1
|
Guyon L, Guez J, Toupance B, Heyer E, Chaix R. Patrilineal segmentary systems provide a peaceful explanation for the post-Neolithic Y-chromosome bottleneck. Nat Commun 2024; 15:3243. [PMID: 38658560 PMCID: PMC11043392 DOI: 10.1038/s41467-024-47618-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 04/08/2024] [Indexed: 04/26/2024] Open
Abstract
Studies have found a pronounced decline in male effective population sizes worldwide around 3000-5000 years ago. This bottleneck was not observed for female effective population sizes, which continued to increase over time. Until now, this remarkable genetic pattern was interpreted as the result of an ancient structuring of human populations into patrilineal groups (gathering closely related males) violently competing with each other. In this scenario, violence is responsible for the repeated extinctions of patrilineal groups, leading to a significant reduction in male effective population size. Here, we propose an alternative hypothesis by modelling a segmentary patrilineal system based on anthropological literature. We show that variance in reproductive success between patrilineal groups, combined with lineal fission (i.e., the splitting of a group into two new groups of patrilineally related individuals), can lead to a substantial reduction in the male effective population size without resorting to the violence hypothesis. Thus, a peaceful explanation involving ancient changes in social structures, linked to global changes in subsistence systems, may be sufficient to explain the reported decline in Y-chromosome diversity.
Collapse
Affiliation(s)
- Léa Guyon
- Eco-Anthropologie (UMR 7206), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, Paris, 75116, France.
| | - Jérémy Guez
- Eco-Anthropologie (UMR 7206), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, Paris, 75116, France
- Université Paris-Saclay, CNRS, INRIA, Laboratoire Interdisciplinaire des Sciences du Numérique, Orsay, 91400, France
| | - Bruno Toupance
- Eco-Anthropologie (UMR 7206), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, Paris, 75116, France
- Université Paris Cité, Eco-anthropologie, Paris, F-75006, France
| | - Evelyne Heyer
- Eco-Anthropologie (UMR 7206), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, Paris, 75116, France
| | - Raphaëlle Chaix
- Eco-Anthropologie (UMR 7206), Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, Paris, 75116, France.
| |
Collapse
|
2
|
Lampitto M, Barchi M. Recent advances in mechanisms ensuring the pairing, synapsis and segregation of XY chromosomes in mice and humans. Cell Mol Life Sci 2024; 81:194. [PMID: 38653846 DOI: 10.1007/s00018-024-05216-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/04/2024] [Accepted: 03/20/2024] [Indexed: 04/25/2024]
Abstract
Sex chromosome aneuploidies are among the most common variations in human whole chromosome copy numbers, with an estimated prevalence in the general population of 1:400 to 1:1400 live births. Unlike whole-chromosome aneuploidies of autosomes, those of sex chromosomes, such as the 47, XXY aneuploidy that causes Klinefelter Syndrome (KS), often originate from the paternal side, caused by a lack of crossover (CO) formation between the X and Y chromosomes. COs must form between all chromosome pairs to pass meiotic checkpoints and are the product of meiotic recombination that occurs between homologous sequences of parental chromosomes. Recombination between male sex chromosomes is more challenging compared to both autosomes and sex chromosomes in females, as it is restricted within a short region of homology between X and Y, called the pseudo-autosomal region (PAR). However, in normal individuals, CO formation occurs in PAR with a higher frequency than in any other region, indicating the presence of mechanisms that promote the initiation and processing of recombination in each meiotic division. In recent years, research has made great strides in identifying genes and mechanisms that facilitate CO formation in the PAR. Here, we outline the most recent and relevant findings in this field. XY chromosome aneuploidy in humans has broad-reaching effects, contributing significantly also to Turner syndrome, spontaneous abortions, oligospermia, and even infertility. Thus, in the years to come, the identification of genes and mechanisms beyond XY aneuploidy is expected to have an impact on the genetic counseling of a wide number of families and adults affected by these disorders.
Collapse
Affiliation(s)
- Matteo Lampitto
- Section of Anatomy, Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Marco Barchi
- Section of Anatomy, Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy.
- Section of Anatomy, Department of Medicine, Saint Camillus International University of Health Sciences, Rome, Italy.
| |
Collapse
|
3
|
Gutiérrez-Hurtado IA, Sánchez-Méndez AD, Becerra-Loaiza DS, Rangel-Villalobos H, Torres-Carrillo N, Gallegos-Arreola MP, Aguilar-Velázquez JA. Loss of the Y Chromosome: A Review of Molecular Mechanisms, Age Inference, and Implications for Men's Health. Int J Mol Sci 2024; 25:4230. [PMID: 38673816 DOI: 10.3390/ijms25084230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 03/29/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Until a few years ago, it was believed that the gradual mosaic loss of the Y chromosome (mLOY) was a normal age-related process. However, it is now known that mLOY is associated with a wide variety of pathologies in men, such as cardiovascular diseases, neurodegenerative disorders, and many types of cancer. Nevertheless, the mechanisms that generate mLOY in men have not been studied so far. This task is of great importance because it will allow focusing on possible methods of prophylaxis or therapy for diseases associated with mLOY. On the other hand, it would allow better understanding of mLOY as a possible marker for inferring the age of male samples in cases of human identification. Due to the above, in this work, a comprehensive review of the literature was conducted, presenting the most relevant information on the possible molecular mechanisms by which mLOY is generated, as well as its implications for men's health and its possible use as a marker to infer age.
Collapse
Affiliation(s)
- Itzae Adonai Gutiérrez-Hurtado
- Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Guadalajara 44340, Jalisco, Mexico
| | - Astrid Desireé Sánchez-Méndez
- Laboratorio de Ciencias Morfológico Forenses y Medicina Molecular, Departamento de Morfología, Centro Universitario de Ciencias de la Salud, Guadalajara 44340, Jalisco, Mexico
- Doctorado en Genética Humana, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | | | - Héctor Rangel-Villalobos
- Instituto de Investigación en Genética Molecular, Departamento de Ciencias Médicas y de la Vida, Centro Universitario de la Ciénega, Universidad de Guadalajara, Ocotlán 47820, Jalisco, Mexico
| | - Norma Torres-Carrillo
- Departamento de Microbiología y Patología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | - Martha Patricia Gallegos-Arreola
- División de Genética, Centro de Investigación Biomédica de Occidente (CIBO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara 44340, Jalisco, Mexico
| | - José Alonso Aguilar-Velázquez
- Laboratorio de Ciencias Morfológico Forenses y Medicina Molecular, Departamento de Morfología, Centro Universitario de Ciencias de la Salud, Guadalajara 44340, Jalisco, Mexico
| |
Collapse
|
4
|
Eskandarion MR, Tabrizi AA, Shirkoohi R, Raoofian R, Naji M, Pazhoomand R, Salari H, Samadirad B, Sabouri A, Zohour MM, Namazi H, Farhadi P, Baratieh Z, Sayyari M, Dadgarmoghaddam M, Safdarian E, Nikbakht A, Golshan F, Baybordi F, Madhaji E, ShohodiFar S, Tabasi M, Mohebbi R. Haplotype diversity of 17 Y-STR in the Iranian population. BMC Genomics 2024; 25:332. [PMID: 38566001 PMCID: PMC10986111 DOI: 10.1186/s12864-024-10217-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 03/12/2024] [Indexed: 04/04/2024] Open
Abstract
The current study aimed to evaluate Y chromosome haplotypes obtained from 1353 unrelated Iranian males using the AmpFlSTRTM YfilerTM kit; 1353 out of the 1353 identified haplotypes were unique. The haplotype diversity (HD) and discriminating capacity (DC) values were 1.00000 and 0.997, respectively. Analysis of genetic distance was performed using molecular variance (AMOVA) and multidimensional scaling plots (MDS), revealing a statistically significant difference between the study population and previous data reported for other Iranian populations and other neighboring countries. The present findings are likely to be useful for forensic casework analyses and kinship investigations.
Collapse
Affiliation(s)
- Mohammad Reza Eskandarion
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
- Cancer Research Institute, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Reza Shirkoohi
- Cancer Research Institute, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Raoofian
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | - Masume Naji
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | - Reza Pazhoomand
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | - Hooman Salari
- Plant Genetics and Production, Razi University, Kermanshah, Iran
| | - Bahram Samadirad
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | - Alireza Sabouri
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | | | - Hadi Namazi
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | - Pegah Farhadi
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | - Zohre Baratieh
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | - Minoo Sayyari
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | - Maliheh Dadgarmoghaddam
- Department of Community Medicine, School of Medicine, Mashhad University of Medical Science, Mashhad, Iran
| | - Esmat Safdarian
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | - Afrooz Nikbakht
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | - Farnaz Golshan
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | - Fatemeh Baybordi
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | - Elham Madhaji
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | - Shadi ShohodiFar
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | - Mohsen Tabasi
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
- Department of Molecular Biology, Pasteur Institute of Iran, Pasteur Ave, Tehran, Iran
| | - Ramezan Mohebbi
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| |
Collapse
|
5
|
Englinger B, Shariat SF. Re: The Complete Sequence of a Human Y Chromosome. Eur Urol 2024; 85:393. [PMID: 38007312 DOI: 10.1016/j.eururo.2023.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 11/14/2023] [Indexed: 11/27/2023]
Affiliation(s)
- Bernhard Englinger
- Department of Urology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria; Center for Cancer Research and Comprehensive Cancer Center, Medical University Vienna, Vienna, Austria.
| | - Shahrokh F Shariat
- Department of Urology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria; Department of Urology, Weill Cornell Medical College, New York, USA; Department of Urology, University of Texas Southwestern, Dallas, TX, USA; Department of Urology, Second Faculty of Medicine, Charles University, Prague, Czechia; Institute for Urology, University of Jordan, Amman, Jordan
| |
Collapse
|
6
|
Bretschneider A, Mazanec J, Wittmeier P, Flux AL, Schmidt D, Hummel S. X-chromosomal STRs in aDNA kinship analysis. Anthropol Anz 2024; 81:131-138. [PMID: 37580949 DOI: 10.1127/anthranz/2023/1714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 06/27/2023] [Accepted: 06/27/2023] [Indexed: 08/16/2023]
Abstract
The analysis of ancient DNA (aDNA) from human skeletal remains can provide useful insights when investigating archaeological finds. One popular application of aDNA is to examine genealogical relationships between individuals recovered at the same archaeological site. For the reconstruction of genealogical relationships, several genetic markers are commonly used: autosomal STRs, mitochondrial lineages (based on SNP-analysis) and Y-chromosomal haplotypes (based on Y-STR-analysis). In this paper, we present the additional opportunities that X-STRs provide in aDNA kinship reconstruction, especially in deficiency cases and for the examination of father-daughter relationships. Possible applications are demonstrated on a range of different kinship reconstructions: confirmation of half-siblingship in the Lichtenstein cave (Germany), exclusion of two potential father-daughter relationships in Goslar (Germany), investigation of three siblingships in Boilstädt (Germany) as well as the confirmation of a father-daughter relationship in Stolpe (Germany). This study shows that the analysis of X-STRs can contribute to the investigation of relationship constellations otherwise difficult to approach (e.g. father-daughter relationships) and that X-STRs are useful to support and complement autosomal STRs, mtDNA and Y-STR data.
Collapse
Affiliation(s)
- Anna Bretschneider
- Department of Historical Anthropology & Human Ecology, University of Göttingen, Bürgerstraße 50, 37073, Göttingen, Germany
| | - Janine Mazanec
- Department of Historical Anthropology & Human Ecology, University of Göttingen, Bürgerstraße 50, 37073, Göttingen, Germany
| | - Patrick Wittmeier
- Department of Historical Anthropology & Human Ecology, University of Göttingen, Bürgerstraße 50, 37073, Göttingen, Germany
| | - Anna Lena Flux
- Department of Historical Anthropology & Human Ecology, University of Göttingen, Bürgerstraße 50, 37073, Göttingen, Germany
| | - Diane Schmidt
- Hessisches Landeskriminalamt, Hölderlinstraße 1-5, 65187, Wiesbaden, Germany
| | - Susanne Hummel
- Department of Historical Anthropology & Human Ecology, University of Göttingen, Bürgerstraße 50, 37073, Göttingen, Germany
| |
Collapse
|
7
|
Mattisson J, Halvardson J, Davies H, Bruhn-Olszewska B, Olszewski P, Danielsson M, Bjurling J, Lindberg A, Zaghlool A, Rychlicka-Buniowska E, Dumanski JP, Forsberg LA. Loss of chromosome Y in regulatory T cells. BMC Genomics 2024; 25:243. [PMID: 38443832 PMCID: PMC10913415 DOI: 10.1186/s12864-024-10168-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 02/28/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Mosaic loss of chromosome Y (LOY) in leukocytes is the most prevalent somatic aneuploidy in aging humans. Men with LOY have increased risks of all-cause mortality and the major causes of death, including many forms of cancer. It has been suggested that the association between LOY and disease risk depends on what type of leukocyte is affected with Y loss, with prostate cancer patients showing higher levels of LOY in CD4 + T lymphocytes. In previous studies, Y loss has however been observed at relatively low levels in this cell type. This motivated us to investigate whether specific subsets of CD4 + T lymphocytes are particularly affected by LOY. Publicly available, T lymphocyte enriched, single-cell RNA sequencing datasets from patients with liver, lung or colorectal cancer were used to study how LOY affects different subtypes of T lymphocyte. To validate the observations from the public data, we also generated a single-cell RNA sequencing dataset comprised of 23 PBMC samples and 32 CD4 + T lymphocytes enriched samples. RESULTS Regulatory T cells had significantly more LOY than any other studied T lymphocytes subtype. Furthermore, LOY in regulatory T cells increased the ratio of regulatory T cells compared with other T lymphocyte subtypes, indicating an effect of Y loss on lymphocyte differentiation. This was supported by developmental trajectory analysis of CD4 + T lymphocytes culminating in the regulatory T cells cluster most heavily affected by LOY. Finally, we identify dysregulation of 465 genes in regulatory T cells with Y loss, many involved in the immunosuppressive functions and development of regulatory T cells. CONCLUSIONS Here, we show that regulatory T cells are particularly affected by Y loss, resulting in an increased fraction of regulatory T cells and dysregulated immune functions. Considering that regulatory T cells plays a critical role in the process of immunosuppression; this enrichment for regulatory T cells with LOY might contribute to the increased risk for cancer observed among men with Y loss in leukocytes.
Collapse
Affiliation(s)
- Jonas Mattisson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jonatan Halvardson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Hanna Davies
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Bożena Bruhn-Olszewska
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Paweł Olszewski
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Poland
| | - Marcus Danielsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Josefin Bjurling
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Amanda Lindberg
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ammar Zaghlool
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Jan P Dumanski
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Poland
| | - Lars A Forsberg
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- The Beijer Laboratory, Uppsala University, Uppsala, Sweden
| |
Collapse
|
8
|
Watahiki H, Fujii K, Fukagawa T, Mita Y, Kitayama T, Mizuno N. Y chromosome haplogroup N in a Japanese population is classified into three subclades, and two DYS385 loci, a duplicated Y-STR, are duplicated again in subclade N-M1819. Leg Med (Tokyo) 2024; 67:102390. [PMID: 38190775 DOI: 10.1016/j.legalmed.2023.102390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/21/2023] [Accepted: 12/28/2023] [Indexed: 01/10/2024]
Abstract
DYS385 is one of the major Y chromosome short tandem repeats (Y-STRs) in forensic genetics and exists as 2 copies in the human Y chromosome palindrome P4 region. In this study, we found that some samples were estimated to have ≥ 4 copies of DYS385 in Y chromosome haplogroup N in a Japanese population. Y chromosome haplogroup N is distributed widely in eastern/central Asia, Siberia, and eastern/northern Europe, and is also observed in Japan; however, little is known about haplogroup N subclades in the Japanese population. To reveal the link between increased DYS385 copy number and haplogroup N subclades, we sequenced single nucleotide polymorphisms to classify the subclades. As a result, the Japanese Y chromosomes of haplogroup N were classified into three subclades, and an increased DYS385 copy number was specific to subclade N-M1819* (N1b2*). These results are of use in forensic DNA analysis because Y-STR copy number is important for the interpretation of Y-STR typing results of male DNA mixtures and kinship analysis. We also found that DYS458.1 microvariants (DYS458 intermediate alleles with single-nucleotide insertion) were observed only in subclade N-CTS962 (N1b1b∼) samples. Given that previous studies reported that DYS458.1 microvariants are observed in Y chromosomes of haplogroup N in other populations, DYS458.1 might be used to infer haplogroup N subclades without limitation to the Japanese population. The results of this study will be beneficial not only to forensic genetics but also to anthropological studies.
Collapse
Affiliation(s)
- Haruhiko Watahiki
- National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan.
| | - Koji Fujii
- National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Takashi Fukagawa
- National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Yusuke Mita
- National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Tetsushi Kitayama
- National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Natsuko Mizuno
- National Research Institute of Police Science, 6-3-1, Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| |
Collapse
|
9
|
Wang Y, Sano S. Why Y matters? The implication of loss of Y chromosome in blood and cancer. Cancer Sci 2024; 115:706-714. [PMID: 38258457 PMCID: PMC10921008 DOI: 10.1111/cas.16072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/23/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
Hematopoietic mosaic loss of Y chromosome (mLOY) has emerged as a potential male-specific accelerator of biological aging, increasing the risk of various age-related diseases, including cancer. Importantly, mLOY is not confined to hematopoietic cells; its presence has also been observed in nonhematological cancer cells, with the impact of this presence previously unknown. Recent studies have revealed that, whether occurring in leukocytes or cancer cells, mLOY plays a role in promoting the development of an immunosuppressive tumor microenvironment. This occurs through the modulation of tumor-infiltrating immune cells, ultimately enabling cancer cells to evade the vigilant immune system. In this review, we illuminate recent progress concerning the effects of hematopoietic mLOY and cancer mLOY on cancer progression. Examining cancer progression from the perspective of LOY adds a new layer to our understanding of cancer immunity, promising insights that hold the potential to identify innovative and potent immunotherapy targets for cancer.
Collapse
Affiliation(s)
- Ying Wang
- Department of CardiologyThe Second Affiliated Hospital of Army Medical UniversityChongqingChina
| | - Soichi Sano
- Laboratory of Cardiovascular MosaicismNational Cerebral and Cardiovascular CenterOsakaJapan
| |
Collapse
|
10
|
Graziani A, Merico M, Grande G, Di Mambro A, Vinanzi C, Rocca MS, Selice R, Ferlin A. A cryptozoospermic infertile male with Y chromosome AZFc microdeletion and low FSH levels due to a simultaneous polymorphism in the FSHB gene: a case report. Hum Reprod 2024; 39:504-508. [PMID: 38224259 DOI: 10.1093/humrep/dead277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 12/13/2023] [Indexed: 01/16/2024] Open
Abstract
Genetic causes account for 10-15% of male factor infertility, making the genetic investigation an essential and useful tool, mainly in azoospermic and severely oligozoospermic men. In these patients, the most frequent findings are chromosomal abnormalities and Y chromosome long arm microdeletions, which cause a primary severe spermatogenic impairment with classically increased levels of FSH. On the other hand, polymorphisms in the FSH receptor (FSHR) and FSH beta chain (FSHB) genes have been associated with different FSH plasma levels, due to variations in the receptor sensitivity (FSHR) or in the production of FSH from the pituitary gland (FSHB). Here, we describe an unusual patient with a combined genetic alteration (classic AZFc deletion of the Y chromosome and TT homozygosity for the -211G>T polymorphism in the FSHB gene (rs10835638)), presenting with cryptozoospermia, severe hypospermatogenesis, and normal LH and testosterone plasma concentrations, but low FSH levels. The patient partially benefitted from treatment with FSH (150 IU three times/week for 6 months) which allowed him to cryopreserve enough motile spermatozoa to be used for intracytoplasmic sperm injection. According to our knowledge, this is the first report of an infertile man with AZFc microdeletion with low FSH plasma concentrations related to homozygosity for the -211G>T polymorphism in the FSHB gene.
Collapse
Affiliation(s)
| | - Maurizio Merico
- Department of Systems Medicine, Unit of Andrology and Reproductive Medicine, University Hospital of Padova, Padova, Italy
| | - Giuseppe Grande
- Department of Systems Medicine, Unit of Andrology and Reproductive Medicine, University Hospital of Padova, Padova, Italy
| | - Antonella Di Mambro
- Department of Systems Medicine, Unit of Andrology and Reproductive Medicine, University Hospital of Padova, Padova, Italy
| | - Cinzia Vinanzi
- Department of Systems Medicine, Unit of Andrology and Reproductive Medicine, University Hospital of Padova, Padova, Italy
| | - Maria Santa Rocca
- Department of Systems Medicine, Unit of Andrology and Reproductive Medicine, University Hospital of Padova, Padova, Italy
| | - Riccardo Selice
- Department of Systems Medicine, Unit of Andrology and Reproductive Medicine, University Hospital of Padova, Padova, Italy
| | - Alberto Ferlin
- Department of Medicine, University of Padova, Padova, Italy
- Department of Systems Medicine, Unit of Andrology and Reproductive Medicine, University Hospital of Padova, Padova, Italy
| |
Collapse
|
11
|
Xie S, Ma Y, Liu Y, Tao D, Wang Z, Yang Y. Primary azoospermia factor C duplication associated with spermatogenic impariment: a case-control study based on Y-chromosome haplogrouping in a Han Chinese population. Andrology 2024; 12:561-569. [PMID: 37594248 DOI: 10.1111/andr.13510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 06/22/2023] [Accepted: 08/06/2023] [Indexed: 08/19/2023]
Abstract
BACKGROUND Azoospermia factor C (AZFc) in the male-specific region of Y-chromosome (MSY) presents wide structure variation mainly due to frequent non-allele homologous recombination, leading to significant copy number variation of the AZFc-linked coding sequences involving in spermatogenesis. A large number of studies had been conducted to investigate the association between AZFc deletions and male infertility in certain Y chromosome genetic backgrounds, however, the influence of primary AZFc duplication on spermatogenesis remained controversial and the cause of the discrepant outcomes is unknown. METHODS In the present study, a total of 1,102 unrelated Han Chinese males without any detectable AZF deletions were recruited from 2014 to 2019, including 411 controls with normozoospermia and 691 patients with idiopathic spermatogenic failure. Using multiple paralog ratio tests (PRTs), the structure duplications were classified by the copy number of the AZFc-linked amplicons and genes. The Y-chromosome haplogroup (Y-hg) was categorized by genetyping of MSY-linked polymorphism loci. The association of primary AZFc duplication with spermatogenic phenotype was investigated in males with the same Y-hg. RESULTS Within Y-hg O3* group, the frequency of the gr/gr duplication in patients is significantly higher than that of controls (P = 1.29×10-3 , odds ratio (OR) 7.64, 95% confidence interval (CI) 1.79-32.57). Moreover, Y-hg O3* males with the gr/gr duplication presented a significantly lower sperm production compared with non-AZFc duplicated ones (sperm concentration: P = 1.46×10-3 ; total sperm count: P = 1.82 ×10-3 ). The b2/b3 duplication were identified clustered in Y-hg Cα2*, and the significant difference in the distribution was not observed between patients with spermatogenic failure and controls. CONCLUSION The results suggest that, in the Han Chinese population, the gr/gr duplication is a predisposing genetic factor for spermatogenic impairment in males harboring Y-hg O3* . Meanwhile, the b2/b3 duplication may be fixed on a yet-unidentified subbranch of Y-hg Cα2* without significantly deleterious effect on spermatogenesis. Our findings provide evidence that the difference in the Y-hg composition may cause the discrepancy on the association of AZFc duplication with spermatogenic failure among the studied populations.
Collapse
Affiliation(s)
- Shengyu Xie
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China School of medicine, Sichuan University, Chengdu, China
| | - Yongyi Ma
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China School of medicine, Sichuan University, Chengdu, China
- Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, China
| | - Yunqiang Liu
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China School of medicine, Sichuan University, Chengdu, China
| | - Dachang Tao
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China School of medicine, Sichuan University, Chengdu, China
| | - Zhaokun Wang
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China School of medicine, Sichuan University, Chengdu, China
| | - Yuan Yang
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China School of medicine, Sichuan University, Chengdu, China
| |
Collapse
|
12
|
Krausz C, Navarro-Costa P, Wilke M, Tüttelmann F. EAA/EMQN best practice guidelines for molecular diagnosis of Y-chromosomal microdeletions: State of the art 2023. Andrology 2024; 12:487-504. [PMID: 37674303 DOI: 10.1111/andr.13514] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 09/08/2023]
Abstract
Testing for AZoospermia Factor (AZF) deletions of the Y chromosome is a key component of the diagnostic workup of azoospermic and severely oligozoospermic men. This revision of the 2013 European Academy of Andrology (EAA) and EMQN CIC (previously known as the European Molecular Genetics Quality Network) laboratory guidelines summarizes recent clinically relevant advances and provides an update on the results of the external quality assessment program jointly offered by both organizations. A basic multiplex PCR reaction followed by a deletion extension analysis remains the gold-standard methodology to detect and correctly interpret AZF deletions. Recent data have led to an update of the sY84 reverse primer sequence, as well as to a refinement of what were previously considered as interchangeable border markers for AZFa and AZFb deletion breakpoints. More specifically, sY83 and sY143 are no longer recommended for the deletion extension analysis, leaving sY1064 and sY1192, respectively, as first-choice markers. Despite the transition, currently underway in several countries, toward a diagnosis based on certified kits, it should be noted that many of these commercial products are not recommended due to an unnecessarily high number of tested markers, and none of those currently available are, to the best of our knowledge, in accordance with the new first-choice markers for the deletion extension analysis. The gr/gr partial AZFc deletion remains a population-specific risk factor for impaired sperm production and a predisposing factor for testicular germ cell tumors. Testing for this deletion type is, as before, left at the discretion of the diagnostic labs and referring clinicians. Annual participation in an external quality control program is strongly encouraged, as the 22-year experience of the EMQN/EAA scheme clearly demonstrates a steep decline in diagnostic errors and an improvement in reporting practice.
Collapse
Affiliation(s)
- Csilla Krausz
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, University Hospital Careggi, Florence, Italy
| | - Paulo Navarro-Costa
- EvoReproMed Lab, Environmental Health Institute (ISAMB), Associate Laboratory TERRA, Faculty of Medicine, University of Lisbon, Lisbon, Portugal
- Gulbenkian Science Institute, Oeiras, Portugal
| | - Martina Wilke
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Frank Tüttelmann
- Institute of Reproductive Genetics, University of Münster, Münster, Germany
| |
Collapse
|
13
|
Li JP, Zhang FB, Li LJ, Chen WK, Wu JG, Tian YH, Liang ZY, Chen C, Jin F. Y chromosome polymorphisms contribute to an increased risk of non-obstructive azoospermia: a retrospective study of 32,055 Chinese men. J Assist Reprod Genet 2024; 41:757-765. [PMID: 38270748 PMCID: PMC10957810 DOI: 10.1007/s10815-024-03022-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 01/04/2024] [Indexed: 01/26/2024] Open
Abstract
PURPOSE To investigate the prevalence of Y chromosome polymorphisms in Chinese men and analyze their associations with male infertility and female adverse pregnancy outcomes. METHODS The clinical data of 32,055 Chinese men who underwent karyotype analysis from October 2014 to September 2019 were collected. Fisher's exact test, chi-square test, or Kruskal-Wallis test was used to analyze the effects of Y chromosome polymorphism on semen parameters, azoospermia factor (AZF) microdeletions, and female adverse pregnancy outcomes. RESULTS The incidence of Y chromosome polymorphic variants was 1.19% (381/32,055) in Chinese men. The incidence of non-obstructive azoospermia (NOA) was significantly higher in men with the Yqh- variant than that in men with normal karyotype and other Y chromosome polymorphic variants (p < 0.050). The incidence of AZF microdeletions was significantly different among the normal karyotype and different Y chromosome polymorphic variant groups (p < 0.001). The detection rate of AZF microdeletions was 28.92% (24/83) in the Yqh- group and 2.50% (3/120) in the Y ≤ 21 group. The AZFb + c region was the most common AZF microdeletion (78.57%, 22/28), followed by AZFc microdeletion (7.14%,2/28) in NOA patients with Yqh- variants. There was no significant difference in the distribution of female adverse pregnancy outcomes among the normal karyotype and different Y chromosome polymorphic variant groups (p = 0.528). CONCLUSIONS Patients with 46,XYqh- variant have a higher incidence of NOA and AZF microdeletions than patients with normal karyotype and other Y chromosome polymorphic variants. Y chromosome polymorphic variants do not affect female adverse pregnancy outcomes.
Collapse
Affiliation(s)
- Jing-Ping Li
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Feng-Bin Zhang
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Le-Jun Li
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Wei-Kang Chen
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Jing-Gen Wu
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Yong-Hong Tian
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Zhong-Yan Liang
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Chong Chen
- Department of Ultrasound, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Fan Jin
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China.
| |
Collapse
|
14
|
Xin Z, Xin J, Jun L, Lan Y, Li-Xin Z, Cai-Xia L, Jiang H, Li J. Paternal genetic structure analysis of the modern Han populations based on Y-SNP and Y-STR. Yi Chuan 2024; 46:149-167. [PMID: 38340005 DOI: 10.16288/j.yczz.23-260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
Abstract
The Han populations represent the largest ethnic group in China. Previous studies have primarily focused on investigating their genetic origins, migration and integration, as well as paternal genetic relationships within specific regional Han populations. However, a comprehensive analysis of the global paternal genetic structure of Han populations is lacking. In this study, we performed Y-chromosome sequencing on 362 unrelated male samples from Chinese Han individuals collected from Qinghai, Sichuan and Liaoning provinces. We then integrated relevant data from reported studies. Our final dataset comprised 1830 samples from 16 Han populations across 15 provinces in China, encompassing information on 89 Y-SNPs and 16 Y-STRs. Statistical analyses were conducted to assess Y-STR haplotype diversity (HD) and Y-SNP haplogroup frequencies. Additionally, we employed principal component analysis (PCA), phylogenetic tree and haplotype network to explore genetic differentiation within Han populations and the genetic relationships between Han populations and ethnic minorities surrounding them. Our results demonstrated that the O-M175 haplogroup represents the predominant paternal lineage in Han populations, with frequencies ranging from 60.53% (Qinghai Han) to 92.7% (Guangdong Han). Moreover, the subclades downstream of O-M175 showed distinct regional variations in their distribution patterns. The O2-M122 haplogroup was prevalent in all Han populations and demonstrated a gradual decline in frequency from north to south. Conversely, the distribution frequency of the O1b-M268 haplogroup decreased from south to north, particularly showed significant presence among Han populations in the Lingnan region. Haplogroup O1a-M119 distributed more frequently in the central Han populations. Our findings revealed that Chinese Han populations can be categorized into three subgroups: northern, central, and southern. Notably, there were significant differences among Han in Qinghai and other regions. Regarding the genetic relationships between Han populations and surrounding ethnic minorities, we observed a closer genetic affinity between different Han populations, but northern Han demonstrated a stronger relationship with the Hui ethnic group, while southern Han exhibited a closer connection with the Gelao and Li ethnic groups. In summary, this study presented a systematic analysis of haplogroup distribution, genetic substructure of Han populations and genetic relationships between Han populations and surrounding ethnic minorities based on 89 Y-SNPs and 16 Y-STRs systematically. Our research supplemented valuable insights into population genetics and forensic genetics, and provided data support for the forensic application of Y chromosome. The integration of Y-SNP haplogroups with Y-STR haplotypes offers enhanced understanding of the genetic substructure within Han populations, which holds significance for both population genetics research and forensic science applications.
Collapse
Affiliation(s)
- Zhu Xin
- Institute of Forensic Medicine, Guizhou Medical University, Guiyang 550004, China
- Key Laboratory of Forensic Genetics, Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing 100038, China
| | - Jin Xin
- Public Security Department of Hainan Province, Haikou 570203, China
| | - Liu Jun
- Key Laboratory of Forensic Genetics, Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing 100038, China
- Shanxi Medical University, Taiyuan 030001, China
| | - Yang Lan
- Key Laboratory of Forensic Genetics, Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing 100038, China
- Shanxi Medical University, Taiyuan 030001, China
| | - Zou Li-Xin
- Key Laboratory of Forensic Genetics, Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing 100038, China
- Jiangsu Normal University, Xuzhou 221116, China
| | - Li Cai-Xia
- Institute of Forensic Medicine, Guizhou Medical University, Guiyang 550004, China
- Key Laboratory of Forensic Genetics, Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing 100038, China
| | - Huang Jiang
- Institute of Forensic Medicine, Guizhou Medical University, Guiyang 550004, China
| | - Jiang Li
- Key Laboratory of Forensic Genetics, Beijing Engineering Research Center of Crime Scene Evidence Examination, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing 100038, China
| |
Collapse
|
15
|
Bukayev A, Aidarov B, Fesenko D, Saidamarova V, Ivanovsky I, Maltseva E, Naizabayeva D, Bukayeva A, Faizov B, Pylev V, Darmenov A, Skiba Y, Balanovska E, Zhabagin M. Genotype data for 60 SNP genetic markers associated with eye, hair, skin color, ABO blood group, sex, core Y-chromosome haplogroups in Kazakh population. BMC Res Notes 2024; 17:51. [PMID: 38369539 PMCID: PMC10874529 DOI: 10.1186/s13104-024-06712-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 02/01/2024] [Indexed: 02/20/2024] Open
Abstract
OBJECTIVES The collection of genotype data was conducted as an essential part of a pivotal research project with the goal of examining the genetic variability of skin, hair, and iris color among the Kazakh population. The data has practical application in the field of forensic DNA phenotyping (FDA). Due to the limited size of forensic databases from Central Asia (Kazakhstan), it is practically impossible to obtain an individual identification result based on forensic profiling of short tandem repeats (STRs). However, the pervasive use of the FDA necessitates validation of the currently employed set of genetic markers in a variety of global populations. No such data existed for the Kazakhs. The Phenotype Expert kit (DNA Research Center, LLC, Russia) was used for the first time in this study to collect data. DATA DESCRIPTION The present study provides genotype data for a total of 60 SNP genetic markers, which were analyzed in a sample of 515 ethnic Kazakhs. The dataset comprises a total of 41 single nucleotide polymorphisms (SNPs) obtained from the HIrisPlex-S panel. Additionally, there are 4 SNPs specifically related to the AB0 gene, 1 marker associated with the AMELX/Y genes, and 14 SNPs corresponding to the primary haplogroups of the Y chromosome. The aforementioned data could prove valuable to researchers with an interest in investigating genetic variability and making predictions about phenotype based on eye color, hair color, skin color, AB0 blood group, gender, and biogeographic origin within the male lineage.
Collapse
Affiliation(s)
- Alizhan Bukayev
- National Center for Biotechnology, Astana, 010000, Republic of Kazakhstan
| | - Baglan Aidarov
- National Center for Biotechnology, Astana, 010000, Republic of Kazakhstan
| | - Denis Fesenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Viktoriya Saidamarova
- Karaganda Academy of the Ministry of Internal Affairs of the Republic of Kazakhstan Named After Barimbek Beisenov, Karaganda, 100000, Republic of Kazakhstan
| | | | - Elina Maltseva
- Almaty Branch of the National Center for Biotechnology, Almaty, 050054, Kazakhstan
- Tethys Scientific Society, Almaty, 050063, Kazakhstan
| | - Dinara Naizabayeva
- Almaty Branch of the National Center for Biotechnology, Almaty, 050054, Kazakhstan
| | - Ayagoz Bukayeva
- National Center for Biotechnology, Astana, 010000, Republic of Kazakhstan
| | - Bekzhan Faizov
- National Center for Biotechnology, Astana, 010000, Republic of Kazakhstan
| | - Vladimir Pylev
- Bochkov Research Centre of Medical Genetics, Moscow, 115522, Russia
| | - Akynkali Darmenov
- Karaganda Academy of the Ministry of Internal Affairs of the Republic of Kazakhstan Named After Barimbek Beisenov, Karaganda, 100000, Republic of Kazakhstan
| | - Yuriy Skiba
- Almaty Branch of the National Center for Biotechnology, Almaty, 050054, Kazakhstan
| | - Elena Balanovska
- Bochkov Research Centre of Medical Genetics, Moscow, 115522, Russia
| | - Maxat Zhabagin
- National Center for Biotechnology, Astana, 010000, Republic of Kazakhstan.
| |
Collapse
|
16
|
Ralf A, van Wersch B, Montiel González D, Kayser M. Male Pedigree Toolbox: A Versatile Software for Y-STR Data Analyses. Genes (Basel) 2024; 15:227. [PMID: 38397216 PMCID: PMC10887500 DOI: 10.3390/genes15020227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Y-chromosomal short tandem repeats (Y-STRs) are widely used in forensic, genealogical, and population genetics. With the recent increase in the number of rapidly mutating (RM) Y-STRs, an unprecedented level of male differentiation can be achieved, widening and improving the applications of Y-STRs in various fields, including forensics. The growing complexity of Y-STR data increases the need for automated data analyses, but dedicated software tools are scarce. To address this, we present the Male Pedigree Toolbox (MPT), a software tool for the automated analysis of Y-STR data in the context of patrilineal genealogical relationships. The MPT can estimate mutation rates and male relative differentiation rates from input Y-STR pedigree data. It can aid in determining ancestral haplotypes within a pedigree and visualize the genetic variation within pedigrees in all branches of family trees. Additionally, it can provide probabilistic classifications using machine learning, helping to establish or prove the structure of the pedigree and the level of relatedness between males, even for closely related individuals with highly similar haplotypes. The tool is flexible and easy to use and can be adjusted to any set of Y-STR markers by modifying the intuitive input file formats. We introduce the MPT software tool v1.0 and make it publicly available with the goal of encouraging and supporting forensic, genealogical, and other geneticists in utilizing the full potential of Y-STRs for both research purposes and practical applications, including criminal casework.
Collapse
Affiliation(s)
- Arwin Ralf
- Department of Genetic Identification, Erasmus MC, University Medical Center Rotterdam, 3015 CN Rotterdam, The Netherlands
| | | | | | | |
Collapse
|
17
|
Rojas MG, Pozzi E, Ramasamy R. Unlocking the mystery of the human Y chromosome. Nat Rev Urol 2024; 21:65-66. [PMID: 37803196 DOI: 10.1038/s41585-023-00826-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/08/2023]
Affiliation(s)
- Miguel G Rojas
- Desai Sethi Urology Institute, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Edoardo Pozzi
- Desai Sethi Urology Institute, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Ranjith Ramasamy
- Desai Sethi Urology Institute, Miller School of Medicine, University of Miami, Miami, FL, USA.
| |
Collapse
|
18
|
Luis JR, Palencia-Madrid L, Runfeldt G, Garcia-Bertrand R, Herrera RJ. Delineating the dispersal of Y-chromosome sub-haplogroup O2a2b-P164 among Austronesian-speaking populations. Sci Rep 2024; 14:2066. [PMID: 38267477 PMCID: PMC10808098 DOI: 10.1038/s41598-024-52293-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 01/16/2024] [Indexed: 01/26/2024] Open
Abstract
This article reports on an exploration of the Y-chromosome sub-haplogroup O2a2b-P164 in Austronesian-speaking populations. Moderate to high abundance of the P 164 mutation is seen in the West Pacific including the Amis of Formosa (36%) and the Filipinos of Mindanao (50%) as well as in the Kiritimati of Micronesia (70%), and Tonga and Samoa of West Polynesia (54% and 33%, respectively), and it drops to low frequencies in populations of East Polynesia. The communities of Polynesia and Micronesia exhibit considerable inter- and intra-population haplotype sharing suggesting extensive population affinity. The observed affinities, as well as the ages and diversity values within the P 164 sub-haplogroup among Austronesian-speaking populations signal an ancestral migration route and relationships that link the Amis of Taiwan with distant communities in West and East Polynesia, Micronesia, and the Maori of New Zealand. High resolution sequencing of the Austronesian Y chromosome indicate that the P 164 lineage originated about 19,000 ya and then split into three branches separating the Ami aborigines, Southeast Asian and Polynesian/Micronesian populations about 4700 ya, roughly coinciding with the initiation of the Austronesian diaspora. The Y-chromosomes of all the Polynesian and Micronesian population examined belong to the new FT 257096 haplogroup.
Collapse
Affiliation(s)
- Javier Rodriguez Luis
- Area de Antropología, Facultad de Biología, Universidad de Santiago de Compostela, Campus Sur s/n, 15782, Santiago de Compostela, Spain
| | - Leire Palencia-Madrid
- BIOMICs Research Group, Dpto. Z. y Biologia Celular A., Lascaray Research Centre, University of the Basque Country UPV/EHU, 01006, Vitoria-Gasteiz, Spain
| | | | - Ralph Garcia-Bertrand
- Department of Molecular Biology, Colorado College, 14 East Cache La Poudre Street, Colorado Springs, CO, 80903-3294, USA
| | - Rene J Herrera
- Department of Molecular Biology, Colorado College, 14 East Cache La Poudre Street, Colorado Springs, CO, 80903-3294, USA.
| |
Collapse
|
19
|
Marinaro JA, Punjani N, Gal J, Mielnik A, Schlegel PN. Sperm production is stable over time for men with azoospermia factor c Y-chromosome microdeletions. Fertil Steril 2024; 121:117-120. [PMID: 37717811 DOI: 10.1016/j.fertnstert.2023.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 09/10/2023] [Accepted: 09/11/2023] [Indexed: 09/19/2023]
Affiliation(s)
| | - Nahid Punjani
- Department of Urology, Mayo Clinic, Scottsdale, Arizona
| | - Jonathan Gal
- Department of Urology, Weill Cornell Medicine, New York, New York
| | - Anna Mielnik
- Department of Urology, Weill Cornell Medicine, New York, New York
| | - Peter N Schlegel
- Department of Urology, Weill Cornell Medicine, New York, New York.
| |
Collapse
|
20
|
Sumapraja K, Pangastuti NP, Ikhsan M, Harzif AK, Maidarti M. Combined clinical and ultrasound criteria could accurately predict the Y chromosome in primary amenorrhea patient. Sci Rep 2023; 13:22096. [PMID: 38086929 PMCID: PMC10716374 DOI: 10.1038/s41598-023-49570-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 12/09/2023] [Indexed: 12/18/2023] Open
Abstract
This study aimed to assess the combined clinical and ultrasound criteria as a diagnostic tool for screening the Y chromosome related to primary amenorrhea. This cross-sectional study involving 59 subjects was taken from medical records at the Reproductive Immunoendocrinology Polyclinic of Cipto Mangunkusumo General Hospital, Jakarta, Indonesia. The medical records of subjects were then cross-checked with karyotyping analysis results. Sensitivity, specificity, and predictive values were analyzed to assess the criteria. Two subjects were presented with a Y chromosome, and one without a Y chromosome was misclassified into another group. After analysis, we found that combined clinical and ultrasound criteria could predict the Y chromosome related to primary amenorrhea with 95.9% accuracy, with sensitivity and specificity of 80% and 97.96%, respectively. Combined clinical and ultrasound criteria (introduced as Kanadi Sumapraja Criteria) could be used as a diagnostic tool for screening a Y chromosome related to primary amenorrhea.
Collapse
Affiliation(s)
- Kanadi Sumapraja
- Reproductive Immunoendocrinology Division, Department of Obstetrics and Gynecology, Faculty of Medicine, Universitas Indonesia - Dr. Cipto Mangunkusumo General Hospital, Jalan Pangeran Diponegoro No. 71, Jakarta, 10320, Indonesia.
- Yasmin IVF Clinic, Dr. Cipto Mangunkusumo General Hospital, Jakarta, Indonesia.
- Human Reproduction, Infertility, and Family Planning Cluster, Faculty of Medicine, Indonesia Reproductive Medicine Research and Training Center, Universitas Indonesia, Jakarta, 10430, Indonesia.
| | - Niken Pudji Pangastuti
- Reproductive Immunoendocrinology Division, Department of Obstetrics and Gynecology, Faculty of Medicine, Universitas Indonesia - Dr. Cipto Mangunkusumo General Hospital, Jalan Pangeran Diponegoro No. 71, Jakarta, 10320, Indonesia
| | - Muhammad Ikhsan
- Reproductive Immunoendocrinology Division, Department of Obstetrics and Gynecology, Faculty of Medicine, Universitas Indonesia - Dr. Cipto Mangunkusumo General Hospital, Jalan Pangeran Diponegoro No. 71, Jakarta, 10320, Indonesia
| | - Achmad Kemal Harzif
- Reproductive Immunoendocrinology Division, Department of Obstetrics and Gynecology, Faculty of Medicine, Universitas Indonesia - Dr. Cipto Mangunkusumo General Hospital, Jalan Pangeran Diponegoro No. 71, Jakarta, 10320, Indonesia
- Yasmin IVF Clinic, Dr. Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
- Human Reproduction, Infertility, and Family Planning Cluster, Faculty of Medicine, Indonesia Reproductive Medicine Research and Training Center, Universitas Indonesia, Jakarta, 10430, Indonesia
| | - Mila Maidarti
- Reproductive Immunoendocrinology Division, Department of Obstetrics and Gynecology, Faculty of Medicine, Universitas Indonesia - Dr. Cipto Mangunkusumo General Hospital, Jalan Pangeran Diponegoro No. 71, Jakarta, 10320, Indonesia
- Yasmin IVF Clinic, Dr. Cipto Mangunkusumo General Hospital, Jakarta, Indonesia
- Human Reproduction, Infertility, and Family Planning Cluster, Faculty of Medicine, Indonesia Reproductive Medicine Research and Training Center, Universitas Indonesia, Jakarta, 10430, Indonesia
| |
Collapse
|
21
|
Han N, Liu X. AZF microdeletion affects semen parameters, sex hormone levels, and chromosome karyotypes in infertile men in Xinjiang. Cell Mol Biol (Noisy-le-grand) 2023; 69:106-111. [PMID: 38158680 DOI: 10.14715/cmb/2023.69.13.17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Indexed: 01/03/2024]
Abstract
This study aimed to analyze the correlation between the microdeletion of different regions of the azoospermia factor (AZF) gene and semen parameters, sex hormone levels, and karyotypes in infertile males by retrospective study. This was performed to obtain a comprehensive understanding of the clinical data of AZF microdeletion in infertile males, to guide clinical diagnoses and treatments, and to improve the efficacy and safety of assisted reproductive technology. For this purpose, Fifty-seven patients with AZF microdeletions and complete data were selected from 1916 patients with AZF microdeletions in our hospital from January 2020 to August 2022. The correlation between semen parameters, sex hormone levels, and chromosome karyotypes of these 57 patients was analyzed. Results showed that among the 57 patients with AZF microdeletions, the region with the highest microdeletion rate was AZFc with 57.89%; single or combined deletions in AZFa and AZFb regions resulted in azoospermia. The deletion frequency of AZFc in the oligospermia group was significantly higher than that in the azoospermia group, and the deletion frequencies of AZFb and AZFb + c in the azoospermia group were significantly higher than those in the oligospermia group (P<0.05). There were statistically significant differences in follicle-stimulating hormone (FSH) and luteinizing hormone (LH) levels, and chromosome karyotypes between patients with azoospermia and oligospermia (P<0.05). Statistically significant differences were observed in prolactin (PRL), FSH, testosterone (T), LH levels, and chromosome karyotypes of patients in different AZF microdeletion regions (P<0.05). In conclusion, AZF microdeletions can lead to a decline in semen quality in men, and different types of deletions have different effects on semen parameters, sex hormone levels, and karyotype analysis. Further treatments should be selected based on the AZF microdeletion area.
Collapse
Affiliation(s)
- Ningning Han
- Department of Prenatal Diagnosis, Reproductive Medicine Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011 Xinjiang, China.
| | - Xiaoran Liu
- Department of Prenatal Diagnosis, Reproductive Medicine Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011 Xinjiang, China.
| |
Collapse
|
22
|
Chen D, Fan G, Zhu X, Chen Q, Chen X, Gao F, Guo Z, Luo P, Gao Y. Y chromosome microdeletions in Chinese men with infertility: prevalence, phenotypes, and intracytoplasmic sperm injection outcomes. Reprod Biol Endocrinol 2023; 21:116. [PMID: 38053137 DOI: 10.1186/s12958-023-01168-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 11/28/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND The incidence of Y chromosome microdeletions varies among men with infertility across regions and ethnicities worldwide. However, comprehensive epidemiological studies on Y chromosome microdeletions in Chinese men with infertility are lacking. We aimed to investigate Y chromosome microdeletions prevalence among Chinese men with infertility and its correlation with intracytoplasmic sperm injection (ICSI) outcomes. METHODS This single-center retrospective study included 4,714 men with infertility who were evaluated at the Reproductive Center of the First Affiliated Hospital of Sun Yat-sen University between May 2017 and January 2021. Semen analysis and Y-chromosome microdeletion via multiplex polymerase chain reaction were conducted on the men. The study compared outcomes of 36 ICSI cycles from couples with male azoospermia factor (AZF)cd deletions with those of a control group, which included 72 ICSI cycles from couples without male Y chromosome microdeletions, during the same period. Both groups underwent ICSI treatment using ejaculated sperm. RESULTS Among 4,714 Chinese men with infertility, 3.31% had Y chromosome microdeletions. The combined deletion of sY254 and sY255 in the AZFc region and sY152 in the AZFd region was the prevalent pattern of Y chromosome microdeletion, with 3.05% detection rate. The detection rates of AZF deletions in patients with normal total sperm count, mild oligozoospermia, severe oligozoospermia, cryptozoospermia, and azoospermia were 0.17%, 1.13%, 5.53%, 71.43%, and 7.54%, respectively. Compared with the control group, the AZFcd deletion group exhibited no significant difference in the laboratory results or pregnancy outcomes of ICSI cycles using ejaculated sperm. CONCLUSIONS This is the largest epidemiological study on Y chromosome microdeletions in Chinese men with infertility. The study results underline the necessity for detecting Y chromosome microdeletion in men with infertility and severe sperm count abnormalities, especially those with cryptozoospermia. The combined deletion of sY254 and sY255 in the AZFc region and sY152 in the AZFd region was the most prevalent Y chromosome microdeletion pattern. Among patients with AZFcd deletion and ejaculated sperm, ICSI treatment can result in pregnancy outcomes, similar to those without AZFcd deletion.
Collapse
Affiliation(s)
- Dongjia Chen
- Reproductive Medicine Center, Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangdong Provincial Clinical Research Center for obstetrical and gynecological diseases, The First Affiliated Hospital, Sun Yat-sen University, 510080, Guangzhou, China
| | - Guoqing Fan
- Reproductive Medicine Center, Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangdong Provincial Clinical Research Center for obstetrical and gynecological diseases, The First Affiliated Hospital, Sun Yat-sen University, 510080, Guangzhou, China
| | - Xianqing Zhu
- Reproductive Medicine Center, Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangdong Provincial Clinical Research Center for obstetrical and gynecological diseases, The First Affiliated Hospital, Sun Yat-sen University, 510080, Guangzhou, China
| | - Qinyun Chen
- Reproductive Medicine Center, Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangdong Provincial Clinical Research Center for obstetrical and gynecological diseases, The First Affiliated Hospital, Sun Yat-sen University, 510080, Guangzhou, China
| | - Xuren Chen
- Reproductive Medicine Center, Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangdong Provincial Clinical Research Center for obstetrical and gynecological diseases, The First Affiliated Hospital, Sun Yat-sen University, 510080, Guangzhou, China
| | - Feng Gao
- Reproductive Medicine Center, Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangdong Provincial Clinical Research Center for obstetrical and gynecological diseases, The First Affiliated Hospital, Sun Yat-sen University, 510080, Guangzhou, China
| | - Zexin Guo
- Reproductive Medicine Center, Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangdong Provincial Clinical Research Center for obstetrical and gynecological diseases, The First Affiliated Hospital, Sun Yat-sen University, 510080, Guangzhou, China
| | - Peng Luo
- Reproductive Medicine Center, Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangdong Provincial Clinical Research Center for obstetrical and gynecological diseases, The First Affiliated Hospital, Sun Yat-sen University, 510080, Guangzhou, China
| | - Yong Gao
- Reproductive Medicine Center, Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangdong Provincial Clinical Research Center for obstetrical and gynecological diseases, The First Affiliated Hospital, Sun Yat-sen University, 510080, Guangzhou, China.
| |
Collapse
|
23
|
Sequencing the Y Chromosome. Am J Med Genet A 2023; 191:2798-9. [PMID: 37955261 DOI: 10.1002/ajmg.a.62841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 10/13/2023] [Accepted: 11/05/2023] [Indexed: 11/14/2023]
|
24
|
Ghorbel M, Baklouti-Gargouri S, Keskes R, Sellami A, McElreavy K, Ammar-Keskes L. Y-chromosome haplogroups and Azoospermia Factor (AZF) analysis in Tunisian infertile male. HUM FERTIL 2023; 26:1238-1247. [PMID: 36591797 DOI: 10.1080/14647273.2022.2163194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 07/01/2022] [Indexed: 01/03/2023]
Abstract
The aim of the present study was to clarify the implication of Y chromosome genetic variations and haplogroups in Tunisian infertile men. A total of 27 Y-chromosomal binary markers partial microdeletions (gr/gr, b1/b3 and b2/b3) and copy number variation of DAZ and CDY genes in the AZFc region were analysed in 131 Tunisian infertile men with spermatogenic failure and severe reduced sperm concentrations and in 85 normospermic men as controls. Eleven different haplogroups in the overall population study (E3b2; J1J*, E1, E3b*, F, G, K, P/Q, R*, R1* and R1a1) were found. Interestingly, the J1J* haplogroup was significantly more frequent in azoo/oligospermic patients than in normospermic men (35.1% and 22.3%, respectively (p value = 0.04)). Results showed also that patients without DAZ/CDY1 copies loss and without partial microdeletions belonged to the R1 haplogroup. The relative high frequencies of two haplogroups, E3b2 (35.1%) and J (30%) was confirmed in Tunisia. We reported in the present study and for the first time, that J1J* haplogroup may confer a risk factor for infertility in the Tunisian population and we suggested that R1 haplogroup may ensure certain stability to Y-chromosome in Tunisian men.
Collapse
Affiliation(s)
- Myriam Ghorbel
- Faculty of Medicine, Laboratory of Human Molecular Genetics, Universite de Sfax Faculte de Medecine de Sfax, Sfax, Tunisia
| | - Siwar Baklouti-Gargouri
- Faculty of Medicine, Laboratory of Human Molecular Genetics, Universite de Sfax Faculte de Medecine de Sfax, Sfax, Tunisia
| | - Rim Keskes
- Faculty of Medicine, Laboratory of Human Molecular Genetics, Universite de Sfax Faculte de Medecine de Sfax, Sfax, Tunisia
| | - Afifa Sellami
- Faculty of Medicine, Laboratory of Histology & Embryology, Universite de Sfax Faculte de Medecine de Sfax, Sfax, Tunisia
| | - Ken McElreavy
- Human Developmental Genetics Unit, Institut Pasteur, Paris, France
| | - Leila Ammar-Keskes
- Faculty of Medicine, Laboratory of Human Molecular Genetics, Universite de Sfax Faculte de Medecine de Sfax, Sfax, Tunisia
- Faculty of Medicine, Laboratory of Histology & Embryology, Universite de Sfax Faculte de Medecine de Sfax, Sfax, Tunisia
| |
Collapse
|
25
|
From AI to the Y chromosome (and everything in between). Nat Biotechnol 2023; 41:1661-2. [PMID: 38049559 DOI: 10.1038/s41587-023-02076-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2023]
|
26
|
Mut P, Bertoni B, Sapiro R, Hidalgo PC, Torres A, Azambuja C, Sans M. Insights into the Y chromosome human diversity in Uruguay. Am J Hum Biol 2023; 35:e23963. [PMID: 37493343 DOI: 10.1002/ajhb.23963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 04/26/2023] [Accepted: 07/04/2023] [Indexed: 07/27/2023] Open
Abstract
BACKGROUND With regard to the origin of its population and microevolutionary processes, Uruguay exhibits distinctive features that distinguish it from other countries in Latin America, while at the same time sharing several similarities. In this article, we will focus on the variability of paternal genetic lineages in two geographical regions with different histories that can be considered as examples of distinct populations for the continent. In general terms, the genetic diversity is a result of different demographic processes related to the American conquest and colonisation. These resulted in distinct ancestral components which vary geographical and depend on the distribution by sex within these components. In Uruguay, native maternal haplogroups are significantly more frequent in the North. Although there are several studies about the geneticvariability of Uruguay, little is known about male genetic lineages. AIMS The aim of this work is to present an updated study of the male genetic variability of the Uruguayan population. METHODS We analyzed 13 biallelic markers and 27 STRs located in the male-specific region of the Y chromosome for 157 males: 98 from the capital, Montevideo, and 59 from Tacuarembó. RESULTS Almost all haplogroups found in both locations are European (99% and 93.2% respectively). One Sub-Saharan African haplogroup was found in Montevideo (1%) and 2 in Tacuarembó (3%), while Native haplogroups were found only in Tacuarembó, evidencing a strong sex-biased admixture. By crossing genetic and genealogical information we could relate European haplogroups with different waves and times of migrations. DISCUSSION Network analysis indicated a very diverse male population, suggesting that European migrants came from heterogeneous geographic locations and in different waves. Tacuarembó has closer population affinities with Iberian populations while Montevideo is more diverse. Male population expansion expansion, can be explained by the large number of migrants that arrived during the XIX century and the first half of the XX century. CONCLUSIONS The Uruguayan male gene pool is the result of several migration waves with diverse origins, with strong sex-biased admixture that can be explained by the European migration, the violence against the indigenous males, and the segregation of the Africansadmixture that can be explained due to European migration, violence against Natives, and segregation against African males.admixture that can be explained due to European migration, violence against Natives, and segregation against African males.admixture that can be explained due to European migration, violence against Natives, and segregation against African males.admixture that can be explained due to European migration, violence against Natives, and segregation of hte Africans.
Collapse
Affiliation(s)
- Patricia Mut
- Departamento de Antropología Biológica, Facultad de Humanidades y Ciencias de la Educación, UdelaR, Montevideo, Uruguay
| | - Bernardo Bertoni
- Departamento de Genética, Facultad de Medicina, UdelaR, Montevideo, Uruguay
| | - Rossana Sapiro
- Departamento de Histología y Embriología, Facultad de Medicina, UdelaR, Montevideo, Uruguay
| | - Pedro C Hidalgo
- Polo de Desarrollo Universitario Diversidad Genética Humana, Centro Universitario Noreste, Tacuarembó, Uruguay
| | | | | | - Mónica Sans
- Departamento de Antropología Biológica, Facultad de Humanidades y Ciencias de la Educación, UdelaR, Montevideo, Uruguay
| |
Collapse
|
27
|
Zupanič Pajnič I, Mlinšek T, Počivavšek T, Leskovar T. Genetic sexing of subadult skeletal remains. Sci Rep 2023; 13:20463. [PMID: 37993531 PMCID: PMC10665466 DOI: 10.1038/s41598-023-47836-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 11/19/2023] [Indexed: 11/24/2023] Open
Abstract
When subadult skeletons need to be identified, biological sex diagnosis is one of the first steps in the identification process. Sex assessment of subadults using morphological features is unreliable, and molecular genetic methods were applied in this study. Eighty-three ancient skeletons were used as models for poorly preserved DNA. Three sex-informative markers on the Y and X chromosome were used for sex identification: a qPCR test using the PowerQuant Y target included in PowerQuant System (Promega), the amelogenin test included in ESI 17 Fast STR kit (Promega), and a Y-STR amplification test using the PowerPlex Y-23 kit (Promega). Sex was successfully determined in all but five skeletons. Successful PowerQuant Y-target, Y-amelogenin, and Y-chromosomal STR amplifications proved the presence of male DNA in 35 skeletons, and in 43 subadults female sex was established. No match was found between the genetic profiles of subadult skeletons, and the elimination database and negative control samples produced no profiles, indicating no contamination issue. Our study shows that genetic sex identification is a very successful approach for biological sexing of subadult skeletons whose sex cannot be assessed by anthropological methods. The results of this study are applicable for badly preserved subadult skeletons from routine forensic casework.
Collapse
Affiliation(s)
- Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia.
| | - Teo Mlinšek
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia
| | - Tadej Počivavšek
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia
| | - Tamara Leskovar
- Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Ljubljana, Slovenia
| |
Collapse
|
28
|
Fu D, Adnan A, Yao J, Aldayan NH, Wang CC, Hongyi C. Unraveling the paternal genetic structure and forensic traits of the Hui population in Liaoning Province, China using Y-chromosome analysis. BMC Genomics 2023; 24:691. [PMID: 37978341 PMCID: PMC10655310 DOI: 10.1186/s12864-023-09774-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 10/30/2023] [Indexed: 11/19/2023] Open
Abstract
The Hui people are the second-largest ethnic minority in China, and they are distributed throughout the country. A previous study explored the paternal genetic structure of the Hui population in nine different regions of China, but it overlooked the Liaoning province. In this study, we examined the paternal genetic makeup and forensic traits of the Hui population in Liaoning province by analyzing 157 Y-chromosome single nucleotide polymorphisms (Y-SNPs) and 26 short tandem repeats (Y-STRs). We successfully genotyped 282 unrelated male individuals from the Hui population of Liaoning province using the SNaPshot® single base extension assay and Goldeneye™ Y26 system kit (PEOPLESPOT R&D, Beijing, China). The results revealed high haplotypic diversity (0.9998) and identified 46 terminal haplogroups for the Hui population. Additional analyses, such as heat maps, principal component analysis (PCA), genetic distance (FST), Multidimensional scaling (MDS) analysis, and median-joining network (MJ) analysis, showed that the Hui population could be classified into three groups: Northwest Hui populations (NWH), including Liaoning, Xinjiang, Qinghai, Gansu, Ningxia, Shaanxi, and Henan; Hui populations from Sichuan and Shandong (SSH); and Yunnan Hui populations (YNH). Pairwise genetic distance (Rst) comparisons with other Chinese populations revealed that the Hui population displayed genetic affinity with the Han population. The comprehensive understanding of the Hui population in Liaoning province, explored by Y-SNPs and Y-STRs, can be utilized to interpret their genetic structure and enhance the accuracy of forensic databases.
Collapse
Affiliation(s)
- Dazhi Fu
- First Affiliated Hospital of China Medical University, 155 Heping District, Shenyang, 110001, China
| | - Atif Adnan
- Department of Forensic Sciences, Collage of Criminal Justice, Naif Arab University for Security Sciences, Riyadh, Saudi Arabia.
| | - Jun Yao
- Department of Forensic Biology and Genetics, School of Forensic Medicine, China Medical University, Shenyang, 110001, China
| | - Noura H Aldayan
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Ibn Abdulaziz University, Al-Kharj, 16273, Saudi Arabia
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, Fujian, People's Republic of China.
| | - Cao Hongyi
- First Affiliated Hospital of China Medical University, 155 Heping District, Shenyang, 110001, China.
- Department of Pathology, School of Basic Medical Sciences, China Medical University, Shenyang, 110001, China.
| |
Collapse
|
29
|
Schurr TG, Shengelia R, Shamoon-Pour M, Chitanava D, Laliashvili S, Laliashvili I, Kibret R, Kume-Kangkolo Y, Akhvlediani I, Bitadze L, Mathieson I, Yardumian A. Genetic Analysis of Mingrelians Reveals Long-Term Continuity of Populations in Western Georgia (Caucasus). Genome Biol Evol 2023; 15:evad198. [PMID: 37935112 PMCID: PMC10665041 DOI: 10.1093/gbe/evad198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/26/2023] [Accepted: 10/28/2023] [Indexed: 11/09/2023] Open
Abstract
To elucidate the population history of the Caucasus, we conducted a survey of genetic diversity in Samegrelo (Mingrelia), western Georgia. We collected DNA samples and genealogical information from 485 individuals residing in 30 different locations, the vast majority of whom being Mingrelian speaking. From these DNA samples, we generated mitochondrial DNA (mtDNA) control region sequences for all 485 participants (female and male), Y-short tandem repeat haplotypes for the 372 male participants, and analyzed all samples at nearly 590,000 autosomal single nucleotide polymorphisms (SNPs) plus around 33,000 on the sex chromosomes, with 27,000 SNP removed for missingness, using the GenoChip 2.0+ microarray. The resulting data were compared with those from populations from Anatolia, the Caucasus, the Near East, and Europe. Overall, Mingrelians exhibited considerable mtDNA haplogroup diversity, having high frequencies of common West Eurasian haplogroups (H, HV, I, J, K, N1, R1, R2, T, U, and W. X2) and low frequencies of East Eurasian haplogroups (A, C, D, F, and G). From a Y-chromosome standpoint, Mingrelians possessed a variety of haplogroups, including E1b1b, G2a, I2, J1, J2, L, Q, R1a, and R1b. Analysis of autosomal SNP data further revealed that Mingrelians are genetically homogeneous and cluster with other modern-day South Caucasus populations. When compared with ancient DNA samples from Bronze Age archaeological contexts in the broader region, these data indicate that the Mingrelian gene pool began taking its current form at least by this period, probably in conjunction with the formation of a distinct linguistic community.
Collapse
Affiliation(s)
- Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ramaz Shengelia
- Department of the History of Medicine, Tbilisi State Medical University, Tbilisi, Georgia
| | - Michel Shamoon-Pour
- First-year Research Immersion, Binghamton University, Binghamton, New York, USA
| | - David Chitanava
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi, Georgia
| | - Shorena Laliashvili
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi, Georgia
| | - Irma Laliashvili
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi, Georgia
| | - Redate Kibret
- Department of History and Social Science, Bryn Athyn College, Bryn Athyn, Pennsylvania, USA
| | - Yanu Kume-Kangkolo
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Lia Bitadze
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi, Georgia
| | - Iain Mathieson
- Department of Genetics, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Aram Yardumian
- Department of History and Social Science, Bryn Athyn College, Bryn Athyn, Pennsylvania, USA
| |
Collapse
|
30
|
First Complete Sequence of Human Y Chromosome Assembled. Genet Test Mol Biomarkers 2023; 27:355-6. [PMID: 38019144 DOI: 10.1089/gtmb.2023.29078.eag] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023] Open
|
31
|
Yu HX, Zhang XP, Bai Y, Liu KJ, Li H, Li YL, Sun J, Wei LH. The formation of proto-austronesians: insights from a revised phylogeography of the paternal founder lineage. Mol Genet Genomics 2023; 298:1301-1308. [PMID: 37498359 DOI: 10.1007/s00438-023-02054-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 07/01/2023] [Indexed: 07/28/2023]
Abstract
OBJECTIVES Previous studies suggested that the Y-chromosome haplogroups O2-N6-B451-AM01756 and O1a-M119 are two founder lineages of proto-Austronesians at about five thousand years ago. The objective of this study was to investigate the formation of proto-Austronesians from the perspective of the paternal gene pool. MATERIALS AND METHODS In this study, we developed a highly evised phylogenetic tree with age estimates for haplogroup O2-N6 and early branches of O1a-M119 (M110, F1036, and F819). In addition, we also explored the geographical distribution of eight sub-branches of O2-N6 and O1a-M119, and spatial autocorrelation analysis was conducted for each sub-branch. RESULTS The paternal lineage combination of proto-Austronesians is a small subset of a diverse gene pool of populations from the mainland of East Asia. The distribution map and results of the spatial autocorrelation analysis suggested that the eastern coastal region of northern China is likely the source of lineage O2-N6 while the coastal region of southeastern China is likely the diffusion center of early branches of O1a-M119. We developed an evolutionary diagram for Austronesians and their ancestors in the past 18,000 years. DISCUSSION We proposed that the millet farming community in North China is the common ancestor group of the Austronesians and the Han people, while the diverse ancient people in the southeast coastal areas of East Asia form the common ancestor group of the Austronesians and the East Asian mainland population. The demographic history of multiple ancestral groups of the most recent common ancestor group itself in the more ancient period is helpful to understand the deep roots of the genetic components and cultural traditions of Austronesians.
Collapse
Affiliation(s)
- Hui-Xin Yu
- Institute of Humanities and Human Sciences, School of Ethnology and Anthropology, Inner Mongolia Normal University, Hohhot, 010028, China
| | - Xian-Peng Zhang
- Institute of Humanities and Human Sciences, School of Ethnology and Anthropology, Inner Mongolia Normal University, Hohhot, 010028, China
| | - Yun Bai
- College of Life Science and Technology, Inner Mongolia Normal University, Hohhot, 021002, China
| | - Kai-Jun Liu
- School of International Tourism and Culture, Guizhou Normal University, Guiyang, 550001, China
| | - Hui Li
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, 200438, China
| | - Yong-Lan Li
- Institute of Humanities and Human Sciences, School of Ethnology and Anthropology, Inner Mongolia Normal University, Hohhot, 010028, China
| | - Jin Sun
- School of Literature and Media, Xingyi Normal University for Nationalities, Xingyi, 562400, China.
| | - Lan-Hai Wei
- B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, 200438, China.
| |
Collapse
|
32
|
Ashirbekov Y, Seidualy M, Abaildayev A, Maxutova A, Zhunussova A, Akilzhanova A, Sharipov K, Sabitov Z, Zhabagin M. Genetic polymorphism of Y-chromosome in Kazakh populations from Southern Kazakhstan. BMC Genomics 2023; 24:649. [PMID: 37891458 PMCID: PMC10612363 DOI: 10.1186/s12864-023-09753-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND The Kazakhs are one of the biggest Turkic-speaking ethnic groups, controlling vast swaths of land from the Altai to the Caspian Sea. In terms of area, Kazakhstan is ranked ninth in the world. Northern, Eastern, and Western Kazakhstan have already been studied in relation to genetic polymorphism 27 Y-STR. However, current information on the genetic polymorphism of the Y-chromosome of Southern Kazakhstan is limited only by 17 Y-STR and no geographical study of other regions has been studied at this variation. RESULTS The Kazakhstan Y-chromosome Haplotype Reference Database was expanded with 468 Kazakh males from the Zhambyl and Turkestan regions of South Kazakhstan by having their 27 Y-STR loci and 23 Y-SNP markers analyzed. Discrimination capacity (DC = 91.23%), haplotype match probability (HPM = 0.0029) and haplotype diversity (HD = 0.9992) are defined. Most of this Y-chromosome variability is attributed to haplogroups C2a1a1b1-F1756 (2.1%), C2a1a2-M48 (7.3%), C2a1a3-F1918 (33.3%) and C2b1a1a1a-M407 (6%). Median-joining network analysis was applied to understand the relationship between the haplotypes of the three regions. In three genetic layer can be described the position of the populations of the Southern region of Kazakhstan-the geographic Kazakh populations of Kazakhstan, the Kazakh tribal groups, and the people of bordering Asia. CONCLUSION The Kazakhstan Y-chromosome Haplotype Reference Database was formed for 27 Y-STR loci with a total sample of 1796 samples of Kazakhs from 16 regions of Kazakhstan. The variability of the Y-chromosome of the Kazakhs in a geographical context can be divided into four main clusters-south, north, east, west. At the same time, in the genetic space of tribal groups, the population of southern Kazakhs clusters with tribes from the same region, and genetic proximity is determined with the populations of the Hazaras of Afghanistan and the Mongols of China.
Collapse
Affiliation(s)
- Yeldar Ashirbekov
- M. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Kazakhstan
| | - Madina Seidualy
- National Center for Biotechnology, Astana, Kazakhstan
- Nazarbayev University, Astana, Kazakhstan
| | - Arman Abaildayev
- M. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Kazakhstan
| | | | | | | | - Kamalidin Sharipov
- M. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Kazakhstan
| | - Zhaxylyk Sabitov
- Research Institute for Jochi Ulus Studies, Astana, Republic of Kazakhstan
- L.N. Gumilyov Eurasian National University, Astana, Republic of Kazakhstan
| | - Maxat Zhabagin
- National Center for Biotechnology, Astana, Kazakhstan.
- Nazarbayev University, Astana, Kazakhstan.
| |
Collapse
|
33
|
郭 科建, 黄 磊, 李 士林, 殷 才湧, 汤 真. [Polymorphism and mutation investigation of 37 Y-STR loci in Shandong Han population]. Fa Yi Xue Za Zhi 2023; 39:501-506. [PMID: 38006271 DOI: 10.12116/j.issn.1004-5619.2022.520903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/26/2023]
|
34
|
Silcocks M, Dunstan SJ. Parallel signatures of Mycobacterium tuberculosis and human Y-chromosome phylogeography support the Two Layer model of East Asian population history. Commun Biol 2023; 6:1037. [PMID: 37833496 PMCID: PMC10575886 DOI: 10.1038/s42003-023-05388-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
The Two Layer hypothesis is fast becoming the favoured narrative describing East Asian population history. Under this model, hunter-gatherer groups who initially peopled East Asia via a route south of the Himalayas were assimilated by agriculturalist migrants who arrived via a northern route across Eurasia. A lack of ancient samples from tropical East Asia limits the resolution of this model. We consider insight afforded by patterns of variation within the human pathogen Mycobacterium tuberculosis (Mtb) by analysing its phylogeographic signatures jointly with the human Y-chromosome. We demonstrate the Y-chromosome lineages enriched in the traditionally hunter-gatherer groups associated with East Asia's first layer of peopling to display deep roots, low long-term effective population size, and diversity patterns consistent with a southern entry route. These characteristics mirror those of the evolutionarily ancient Mtb lineage 1. The remaining East Asian Y-chromosome lineage is almost entirely absent from traditionally hunter-gatherer groups and displays spatial and temporal characteristics which are incompatible with a southern entry route, and which link it to the development of agriculture in modern-day China. These characteristics mirror those of the evolutionarily modern Mtb lineage 2. This model paves the way for novel host-pathogen coevolutionary research hypotheses in East Asia.
Collapse
Affiliation(s)
- Matthew Silcocks
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia.
| | - Sarah J Dunstan
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| |
Collapse
|
35
|
Zhao GB, Miao L, Wang M, Yuan JH, Wei LH, Feng YS, Zhao J, Kang KL, Zhang C, Ji AQ, He G, Wang L. Developmental validation of a high-resolution panel genotyping 639 Y-chromosome SNP and InDel markers and its evolutionary features in Chinese populations. BMC Genomics 2023; 24:611. [PMID: 37828453 PMCID: PMC10568895 DOI: 10.1186/s12864-023-09709-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/02/2023] [Indexed: 10/14/2023] Open
Abstract
Uniparental-inherited haploid genetic marker of Y-chromosome single nucleotide polymorphisms (Y-SNP) have the power to provide a deep understanding of the human evolutionary past, forensic pedigree, and bio-geographical ancestry information. Several international cross-continental or regional Y-panels instead of Y-whole sequencing have recently been developed to promote Y-tools in forensic practice. However, panels based on next-generation sequencing (NGS) explicitly developed for Chinese populations are insufficient to represent the Chinese Y-chromosome genetic diversity and complex population structures, especially for Chinese-predominant haplogroup O. We developed and validated a 639-plex panel including 633 Y-SNPs and 6 Y-Insertion/deletions, which covered 573 Y haplogroups on the Y-DNA haplogroup tree. In this panel, subgroups from haplogroup O accounted for 64.4% of total inferable haplogroups. We reported the sequencing metrics of 354 libraries sequenced with this panel, with the average sequencing depth among 226 individuals being 3,741×. We illuminated the high level of concordance, accuracy, reproducibility, and specificity of the 639-plex panel and found that 610 loci were genotyped with as little as 0.03 ng of genomic DNA in the sensitivity test. 94.05% of the 639 loci were detectable in male-female mixed DNA samples with a mix ratio of 1:500. Nearly all of the loci were genotyped correctly when no more than 25 ng/μL tannic acid, 20 ng/μL humic acid, or 37.5 μM hematin was added to the amplification mixture. More than 80% of genotypes were obtained from degraded DNA samples with a degradation index of 11.76. Individuals from the same pedigree shared identical genotypes in 11 male pedigrees. Finally, we presented the complex evolutionary history of 183 northern Chinese Hans and six other Chinese populations, and found multiple founding lineages that contributed to the northern Han Chinese gene pool. The 639-plex panel proved an efficient tool for Chinese paternal studies and forensic applications.
Collapse
Affiliation(s)
- Guang-Bin Zhao
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Lei Miao
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Mengge Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510275, China
| | - Jia-Hui Yuan
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Lan-Hai Wei
- School of Ethnology and Anthropology, Inner Mongolia Normal University, Inner Mongolia, 010028, China
| | - Yao-Sen Feng
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Jie Zhao
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Ke-Lai Kang
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Chi Zhang
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - An-Quan Ji
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China.
| | - Guanglin He
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China.
| | - Le Wang
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China.
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China.
| |
Collapse
|
36
|
Abstract
Unreliable protein-based tools are impeding sex-based research.
Collapse
Affiliation(s)
- Bradley D Gelfand
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Jayakrishna Ambati
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, VA, USA
| |
Collapse
|
37
|
Fu J, Song B, Qian J, He T, Chen H, Cheng J, Fu J. Genetic Polymorphism Analysis of 24 Y-STRs in a Han Chinese Population in Luzhou, Southwest China. Genes (Basel) 2023; 14:1904. [PMID: 37895253 PMCID: PMC10606688 DOI: 10.3390/genes14101904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 09/27/2023] [Accepted: 09/30/2023] [Indexed: 10/29/2023] Open
Abstract
Han is the largest of China's 56 ethnic groups and the most populous ethnic group in the world. The Luzhou region is located in southwest China, at the junction of three provinces. The unique historical factors contribute to the genetic polymorphism information. Short tandem repeats (STRs) are highly polymorphic, but the polymorphism of the Y chromosomal STRs (Y-STRs) loci in the Luzhou region is still unclear. It is of great significance to provide Y-STRs genetic data for the Han population from the Luzhou areas of southwest China. A total of 910 unrelated male individuals of the Han population from the Luzhou area were recruited, and 24 Y-STRs were analyzed. The population structure and phylogenetic relationships were compared with those of another 11 related Han populations. A total of 893 different haplotypes were achieved from 910 samples, of which 877 (98.21%) haplotypes were unique. Haplotype diversity and discrimination were 0.999956 and 0.981319, respectively. The lowest genetic diversity of DYS437 is 0.4321, and the highest genetic diversity of DYS385a/b is 0.9642. Pair-to-pair genetic distance and relative probability values indicate that Luzhou Han people are close to Sichuan Han people, Guangdong Han people, and Hunan Han people, which is consistent with geographical distribution, historical influence, and economic development. The 24 Y-STR markers of the southwest Luzhou Han population were highly polymorphic, which provided us with genetic polymorphism information and enriched the population genetic database. Therefore, it is of great value to our forensic applications and population genetics research.
Collapse
Affiliation(s)
- Jiewen Fu
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, China; (J.F.); (B.S.); (J.Q.); (T.H.); (J.C.)
- School for Basic Medicine, Southwest Medical University, Luzhou 646000, China
- Laboratory of Forensic DNA, The Judicial Authentication Center, Southwest Medical University, Luzhou 646000, China
| | - Binghui Song
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, China; (J.F.); (B.S.); (J.Q.); (T.H.); (J.C.)
- Laboratory of Forensic DNA, The Judicial Authentication Center, Southwest Medical University, Luzhou 646000, China
| | - Jie Qian
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, China; (J.F.); (B.S.); (J.Q.); (T.H.); (J.C.)
| | - Ting He
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, China; (J.F.); (B.S.); (J.Q.); (T.H.); (J.C.)
| | - Hanchun Chen
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Central South University, Changsha 410013, China;
| | - Jingliang Cheng
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, China; (J.F.); (B.S.); (J.Q.); (T.H.); (J.C.)
- Laboratory of Forensic DNA, The Judicial Authentication Center, Southwest Medical University, Luzhou 646000, China
| | - Junjiang Fu
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, China; (J.F.); (B.S.); (J.Q.); (T.H.); (J.C.)
- Laboratory of Forensic DNA, The Judicial Authentication Center, Southwest Medical University, Luzhou 646000, China
| |
Collapse
|
38
|
Song W, Zhou S, Yu W, Fan Y, Liang X. Genetic analysis of 42 Y-STR loci in Han and Manchu populations from the three northeastern provinces in China. BMC Genomics 2023; 24:578. [PMID: 37770896 PMCID: PMC10537175 DOI: 10.1186/s12864-023-09636-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 08/30/2023] [Indexed: 09/30/2023] Open
Abstract
BACKGROUND Y-STR polymorphisms are useful in tracing genealogy and understanding human origins and migration history. This study aimed to fill a knowledge gap in the genetic diversity, structure, and haplogroup distribution of the Han and Manchu populations from the three northeastern provinces in China (Liaoning, Jilin, and Heilongjiang). METHODS A total of 1,048 blood samples were collected from unrelated males residing in Dalian. Genotyping was performed using the AGCU Y37 + 5 Amplification Kit, and the genotype data were analyzed to determine allele and haplotype frequencies, genetic and haplotype diversity, discrimination capacity, and haplotype match probability. Population pairwise genetic distances (Fst) were calculated to compare the genetic relationships among Han and Manchu populations from Northeast China and other 23 populations using 27 Yfiler Plus loci set. Multi-dimensional scaling and phylogenetic analysis were employed to visualize the genetic relationships among the 27 populations. Moreover, haplogroups were predicted based on 27 Yfiler Plus loci set. RESULTS The Han populations from Northeast China exhibited genetic affinities with both Han populations from the Central Plain and the Sichuan Qiang population, despite considerable geographical distances. Conversely, the Manchu population displayed a relatively large genetic distance from other populations. The haplogroup analysis revealed the prevalence of haplogroups E1b1b, O1b, O2, and Q in the studied populations, with variations observed among different ethnic groups. CONCLUSION The study contributes to our understanding of genetic diversity and history of the Han and Manchu populations in Northeast China, the genetic relationships between populations, and the intricate processes of migration, intermarriage, and cultural integration that have shaped the region's genetic landscape.
Collapse
Affiliation(s)
- Wenqian Song
- Institute of Forensic Science, Dalian Blood Center, Liaoning, China
| | - Shihang Zhou
- Institute of Forensic Science, Dalian Blood Center, Liaoning, China
| | - Weijian Yu
- Institute of Forensic Science, Dalian Blood Center, Liaoning, China
| | - Yaxin Fan
- Institute of Forensic Science, Dalian Blood Center, Liaoning, China
| | - Xiaohua Liang
- Institute of Forensic Science, Dalian Blood Center, Liaoning, China.
| |
Collapse
|
39
|
Sandoval JR, Revollo S, Cuellar C, Lacerda DR, Jota MS, Fujita R, Santos FR. Genetic portrait of the Amazonian communities of Peru and Bolivia: The legacy of the Takanan-speaking people. Ann Hum Genet 2023; 87:210-221. [PMID: 37161738 DOI: 10.1111/ahg.12510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 04/24/2023] [Accepted: 04/27/2023] [Indexed: 05/11/2023]
Abstract
During the colonial period in South America, many autochthonous populations were affected by relocation by European missionary reductions and other factors that impacted and reconfigured their genetic makeup. Presently, the descendants of some "reduced" and other isolated groups are distributed in the Amazonian areas of Peru, Bolivia, and Brazil, and among them, speakers of Takanan and Panoan languages. Based on linguistics, these peoples should be closely related, but so far no DNA comparison studies have been conducted to corroborate a genetic relationship. To clarify these questions, we used a set of 15 short tandem repeats of the non-recombining part of the Y-chromosome (Y-STRs) and mitochondrial DNA (mtDNA) control region sequence data. Paternal line comparisons showed the Takanan-speaking peoples from Peru and Bolivia descended from recent common ancestors; one group was related to Arawakan, Jivaroan, and Cocama and the other to Panoan speakers, consistent with linguistics. Also, a genetic affinity for maternal lines was observed between some Takanan speakers and individuals who spoke different Amazonian languages. Our results supported a shared ancestry of Takanan, Panoan, Cocama, and Jivaroan-speaking communities who appeared to be related to each other and came likely from an early Arawak expansion in the western Amazonia of South America.
Collapse
Affiliation(s)
- José R Sandoval
- Centro de Genética y Biología Molecular (CGBM), Instituto de Investigación, Facultad de Medicina Humana, Universidad de San Martín de Porres, Lima, Perú
- Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | - Daniela R Lacerda
- Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Marilza S Jota
- Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ricardo Fujita
- Centro de Genética y Biología Molecular (CGBM), Instituto de Investigación, Facultad de Medicina Humana, Universidad de San Martín de Porres, Lima, Perú
| | - Fabricio R Santos
- Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| |
Collapse
|
40
|
Hallast P, Ebert P, Loftus M, Yilmaz F, Audano PA, Logsdon GA, Bonder MJ, Zhou W, Höps W, Kim K, Li C, Hoyt SJ, Dishuck PC, Porubsky D, Tsetsos F, Kwon JY, Zhu Q, Munson KM, Hasenfeld P, Harvey WT, Lewis AP, Kordosky J, Hoekzema K, O'Neill RJ, Korbel JO, Tyler-Smith C, Eichler EE, Shi X, Beck CR, Marschall T, Konkel MK, Lee C. Assembly of 43 human Y chromosomes reveals extensive complexity and variation. Nature 2023; 621:355-364. [PMID: 37612510 PMCID: PMC10726138 DOI: 10.1038/s41586-023-06425-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 07/11/2023] [Indexed: 08/25/2023]
Abstract
The prevalence of highly repetitive sequences within the human Y chromosome has prevented its complete assembly to date1 and led to its systematic omission from genomic analyses. Here we present de novo assemblies of 43 Y chromosomes spanning 182,900 years of human evolution and report considerable diversity in size and structure. Half of the male-specific euchromatic region is subject to large inversions with a greater than twofold higher recurrence rate compared with all other chromosomes2. Ampliconic sequences associated with these inversions show differing mutation rates that are sequence context dependent, and some ampliconic genes exhibit evidence for concerted evolution with the acquisition and purging of lineage-specific pseudogenes. The largest heterochromatic region in the human genome, Yq12, is composed of alternating repeat arrays that show extensive variation in the number, size and distribution, but retain a 1:1 copy-number ratio. Finally, our data suggest that the boundary between the recombining pseudoautosomal region 1 and the non-recombining portions of the X and Y chromosomes lies 500 kb away from the currently established1 boundary. The availability of fully sequence-resolved Y chromosomes from multiple individuals provides a unique opportunity for identifying new associations of traits with specific Y-chromosomal variants and garnering insights into the evolution and function of complex regions of the human genome.
Collapse
Affiliation(s)
- Pille Hallast
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Peter Ebert
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
- Core Unit Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany
| | - Mark Loftus
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC, USA
- Center for Human Genetics, Clemson University, Greenwood, SC, USA
| | - Feyza Yilmaz
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Peter A Audano
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Glennis A Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Marc Jan Bonder
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Weichen Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Wolfram Höps
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Kwondo Kim
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Chong Li
- Department of Computer and Information Sciences, Temple University, Philadelphia, PA, USA
| | - Savannah J Hoyt
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Philip C Dishuck
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Fotios Tsetsos
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Jee Young Kwon
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Qihui Zhu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Patrick Hasenfeld
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - William T Harvey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Alexandra P Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Jennifer Kordosky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Rachel J O'Neill
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
- The University of Connecticut Health Center, Farmington, CT, USA
| | - Jan O Korbel
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Xinghua Shi
- Department of Computer and Information Sciences, Temple University, Philadelphia, PA, USA
| | - Christine R Beck
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
- The University of Connecticut Health Center, Farmington, CT, USA
| | - Tobias Marschall
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University, Düsseldorf, Germany
| | - Miriam K Konkel
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC, USA
- Center for Human Genetics, Clemson University, Greenwood, SC, USA
| | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
| |
Collapse
|
41
|
Rhie A, Nurk S, Cechova M, Hoyt SJ, Taylor DJ, Altemose N, Hook PW, Koren S, Rautiainen M, Alexandrov IA, Allen J, Asri M, Bzikadze AV, Chen NC, Chin CS, Diekhans M, Flicek P, Formenti G, Fungtammasan A, Garcia Giron C, Garrison E, Gershman A, Gerton JL, Grady PGS, Guarracino A, Haggerty L, Halabian R, Hansen NF, Harris R, Hartley GA, Harvey WT, Haukness M, Heinz J, Hourlier T, Hubley RM, Hunt SE, Hwang S, Jain M, Kesharwani RK, Lewis AP, Li H, Logsdon GA, Lucas JK, Makalowski W, Markovic C, Martin FJ, Mc Cartney AM, McCoy RC, McDaniel J, McNulty BM, Medvedev P, Mikheenko A, Munson KM, Murphy TD, Olsen HE, Olson ND, Paulin LF, Porubsky D, Potapova T, Ryabov F, Salzberg SL, Sauria MEG, Sedlazeck FJ, Shafin K, Shepelev VA, Shumate A, Storer JM, Surapaneni L, Taravella Oill AM, Thibaud-Nissen F, Timp W, Tomaszkiewicz M, Vollger MR, Walenz BP, Watwood AC, Weissensteiner MH, Wenger AM, Wilson MA, Zarate S, Zhu Y, Zook JM, Eichler EE, O'Neill RJ, Schatz MC, Miga KH, Makova KD, Phillippy AM. The complete sequence of a human Y chromosome. Nature 2023; 621:344-354. [PMID: 37612512 PMCID: PMC10752217 DOI: 10.1038/s41586-023-06457-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 07/19/2023] [Indexed: 08/25/2023]
Abstract
The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure that includes long palindromes, tandem repeats and segmental duplications1-3. As a result, more than half of the Y chromosome is missing from the GRCh38 reference sequence and it remains the last human chromosome to be finished4,5. Here, the Telomere-to-Telomere (T2T) consortium presents the complete 62,460,029-base-pair sequence of a human Y chromosome from the HG002 genome (T2T-Y) that corrects multiple errors in GRCh38-Y and adds over 30 million base pairs of sequence to the reference, showing the complete ampliconic structures of gene families TSPY, DAZ and RBMY; 41 additional protein-coding genes, mostly from the TSPY family; and an alternating pattern of human satellite 1 and 3 blocks in the heterochromatic Yq12 region. We have combined T2T-Y with a previous assembly of the CHM13 genome4 and mapped available population variation, clinical variants and functional genomics data to produce a complete and comprehensive reference sequence for all 24 human chromosomes.
Collapse
Affiliation(s)
- Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sergey Nurk
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Oxford Nanopore Technologies Inc., Oxford, UK
| | - Monika Cechova
- Faculty of Informatics, Masaryk University, Brno, Czech Republic
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Savannah J Hoyt
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Dylan J Taylor
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Nicolas Altemose
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Paul W Hook
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mikko Rautiainen
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ivan A Alexandrov
- Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
- Center for Algorithmic Biotechnology, Saint Petersburg State University, St Petersburg, Russia
- Department of Anatomy and Anthropology and Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Jamie Allen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Mobin Asri
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Andrey V Bzikadze
- Graduate Program in Bioinformatics and Systems Biology, University of California, San Diego, CA, USA
| | - Nae-Chyun Chen
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Chen-Shan Chin
- GeneDX Holdings Corp, Stamford, CT, USA
- Foundation of Biological Data Science, Belmont, CA, USA
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | | | | | - Carlos Garcia Giron
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Erik Garrison
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Ariel Gershman
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jennifer L Gerton
- Stowers Institute for Medical Research, Kansas City, MO, USA
- University of Kansas Medical Center, Kansas City, MO, USA
| | - Patrick G S Grady
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Andrea Guarracino
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
- Genomics Research Centre, Human Technopole, Milan, Italy
| | - Leanne Haggerty
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Reza Halabian
- Institute of Bioinformatics, Faculty of Medicine, University of Münster, Münster, Germany
| | - Nancy F Hansen
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Robert Harris
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Gabrielle A Hartley
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - William T Harvey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Marina Haukness
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Jakob Heinz
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Stephen Hwang
- XDBio Program, Johns Hopkins University, Baltimore, MD, USA
| | - Miten Jain
- Department of Bioengineering, Department of Physics, Northeastern University, Boston, MA, USA
| | - Rupesh K Kesharwani
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Alexandra P Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Glennis A Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Julian K Lucas
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Wojciech Makalowski
- Institute of Bioinformatics, Faculty of Medicine, University of Münster, Münster, Germany
| | - Christopher Markovic
- Genome Technology Access Center at the McDonnell Genome Institute, Washington University, St. Louis, MO, USA
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ann M Mc Cartney
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rajiv C McCoy
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Jennifer McDaniel
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Brandy M McNulty
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Paul Medvedev
- Department of Computer Science and Engineering, Pennsylvania State University, University Park, PA, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
- Center for Computational Biology and Bioinformatics, Pennsylvania State University, University Park, PA, USA
| | - Alla Mikheenko
- Center for Algorithmic Biotechnology, Saint Petersburg State University, St Petersburg, Russia
- UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Hugh E Olsen
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Nathan D Olson
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Luis F Paulin
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Tamara Potapova
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Fedor Ryabov
- Masters Program in National Research University Higher School of Economics, Moscow, Russia
| | - Steven L Salzberg
- Departments of Biomedical Engineering, Computer Science, and Biostatistics, Johns Hopkins University, Baltimore, MD, USA
| | | | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
- Department of Computer Science, Rice University, Houston, TX, USA
| | | | | | - Alaina Shumate
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | | | - Likhitha Surapaneni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Angela M Taravella Oill
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Marta Tomaszkiewicz
- Department of Biology, Pennsylvania State University, University Park, PA, USA
- Department of Biomedical Engineering, Pennsylvania State University, State College, PA, USA
| | - Mitchell R Vollger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Brian P Walenz
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Allison C Watwood
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | | | | | - Melissa A Wilson
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Samantha Zarate
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Yiming Zhu
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Justin M Zook
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Investigator, Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Rachel J O'Neill
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA
| | - Michael C Schatz
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Karen H Miga
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Kateryna D Makova
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
42
|
Xavier C, Sutter C, Amory C, Niederstätter H, Parson W. NuMY-A qPCR Assay Simultaneously Targeting Human Autosomal, Y-Chromosomal, and Mitochondrial DNA. Genes (Basel) 2023; 14:1645. [PMID: 37628695 PMCID: PMC10454206 DOI: 10.3390/genes14081645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/13/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
The accurate quantification of DNA in forensic samples is of utmost importance. These samples are often present in limited amounts; therefore, it is indicated to use the appropriate analysis route with the optimum DNA amount (when possible). Also, DNA quantification can inform about the degradation stage and therefore support the decision on which downstream genotyping method to use. Consequently, DNA quantification aids in getting the best possible results from a forensic sample, considering both its DNA quantity and quality limitations. Here, we introduce NuMY, a new quantitative real-time PCR (qPCR) method for the parallel quantification of human nuclear (n) and mitochondrial (mt) DNA, assessing the male portion in mixtures of both sexes and testing for possible PCR inhibition. NuMY is based on previous work and follows the MIQE guidelines whenever applicable. Although quantification of nuclear (n)DNA by simultaneously analyzing autosomal and male-specific targets is available in commercial qPCR kits, tools that include the quantification of mtDNA are sparse. The quantification of mtDNA has proven relevant for samples with low nDNA content when conventional DNA fingerprinting techniques cannot be followed. Furthermore, the development and use of new massively parallel sequencing assays that combine multiple marker types, i.e., autosomal, Y-chromosomal, and mtDNA, can be optimized when precisely knowing the amount of each DNA component present in the input sample. For high-quality DNA extracts, NuMY provided nDNA results comparable to those of another quantification technique and has also proven to be a reliable tool for challenging, forensically relevant samples such as mixtures, inhibited, and naturally degraded samples.
Collapse
Affiliation(s)
- Catarina Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.S.); (C.A.); (H.N.)
- i3S—Institute for Research and Innovation in Health, University of Porto, 4099-002 Porto, Portugal
| | - Charlotte Sutter
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.S.); (C.A.); (H.N.)
| | - Christina Amory
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.S.); (C.A.); (H.N.)
| | - Harald Niederstätter
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.S.); (C.A.); (H.N.)
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, 6020 Innsbruck, Austria; (C.S.); (C.A.); (H.N.)
- Forensic Science Program, The Pennsylvania State University, University Park, PA 16801, USA
| |
Collapse
|
43
|
Kuroki Y, Fukami M. Y Chromosome Genomic Variations and Biological Significance in Human Diseases and Health. Cytogenet Genome Res 2023; 163:5-13. [PMID: 37562362 DOI: 10.1159/000531933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 07/10/2023] [Indexed: 08/12/2023] Open
Abstract
The Y chromosome is a haploid genome unique to males with no genes essential for life. It is easily transmitted to the next generation without being repaired by recombination, even if a major genomic structural alteration occurs. On the other hand, the Y chromosome genome is basically a region transmitted only from father to son, reflecting a male-specific inheritance between generations. The Y chromosome exhibits genomic structural differences among different ethnic groups and individuals. The Y chromosome was previously thought to affect only male-specific phenotypes, but recent studies have revealed associations between the Y chromosomes and phenotypes common to both males and females, such as certain types of cancer and neuropsychiatric disorders. This evidence was discovered with the finding of the mosaic loss of the Y chromosome in somatic cells. This phenomenon is also affected by environmental factors, such as smoking and aging. In the past, functional analysis of the Y chromosome has been elucidated by assessing the function of Y chromosome-specific genes and the association between Y chromosome haplogroups and human phenotypes. These studies are currently being conducted intensively. Additionally, the recent advance of large-scale genome cohort studies has increased the amount of Y chromosome genomic information available for analysis, making it possible to conduct more precise studies of the relationship between genome structures and phenotypes. In this review, we will introduce recent analyses using large-scale genome cohort data and previously reported association studies between Y chromosome haplogroups and human phenotypes, such as male infertility, cancer, cardiovascular system traits, and neuropsychiatric disorders. The function and biological role of the Y chromosome in human phenotypes will also be discussed.
Collapse
Affiliation(s)
- Yoko Kuroki
- Department of Genome Medicine, National Center for Child Health and Development, Tokyo, Japan
- Division of Collaborative Research, National Center for Child Health and Development, Tokyo, Japan
- Division of Diversity Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Maki Fukami
- Division of Diversity Research, National Research Institute for Child Health and Development, Tokyo, Japan
- Department of Molecular Endocrinology, National Center for Child Health and Development, Tokyo, Japan
| |
Collapse
|
44
|
Demanelis K, Delgado DA, Tong L, Jasmine F, Ahmed A, Islam T, Parvez F, Kibriya MG, Graziano JH, Ahsan H, Pierce BL. Somatic loss of the Y chromosome is associated with arsenic exposure among Bangladeshi men. Int J Epidemiol 2023; 52:1035-1046. [PMID: 36130227 PMCID: PMC10695470 DOI: 10.1093/ije/dyac176] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 09/01/2022] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Arsenic exposure increases the risk of several cancers in humans and contributes to genomic instability. Somatic loss of the Y chromosome (LoY) is a potential biomarker of genomic instability and cancer risk. Smoking is associated with LoY, but few other carcinogens have been investigated. We tested the cross-sectional association between arsenic exposure and LoY in leukocytes among genotyped Bangladeshi men (age 20-70 years) from the Health Effects of Arsenic Longitudinal Study. METHODS We extracted the median of logR-ratios from probes on the Y chromosome (mLRR-chrY) from genotyping arrays (n = 1364) and estimated the percentage of cells with LoY (% LoY) from mLRR-chrY. We evaluated the association between arsenic exposure (measured in drinking water and urine) and LoY using multivariable linear and logistic regression models. The association between LoY and incident arsenic-induced skin lesions was also examined. RESULTS Ten percent of genotyped men had LoY in at least 5% of cells and % LoY increased with age. Among men randomly selected for genotyping (n = 778), higher arsenic in drinking water, arsenic consumed and urinary arsenic were associated with increased % LoY (P = 0.006, P = 0.06 and P = 0.13, respectively). LoY was associated with increased risk of incident skin lesions (P = 0.008). CONCLUSION Arsenic exposure was associated with increased LoY, providing additional evidence that arsenic contributes to genomic instability. LoY was associated with developing skin lesions, a risk factor for cancer, suggesting that LoY may be a biomarker of susceptibility in arsenic-exposed populations. The effect of arsenic on somatic events should be further explored in cancer-prone tissue types.
Collapse
Affiliation(s)
- Kathryn Demanelis
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA
| | - Dayana A Delgado
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA
| | - Lin Tong
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA
| | - Farzana Jasmine
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA
| | | | | | - Faruque Parvez
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Muhammad G Kibriya
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA
| | - Joseph H Graziano
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Habibul Ahsan
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
- Comprehensive Cancer Center, The University of Chicago, Chicago, IL, USA
- Departments of Medicine and Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Brandon L Pierce
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
- Comprehensive Cancer Center, The University of Chicago, Chicago, IL, USA
| |
Collapse
|
45
|
Lucotte EA, Guðmundsdóttir VB, Jensen JM, Skov L, Macià MC, Almstrup K, Schierup MH, Helgason A, Stefansson K. Characterizing the evolution and phenotypic impact of ampliconic Y chromosome regions. Nat Commun 2023; 14:3990. [PMID: 37414752 PMCID: PMC10326017 DOI: 10.1038/s41467-023-39644-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 06/22/2023] [Indexed: 07/08/2023] Open
Abstract
A major part of the human Y chromosome consists of palindromes with multiple copies of genes primarily expressed in testis, many of which have been claimed to affect male fertility. Here we examine copy number variation in these palindromes based on whole genome sequence data from 11,527 Icelandic men. Using a subset of 7947 men grouped into 1449 patrilineal genealogies, we infer 57 large scale de novo copy number mutations affecting palindrome 1. This corresponds to a mutation rate of 2.34 × 10-3 mutations per meiosis, which is 4.1 times larger than our phylogenetic estimate of the mutation rate (5.72 × 10-4), suggesting that de novo mutations on the Y are lost faster than expected under neutral evolution. Although simulations indicate a selection coefficient of 1.8% against non-reference copy number carriers, we do not observe differences in fertility among sequenced men associated with their copy number genotype, but we lack statistical power to detect differences resulting from weak negative selection. We also perform association testing of a diverse set of 341 traits to palindromic copy number without any significant associations. We conclude that large-scale palindrome copy number variation on the Y chromosome has little impact on human phenotype diversity.
Collapse
Affiliation(s)
- Elise A Lucotte
- Bioinformatics Research Centre, Aarhus University, Dk-8000, Aarhus C., Denmark.
- Ecologie Systematique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, 91198, Gif-sur-Yvette, France.
| | - Valdís Björt Guðmundsdóttir
- deCODE genetics/Amgen Inc., 101, Reykjavik, Iceland
- Department of Anthropology, University of Iceland, 101, Reykjavik, Iceland
| | - Jacob M Jensen
- Bioinformatics Research Centre, Aarhus University, Dk-8000, Aarhus C., Denmark
| | - Laurits Skov
- Bioinformatics Research Centre, Aarhus University, Dk-8000, Aarhus C., Denmark
| | - Moisès Coll Macià
- Bioinformatics Research Centre, Aarhus University, Dk-8000, Aarhus C., Denmark
| | - Kristian Almstrup
- Department of Growth and Reproduction, Rigshospitalet, Copenhagen, Denmark
| | - Mikkel H Schierup
- Bioinformatics Research Centre, Aarhus University, Dk-8000, Aarhus C., Denmark
| | - Agnar Helgason
- deCODE genetics/Amgen Inc., 101, Reykjavik, Iceland.
- Department of Anthropology, University of Iceland, 101, Reykjavik, Iceland.
| | - Kari Stefansson
- deCODE genetics/Amgen Inc., 101, Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, 101, Reykjavik, Iceland
| |
Collapse
|
46
|
Ge J, Crysup B, Peters D, Franco R, Liu M, Wang X, Huang M, Budowle B. MPKin-YSTR: Interpretation of Y chromosome STR haplotypes for missing persons cases. Electrophoresis 2023; 44:1080-1087. [PMID: 37016479 DOI: 10.1002/elps.202200225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 03/22/2023] [Accepted: 03/30/2023] [Indexed: 04/06/2023]
Abstract
Y chromosome Short Tandem Repeat (STR) haplotypes have been used in assisting forensic investigations primarily for identification and male lineage determination. The current SWGDAM interpretation guidelines for Y-STR typing provide helpful guidance on those purposes but do not address the issue of kinship analysis with Y-STR haplotypes. Because of the high mutation rate of Y-STRs, there are complex missing person cases in which inconsistent Y-STR haplotypes between true paternal lineage relatives will arise and cases with two or more male references in the same lineage and yet differ in their haplotypes. Therefore, more useful methods are needed for interpreting the Y-STR haplotype data. Computational methods and interpretation guidelines have been developed specifically addressing this issue, either using a mismatch-based counting method or a pedigree likelihood ratio method. In this study, a software program, MPKin-YSTR, was developed by implementing those more sophisticated methods. This software should be able to improve the interpretation of complex cases with Y-STR haplotype evidence. Thus, more biological evidence will be interpreted, which in turn will result in more investigation leads to help solve crimes.
Collapse
Affiliation(s)
- Jianye Ge
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, USA
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Benjamin Crysup
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Dixie Peters
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Romy Franco
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Muyi Liu
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Xuewen Wang
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Meng Huang
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, Fort Worth, Texas, USA
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, Texas, USA
| |
Collapse
|
47
|
Abdel-Hafiz HA, Schafer JM, Chen X, Xiao T, Gauntner TD, Li Z, Theodorescu D. Y chromosome loss in cancer drives growth by evasion of adaptive immunity. Nature 2023; 619:624-631. [PMID: 37344596 PMCID: PMC10975863 DOI: 10.1038/s41586-023-06234-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 05/18/2023] [Indexed: 06/23/2023]
Abstract
Loss of the Y chromosome (LOY) is observed in multiple cancer types, including 10-40% of bladder cancers1-6, but its clinical and biological significance is unknown. Here, using genomic and transcriptomic studies, we report that LOY correlates with poor prognoses in patients with bladder cancer. We performed in-depth studies of naturally occurring LOY mutant bladder cancer cells as well as those with targeted deletion of Y chromosome by CRISPR-Cas9. Y-positive (Y+) and Y-negative (Y-) tumours grew similarly in vitro, whereas Y- tumours were more aggressive than Y+ tumours in immune-competent hosts in a T cell-dependent manner. High-dimensional flow cytometric analyses demonstrated that Y- tumours promote striking dysfunction or exhaustion of CD8+ T cells in the tumour microenvironment. These findings were validated using single-nuclei RNA sequencing and spatial proteomic evaluation of human bladder cancers. Of note, compared with Y+ tumours, Y- tumours exhibited an increased response to anti-PD-1 immune checkpoint blockade therapy in both mice and patients with cancer. Together, these results demonstrate that cancer cells with LOY mutations alter T cell function, promoting T cell exhaustion and sensitizing them to PD-1-targeted immunotherapy. This work provides insights into the basic biology of LOY mutation and potential biomarkers for improving cancer immunotherapy.
Collapse
Affiliation(s)
- Hany A Abdel-Hafiz
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Johanna M Schafer
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center-The James, Columbus, OH, USA
- Roche Diagnostics Solutions, Oro Valley, AZ, USA
| | - Xingyu Chen
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Tong Xiao
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center-The James, Columbus, OH, USA
| | - Timothy D Gauntner
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center-The James, Columbus, OH, USA
| | - Zihai Li
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center-The James, Columbus, OH, USA
| | - Dan Theodorescu
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
- Cedars-Sinai Cancer Center, Los Angeles, CA, USA.
| |
Collapse
|
48
|
Small AM, Libby P. Why Y? The Y chromosome may serve a cardiovascular purpose after all. Eur Heart J 2023; 44:1953-1955. [PMID: 36932705 PMCID: PMC10232269 DOI: 10.1093/eurheartj/ehad125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/19/2023] Open
Affiliation(s)
- Aeron M Small
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School Boston, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Peter Libby
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School Boston, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| |
Collapse
|
49
|
张 世, 蹇 慧, 王 倩, 王 威, 丁 艳, 张 宵, 徐 冬, 杜 冰, 金 波. [Polymorphism and Mutation Rate of 20 Rapidly Mutating Y-Chromosomal Short Tandem Repeats in Chinese Han Population of Sichuan Province]. Sichuan Da Xue Xue Bao Yi Xue Ban 2023; 54:367-373. [PMID: 36949700 PMCID: PMC10409182 DOI: 10.12182/20230260308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Indexed: 03/24/2023]
Abstract
Objective To explore the applicability of 20 rapidly mutating Y-chromosomal short tandem repeats (RM Y-STRs) in Chinese Han population of Sichuan province. Methods Two RM Y-STR multiple amplification systems (RM1, including DYF404S1, DYF399S1, DYS547, DYS526a/b, DYS626, DYF403S1a/b, and DYS612, and RM2, including DYS1003, DYS1007, DYR88, DYS712, DYS711, DYS724, and DYF1002, with 14 RM Y-STR loci in total) and Y41SE-V1.2 (including 6 RM Y-STR loci of DYS627, DYS576, DYF387S1, DYS518, DYS570, and DYS449, 30 ordinary Y-chromosomal short tandem repeats [Y-STR] loci, and 1 Indel locus) were used for the amplification and typing of 200 unrelated males and 260 father-son pairs. The polymorphisms and mutation rates of 20 RM Y-STRs and 30 ordinary Y-STRs in Chinese Han population of Sichuan province were investigated and compared. Results In the 200 unrelated males, the gene diversity (GD) of 20 RM Y-STR loci ranged from 0.7910 to 0.9975, and there were 200 haplotypes. Haplotype diversity (HD) was 1 and the discriminative capacity (DC) was 1. A total of 198 haplotypes were found in Y41se-v1.2 (the 30 Y-STRs), with 4 cases sharing two haplotypes, the haplotype diversity being 0.9999, and the discriminative capacity being 0.99. A total of 68 mutations were found at the 20 RM Y-STRs loci in the 260 father-son pairs, and there was slightly more increase than decrease of allele repeats (1.19∶1), with the mutation rate ranging from <3.85×10 -3 (95% C I: 0.00-1.41×10 -2) to 2.69×10 -2 (95% CI: 1.09×10 -2-5.47×10 -2), and the average mutation rate being 1.19×10 -2 (95% CI: 9.20×10 -3-1.51×10 -2). The 20 RM Y-STRs and the Y41SE-V1.2 (the 30 Y-STRs) could be used to distinguish 22.3% and 13.8% father-son pairs, respectively. Conclusion The 20 RM Y-STRs have high gene and haplotype diversity and paternal lineage differentiation rate in Chinese Han population of Sichuan province, showing great potential for application in Chinese Han population of Sichuan province.
Collapse
Affiliation(s)
- 世林 张
- 川北医学院基础医学与法医学研究所 (南充 637000)Institute of Basic Medicine Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong 637000, China
| | - 慧 蹇
- 川北医学院基础医学与法医学研究所 (南充 637000)Institute of Basic Medicine Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong 637000, China
| | - 倩 王
- 川北医学院基础医学与法医学研究所 (南充 637000)Institute of Basic Medicine Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong 637000, China
| | - 威 王
- 川北医学院基础医学与法医学研究所 (南充 637000)Institute of Basic Medicine Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong 637000, China
| | - 艳杰 丁
- 川北医学院基础医学与法医学研究所 (南充 637000)Institute of Basic Medicine Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong 637000, China
| | - 宵 张
- 川北医学院基础医学与法医学研究所 (南充 637000)Institute of Basic Medicine Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong 637000, China
| | - 冬冬 徐
- 川北医学院基础医学与法医学研究所 (南充 637000)Institute of Basic Medicine Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong 637000, China
| | - 冰 杜
- 川北医学院基础医学与法医学研究所 (南充 637000)Institute of Basic Medicine Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong 637000, China
| | - 波 金
- 川北医学院基础医学与法医学研究所 (南充 637000)Institute of Basic Medicine Sciences and Forensic Medicine, North Sichuan Medical College, Nanchong 637000, China
| |
Collapse
|
50
|
Bardan F, Higgins D, Austin JJ. A custom hybridisation enrichment forensic intelligence panel to infer biogeographic ancestry, hair and eye colour, and Y chromosome lineage. Forensic Sci Int Genet 2023; 63:102822. [PMID: 36525814 DOI: 10.1016/j.fsigen.2022.102822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 11/02/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022]
Abstract
Massively parallel sequencing can provide genetic data for hundreds to thousands of loci in a single assay for various types of forensic testing. However, available commercial kits require an initial PCR amplification of short-to-medium sized targets which limits their application for highly degraded DNA. Development and optimisation of large PCR multiplexes also prevents creation of custom panels that target different suites of markers for identity, biogeographic ancestry, phenotype, and lineage markers (Y-chromosome and mtDNA). Hybridisation enrichment, an alternative approach for target enrichment prior to sequencing, uses biotinylated probes to bind to target DNA and has proven successful on degraded and ancient DNA. We developed a customisable hybridisation capture method, that uses individually mixed baits to allow tailored and targeted enrichment to specific forensic questions of interest. To allow collection of forensic intelligence data, we assembled and tested a custom panel of hybridisation baits to infer biogeographic ancestry, hair and eye colour, and paternal lineage (and sex) on modern male and female samples with a range of self-declared ancestries and hair/eye colour combinations. The panel correctly estimated biogeographic ancestry in 9/12 samples (75%) but detected European admixture in three individuals from regions with admixed demographic history. Hair and eye colour were predicted correctly in 83% and 92% of samples respectively, where intermediate eye colour and blond hair were problematic to predict. Analysis of Y-chromosome SNPs correctly assigned sex and paternal haplogroups, the latter complementing and supporting biogeographic ancestry predictions. Overall, we demonstrate the utility of this hybridisation enrichment approach to forensic intelligence testing using a combined suite of biogeographic ancestry, phenotype, and Y-chromosome SNPs for comprehensive biological profiling.
Collapse
Affiliation(s)
- Felicia Bardan
- Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, South Australia, Australia
| | - Denice Higgins
- Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, South Australia, Australia; School of Dentistry, Health and Medical Sciences, The University of Adelaide, South Australia, Australia
| | - Jeremy J Austin
- Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, South Australia, Australia.
| |
Collapse
|