fuelling a rise of 'citizen scientists', whose interest in resequencing their own Y chromosomes is generating a wealth of new data.
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Y chromosome polymorphisms may contribute to an increased risk of male-induced unexplained recurrent miscarriage. Biosci Rep 2017; 37:BSR20160528. [PMID: 28183871 PMCID: PMC5469323 DOI: 10.1042/bsr20160528] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 01/22/2017] [Accepted: 01/30/2017] [Indexed: 12/11/2022] Open
Abstract
The present study aims to explore the relationship between the Y chromosome polymorphisms (1qh+, inv(9), 9qh+, 16qh+, group D/G, Yqh– and Yqh+) and the risk of unexplained recurrent miscarriage (URM). A total of 507 couples with URM were recruited as case group and 465 healthy couples as control group. The Y chromosome polymorphisms of the male individuals were analysed with the G-banding technique, and the results of the chromosome G-banding analysis were determined using the International Naming Standards of Human Genetics (ISCN). Logistic regression analysis was used to analyse the risk factors for URM. The detection rate of Y chromosome polymorphisms in the case group (12.03%) was higher than that in the control group (2.15%). Y chromosome polymorphisms were detected at significantly higher rates in the case group than in the control group. Using the normal Y chromosomes in individuals of the case group as reference, the partners of their counterparts were more likely to experience miscarriage. The couples who were Y chromosome-polymorphism carriers had shorter gestational age, increased frequency of URM and longer average interval between pregnancies. The results of logistic regression analysis revealed that Y chromosome polymorphisms, shorter gestational age, a higher frequency of miscarriage and longer pregnancy interval were independent risk factors for URM. Y chromosome polymorphisms may be associated with the risk of URM and may play an important role in the development of URM.
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Liu XY, Zhang HY, Pang DX, Xue LT, Yang X, Li YS, Liu RZ. AZFa Microdeletions: Occurrence in Chinese Infertile Men and Novel Deletions Revealed by Semiconductor Sequencing. Urology 2017; 107:76-81. [PMID: 28456540 DOI: 10.1016/j.urology.2017.04.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 03/27/2017] [Accepted: 04/17/2017] [Indexed: 11/15/2022]
Abstract
OBJECTIVE To evaluate the frequency of azoospermia factor (AZFa) microdeletions among infertile men and establish a new high-throughput sequencing method to detect novel deletion types. MATERIALS AND METHODS A total of 3731 infertile men were included. Karyotype analysis was performed using G-band staining of peripheral blood lymphocytes. Polymerase chain reaction (PCR) amplification using specific sequence-tagged sites (STS) was performed to screen for AZF region microdeletions of the Y chromosome. A novel semiconductor sequencing method was established to detect high-resolution AZFa microdeletions. RESULTS Of 3731 infertile men, 341 (9.14%) had microdeletions in AZFa, AZFb, or AZFc. Thirteen of these (3.81%) had a deletion in the AZFa region (mean age: 27.3 ± 4 years, range: 22-34), which included 12 subjects with a normal karyotype (46, XY) and 1 with Klinefelter syndrome (47, XXY). Four of 10 subjects with complete AZFa microdeletions (sY86 and sY84 loss) underwent semiconductor sequencing. They all had DNA sequence deletions from nt 14469266 to 15195932, whereas their fathers had no deletions. One subject with partial AZFa microdeletion (sY86 loss) and his father underwent semiconductor sequencing and STS-PCR analysis. The same deletion (sY86 loss with DNA sequence deletion from nt 14469266 to 14607672) was identified in both subjects. Forty sperm donators and 50 infertile men showed no AZFa microdeletions by either method. CONCLUSION AZFa deletions are present at a low frequency in men with azoospermia or oligozoospermia. Novel sequencing methods can be used for these patients to reveal high-resolution AZFa microdeletions.
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Affiliation(s)
- Xiang-Yin Liu
- Center for Reproductive Medicine, Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China; Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, China
| | - Hong-Yang Zhang
- Center for Reproductive Medicine, Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China
| | - Da-Xin Pang
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, China
| | - Lin-Tao Xue
- Reproductive Medical and Genetic Center, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Xiao Yang
- Center for Reproductive Medicine, Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China
| | - Yu-Shuai Li
- Peking Jabrehoo Med Tech., Ltd, Beijing, China
| | - Rui-Zhi Liu
- Center for Reproductive Medicine, Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China.
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Human Y chromosome copy number variation in the next generation sequencing era and beyond. Hum Genet 2017; 136:591-603. [PMID: 28378101 PMCID: PMC5418319 DOI: 10.1007/s00439-017-1788-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 03/25/2017] [Indexed: 11/16/2022]
Abstract
The human Y chromosome provides a fertile ground for structural rearrangements owing to its haploidy and high content of repeated sequences. The methodologies used for copy number variation (CNV) studies have developed over the years. Low-throughput techniques based on direct observation of rearrangements were developed early on, and are still used, often to complement array-based or sequencing approaches which have limited power in regions with high repeat content and specifically in the presence of long, identical repeats, such as those found in human sex chromosomes. Some specific rearrangements have been investigated for decades; because of their effects on fertility, or their outstanding evolutionary features, the interest in these has not diminished. However, following the flourishing of large-scale genomics, several studies have investigated CNVs across the whole chromosome. These studies sometimes employ data generated within large genomic projects such as the DDD study or the 1000 Genomes Project, and often survey large samples of healthy individuals without any prior selection. Novel technologies based on sequencing long molecules and combinations of technologies, promise to stimulate the study of Y-CNVs in the immediate future.
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Tomaszkiewicz M, Medvedev P, Makova KD. Y and W Chromosome Assemblies: Approaches and Discoveries. Trends Genet 2017; 33:266-282. [DOI: 10.1016/j.tig.2017.01.008] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 12/05/2016] [Accepted: 01/24/2017] [Indexed: 01/19/2023]
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Abstract
The great apes (orangutans, gorillas, chimpanzees, bonobos and humans) descended from a common ancestor around 13 million years ago, and since then their sex chromosomes have followed very different evolutionary paths. While great-ape X chromosomes are highly conserved, their Y chromosomes, reflecting the general lability and degeneration of this male-specific part of the genome since its early mammalian origin, have evolved rapidly both between and within species. Understanding great-ape Y chromosome structure, gene content and diversity would provide a valuable evolutionary context for the human Y, and would also illuminate sex-biased behaviours, and the effects of the evolutionary pressures exerted by different mating strategies on this male-specific part of the genome. High-quality Y-chromosome sequences are available for human and chimpanzee (and low-quality for gorilla). The chromosomes differ in size, sequence organisation and content, and while retaining a relatively stable set of ancestral single-copy genes, show considerable variation in content and copy number of ampliconic multi-copy genes. Studies of Y-chromosome diversity in other great apes are relatively undeveloped compared to those in humans, but have nevertheless provided insights into speciation, dispersal, and mating patterns. Future studies, including data from larger sample sizes of wild-born and geographically well-defined individuals, and full Y-chromosome sequences from bonobos, gorillas and orangutans, promise to further our understanding of population histories, male-biased behaviours, mutation processes, and the functions of Y-chromosomal genes.
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