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Dai Z, Chen H, Feng K, Li T, Liu W, Zhou Y, Yang D, Xue B, Zhu J. Promoter hypermethylation of Y-chromosome gene PRKY as a potential biomarker for the early diagnosis of prostate cancer. Epigenomics 2024:1-16. [PMID: 38979582 DOI: 10.1080/17501911.2024.2365625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 06/04/2024] [Indexed: 07/10/2024] Open
Abstract
Aim: To develop a methylation marker of Y-chromosome gene in the early diagnosis of prostate cancer (PCa). Materials & methods: We utilized bioinformatics analysis to identify the expression and promoter methylation of Y-chromosome gene PRKY in PCa and other common malignancies. Single-center experiments were conducted to validate the diagnostic value of PRKY promoter methylation in PCa. Results: PRKY expression was significantly down-regulated in PCa and its mechanism may be related to promoter methylation. PRKY promoter methylation is highly specific for the diagnosis of early PCa, which may be superior to prostate-specific antigen, mpMRI and other excellent molecular biomarkers. Conclusion: PRKY promoter methylation may be a potential marker for the early and accurate diagnosis of PCa.
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Affiliation(s)
- Zheng Dai
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
- Department of Urology, The Third Affiliated Hospital of Anhui Medical University, Hefei, 230061, China
| | - Hongbing Chen
- Department of Urology, The Third Affiliated Hospital of Anhui Medical University, Hefei, 230061, China
| | - Kaiwen Feng
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Tuoxin Li
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Weifeng Liu
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Yibin Zhou
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Dongrong Yang
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Boxin Xue
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Jin Zhu
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
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Gabriele A, Chierto E, Gino S, Inturri S, Aneli S, Robino C. Privacy and ethical challenges of the Amelogenin sex test in forensic paternity/kinship analysis: Insights from a 13-year case history. Forensic Sci Int Synerg 2023; 7:100440. [PMID: 37840559 PMCID: PMC10568343 DOI: 10.1016/j.fsisyn.2023.100440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 09/07/2023] [Accepted: 09/14/2023] [Indexed: 10/17/2023]
Abstract
The Amelogenin sex test included in forensic DNA typing kits has the potential to identify congenital conditions such as differences/disorders of sex development (DSD). It can also reveal mismatches between genotypic sex and gender marker in identity documents of transgender persons who obtained legal gender recognition. In a 13-year case history of paternity/kinship tests, involving n = 962 females and n = 1001 males, two mismatches between Amelogenin sex test (male) and gender marker (female), and three cases of chromosomal DSD (Klinefelter syndrome) were observed. The concrete risk of observing Amelogenin anomalies, their potential causes, and the context in which they occur (forensic, i.e. non-medical) mean that laboratory operators are called to strike a complex balance between privacy interests and individual health rights when providing preliminary information and reporting Amelogenin incidental findings. This case history argues for the need of a more responsible approach towards the Amelogenin sex test in the forensic community.
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Affiliation(s)
- Alessandro Gabriele
- Department of Public Health Sciences and Pediatrics, University of Turin, C.so Galileo Galilei 22, 10126, Turin, Italy
| | - Elena Chierto
- Department of Public Health Sciences and Pediatrics, University of Turin, C.so Galileo Galilei 22, 10126, Turin, Italy
| | - Sarah Gino
- Department of Health Sciences, University of Eastern Piedmont, Via Solaroli 17, 28100, Novara, Italy
| | - Serena Inturri
- Department of Public Health Sciences and Pediatrics, University of Turin, C.so Galileo Galilei 22, 10126, Turin, Italy
| | - Serena Aneli
- Department of Public Health Sciences and Pediatrics, University of Turin, C.so Galileo Galilei 22, 10126, Turin, Italy
| | - Carlo Robino
- Department of Public Health Sciences and Pediatrics, University of Turin, C.so Galileo Galilei 22, 10126, Turin, Italy
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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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Sharma S, Yadav R, Sahajpal V, Kumari L, Sharma A. A Comparative Study on the Frequency of Amelogenin Y Deletion in a Brahmin Population of Haryana and Rajasthan State with Other Indian and Global Populations. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422030139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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5
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Chen PF, Kuan LC, Kao CC, Hsu HK, Chen M, Kuo TC, Kuo PL. Complex rearrangements of Y chromosome suggest RPS4Y1 as lymphedema candidate gene. Taiwan J Obstet Gynecol 2022; 61:170-173. [PMID: 35181033 DOI: 10.1016/j.tjog.2021.11.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2021] [Indexed: 11/20/2022] Open
Abstract
OBJECTIVE Cystic hygromas are frequently encountered in fetus with Turner syndrome (TS). Nevertheless, identification of genetic loci responsible for the cystic hygroma has been problematic. Here, we tried to elucidate the candidate gene for cystic hygroma through a rare case of complex Y chromosomal rearrangements involving duplication of partial Yq and monosomy of partial Yp. CASE REPORT A 30-year-old woman, gravida 1 para 0, was diagnosed with fetal cystic hygroma at 12 weeks of gestation. The genetic analysis of the product of conception revealed complex rearrangement of Y chromosome: microdeletion in Yp11.2p11.31 and microduplicatin in Yq11.223q11.23. The deleted region spans about 6.25 Mb and includes 76 genes, including SRY. The duplicated region spans about 4.76 Mb and includes 145 genes. CONCLUSION From this rare case with non-mosaic complex Y-chromosome rearrangements, we could narrow down Turner stigmata critical region to Yp11.2~p11.3. We also propose RPS4Y1 as lymphedema candidate gene.
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Affiliation(s)
- Po-Fan Chen
- Department of Obstetrics and Gynecology, National Cheng Kung University Hospital and College of Medicine, Tainan, Taiwan
| | - Long-Ching Kuan
- Department of Obstetrics and Gynecology, Kuo General Hospital, Tainan, Taiwan
| | - Chiu-Ching Kao
- Department of Obstetrics and Gynecology, National Cheng Kung University Hospital and College of Medicine, Tainan, Taiwan
| | - Hui-Kuo Hsu
- Department of Obstetrics and Gynecology, National Cheng Kung University Hospital and College of Medicine, Tainan, Taiwan
| | - Ming Chen
- Department of Genomic Medicine, And Center for Medical Genetics, Changhua Christian Hospital, Changhua, Taiwan
| | - Tsung-Cheng Kuo
- Department of Obstetrics and Gynecology, Kuo General Hospital, Tainan, Taiwan.
| | - Pao-Lin Kuo
- Department of Obstetrics and Gynecology, National Cheng Kung University Hospital and College of Medicine, Tainan, Taiwan.
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A novel mutation at the AMEL primer binding region on the Y chromosome in AMELY negative male. Int J Legal Med 2022; 136:519-526. [DOI: 10.1007/s00414-022-02781-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 01/19/2022] [Indexed: 10/19/2022]
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7
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The Y chromosome and its use in forensic DNA analysis. Emerg Top Life Sci 2021; 5:427-441. [PMID: 34533187 PMCID: PMC8457770 DOI: 10.1042/etls20200339] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 08/13/2021] [Accepted: 08/24/2021] [Indexed: 11/17/2022]
Abstract
Originally relatively ignored in forensic investigations because its genetic analysis lacks inference of individual identification, the value of Y chromosome analysis has been proven in cases of sexual assault, particularly where the amount of material left by a male assailant is limited in comparison with female DNA. All routine analysis of autosomal DNA, however, targets a gene (AMELY) on the Y chromosome in order to identify the sex of the DNA source and this is discussed in the context of the genetic structure of this male-specific chromosome. Short-tandem repeat markers on the chromosome are tested in dedicated multiplexes that have developed over time and these are described alongside international guidance as to their use in a forensic setting. As a marker of lineage, the Y chromosome provides additional tools to assist in the inference of ancestry, both geographical and familial and the value of Y chromosome testing is illustrated through descriptions of cases of criminal and historical interest. A decision to analyse the Y chromosome has to be considered in the context, not only of the circumstances of the case, but also with regard to the ethical questions it might raise, and these are discussed in relation to the cases that have been described in more detail in the accompanying online supplementary material.
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Chen S, Zhang Q, Chu L, Chang C, Chen Y, Bao Z, Peng W, Zhang L, Li S, Liu C, Zhu H, Yu F, Chen X, Jiang L, Lu D, Jiang Z, Jin L, Xu C. Comprehensive copy number analysis of Y chromosome-linked loci for detection of structural variations and diagnosis of male infertility. J Hum Genet 2021; 67:107-114. [PMID: 34462535 DOI: 10.1038/s10038-021-00973-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 07/18/2021] [Accepted: 08/17/2021] [Indexed: 11/09/2022]
Abstract
Infertility affects about 15% of heterosexual couples and male factors account for ~45-50% of clinical cases. Genetic factors play an important role in male infertility and thus we try to develop a cost-effective method for screening the genetic factors in male infertility. In our retrospective proof-of-concept study, we employed the high-throughput ligation-dependent probe amplification (HLPA) to examine the copy number by 115 genomic loci covering the Y chromosome, and 5 loci covering the X chromosome-specific region. We identified 8 sex chromosome aneuploid people from the low sperm concentration (LSC) group, and Y chromosome-specific microdeletion/duplications in 211 samples from the LSC group, and in 212 samples from the control group. 35 samples showed complete loss of AZFc (BPY2 to CDY1B deletion), which was not observed in controls. Nevertheless, a partial loss of AZFc (BPY2 to BPY2B deletion) was detected at comparable frequencies in both groups (68/211 vs. 108/212, respectively). And we further found structural variations in 28.6 and 26.9% samples from infertility and fertility groups. Moreover, we found that there were lower copy numbers for heterochromatic sequences in men with LSC. Especially, we reported that ultra-low relative copy number (RCN) (<0.5) type and low RCN (0.5 to <0.75) type in Yq12 were more often in the LSC group for the first time. Our results not only shed light on the potential role of low RCN in Yq12 in male infertility but also showed that HLPA can be a powerful and cost-effective tool for clinical screening in male infertility.
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Affiliation(s)
- Songchang Chen
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China.,The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Orignal Diseases, Shanghai, China
| | - Qian Zhang
- The First Hospital Affiliated to Army Medical University, Chongqing, China
| | - Liming Chu
- Genesky Diagnostics (Suzhou) Inc., Suzhou, Jiangsu, China
| | - Chunxin Chang
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Orignal Diseases, Shanghai, China
| | - Yiyao Chen
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Orignal Diseases, Shanghai, China
| | - Zhongwei Bao
- The First Hospital Affiliated to Army Medical University, Chongqing, China
| | - Weihua Peng
- The First Hospital Affiliated to Army Medical University, Chongqing, China
| | - Lanlan Zhang
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Orignal Diseases, Shanghai, China
| | - Shuyuan Li
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Orignal Diseases, Shanghai, China
| | - Chao Liu
- Genesky Diagnostics (Suzhou) Inc., Suzhou, Jiangsu, China
| | - Huanhuan Zhu
- Genesky Diagnostics (Suzhou) Inc., Suzhou, Jiangsu, China
| | - Feng Yu
- Genesky Diagnostics (Suzhou) Inc., Suzhou, Jiangsu, China
| | - Xiaoyan Chen
- Genesky Diagnostics (Suzhou) Inc., Suzhou, Jiangsu, China
| | - Lili Jiang
- Genesky Diagnostics (Suzhou) Inc., Suzhou, Jiangsu, China
| | - Daru Lu
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Zhengwen Jiang
- Genesky Diagnostics (Suzhou) Inc., Suzhou, Jiangsu, China.
| | - Li Jin
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China. .,Shanghai Key Laboratory of Embryo Orignal Diseases, Shanghai, China.
| | - Chenming Xu
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China. .,The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China. .,Shanghai Key Laboratory of Embryo Orignal Diseases, Shanghai, China.
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Muinde JM, Chandra Bhanu DR, Neumann R, Oduor RO, Kanja W, Kimani JK, Mutugi MW, Smith L, Jobling MA, Wetton JH. Geographical and linguistic structure in the people of Kenya demonstrated using 21 autosomal STRs. Forensic Sci Int Genet 2021; 53:102535. [PMID: 34051692 DOI: 10.1016/j.fsigen.2021.102535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 05/11/2021] [Accepted: 05/16/2021] [Indexed: 11/15/2022]
Abstract
Kenya is a diverse and populous nation that employs DNA evidence in its criminal justice system, and therefore requires reliable information on autosomal STR allele frequency variation across the country and in its many ethnic groups. In order to provide reference data and to assess population structure, we analysed the 21 autosomal STRs in the GlobalFiler multiplex in a sample of 510 indigenous Kenyans representing the country's eight former provinces, 43 of its 47 counties, three main linguistic families and all 29 ethnic groups that each comprise >0.5% of the 2019 census population. The indigenous population originated from successive migrations of Cushitic, Nilotic and Bantu speaking groups who settled in regions that suited their distinctive sustenance lifestyles. Consequently, they now largely reside in a patchwork of communities with strong associations with particular counties and provinces and limited degrees of inter-group marriage, as shown by DNA donors' ancestry details. We found significant genetic differentiation between the three Nilotic language sub-families, with Western Nilotes (the Luo ethnic group) showing greater similarity to the Bantu than the Southern and Eastern Nilotes which themselves showed closer affinity to the Cushitic speakers. This concurs with previous genetic, linguistic and social studies. Comparisons with other African populations also showed that linguistic affiliation is a stronger factor than geography. This study revealed several rare off-ladder alleles whose structure was determined by Sanger sequencing. Among the unusual features that could affect profile interpretation were a deletion of Amelogenin Y but no other forensic marker (autosomal or Y-chromosomal), a triallelic pattern at TPOX and an extremely short SE33 allele falling within the expected size range of D7S820. Compared with the currently implemented Identifiler multiplex, Random Match Probabilities decreased from 6.4 × 10-19 to 3.9 × 10-27. The appreciation of local population structure provided by the geographically and ethnically representative sample in this study highlights the structured genetic landscape of Kenya.
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Affiliation(s)
- Jane Mbithe Muinde
- Department of Biochemistry, Microbiology & Biotechnology, Kenyatta University, Nairobi, Kenya
| | | | - Rita Neumann
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK
| | - Richard Okoth Oduor
- Department of Biochemistry, Microbiology & Biotechnology, Kenyatta University, Nairobi, Kenya
| | | | | | | | - Lisa Smith
- Department of Criminology, University of Leicester, Leicester, UK
| | - Mark A Jobling
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.
| | - Jon H Wetton
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.
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Mishra A, Dhali A, Reddy IJ, Kolte AP. Sexing of pre-implantation ovine embryos through polymerase chain reaction-based amplification of GAPDH, SRY and AMEL genes. Reprod Domest Anim 2020; 55:885-892. [PMID: 32379910 DOI: 10.1111/rda.13699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 04/24/2020] [Indexed: 11/27/2022]
Abstract
The ability to identify the sex of embryo and control of sex ratio has a great commercial importance to livestock industry. Prediction of embryonic sex could be useful in the management decisions of sex selection in breeding programs. Several methods have been attempted to determine the sex but the polymerase chain reaction (PCR)-based sexing method is generally favoured, as it is cost effective, simple and reliable. The aim of the present study was to identify sex of sheep embryos produced in vitro through amplification of glyceraldehyde 3-phosphate dehydrogenase (GAPDH), sex-determining region Y (SRY) and amelogenin genes present in genomic DNA (gDNA) of embryos through PCR. To avoid false interpretation of the result by no amplification of SRY in female embryos, a duplex PCR was approached to amplify combinedly SRY and GAPDH genes. Sex-specific blood was used in PCR as positive control. In vitro sheep embryos were produced as per standardized protocol of laboratory. Sexing of sex-specific blood and in vitro produced embryos were approached though PCR to amplify the respective genes using gDNA present in the sample without its traditional isolation. The accuracy of sex prediction for embryos was 100% by this procedure.
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Affiliation(s)
- Ashish Mishra
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, India
| | - Arindam Dhali
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, India
| | - Ippala J Reddy
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, India
| | - Atul P Kolte
- ICAR-National Institute of Animal Nutrition and Physiology, Bangalore, India
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Egger S, Wand D, Scheurer E, Schulz I, Dion D, Balitzki B. Fehlerhafte Geschlechtsbestimmung aufgrund partieller Deletion des Y-Chromosoms. Rechtsmedizin (Berl) 2020. [DOI: 10.1007/s00194-020-00373-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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Dash HR, Rawat N, Das S. Alternatives to amelogenin markers for sex determination in humans and their forensic relevance. Mol Biol Rep 2020; 47:2347-2360. [DOI: 10.1007/s11033-020-05268-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 01/20/2020] [Indexed: 12/15/2022]
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The Role of Number of Copies, Structure, Behavior and Copy Number Variations (CNV) of the Y Chromosome in Male Infertility. Genes (Basel) 2019; 11:genes11010040. [PMID: 31905733 PMCID: PMC7016774 DOI: 10.3390/genes11010040] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/17/2019] [Accepted: 12/23/2019] [Indexed: 12/11/2022] Open
Abstract
The World Health Organization (WHO) defines infertility as the inability of a sexually active, non-contracepting couple to achieve spontaneous pregnancy within one year. Statistics show that the two sexes are equally at risk. Several causes may be responsible for male infertility; however, in 30–40% of cases a diagnosis of idiopathic male infertility is made in men with normal urogenital anatomy, no history of familial fertility-related diseases and a normal panel of values as for endocrine, genetic and biochemical markers. Idiopathic male infertility may be the result of gene/environment interactions, genetic and epigenetic abnormalities. Numerical and structural anomalies of the Y chromosome represent a minor yet significant proportion and are the topic discussed in this review. We searched the PubMed database and major search engines for reports about Y-linked male infertility. We present cases of Y-linked male infertility in terms of (i) anomalies of the Y chromosome structure/number; (ii) Y chromosome misbehavior in a normal genetic background; (iii) Y chromosome copy number variations (CNVs). We discuss possible explanations of male infertility caused by mutations, lower or higher number of copies of otherwise wild type, Y-linked sequences. Despite Y chromosome structural anomalies are not a major cause of male infertility, in case of negative results and of normal DNA sequencing of the ascertained genes causing infertility and mapping on this chromosome, we recommend an analysis of the karyotype integrity in all cases of idiopathic fertility impairment, with an emphasis on the structure and number of this chromosome.
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Dunkelmann B, Helm K, Grießner I, Zahrer W, Müller E, Kastinger T, Kreindl G, Cemper-Kiesslich J, Neuhuber F. Intersexuality as a potential source of error in sex determination using forensic multiplex kits. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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15
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Timasheva YR, Tuktarova IA, Gizullina LI, Sundyrev EY, Mustafina OE. [Molecular-genetic analysis of a rare forensic case of partial deletion of the Y-chromosome]. Sud Med Ekspert 2019; 62:19-21. [PMID: 31407701 DOI: 10.17116/sudmed20196204119] [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: 11/17/2022]
Abstract
The amelogenin gene encodes dental enamel protein and is present in humans in two forms - AMELX and AMELY, located on the X- and Y-chromosomes, respectively. This rare case depicts a partial deletion of the AMELY gene. In the Into-Stil LLC laboratory, we performed the genetic testing of the DNA samples extracted from buccal epithelial cells of the alleged father and the disputed child (a boy). Genotyping was carried out using COrDIS Plus ('Gordis', Russian Federation) and AmpFLSTR Identifiler Direct PCR Amplification ('Applied Biosystems', USA) Kits. Our findings have demonstrated that both the alleged father and the disputed child lacked the fragments corresponding with the AMELY gene. Using both STR-systems, we detected, in the disputed child's genome, the allele formally identical to the allele in the genome of the alleged father. Further analysis using the COrDYS ('Gordis', Russian Federation) kit allowed us to detect the amplified fragments corresponding with all the STR loci of Y chromosome, except DYS576 and DYS449, which confirmed that both studied individuals belonged to male biological sex.
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Affiliation(s)
- Ya R Timasheva
- Physiological Genetics Laboratory of the Institute of Biochemistry and Genetics of the Ufa Branch of the Russian Academy of Sciences, Ufa, Russia 450054; Department of Medical Genetics and Fundamental Medicine, Bashkir State Medical University, Ufa, Russia 450000
| | - I A Tuktarova
- Physiological Genetics Laboratory of the Institute of Biochemistry and Genetics of the Ufa Branch of the Russian Academy of Sciences, Ufa, Russia 450054; OOO Into Steel, Ufa, Russia, 450044
| | | | | | - O E Mustafina
- Physiological Genetics Laboratory of the Institute of Biochemistry and Genetics of the Ufa Branch of the Russian Academy of Sciences, Ufa, Russia 450054
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Cheng JB, Liu Q, Long F, Huang DX, Yi SH. Analysis of the Yp11.2 Deletion Region of Phenotypically Normal Males with an AMELY-Null Allele in the Chinese Han Population. Genet Test Mol Biomarkers 2019; 23:359-362. [PMID: 30994363 DOI: 10.1089/gtmb.2018.0231] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Aim: The amelogenin gene is a widely used gender marker for forensic DNA profiling. Males who have the amelogenin Y (AMELY) allele deletion can be mistakenly identified as females if genotyping is performed only on the amelogenin gene. The aim of this study was to investigate the frequency of the AMELY allele deletion in the Chinese Han population and analyze the possible genetic variation on the Y chromosome. Materials and Methods: The amelogenin gene of 12,735 unrelated males from the Chinese Han population were genotyped using common forensic short tandem repeat (STR) kits. The AMELY allele deletion was verified by redesigned primers and sequencing. Eighteen Y-specific sequence tagged sites (STSs) on the Yp11.2 region were selected to delineate the deletion breakpoints on the Y chromosome. Results: Three males were confirmed to have no AMELY allele. The frequency rate of the AMELY-null allele was 0.236% (3/12,735) in the Chinese Han population of Central China; 2.73 Mb of sequence on the Y chromosome were absent in all the AMELY-negative samples. The deleted region was mapped using SRY, AMELY, 5 Y-STRs, and 18 STSs, which belong to the class I deleted pattern. The three unrelated males shared the same Y-STR haplotype with four males from other Chinese populations, all of whom have the AMELY-null allele. The haplogroup of these males was identified as the O3 haplogroup. Conclusion: The AMELY allele deletion in the Chinese population was accompanied by the deletion of the Y-STR loci on the Yp11.2 region. Therefore, another Y-specific marker should be tested simultaneously when unknown samples are examined as part of a criminal investigation.
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Affiliation(s)
- Juan Bo Cheng
- 1 Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Quan Liu
- 2 Hubei Key Laboratory of Forensic Science (Hubei University of Police), Wuhan, China
| | - Fei Long
- 1 Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dai Xin Huang
- 1 Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shao Hua Yi
- 1 Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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San Roman AK, Page DC. A strategic research alliance: Turner syndrome and sex differences. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2019; 181:59-67. [PMID: 30790449 DOI: 10.1002/ajmg.c.31677] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 01/06/2019] [Indexed: 12/11/2022]
Abstract
Sex chromosome constitution varies in the human population, both between the sexes (46,XX females and 46,XY males), and within the sexes (e.g., 45,X and 46,XX females, and 47,XXY and 46,XY males). Coincident with this genetic variation are numerous phenotypic differences between males and females, and individuals with sex chromosome aneuploidy. However, the molecular mechanisms by which sex chromosome constitution impacts phenotypes at the cellular, tissue, and organismal levels remain largely unexplored. Thus, emerges a fundamental question connecting the study of sex differences and sex chromosome aneuploidy syndromes: How does sex chromosome constitution influence phenotype? Here, we focus on Turner syndrome (TS), associated with the 45,X karyotype, and its synergies with the study of sex differences. We review findings from evolutionary studies of the sex chromosomes, which identified genes that are most likely to contribute to phenotypes as a result of variation in sex chromosome constitution. We then explore strategies for investigating the direct effects of the sex chromosomes, and the evidence for specific sex chromosome genes impacting phenotypes. In sum, we argue that integrating the study of TS with sex differences offers a mutually beneficial alliance to identify contributions of the sex chromosomes to human development, health, and disease.
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Affiliation(s)
| | - David C Page
- Whitehead Institute, Cambridge, Massachusetts.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
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D'Atanasio E, Bonito M, Iacovacci G, Berti A, Trombetta B, Cruciani F. Identification and molecular characterisation of an AMEL-X null allele due to an Alu insertion. Forensic Sci Int Genet 2018; 38:e1-e4. [PMID: 30413337 DOI: 10.1016/j.fsigen.2018.10.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 10/18/2018] [Accepted: 10/31/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Eugenia D'Atanasio
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Rome, Italy
| | - Maria Bonito
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Rome, Italy
| | - Giuseppe Iacovacci
- Banca Dati Nazionale del DNA, Direzione Centrale di Polizia Criminale, Rome, Italy
| | - Andrea Berti
- Carabinieri, Reparto Investigazioni Scientifiche di Roma, Sezione di Biologia, Rome, Italy
| | - Beniamino Trombetta
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Rome, Italy
| | - Fulvio Cruciani
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Rome, Italy; Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Rome, Italy.
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19
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Genetic characterization of Y-chromosomal STRs in Hazara ethnic group of Pakistan and confirmation of DYS448 null allele. Int J Legal Med 2018; 133:789-793. [DOI: 10.1007/s00414-018-1962-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 10/24/2018] [Indexed: 10/28/2022]
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20
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TBL1Y: a new gene involved in syndromic hearing loss. Eur J Hum Genet 2018; 27:466-474. [PMID: 30341416 DOI: 10.1038/s41431-018-0282-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 09/08/2018] [Accepted: 09/18/2018] [Indexed: 12/16/2022] Open
Abstract
Hereditary hearing loss (HHL) is an extremely heterogeneous disorder with autosomal dominant, recessive, and X-linked forms. Here, we described an Italian pedigree affected by HHL but also prostate hyperplasia and increased ratio of the free/total PSA levels, with the unusual and extremely rare Y-linked pattern of inheritance. Using exome sequencing we found a missense variant (r.206A>T leading to p.Asp69Val) in the TBL1Y gene. TBL1Y is homologous of TBL1X, whose partial deletion has described to be involved in X-linked hearing loss. Here, we demonstrate that it has a restricted expression in adult human cochlea and prostate and the variant identified induces a lower protein stability caused by misfolded mutated protein that impairs its cellular function. These findings indicate that TBL1Y could be considered a novel candidate for HHL.
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21
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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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22
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Kholief M, El Shanawany S, Gomaa R. Sex determination from dental pulp DNA among Egyptians. EGYPTIAN JOURNAL OF FORENSIC SCIENCES 2017. [DOI: 10.1186/s41935-017-0030-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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23
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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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Zhang GW, Guan JQ, Luo ZG, Zhang WX, Wang L, Luo XL, Zuo FY. A tremendous expansion of copy number in crossbred bulls ( × ). J Anim Sci 2017; 94:1398-407. [PMID: 27135999 DOI: 10.2527/jas.2015-9983] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Crossbreeding between cattle () and yak () exhibits significant hybrid advantages in milk yield and meat production. By contrast, cattle-yak F hybrid bulls are sterile. Copy number variations (CNV) of multicopy gene families in male-specific regions of the mammalian Y chromosome (MSY) affect human and animal fertility. The present study investigated CNV of (), (), (), and () in 5 yak breed bulls ( = 63), cattle-yak F ( = 22) and F ( = 2) hybrid bulls, and Chinese Yellow (CY) cattle bulls ( = 10) by quantitative real-time PCR. showed restricted amplification in yak bulls in that the average geometric mean copy number (CN) was estimated to be 4 copies. The most compelling finding is that there is a tremendous expansion of CN in F hybrids (385 copies; 95% confidence interval [CI] = 351-421) and F hybrids (356 copies) compared with the male parent breed CY cattle (142 copies; 95% CI = 95-211). Copy numbers of and were also extensively expanded on the Y chromosome in yak and CY cattle bulls. The geometric mean CN of and were estimated to be 123 (95% CI = 114-132) and 250 copies (95% CI = 233-268) in yak bulls and 71 (95% CI = 61-82) and 133 (95% CI = 107-164) copies in CY cattle, respectively. Yak and CY cattle have 2 copies of the gene on the Y chromosome. Similarly to gene, the F and F hybrid bulls have higher CN of , , and than CY cattle ( < 0.01). These results indicated that the MSY of yak and cattle-yak crossbred hybrids was fundamentally different from cattle MSY in the context of genomic organization. Based on the model of cattle-yak F and F hybrid bull sterility, the CNV of may serve as a potential risk factor for crossbred bull ( × ) infertility. To our knowledge, this is the first study to examine differences in multicopy genes in MSY between yak and cattle-yak bulls.
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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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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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27
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Pathak D, Yadav SK, Rawal L, Ali S. Mutational landscape of the human Y chromosome-linked genes and loci in patients with hypogonadism. J Genet 2016; 94:677-87. [PMID: 26690523 DOI: 10.1007/s12041-015-0582-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Sex chromosome-related anomalies engender plethora of conditions leading to male infertility. Hypogonadotropic hypogonadism (HH) is a rare but well-known cause of male infertility. Present study was conducted to ascertain possible consensus on the alterations of the Y-linked genes and loci in males representing hypogonadism (H), which in turn culminate in reproductive dysfunction. A total of nineteen 46, XY males, clinically diagnosed with H (11 representative HH adults and eight prepubertal boys suspected of having HH) were included in the study. Sequence-tagged site screening,SRY gene sequencing,fluorescence in situ hybridization mapping (FISH), copy number and relative expression studies by real-time PCR were conducted to uncover the altered status of the Y chromosome in the patients. The result showed random microdeletions within the AZFa (73%)/b (78%) and c(26%) regions. Sequencing of the SRY gene showed nucleotide variations within and outside of the HMG box in four males (21%). FISH uncovered mosaicism for SRY, AMELY,DAZ genes and DYZ1 arrays, structural rearrangement for AMELY (31%) and duplication of DAZ (57%) genes. Copy number variation for seven Y-linked genes (2-8 rounds of duplication), DYZ1 arrays (495-6201 copies) and differential expression of SRY,UTY and VCY in the patients' blood were observed. Present work demonstrates the organizational vulnerability of several Y-linked genes in H males. These results are envisaged to be useful during routine diagnosis of H patients.
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Affiliation(s)
- Deepali Pathak
- Molecular Genetics Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067,India.
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28
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van den Berge M, Sijen T. A male and female RNA marker to infer sex in forensic analysis. Forensic Sci Int Genet 2016; 26:70-76. [PMID: 27816848 DOI: 10.1016/j.fsigen.2016.10.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 10/17/2016] [Accepted: 10/24/2016] [Indexed: 01/18/2023]
Abstract
In forensics, DNA profiling is used for the identification of the donor of a trace, while messenger RNA (mRNA) profiling can be applied to identify the cellular origin such as body fluids or organ tissues. The presence of male cell material can be readily assessed by the incorporation of Y-chromosomal markers in quantitation or STR profiling systems. However, no forensic marker exists to positively identify female cell material; merely the presence of female DNA is deduced from the absence of a Y peak, or unbalanced X-Y signals at the Amelogenin locus or unbalanced response of the total and Y-specific quantifier. The presence of two X-chromosomes in female cells invokes dosage compensation, which is achieved through inactivation of one of the X-chromosomes in females. Since this process involves specific RNA molecules, identification of female cellular material may be possible through RNA profiling. Additionally, male material may be identified through RNAs expressed from the Y-chromosome. RNAs preferentially expressed in either sex were assessed for their potential to act as sex markers in forensic RNA assays. To confirm sex-specificity, body fluids and organ tissues of multiple donors of either sex were tested. Additionally, sensitivity of the markers and the suitability of positively identifying male-female mixtures were assessed and degraded samples were used to assess performance of the markers in forensic settings. The addition of sex-specific markers is of added informative value in any RNA profiling system and both markers were incorporated into existing RNA assays that either target body fluids or organs. These are the first forensic assays that enable positive identification of female cellular material.
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Affiliation(s)
- M van den Berge
- Department of Human Biological Traces, Netherlands Forensic Institute, P.O. Box 24044, 2490 AA The Hague, The Netherlands, The Netherlands.
| | - T Sijen
- Department of Human Biological Traces, Netherlands Forensic Institute, P.O. Box 24044, 2490 AA The Hague, The Netherlands, The Netherlands.
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Madel MB, Niederstätter H, Parson W. TriXY-Homogeneous genetic sexing of highly degraded forensic samples including hair shafts. Forensic Sci Int Genet 2016; 25:166-174. [PMID: 27613970 DOI: 10.1016/j.fsigen.2016.09.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 09/01/2016] [Indexed: 02/04/2023]
Abstract
Sexing of biological evidence is an important aspect in forensic investigations. A routinely used molecular-genetic approach to this endeavour is the amelogenin sex test, which is integrated in most commercially available polymerase chain reaction (PCR) kits for human identification. However, this assay is not entirely effective in respect to highly degraded DNA samples. This study presents a homogeneous PCR assay for robust sex diagnosis, especially for the analysis of severely fragmented DNA. The introduced triplex for the X and Y chromosome (TriXY) is based on real-time PCR amplification of short intergenic sequences (<50bp) on both gonosomes. Subsequent PCR product examination and molecular-genetic sex-assignment rely on high-resolution melting (HRM) curve analysis. TriXY was optimized using commercially available multi-donor human DNA preparations of either male or female origin and successfully evaluated on challenging samples, including 46 ancient DNA specimens from archaeological excavations and a total of 16 DNA samples extracted from different segments of eight hair shafts of male and female donors. Additionally, sensitivity and cross-species amplification were examined to further test the assay's utility in forensic investigations. TriXY's closed-tube format avoids post-PCR sample manipulations and, therefore, distinctly reduces the risk of PCR product carry-over contamination and sample mix-up, while reducing labour and financial expenses at the same time. The method is sensitive down to the DNA content of approximately two diploid cells and has proven highly useful on severely fragmented and low quantity ancient DNA samples. Furthermore, it even allowed for sexing of proximal hair shafts with very good results. In summary, TriXY facilitates highly sensitive, rapid, and costeffective genetic sex-determination. It outperforms existing sexing methods both in terms of sensitivity and minimum required template molecule lengths. Therefore, we feel confident that TriXY will prove to be a reliable addition to the toolbox currently used for sex-typing in forensic genetics and other fields of research.
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Affiliation(s)
| | - Harald Niederstätter
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, PA, USA.
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30
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Hallast P, Maisano Delser P, Batini C, Zadik D, Rocchi M, Schempp W, Tyler-Smith C, Jobling MA. Great ape Y Chromosome and mitochondrial DNA phylogenies reflect subspecies structure and patterns of mating and dispersal. Genome Res 2016; 26:427-39. [PMID: 26883546 PMCID: PMC4817767 DOI: 10.1101/gr.198754.115] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 01/25/2016] [Indexed: 12/30/2022]
Abstract
The distribution of genetic diversity in great ape species is likely to have been affected by patterns of dispersal and mating. This has previously been investigated by sequencing autosomal and mitochondrial DNA (mtDNA), but large-scale sequence analysis of the male-specific region of the Y Chromosome (MSY) has not yet been undertaken. Here, we use the human MSY reference sequence as a basis for sequence capture and read mapping in 19 great ape males, combining the data with sequences extracted from the published whole genomes of 24 additional males to yield a total sample of 19 chimpanzees, four bonobos, 14 gorillas, and six orangutans, in which interpretable MSY sequence ranges from 2.61 to 3.80 Mb. This analysis reveals thousands of novel MSY variants and defines unbiased phylogenies. We compare these with mtDNA-based trees in the same individuals, estimating time-to-most-recent common ancestor (TMRCA) for key nodes in both cases. The two loci show high topological concordance and are consistent with accepted (sub)species definitions, but time depths differ enormously between loci and (sub)species, likely reflecting different dispersal and mating patterns. Gorillas and chimpanzees/bonobos present generally low and high MSY diversity, respectively, reflecting polygyny versus multimale–multifemale mating. However, particularly marked differences exist among chimpanzee subspecies: The western chimpanzee MSY phylogeny has a TMRCA of only 13.2 (10.8–15.8) thousand years, but that for central chimpanzees exceeds 1 million years. Cross-species comparison within a single MSY phylogeny emphasizes the low human diversity, and reveals species-specific branch length variation that may reflect differences in long-term generation times.
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Affiliation(s)
- Pille Hallast
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom; Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
| | | | - Chiara Batini
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - Daniel Zadik
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - Mariano Rocchi
- Department of Biology, University of Bari, 70124 Bari, Italy
| | - Werner Schempp
- Institute of Human Genetics, University of Freiburg, 79106 Freiburg, Germany
| | - Chris Tyler-Smith
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Mark A Jobling
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom
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31
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Stewart NA, Molina GF, Mardegan Issa JP, Yates NA, Sosovicka M, Vieira AR, Line SRP, Montgomery J, Gerlach RF. The identification of peptides by nanoLC-MS/MS from human surface tooth enamel following a simple acid etch extraction. RSC Adv 2016. [DOI: 10.1039/c6ra05120k] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Tooth enamel is the hardest, densest and most mineralized tissue in vertebrates.
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Affiliation(s)
| | - Gabriela Ferian Molina
- Department of Morphology
- Physiology, and Basic Pathology
- School of Dentistry of Ribeirão Preto
- University of São Paulo
- 14040-904 Ribeirão Preto
| | - João Paulo Mardegan Issa
- Department of Morphology
- Physiology, and Basic Pathology
- School of Dentistry of Ribeirão Preto
- University of São Paulo
- 14040-904 Ribeirão Preto
| | - Nathan Andrew Yates
- Department of Cell Biology
- University of Pittsburgh School of Medicine
- Pittsburgh
- USA
- Biomedical Mass Spectrometry Center
| | - Mark Sosovicka
- Department of Oral and Maxillofacial Surgery
- School of Dental Medicine
- University of Pittsburgh
- Pittsburgh
- USA
| | - Alexandre Rezende Vieira
- Department of Oral Biology
- School of Dental Medicine
- University of Pittsburgh. 3501 Terrace Street
- Pittsburgh
- USA
| | | | | | - Raquel Fernanda Gerlach
- Department of Morphology
- Physiology, and Basic Pathology
- School of Dentistry of Ribeirão Preto
- University of São Paulo
- 14040-904 Ribeirão Preto
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32
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Espinosa JRF, Ayub Q, Chen Y, Xue Y, Tyler-Smith C. Structural variation on the human Y chromosome from population-scale resequencing. Croat Med J 2015; 56:194-207. [PMID: 26088844 PMCID: PMC4500966 DOI: 10.3325/cmj.2015.56.194] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 05/24/2015] [Indexed: 11/05/2022] Open
Abstract
AIM To investigate the information about Y-structural variants (SVs) in the general population that could be obtained by low-coverage whole-genome sequencing. METHODS We investigated SVs on the male-specific portion of the Y chromosome in the 70 individuals from Africa, Europe, or East Asia sequenced as part of the 1000 Genomes Pilot project, using data from this project and from additional studies on the same samples. We applied a combination of read-depth and read-pair methods to discover candidate Y-SVs, followed by validation using information from the literature, independent sequence and single nucleotide polymorphism-chip data sets, and polymerase chain reaction experiments. RESULTS We validated 19 Y-SVs, 2 of which were novel. Non-reference allele counts ranged from 1 to 64. The regions richest in variation were the heterochromatic segments near the centromere or the DYZ19 locus, followed by the ampliconic regions, but some Y-SVs were also present in the X-transposed and X-degenerate regions. In all, 5 of the 27 protein-coding gene families on the Y chromosome varied in copy number. CONCLUSIONS We confirmed that Y-SVs were readily detected from low-coverage sequence data and were abundant on the chromosome. We also reported both common and rare Y-SVs that are novel.
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Affiliation(s)
| | | | | | | | - Chris Tyler-Smith
- Chris Tyler-Smith,The Wellcome Trust Sanger Institute, Hinxton, Cambs. CB10 1SA, UK,
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33
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Hallast P, Batini C, Zadik D, Maisano Delser P, Wetton JH, Arroyo-Pardo E, Cavalleri GL, de Knijff P, Destro Bisol G, Dupuy BM, Eriksen HA, Jorde LB, King TE, Larmuseau MH, López de Munain A, López-Parra AM, Loutradis A, Milasin J, Novelletto A, Pamjav H, Sajantila A, Schempp W, Sears M, Tolun A, Tyler-Smith C, Van Geystelen A, Watkins S, Winney B, Jobling MA. The Y-chromosome tree bursts into leaf: 13,000 high-confidence SNPs covering the majority of known clades. Mol Biol Evol 2014; 32:661-73. [PMID: 25468874 PMCID: PMC4327154 DOI: 10.1093/molbev/msu327] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Many studies of human populations have used the male-specific region of the Y chromosome (MSY) as a marker, but MSY sequence variants have traditionally been subject to ascertainment bias. Also, dating of haplogroups has relied on Y-specific short tandem repeats (STRs), involving problems of mutation rate choice, and possible long-term mutation saturation. Next-generation sequencing can ascertain single nucleotide polymorphisms (SNPs) in an unbiased way, leading to phylogenies in which branch-lengths are proportional to time, and allowing the times-to-most-recent-common-ancestor (TMRCAs) of nodes to be estimated directly. Here we describe the sequencing of 3.7 Mb of MSY in each of 448 human males at a mean coverage of 51×, yielding 13,261 high-confidence SNPs, 65.9% of which are previously unreported. The resulting phylogeny covers the majority of the known clades, provides date estimates of nodes, and constitutes a robust evolutionary framework for analyzing the history of other classes of mutation. Different clades within the tree show subtle but significant differences in branch lengths to the root. We also apply a set of 23 Y-STRs to the same samples, allowing SNP- and STR-based diversity and TMRCA estimates to be systematically compared. Ongoing purifying selection is suggested by our analysis of the phylogenetic distribution of nonsynonymous variants in 15 MSY single-copy genes.
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Affiliation(s)
- Pille Hallast
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Chiara Batini
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Daniel Zadik
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | | | - Jon H Wetton
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Eduardo Arroyo-Pardo
- Laboratory of Forensic and Population Genetics, Department of Toxicology and Health Legislation, Faculty of Medicine, Complutense University, Madrid, Spain
| | - Gianpiero L Cavalleri
- Molecular and Cellular Therapeutics, The Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Giovanni Destro Bisol
- Istituto Italiano di Antropologia, Rome, Italy Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - Berit Myhre Dupuy
- Division of Forensic Sciences, Norwegian Institute of Public Health, Oslo, Norway
| | - Heidi A Eriksen
- Centre of Arctic Medicine, Thule Institute, University of Oulu, Oulu, Finland Utsjoki Health Care Centre, Utsjoki, Finland
| | - Lynn B Jorde
- Department of Human Genetics, University of Utah Health Sciences Center, Salt Lake City, UT
| | - Turi E King
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Maarten H Larmuseau
- Laboratory of Forensic Genetics and Molecular Archaeology, KU Leuven, Leuven, Belgium Department of Imaging & Pathology, Biomedical Forensic Sciences, KU Leuven, Leuven, Belgium Laboratory of Biodiversity and Evolutionary Genomics, Department of Biology, KU Leuven, Leuven, Belgium
| | | | - Ana M López-Parra
- Laboratory of Forensic and Population Genetics, Department of Toxicology and Health Legislation, Faculty of Medicine, Complutense University, Madrid, Spain
| | | | - Jelena Milasin
- School of Dental Medicine, Institute of Human Genetics, University of Belgrade, Belgrade, Serbia
| | | | - Horolma Pamjav
- Network of Forensic Science Institutes, Institute of Forensic Medicine, Budapest, Hungary
| | - Antti Sajantila
- Department of Forensic Medicine, Hjelt Institute, University of Helsinki, Helsinki, Finland Department of Molecular and Medical Genetics, Institute of Applied Genetics, University of North Texas Health Science Center, Fort Worth, Texas
| | - Werner Schempp
- Institute of Human Genetics, University of Freiburg, Freiburg, Germany
| | - Matt Sears
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Aslıhan Tolun
- Department of Molecular Biology and Genetics, Boğaziçi University, Istanbul, Turkey
| | | | - Anneleen Van Geystelen
- Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven, Belgium
| | - Scott Watkins
- Department of Human Genetics, University of Utah Health Sciences Center, Salt Lake City, UT
| | - Bruce Winney
- Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Mark A Jobling
- Department of Genetics, University of Leicester, Leicester, United Kingdom
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Allwood JS, Harbison SA. "YFlag"--a single-base extension primer based method for gender determination. J Forensic Sci 2014; 60:142-6. [PMID: 25354446 DOI: 10.1111/1556-4029.12553] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 06/21/2013] [Accepted: 10/18/2013] [Indexed: 11/28/2022]
Abstract
Assigning the gender of a DNA contributor in forensic analysis is typically achieved using the amelogenin test. Occasionally, this test produces false-positive results due to deletions occurring on the Y chromosome. Here, a four-marker "YFlag" method is presented to infer gender using single-base extension primers to flag the presence (or absence) of Y-chromosome DNA within a sample to supplement forensic STR profiling. This method offers built-in redundancy, with a single marker being sufficient to detect the presence of male DNA. In a study using 30 male and 30 female individuals, detection of male DNA was achieved with c. 0.03 ng of male DNA. All four markers were present in male/female mixture samples despite the presence of excessive female DNA. In summary, the YFlag system offers a method that is reproducible, specific, and sensitive, making it suitable for forensic use to detect male DNA.
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Affiliation(s)
- Julia S Allwood
- Institute of Environmental Science and Research (ESR Ltd.), Mt Albert Science Centre, Private Bag 92-021, Auckland Mail Centre, Auckland, 1142, New Zealand; School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
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Borovko S, Shyla A, Korban V, Borovko A. Amelogenin test abnormalities revealed in Belarusian population during forensic DNA analysis. Forensic Sci Int Genet 2014; 15:98-104. [PMID: 25458925 DOI: 10.1016/j.fsigen.2014.10.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 10/15/2014] [Indexed: 12/01/2022]
Abstract
Study of gender markers is a part of routine forensic genetic examination of crime scene and reference samples, paternity testing and personal identification. Amelogenin locus as a gender marker is included in majority of forensic STR kits of different manufacturers. In current study we report 11 cases of amelogenin abnormalities identified in males of Belarusian origin: 9 cases of AMELY dropout and 2 cases of AMELX dropout. Cases were obtained from forensic casework (n=9) and paternity testing (n=2) groups. In 4 out of 9 AMELY-negative cases deletion of AMELY was associated with the loss of DYS458 marker. In addition, we identified 3 males with SRY-positive XX male syndrome. Deletion of the long arm of the Y-chromosome was detected in two XX males. Loss of the major part of the Y-chromosome was identified in the third XX male. The presence of two X-chromosomes in XX males was confirmed with the use of Mentype(®) Argus X-8 PCR Amplification Kit. AMELY null allele observed in 2 out of 9 cases with AMELY dropout can be caused by mutation in the primer-binding site of AMELY allele. Primer-binding site mutations of AMELX can result in AMELX dropout identified in 2 cases with amplification failure of AMELX. Our study represents the first report and molecular genetic investigation of amelogenin abnormalities in the Belarusian population.
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Affiliation(s)
- Sergey Borovko
- State Committee of Forensic Examinations of the Republic of Belarus, Volodarskiy str. 2a, 220030 Minsk, Belarus.
| | - Alena Shyla
- State Committee of Forensic Examinations of the Republic of Belarus, Volodarskiy str. 2a, 220030 Minsk, Belarus
| | - Victorya Korban
- State Committee of Forensic Examinations of the Republic of Belarus, Volodarskiy str. 2a, 220030 Minsk, Belarus
| | - Alexandra Borovko
- State Committee of Forensic Examinations of the Republic of Belarus, Volodarskiy str. 2a, 220030 Minsk, Belarus
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Cadamuro VC, Bouakaze C, Croze M, Schiavinato S, Tonasso L, Gérard P, Fausser JL, Gibert M, Dugoujon JM, Braga J, Balaresque P. Determined about sex: sex-testing in 45 primate species using a 2Y/1X sex-typing assay. Forensic Sci Int Genet 2014; 14:96-107. [PMID: 25307201 DOI: 10.1016/j.fsigen.2014.09.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 09/04/2014] [Accepted: 09/15/2014] [Indexed: 11/25/2022]
Abstract
Sex-testing using molecular genetic technique is routinely used in the fields of forensics, population genetics and conservation biology. However, none of the assay used so far allows a non-ambiguous and successful sex determination for human and non-human primate species. The most widely used method, AMELY/X, and its alternatives suffer from a set of drawbacks in humans and can rarely be used in New World primate species. Here, we designed a new sex-typing assay using a multiplexed PCR amplification of UTX and UTY-homologous loci and combined male-specific SRY locus. This method was successfully tested on 1048 samples, including 82 non-human primates from 45 Anthropoidea and Lemuriformes species and 966 human samples from 24 populations (Africans, Europeans, and South Americans). This sex-typing method is applicable across all primate species tested from Hominoidea to Indriidae, and also on various populations with different background origins; it represents a robust and cheap sex-typing assay to be used both by the anthropologist and primatologist communities.
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Affiliation(s)
- Valérie Choesmel Cadamuro
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288-CNRS & Université Paul Sabatier Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Caroline Bouakaze
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288-CNRS & Université Paul Sabatier Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Myriam Croze
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288-CNRS & Université Paul Sabatier Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France; Evolutionary Biology team, Department of Biology II, Ludwig Maximilian University of Munich, LMU BioCenter, Grosshaderner Str. 2, 82152 Planegg-Martinsried, Germany
| | - Stéphanie Schiavinato
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288-CNRS & Université Paul Sabatier Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Laure Tonasso
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288-CNRS & Université Paul Sabatier Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Patrice Gérard
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288-CNRS & Université Paul Sabatier Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Jean-Luc Fausser
- Laboratoire AMIS-UMR5288/CNRS, Institut de Médecine Légale, 11 rue Humann, 67085 Strasbourg Cedex, France
| | - Morgane Gibert
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288-CNRS & Université Paul Sabatier Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Jean-Michel Dugoujon
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288-CNRS & Université Paul Sabatier Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - José Braga
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288-CNRS & Université Paul Sabatier Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France
| | - Patricia Balaresque
- Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), UMR5288-CNRS & Université Paul Sabatier Toulouse III, 37 allées Jules Guesde, 31073 Toulouse Cedex 3, France.
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37
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Dos Santos Godoy GC, Galera BB, Araujo C, Barbosa JS, de Pinho MF, Galera MF, de Medeiros SF. The Low Prevalence of Y Chromosomal Microdeletions is Observed in the Oligozoospermic Men in the Area of Mato Grosso State and Amazonian Region of Brazilian Patients. CLINICAL MEDICINE INSIGHTS. REPRODUCTIVE HEALTH 2014; 8:51-7. [PMID: 25210487 PMCID: PMC4133943 DOI: 10.4137/cmrh.s15475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 05/07/2014] [Accepted: 05/09/2014] [Indexed: 11/05/2022]
Abstract
OBJECTIVE To determine the prevalence of chromosomal abnormalities and microdeletions on Y chromosome in infertile patients with oligozoospermia or azoospermia in Mato Grosso state, Brazil. METHODS This cross-sectional study enrolled 94 men from infertile couples. Karyotype analysis was performed by lymphocyte culture technique. DNA from each sample was extracted using non-enzymatic method. Microdeletions were investigated by polymerase chain reaction (PCR). RESULTS With the use of cytogenetic analysis, five patients (5.3%) had abnormal karyotype, one azoospermic patient (1.1%) had karyotype 46,XY,t(7;1) (qter-p35), one (1.1%) with mild oligozoospermia had karyotype 46,XY,delY(q), and two other azoospermic patients had karyotype 47,XXY, consistent with Klinefelter syndrome (KS). One of them (1.1%) with severe oligozoospermia had karyotype 46,XY,8p+. Microdeletion on Y chromosome was found in the azoospermia factor c (AZFc) region in only one azoospermic patient (1.1%). CONCLUSIONS The prevalence of genetic abnormalities in oligo/azoospermic Brazilian men from infertile couple was 5.3%, and microdeletion on Y chromosome was not a common finding in this population (1.1%).
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Affiliation(s)
| | | | - Claudinéia Araujo
- Faculty of Biology, Federal University of Mato Grosso, UFMT, Cuiabá, MT, Brazil
| | | | | | | | - Sebastião Freitas de Medeiros
- Department of Gynecology and Obstetrics, Faculty of Medicine, UFMT, Cuiabá, MT, Brazil. ; Tropical Institute of Reproductive Medicine and Menopause, Cuiabá, MT, Brazil
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38
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Bellott DW, Hughes JF, Skaletsky H, Brown LG, Pyntikova T, Cho TJ, Koutseva N, Zaghlul S, Graves T, Rock S, Kremitzki C, Fulton RS, Dugan S, Ding Y, Morton D, Khan Z, Lewis L, Buhay C, Wang Q, Watt J, Holder M, Lee S, Nazareth L, Alföldi J, Rozen S, Muzny DM, Warren WC, Gibbs RA, Wilson RK, Page DC. Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators. Nature 2014; 508:494-9. [PMID: 24759411 PMCID: PMC4139287 DOI: 10.1038/nature13206] [Citation(s) in RCA: 432] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 03/06/2014] [Indexed: 12/31/2022]
Abstract
The human X and Y chromosomes evolved from an ordinary pair of autosomes, but
millions of years ago genetic decay ravaged the Y chromosome, and only three percent of
its ancestral genes survived. We reconstructed the evolution of the Y chromosome across
eight mammals to identify biases in gene content and the selective pressures that
preserved the surviving ancestral genes. Our findings indicate that survival was
non-random, and in two cases, convergent across placental and marsupial mammals. We
conclude that the Y chromosome's gene content became specialized through selection
to maintain the ancestral dosage of homologous X-Y gene pairs that function as broadly
expressed regulators of transcription, translation and protein stability. We propose that
beyond its roles in testis determination and spermatogenesis, the Y chromosome is
essential for male viability, and plays unappreciated roles in Turner syndrome and in
phenotypic differences between the sexes in health and disease.
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Affiliation(s)
- Daniel W Bellott
- Whitehead Institute, Howard Hughes Medical Institute, & Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Jennifer F Hughes
- Whitehead Institute, Howard Hughes Medical Institute, & Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Helen Skaletsky
- Whitehead Institute, Howard Hughes Medical Institute, & Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Laura G Brown
- Whitehead Institute, Howard Hughes Medical Institute, & Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Tatyana Pyntikova
- Whitehead Institute, Howard Hughes Medical Institute, & Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Ting-Jan Cho
- Whitehead Institute, Howard Hughes Medical Institute, & Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Natalia Koutseva
- Whitehead Institute, Howard Hughes Medical Institute, & Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Sara Zaghlul
- Whitehead Institute, Howard Hughes Medical Institute, & Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Tina Graves
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Susie Rock
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Colin Kremitzki
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Robert S Fulton
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Yan Ding
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Donna Morton
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Ziad Khan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Lora Lewis
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Christian Buhay
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Qiaoyan Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jennifer Watt
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Michael Holder
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Sandy Lee
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Lynne Nazareth
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jessica Alföldi
- Whitehead Institute, Howard Hughes Medical Institute, & Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Steve Rozen
- Whitehead Institute, Howard Hughes Medical Institute, & Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Wesley C Warren
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Richard K Wilson
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - David C Page
- Whitehead Institute, Howard Hughes Medical Institute, & Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
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Álvarez-Sandoval BA, Manzanilla LR, Montiel R. Sex determination in highly fragmented human DNA by high-resolution melting (HRM) analysis. PLoS One 2014; 9:e104629. [PMID: 25098828 PMCID: PMC4123986 DOI: 10.1371/journal.pone.0104629] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 07/15/2014] [Indexed: 11/19/2022] Open
Abstract
Sex identification in ancient human remains is a common problem especially if the skeletons are sub-adult, incomplete or damaged. In this paper we propose a new method to identify sex, based on real-time PCR amplification of small fragments (61 and 64 bp) of the third exon within the amelogenin gene covering a 3-bp deletion on the AMELX-allele, followed by a High Resolution Melting analysis (HRM). HRM is based on the melting curves of amplified fragments. The amelogenin gene is located on both chromosomes X and Y, showing dimorphism in length. This molecular tool is rapid, sensitive and reduces the risk of contamination from exogenous genetic material when used for ancient DNA studies. The accuracy of the new method described here has been corroborated by using control samples of known sex and by contrasting our results with those obtained with other methods. Our method has proven to be useful even in heavily degraded samples, where other previously published methods failed. Stochastic problems such as the random allele drop-out phenomenon are expected to occur in a less severe form, due to the smaller fragment size to be amplified. Thus, their negative effect could be easier to overcome by a proper experimental design.
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Affiliation(s)
- Brenda A. Álvarez-Sandoval
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, Mexico
| | - Linda R. Manzanilla
- Instituto de Investigaciones Antropológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rafael Montiel
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, Mexico
- * E-mail:
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40
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Yapijakis C, Serefoglou Z, Papadimitriou K, Makrinou E. High frequency of TTTY2-like gene-related deletions in patients with idiopathic oligozoospermia and azoospermia. Andrologia 2014; 47:536-44. [PMID: 24919818 DOI: 10.1111/and.12300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2014] [Indexed: 11/30/2022] Open
Abstract
Genes located on Y chromosome and expressed in testis are likely to be involved in spermatogenesis. TTTY2 is a Y-linked multicopy gene family of unknown function that includes TTTY2L2A and TTTY2L12A at Yq11 and Yp11 loci respectively. Using PCR amplification, we screened for TTTY2L2A- and TTTY2L12A-associated deletions, in 94 Greek men with fertility problems. Patients were divided into three groups as following: group A (n = 28) included men with idiopathic moderate oligozoospermia, group B (n = 34) with idiopathic severe oligozoospermia and azoospermia, and group C (n = 32) with oligo- and azoospermia of various known etiologies. No deletions were detected in group C patients and 50 fertile controls. However, two patients from group A had deletions in TTTY2L2A (7.1%) and six in TTTY2L12A (21.4%), whereas from group B, four patients had deletions in TTTY2L2A (11.8%) and 10 in TTTY2L12A (29.4%). In addition, five patients from both groups A and B (8%) appeared to have deletions in both studied TTTY2 genes, although these are located very far apart. These results indicate that the TTTY2 gene family may play a significant role in spermatogenesis and suggest a possible mechanism of nonhomologous recombinational events that may cause genomic instability and ultimately lead to male infertility.
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Affiliation(s)
- C Yapijakis
- Department of Neurology, University of Athens Medical School, Eginition Hospital, Athens, Greece; Department of Molecular Genetics, "Cephalogenetics" Diagnostic Center, Athens, Greece
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Xie J, Shao C, Xu H, Zhu W, Liu Z, Tang Q, Zhou Y. Deletion mapping of the regions with AMELY from two Chinese males. Leg Med (Tokyo) 2014; 16:290-2. [PMID: 24877595 DOI: 10.1016/j.legalmed.2014.05.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 04/28/2014] [Accepted: 05/05/2014] [Indexed: 10/25/2022]
Abstract
The amelogenin (AMEL) is widely used in many multiplex PCR kits for gender determination. However, the null of amelogenin Y (AMELY) can result in the incorrect genotyping of male samples as females. In this study, we report the deletion of AMELY in two cases with a deletion frequency of 0.019% (2/10526) in our laboratory. The deletion region with AMELY was mapped by using other twelve loci, which shows the class I deletion pattern. Further, the Y chromosome short tandem repeat (Y-STR) typing shows that these two cases share the same haplotype with other two cases from previous reports. The haplogroup of the two cases was predicted as O3 haplogroup with a 100% probability. Altogether, this study will provide evidence to further demonstrate the deletion of AMELY in Chinese population.
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Affiliation(s)
- Jianhui Xie
- Department of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
| | - Chengchen Shao
- Department of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Hongmei Xu
- Department of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Wei Zhu
- Department of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Zhiping Liu
- Department of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Qiqun Tang
- Department of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Yueqin Zhou
- Department of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
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42
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Bartlett JD. Dental enamel development: proteinases and their enamel matrix substrates. ISRN DENTISTRY 2013; 2013:684607. [PMID: 24159389 PMCID: PMC3789414 DOI: 10.1155/2013/684607] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 07/15/2013] [Indexed: 12/31/2022]
Abstract
This review focuses on recent discoveries and delves in detail about what is known about each of the proteins (amelogenin, ameloblastin, and enamelin) and proteinases (matrix metalloproteinase-20 and kallikrein-related peptidase-4) that are secreted into the enamel matrix. After an overview of enamel development, this review focuses on these enamel proteins by describing their nomenclature, tissue expression, functions, proteinase activation, and proteinase substrate specificity. These proteins and their respective null mice and human mutations are also evaluated to shed light on the mechanisms that cause nonsyndromic enamel malformations termed amelogenesis imperfecta. Pertinent controversies are addressed. For example, do any of these proteins have a critical function in addition to their role in enamel development? Does amelogenin initiate crystallite growth, does it inhibit crystallite growth in width and thickness, or does it do neither? Detailed examination of the null mouse literature provides unmistakable clues and/or answers to these questions, and this data is thoroughly analyzed. Striking conclusions from this analysis reveal that widely held paradigms of enamel formation are inadequate. The final section of this review weaves the recent data into a plausible new mechanism by which these enamel matrix proteins support and promote enamel development.
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Affiliation(s)
- John D. Bartlett
- Harvard School of Dental Medicine & Chair, Department of Mineralized Tissue Biology, The Forsyth Institute, 245 First Street, Cambridge MA 02142, USA
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Detection of the deletion on Yp11.2 in a Chinese population. Forensic Sci Int Genet 2013; 8:73-9. [PMID: 24315592 DOI: 10.1016/j.fsigen.2013.07.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2013] [Revised: 06/27/2013] [Accepted: 07/04/2013] [Indexed: 11/20/2022]
Abstract
Sex determination tests based on Amelogenin gene as part of commercial PCR multiplex reaction kits have been widely applied in forensic DNA analysis. Mutations that cause dropout of Y chromosomal Amelogenin gene (AMELY) could lead to errors in gender determination and mixture interpretation. To infer the mechanism and estimate the dropout frequency of AMELY and adjacent Y-STRs, we studied 3 samples with AMELY dropout combined with DYS458 and/or DYS456 and 37 samples with DYS456 dropout. DYS456, DYS458 and AMELY are located in the Yp11.2 region. The singleplex amplification system showed the null alleles could be caused by fragment deletion in Yp11.2 rather than a point mutation in the primer binding region. After detection of the 17 Y-STR and 77 STS markers, the deletion map showed different patterns. The DYS456-AMELY-DYS458 deletion pattern was the largest, breaking from 3.60 Mb to 8.29 Mb in the Y chromosome, and the overall frequency was 0.0077%. The AMELY-DYS458 deletion pattern was broke from 6.74 Mb to 9.17 Mb, with a 0.0155% frequency. The DYS456 negative pattern was concentrated in two main deletion regions, with a 0.8220% frequency. The frequency of all negative pattern was 0.0155%. All the AMELY-DYS458 and DYS456-AMELY-DYS458, and 92% of the DYS456 deletion patterns belonged to Hg O3, the rest belonged to Hg Q. The DYS456 deletion pattern was first reported in Chinese population. The current and previous findings suggest additional gender test for ambiguous sex determination may be required.
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Repnikova EA, Rosenfeld JA, Bailes A, Weber C, Erdman L, McKinney A, Ramsey S, Hashimoto S, Lamb Thrush D, Astbury C, Reshmi SC, Shaffer LG, Gastier-Foster JM, Pyatt RE. Characterization of copy number variation in genomic regions containing STR loci using array comparative genomic hybridization. Forensic Sci Int Genet 2013; 7:475-81. [PMID: 23948316 DOI: 10.1016/j.fsigen.2013.05.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 05/07/2013] [Accepted: 05/23/2013] [Indexed: 10/26/2022]
Abstract
Short tandem repeat (STR) loci are commonly used in forensic casework, familial analysis for human identification, and for monitoring hematopoietic cell engraftment after bone marrow transplant. Unexpected genetic variation leading to sequence and length differences in STR loci can complicate STR typing, and presents challenges in casework interpretation. Copy number variation (CNV) is a relatively recently identified form of genetic variation consisting of genomic regions present at variable copy numbers within an individual compared to a reference genome. Large scale population studies have demonstrated that likely all individuals carry multiple regions with CNV of 1kb in size or greater in their genome. To date, no study correlating genomic regions containing STR loci with CNV has been conducted. In this study, we analyzed results from 32,850 samples sent for clinical array comparative genomic hybridization (CGH) analysis for the presence of CNV at regions containing the 13 CODIS (Combined DNA Index System) STR, and the Amelogenin X (AMELX) and Amelogenin Y (AMELY) loci. Thirty-two individuals with CNV involving STR loci on chromosomes 2, 4, 7, 11, 12, 13, 16, and 21, and twelve with CNV involving the AMELX/AMELY loci were identified. These results were correlated with data from publicly available databases housing information on CNV identified in normal populations and additional clinical cases. These collective results demonstrate the presence of CNV in regions containing 9 of the 13 CODIS STR and AMELX/Y loci. Further characterization of STR profiles within regions of CNV, additional cataloging of these variants in multiple populations, and contributing such examples to the public domain will provide valuable information for reliable use of these loci.
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Affiliation(s)
- Elena A Repnikova
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA
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Veerappa AM, Padakannaya P, Ramachandra NB. Copy number variation-based polymorphism in a new pseudoautosomal region 3 (PAR3) of a human X-chromosome-transposed region (XTR) in the Y chromosome. Funct Integr Genomics 2013; 13:285-93. [PMID: 23708688 DOI: 10.1007/s10142-013-0323-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 03/31/2013] [Accepted: 04/01/2013] [Indexed: 11/26/2022]
Abstract
A 3.5-Mb region of the X chromosome underwent duplication and transposition to the Y chromosome ~5-6 Mya. This X-transposed-region (XTR) originated at Xq21.3 and was inserted at Yp11.2. The two locations have 98.78 % homology and a high concentration of tandem repeats. In whole-genome scans of ten large families with dyslexic members, we identified transposed blocks comprising >102 kb of the Yp11.2 region in its homologous region at Xq21.3 in three females from three different families. Although recombination is known to be limited only to the pseudoautosomal regions (PARs) of the X and Y chromosomes, we report allelic unequal recombination between the XTR region Yp11.2 and Xq21.3, indicating the presence of a new PAR, which we named PAR3. This PAR3 region was also found in 2 % of the general population. An additional layer of justification could be provided from six other dyslexic cases which harbored duplications and deletions in the same Xq21.3 and Yp11.2 regions through allelic unequal recombination.
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Affiliation(s)
- Avinash M Veerappa
- Genomics Laboratory, DOS in Zoology, University of Mysore, Mysore-06, Karnataka, India
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Yadav SK, Kumari A, Ali S. Fate of the human Y chromosome linked genes and loci in prostate cancer cell lines DU145 and LNCaP. BMC Genomics 2013; 14:323. [PMID: 23663454 PMCID: PMC3660188 DOI: 10.1186/1471-2164-14-323] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 05/07/2013] [Indexed: 11/30/2022] Open
Abstract
Background Prostate cancer is a known cause of mortality in men worldwide although the risk factor varies among different ethnic groups. Loss of the Y chromosome is a common chromosomal abnormality observed in the human prostate cancer. Results We screened 51 standard sequence tagged sites (STSs) corresponding to a male-specific region of the Y chromosome (MSY), sequenced the coding region of the SRY gene and assessed the status of the DYZ1 arrays in the human prostate cancer cell lines DU145 and LNCaP. The MSY was found to be intact and coding region of SRY showed no sequence variation in both the cell lines. However, DYZ1 arrays showed sequence and copy number variations. DU145 and LNCaP cells were found to carry 742 and 1945 copies of the DYZ1, respectively per 3.3 pg of genomic DNA. The DYZ1 copies detected in these cell lines are much below the average of that reported in normal human males. Similarly, the number of “TTCCA” repeat and its derivatives within the DYZ1 arrays showed variation compared to those of the normal males. Conclusions Clearly, the DYZ1 is maximally affected in both the cell lines. Work on additional cell lines and biopsied samples would augment our understanding about the susceptibility of this region. Based on the present work, we construe that copy number status of the DYZ1 may be exploited as a supplementary prognostic tool to monitor the occurrence of prostate cancer using biopsied samples.
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Intrachromosomal homologous recombination between inverted amplicons on opposing Y-chromosome arms. Genomics 2013; 102:257-64. [PMID: 23643616 DOI: 10.1016/j.ygeno.2013.04.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 04/23/2013] [Accepted: 04/25/2013] [Indexed: 11/21/2022]
Abstract
Amplicons--large, nearly identical repeats in direct or inverted orientation--are abundant in the male-specific region of the human Y chromosome (MSY) and provide targets for intrachromosomal non-allelic homologous recombination (NAHR). Thus far, NAHR events resulting in deletions, duplications, inversions, or isodicentric chromosomes have been reported only for amplicon pairs located exclusively on the short arm (Yp) or the long arm (Yq). Here we report our finding of four men with Y chromosomes that evidently formed by intrachromosomal NAHR between inverted repeat pairs comprising one amplicon on Yp and one amplicon on Yq. In two men with spermatogenic failure, sister-chromatid crossing-over resulted in pseudoisoYp chromosome formation and loss of distal Yq. In two men with normal spermatogenesis, intrachromatid crossing-over generated pericentric inversions. These findings highlight the recombinogenic nature of the MSY, as intrachromosomal NAHR occurs for nearly all Y-chromosome amplicon pairs, even those located on opposing chromosome arms.
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Deletion of amelogenin Y-locus in forensics: literature revision and description of a novel method for sex confirmation. J Forensic Leg Med 2013; 20:387-91. [PMID: 23756502 DOI: 10.1016/j.jflm.2013.03.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 02/07/2013] [Accepted: 03/03/2013] [Indexed: 11/22/2022]
Abstract
Today, the molecular technique routinely for sex determination in forensics is based the detection of length variations in the X-Y homologous amelogenin gene (AMELX and AMELY). In humans, the amelogenin gene is a single-copy gene located on Xp22.1-Xp22.3 and Yp11.2; the simultaneous detection of the X and Y alleles using polymerase chain reaction (PCR) can lead to gender determination. Several studies have shown that normal males may be typed as females with this test: AMELY deletions may result in no product of amplification and normal males being typed as female as a result of the test (negative male). Considering the consequences of the result obtained using only the amelogenin marker, and the related potential difficulties in interpreting the results, the gender misinterpretation may be troublesome in clinical practice and in forensic casework. In this article, beginning with a review of the incidence of gender-testing failures among different populations, and with the different strategies proposed in the literature in case of doubt regarding the presence of deleted AMEL in the DNA profile, we propose a method for the identification of samples with deleted AMEL that can be applied, as an additional assay, in case of doubt regarding PCR results of sex determination.
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Wang Q, Xue Y, Zhang Y, Long Q, Yang F, Turner D, Fitzgerald T, Ng B, Zhao Y, Chen Y, Liu Q, Yang W, Han D, Quail M, Swerdlow H, Burton J, Fahey C, Ning Z, Hurles M, Carter N, Yang H, Tyler-Smith C, Tyler-Smith C. Genetic basis of Y-linked hearing impairment. Am J Hum Genet 2013; 92:301-6. [PMID: 23352258 DOI: 10.1016/j.ajhg.2012.12.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 11/19/2012] [Accepted: 12/21/2012] [Indexed: 01/21/2023] Open
Abstract
A single Mendelian trait has been mapped to the human Y chromosome: Y-linked hearing impairment. The molecular basis of this disorder is unknown. Here, we report the detailed characterization of the DFNY1 Y chromosome and its comparison with a closely related Y chromosome from an unaffected branch of the family. The DFNY1 chromosome carries a complex rearrangement, including duplication of several noncontiguous segments of the Y chromosome and insertion of ∼160 kb of DNA from chromosome 1, in the pericentric region of Yp. This segment of chromosome 1 is derived entirely from within a known hearing impairment locus, DFNA49. We suggest that a third copy of one or more genes from the shared segment of chromosome 1 might be responsible for the hearing-loss phenotype.
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Hu JCC, Chan HC, Simmer SG, Seymen F, Richardson AS, Hu Y, Milkovich RN, Estrella NMRP, Yildirim M, Bayram M, Chen CF, Simmer JP. Amelogenesis imperfecta in two families with defined AMELX deletions in ARHGAP6. PLoS One 2012; 7:e52052. [PMID: 23251683 PMCID: PMC3522662 DOI: 10.1371/journal.pone.0052052] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 11/12/2012] [Indexed: 11/18/2022] Open
Abstract
Amelogenesis imperfecta (AI) is a group of inherited conditions featuring isolated enamel malformations. About 5% of AI cases show an X-linked pattern of inheritance, which are caused by mutations in AMELX. In humans there are two, non-allelic amelogenin genes: AMELX (Xp22.3) and AMELY (Yp11.2). About 90% of amelogenin expression is from AMELX, which is nested within intron 1 of the gene encoding Rho GTPase activating protein 6 (ARHGAP6). We recruited two AI families and determined that their disease-causing mutations were partial deletions in ARHGAP6 that completely deleted AMELX. Affected males in both families had a distinctive enamel phenotype resembling "snow-capped" teeth. The 96,240 bp deletion in family 1 was confined to intron 1 of ARHGAP6 (g.302534_398773del96240), but removed alternative ARHGAP6 promoters 1c and 1d. Analyses of developing teeth in mice showed that ARHGAP6 is not expressed from these promoters in ameloblasts. The 52,654 bp deletion in family 2 (g.363924_416577del52654insA) removed ARHGAP6 promoter 1d and exon 2, precluding normal expression of ARHGAP6. The male proband of family 2 had slightly thinner enamel with greater surface roughness, but exhibited the same pattern of enamel malformations characteristic of males in family 1, which themselves showed minor variations in their enamel phenotypes. We conclude that the enamel defects in both families were caused by amelogenin insufficiency, that deletion of AMELX results in males with a characteristic snow-capped enamel phenotype, and failed ARHGAP6 expression did not appreciably alter the severity of enamel defects when AMELX was absent.
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Affiliation(s)
- Jan C-C Hu
- Department of Biologic and Materials Sciences, University of Michigan School of Dentistry, Ann Arbor, Michigan, USA.
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