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Adriano MRG, Bortolai A, Madia FAR, da Silva Carvalho GF, Nascimento AM, Zanardo EA, Wolff BM, Waisberg J, Bos-Mikich A, Kulikowski LD, Dias AT. Cytogenetics investigation in 151 Brazilian infertile male patients and genomic analysis in selected cases: experience of 14 years in a public genetic service. BMC Res Notes 2024; 17:67. [PMID: 38444014 PMCID: PMC10916190 DOI: 10.1186/s13104-024-06710-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 01/31/2024] [Indexed: 03/07/2024] Open
Abstract
OBJECTIVES Male infertility accounts for approximately 30% of cases of reproductive failure. The characterization of genetic variants using cytogenomic techniques is essential for the adequate clinical management of these patients. We aimed to conduct a cytogenetic investigation of numerical and structural rearrangements and a genomic study of Y chromosome microdeletions/microduplications in infertile men derived from a single centre with over 14 years of experience. RESULTS We evaluated 151 infertile men in a transversal study using peripheral blood karyotypes and 15 patients with normal karyotypes through genomic investigation by multiplex ligation-dependent probe amplification (MLPA) or polymerase chain reaction of sequence-tagged sites (PCR-STS) techniques. Out of the 151 patients evaluated by karyotype, 13 presented chromosomal abnormalities: two had numerical alterations, and 11 had structural chromosomal rearrangements. PCR-STS detected a BPY2 gene region and RBMY2DP pseudogene region microdeletion in one patient. MLPA analysis allowed the identification of one patient with CDY2B_1 and CDY2B_2 probe duplications (CDY2B and NLGN4Y genes) and one patient with BPY2_1, BPY2_2, and BPY2_4 probe duplications (PRY and RBMY1J genes).
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Affiliation(s)
- Márcia Regina Gimenes Adriano
- Laboratório de Citogenética, Serviço de Laboratório de Análises Clínicas, Instituto de Assistência Médica do Servidor Público do Estado de São Paulo (IAMSPE), São Paulo, SP, 04039-901, Brasil.
| | - Adriana Bortolai
- Laboratório de Citogenética, Serviço de Laboratório de Análises Clínicas, Instituto de Assistência Médica do Servidor Público do Estado de São Paulo (IAMSPE), São Paulo, SP, 04039-901, Brasil
| | - Fabricia Andreia Rosa Madia
- Laboratório de Citogenômica, Departamento de Patologia, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, SP, 05403-000, Brasil
| | - Gleyson Francisco da Silva Carvalho
- Laboratório de Citogenômica, Departamento de Patologia, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, SP, 05403-000, Brasil
| | - Amom Mendes Nascimento
- Laboratório de Citogenômica, Departamento de Patologia, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, SP, 05403-000, Brasil
| | - Evelin Aline Zanardo
- Laboratório de Citogenômica, Departamento de Patologia, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, SP, 05403-000, Brasil
| | - Beatriz Martins Wolff
- Laboratório de Citogenômica, Departamento de Patologia, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, SP, 05403-000, Brasil
| | - Jaques Waisberg
- Laboratório de Citogenética, Serviço de Laboratório de Análises Clínicas, Instituto de Assistência Médica do Servidor Público do Estado de São Paulo (IAMSPE), São Paulo, SP, 04039-901, Brasil
| | - Adriana Bos-Mikich
- Departamento de Ciências Morfológicas, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, 90050-170, Brasil
| | - Leslie Domenici Kulikowski
- Laboratório de Citogenômica, Departamento de Patologia, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, SP, 05403-000, Brasil
| | - Alexandre Torchio Dias
- Laboratório de Citogenética, Serviço de Laboratório de Análises Clínicas, Instituto de Assistência Médica do Servidor Público do Estado de São Paulo (IAMSPE), São Paulo, SP, 04039-901, Brasil
- Laboratório de Citogenômica, Departamento de Patologia, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, SP, 05403-000, Brasil
- Universidade Paulista - UNIP - Instituto de Ciências da Saúde - Curso de Biomedicina, São Paulo, Brasil
- CITOGEM Biotecnologia, São Paulo, Brasil
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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] [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.
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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
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Y chromosome structural variation in infertile men detected by targeted next-generation sequencing. J Assist Reprod Genet 2021; 38:941-948. [PMID: 33454900 DOI: 10.1007/s10815-020-02031-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 12/08/2020] [Indexed: 01/21/2023] Open
Abstract
PURPOSE To provide a validated method to identify copy number variation (CNV) in regions of the Y chromosome of infertile men by next-generation sequencing (NGS). METHODS Semen analysis was used to determine the quality of semen and diagnose infertility. Deletion of the azoospermia factor (AZF) region in the Y chromosome was detected by a routine sequence-tagged-site PCR (STS-PCR) method. We then used the NGS method to detect CNV in the AZF region, including deletions and duplications. RESULTS A total of 326 samples from male infertility patients, family members, and sperm donors were studied between January 2011 and May 2017. AZF microdeletions were detected in 120 patients by STS-PCR, and these results were consistent with the results from NGS. In addition, of the 160 patients and male family members who had no microdeletions detected by STS-PCR, 51 cases were found to exhibit Y chromosome structural variations by the NGS method (31.88%, 51/160). No microdeletions were found in 46 donors by STS-PCR, but the NGS method revealed 11 of these donors (23.91%, 11/46) carried structural variations, which were mainly in the AZFc region, including partial deletions and duplications. CONCLUSION The established NGS method can replace the conventional STS-PCR method to detect Y chromosome microdeletions. The NGS method can detect CNV, such as partial deletion or duplication, and provide details of the abnormal range and size of variations.
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Lassen O, Tabares S, Bertolotto P, Ojeda S, Sembaj A. Preliminary study between Y chromosome haplogroups and chagasic cardiomyopathy manifestations in patients with Chagas disease. Rev Soc Bras Med Trop 2020; 53:e20190566. [PMID: 33174952 PMCID: PMC7670740 DOI: 10.1590/0037-8682-0566-2019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 09/24/2020] [Indexed: 11/22/2022] Open
Abstract
INTRODUCTION Among patients with Chagas disease, men have a higher risk of worse pathological symptoms than women. We aimed to explore the role of the Y chromosome in men diagnosed with Chagas disease and assess the relationship between their ancestry and disease status. METHODS In this comparative study, we analyzed 150 men with unrelated non-chagasic disease (nCD) and 150 men with unrelated chagasic disease (CD). We assessed the serological diagnosis of Chagas disease, biochemical parameters, thoracic X-rays, electrocardiogram, and transthoracic echocardiography and determined the haplogroup by analyzing a set of 17 microsatellites from the Y chromosome. We examined the associations between common Y chromosome haplogroups and the clinical parameters of risk by logistic regression. RESULTS For all patients, the most common haplogroups were R1b (43%), G2a (9%), and E1b1b (9%). The R1b and G2a haplogroup was more frequent in men with nCD and CD, respectively. As expected, we observed a high proportion of symptomatic patients in the CD group independent of the haplogroups. Men from both groups classified as having the R1b haplogroup showed less clinical evidence of disease. Multivariate analysis showed that CD patients without R1b were about five times more likely to have a cardio-thorax index >0.5% (OR [odds ratio] = 5.1, 95% CI [confidence interval] = 3.31-8.17). Men without the R1b haplogroup were 2.5 times more likely to show EcoCG alterations (OR = 2.50, 95% CI = 0.16-3.94). CONCLUSIONS Our results provided evidence that the R1b haplogroup may have a potential protective cardiovascular effect for its carriers.
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Affiliation(s)
- Oscar Lassen
- Cordoba Hospital, Semiology Department UHMI 3, Chagas and Hypertension Office, Córdoba, Argentina
| | - Sandra Tabares
- School of Medicine, Biochemistry and Molecular Biology Department, UNC, Cordoba, Argentina
| | | | - Silvia Ojeda
- School of Mathematics, Astronomy and Physics, UNC, Córdoba, Argentina
| | - Adela Sembaj
- School of Medicine, Biochemistry and Molecular Biology Department, UNC, Cordoba, Argentina
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The Role of Number of Copies, Structure, Behavior and Copy Number Variations (CNV) of the Y Chromosome in Male Infertility. Genes (Basel) 2019; 11:genes11010040. [PMID: 31905733 PMCID: PMC7016774 DOI: 10.3390/genes11010040] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/17/2019] [Accepted: 12/23/2019] [Indexed: 12/11/2022] Open
Abstract
The World Health Organization (WHO) defines infertility as the inability of a sexually active, non-contracepting couple to achieve spontaneous pregnancy within one year. Statistics show that the two sexes are equally at risk. Several causes may be responsible for male infertility; however, in 30–40% of cases a diagnosis of idiopathic male infertility is made in men with normal urogenital anatomy, no history of familial fertility-related diseases and a normal panel of values as for endocrine, genetic and biochemical markers. Idiopathic male infertility may be the result of gene/environment interactions, genetic and epigenetic abnormalities. Numerical and structural anomalies of the Y chromosome represent a minor yet significant proportion and are the topic discussed in this review. We searched the PubMed database and major search engines for reports about Y-linked male infertility. We present cases of Y-linked male infertility in terms of (i) anomalies of the Y chromosome structure/number; (ii) Y chromosome misbehavior in a normal genetic background; (iii) Y chromosome copy number variations (CNVs). We discuss possible explanations of male infertility caused by mutations, lower or higher number of copies of otherwise wild type, Y-linked sequences. Despite Y chromosome structural anomalies are not a major cause of male infertility, in case of negative results and of normal DNA sequencing of the ascertained genes causing infertility and mapping on this chromosome, we recommend an analysis of the karyotype integrity in all cases of idiopathic fertility impairment, with an emphasis on the structure and number of this chromosome.
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Duplications in 19p13.3 are associated with male infertility. J Assist Reprod Genet 2019; 36:2171-2179. [PMID: 31418107 DOI: 10.1007/s10815-019-01547-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 07/24/2019] [Indexed: 02/07/2023] Open
Abstract
PURPOSE To identify genomic imbalances and candidate loci in idiopathic male infertility. METHODS Affymetrix CytoScan 750K Array was used to analyze genomic imbalances and candidate loci in 34 idiopathic infertile cases of different phenotypes (hypo-spermatogenesis, n = 8; maturation arrest, n = 7; and Sertoli cell-only syndrome, n = 13, severe oligozoospermia, n = 6, and 10 normozoospermic fertile men). Ten ethnically matched controls were screened for comparison. RESULTS The cytogenetic array analysis detected a genomic gain at the 19p13.3 region in 9 (26.47%) cases, with the highest frequency in patients with Sertoli cell-only syndrome (SCOS) (38%). Its complete absence in the control group suggests its likely pathogenic nature. In addition to Y-classical, micro, and partial deletions, the duplication in 19p13.3 could serve as a unique biomarker for evaluation of infertility risk. The common region across the individuals harboring the duplication identified STK11, ATP5D, MIDN, CIRBP, and EFNA2 genes which make them strong candidates for further investigations. The largest duplicated region identified in this study displayed a major network of 7 genes, viz., CIRBP, FSTL3, GPX4, GAMT, KISS1R, STK11, and PCSK4, associated with reproductive system development and function. The role of chance was ruled out by screening of ethnically matched controls. CONCLUSION The result clearly indicates the significance of 19p13.3 duplication in infertile men with severe testicular phenotypes. The present study underlines the utility and significance of whole genomic analysis in the cases of male infertility which goes undiagnosed due to limitations in the conventional cytogenetic techniques and for identifying genes that are essential for spermatogenesis.
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Larmuseau MHD, Ottoni C. Mediterranean Y-chromosome 2.0-why the Y in the Mediterranean is still relevant in the postgenomic era. Ann Hum Biol 2018; 45:20-33. [PMID: 29382278 DOI: 10.1080/03014460.2017.1402956] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
CONTEXT Due to its unique paternal inheritance, the Y-chromosome has been a highly popular marker among population geneticists for over two decades. Recently, the advent of cost-effective genome-wide methods has unlocked information-rich autosomal genomic data, paving the way to the postgenomic era. This seems to have announced the decreasing popularity of investigating Y-chromosome variation, which provides only the paternal perspective of human ancestries and is strongly influenced by genetic drift and social behaviour. OBJECTIVE For this special issue on population genetics of the Mediterranean, the aim was to demonstrate that the Y-chromosome still provides important insights in the postgenomic era and in a time when ancient genomes are becoming exponentially available. METHODS A systematic literature search on Y-chromosomal studies in the Mediterranean was performed. RESULTS Several applications of Y-chromosomal analysis with future opportunities are formulated and illustrated with studies on Mediterranean populations. CONCLUSIONS There will be no reduced interest in Y-chromosomal studies going from reconstruction of male-specific demographic events to ancient DNA applications, surname history and population-wide estimations of extra-pair paternity rates. Moreover, more initiatives are required to collect population genetic data of Y-chromosomal markers for forensic research, and to include Y-chromosomal data in GWAS investigations and studies on male infertility.
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Affiliation(s)
- Maarten H D Larmuseau
- a KU Leuven, Forensic Biomedical Sciences , Department of Imaging & Pathology , Leuven , Belgium.,b KU Leuven, Laboratory of Socioecology and Social Evolution , Department of Biology , Leuven , Belgium
| | - Claudio Ottoni
- c Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences , University of Oslo , Oslo , Norway
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Teitz LS, Pyntikova T, Skaletsky H, Page DC. Selection Has Countered High Mutability to Preserve the Ancestral Copy Number of Y Chromosome Amplicons in Diverse Human Lineages. Am J Hum Genet 2018; 103:261-275. [PMID: 30075113 DOI: 10.1016/j.ajhg.2018.07.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/10/2018] [Indexed: 02/07/2023] Open
Abstract
Amplicons-large, highly identical segmental duplications-are a prominent feature of mammalian Y chromosomes. Although they encode genes essential for fertility, these amplicons differ vastly between species, and little is known about the selective constraints acting on them. Here, we develop computational tools to detect amplicon copy number with unprecedented accuracy from high-throughput sequencing data. We find that one-sixth (16.9%) of 1,216 males from the 1000 Genomes Project have at least one deleted or duplicated amplicon. However, each amplicon's reference copy number is scrupulously maintained among divergent branches of the Y chromosome phylogeny, including the ancient branch A00, indicating that the reference copy number is ancestral to all modern human Y chromosomes. Using phylogenetic analyses and simulations, we demonstrate that this pattern of variation is incompatible with neutral evolution and instead displays hallmarks of mutation-selection balance. We also observe cases of amplicon rescue, in which deleted amplicons are restored through subsequent duplications. These results indicate that, contrary to the lack of constraint suggested by the differences between species, natural selection has suppressed amplicon copy number variation in diverse human lineages.
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Dynamic Copy Number Evolution of X- and Y-Linked Ampliconic Genes in Human Populations. Genetics 2018; 209:907-920. [PMID: 29769284 PMCID: PMC6028258 DOI: 10.1534/genetics.118.300826] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 05/15/2018] [Indexed: 11/18/2022] Open
Abstract
Ampliconic genes are multicopy genes often located on sex chromosomes and enriched for testis-expressed genes. Here, Lucotte et al. developed new bioinformatic approaches to investigate the ampliconic gene copy number and their coding... Ampliconic genes are multicopy, with the majority found on sex chromosomes and enriched for testis-expressed genes. While ampliconic genes have been associated with the emergence of hybrid incompatibilities, we know little about their copy number distribution and their turnover in human populations. Here, we explore the evolution of human X- and Y-linked ampliconic genes by investigating copy number variation (CNV) and coding variation between populations using the Simons Genome Diversity Project. We develop a method to assess CNVs using the read depth on modified X and Y chromosome targets containing only one repetition of each ampliconic gene. Our results reveal extensive standing variation in copy number both within and between human populations for several ampliconic genes. For the Y chromosome, we can infer multiple independent amplifications and losses of these gene copies even within closely related Y haplogroups, that diversified < 50,000 years ago. Moreover, X- and Y-linked ampliconic genes seem to have a faster amplification dynamic than autosomal multicopy genes. Looking at expression data from another study, we also find that X- and Y-linked ampliconic genes with extensive CNV are significantly more expressed than genes with no CNV during meiotic sex chromosome inactivation (for both X and Y) and postmeiotic sex chromosome repression (for the Y chromosome only). While we cannot rule out that the XY-linked ampliconic genes are evolving neutrally, this study gives insights into the distribution of copy number within human populations and demonstrates an extremely fast turnover in copy number of these regions.
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Abstract
Differences between genomes can be due to single nucleotide variants (SNPs), translocations, inversions and copy number variants (CNVs, gain or loss of DNA). The latter can range from sub-microscopic events to complete chromosomal aneuploidies. Small CNVs are often benign but those larger than 250 kb are strongly associated with morbid consequences such as developmental disorders and cancer. Detecting CNVs within and between populations is essential to better understand the plasticity of our genome and to elucidate its possible contribution to disease or phenotypic traits.While the link between SNPs and disease susceptibility has been well studied, to date there are still very few published CNV genome-wide association studies; probably owing to the fact that CNV analysis remains a slightly more complex task than SNP analysis (both in term of bioinformatics workflow and uncertainty in the CNV calling leading to high false positive rates and unknown false negative rates). This chapter aims at explaining computational methods for the analysis of CNVs, ranging from study design, data processing and quality control, up to genome-wide association study with clinical traits.
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Affiliation(s)
- Aurélien Macé
- Institute of Social and Preventive Medicine, University Hospital of Lausanne, Lausanne, Switzerland.,Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Zoltán Kutalik
- Institute of Social and Preventive Medicine, University Hospital of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
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Analysis of 62 hybrid assembled human Y chromosomes exposes rapid structural changes and high rates of gene conversion. PLoS Genet 2017; 13:e1006834. [PMID: 28846694 PMCID: PMC5591018 DOI: 10.1371/journal.pgen.1006834] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 09/08/2017] [Accepted: 05/22/2017] [Indexed: 11/21/2022] Open
Abstract
The human Y-chromosome does not recombine across its male-specific part and is therefore an excellent marker of human migrations. It also plays an important role in male fertility. However, its evolution is difficult to fully understand because of repetitive sequences, inverted repeats and the potentially large role of gene conversion. Here we perform an evolutionary analysis of 62 Y-chromosomes of Danish descent sequenced using a wide range of library insert sizes and high coverage, thus allowing large regions of these chromosomes to be well assembled. These include 17 father-son pairs, which we use to validate variation calling. Using a recent method that can integrate variants based on both mapping and de novo assembly, we genotype 10898 SNVs and 2903 indels (max length of 27241 bp) in our sample and show by father-son concordance and experimental validation that the non-recurrent SNP and indel variation on the Y chromosome tree is called very accurately. This includes variation called in a 0.9 Mb centromeric heterochromatic region, which is by far the most variable in the Y chromosome. Among the variation is also longer sequence-stretches not present in the reference genome but shared with the chimpanzee Y chromosome. We analyzed 2.7 Mb of large inverted repeats (palindromes) for variation patterns among the two palindrome arms and identified 603 mutation and 416 gene conversions events. We find clear evidence for GC-biased gene conversion in the palindromes (and a balancing AT mutation bias), but irrespective of this, also a strong bias towards gene conversion towards the ancestral state, suggesting that palindromic gene conversion may alleviate Muller’s ratchet. Finally, we also find a large number of large-scale gene duplications and deletions in the palindromic regions (at least 24) and find that such events can consist of complex combinations of simultaneous insertions and deletions of long stretches of the Y chromosome. The Y chromosome is extraordinary in many respects; it is non-recombining along most of its length, it carries many testis-expressed genes that are often found in palindromes and thus in several copies, and it is generally highly repetitive with very few unique genes. Its evolutionary process is not well understood in general because short-read mapping in such complex sequence is difficult. We combine de novo assembly and mapping to investigate evolution in more than 60% of the length of 62 Y chromosomes of Danish descent. We find that Y chromosome evolution is very dynamic even among the set of closely related Y chromosomes in Denmark with many cases of complex duplications and deletions of large regions including whole genes, clear evidence of GC-biased gene conversion in the palindromes and a tendency for gene conversion to revert mutations to their ancestral state.
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Human Y chromosome copy number variation in the next generation sequencing era and beyond. Hum Genet 2017; 136:591-603. [PMID: 28378101 PMCID: PMC5418319 DOI: 10.1007/s00439-017-1788-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 03/25/2017] [Indexed: 11/16/2022]
Abstract
The human Y chromosome provides a fertile ground for structural rearrangements owing to its haploidy and high content of repeated sequences. The methodologies used for copy number variation (CNV) studies have developed over the years. Low-throughput techniques based on direct observation of rearrangements were developed early on, and are still used, often to complement array-based or sequencing approaches which have limited power in regions with high repeat content and specifically in the presence of long, identical repeats, such as those found in human sex chromosomes. Some specific rearrangements have been investigated for decades; because of their effects on fertility, or their outstanding evolutionary features, the interest in these has not diminished. However, following the flourishing of large-scale genomics, several studies have investigated CNVs across the whole chromosome. These studies sometimes employ data generated within large genomic projects such as the DDD study or the 1000 Genomes Project, and often survey large samples of healthy individuals without any prior selection. Novel technologies based on sequencing long molecules and combinations of technologies, promise to stimulate the study of Y-CNVs in the immediate future.
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Kushima I, Aleksic B, Nakatochi M, Shimamura T, Shiino T, Yoshimi A, Kimura H, Takasaki Y, Wang C, Xing J, Ishizuka K, Oya-Ito T, Nakamura Y, Arioka Y, Maeda T, Yamamoto M, Yoshida M, Noma H, Hamada S, Morikawa M, Uno Y, Okada T, Iidaka T, Iritani S, Yamamoto T, Miyashita M, Kobori A, Arai M, Itokawa M, Cheng MC, Chuang YA, Chen CH, Suzuki M, Takahashi T, Hashimoto R, Yamamori H, Yasuda Y, Watanabe Y, Nunokawa A, Someya T, Ikeda M, Toyota T, Yoshikawa T, Numata S, Ohmori T, Kunimoto S, Mori D, Iwata N, Ozaki N. High-resolution copy number variation analysis of schizophrenia in Japan. Mol Psychiatry 2017; 22:430-440. [PMID: 27240532 DOI: 10.1038/mp.2016.88] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Revised: 04/18/2016] [Accepted: 04/20/2016] [Indexed: 12/30/2022]
Abstract
Recent schizophrenia (SCZ) studies have reported an increased burden of de novo copy number variants (CNVs) and identified specific high-risk CNVs, although with variable phenotype expressivity. However, the pathogenesis of SCZ has not been fully elucidated. Using array comparative genomic hybridization, we performed a high-resolution genome-wide CNV analysis on a mainly (92%) Japanese population (1699 SCZ cases and 824 controls) and identified 7066 rare CNVs, 70.0% of which were small (<100 kb). Clinically significant CNVs were significantly more frequent in cases than in controls (odds ratio=3.04, P=9.3 × 10-9, 9.0% of cases). We confirmed a significant association of X-chromosome aneuploidies with SCZ and identified 11 de novo CNVs (e.g., MBD5 deletion) in cases. In patients with clinically significant CNVs, 41.7% had a history of congenital/developmental phenotypes, and the rate of treatment resistance was significantly higher (odds ratio=2.79, P=0.0036). We found more severe clinical manifestations in patients with two clinically significant CNVs. Gene set analysis replicated previous findings (e.g., synapse, calcium signaling) and identified novel biological pathways including oxidative stress response, genomic integrity, kinase and small GTPase signaling. Furthermore, involvement of multiple SCZ candidate genes and biological pathways in the pathogenesis of SCZ was suggested in established SCZ-associated CNV loci. Our study shows the high genetic heterogeneity of SCZ and its clinical features and raises the possibility that genomic instability is involved in its pathogenesis, which may be related to the increased burden of de novo CNVs and variable expressivity of CNVs.
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Affiliation(s)
- I Kushima
- Institute for Advanced Research, Nagoya University, Nagoya, Japan.,Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - B Aleksic
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - M Nakatochi
- Bioinformatics Section, Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya, Japan
| | - T Shimamura
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - T Shiino
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - A Yoshimi
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - H Kimura
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Y Takasaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - C Wang
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - J Xing
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - K Ishizuka
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - T Oya-Ito
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Y Nakamura
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Y Arioka
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya, Japan
| | - T Maeda
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - M Yamamoto
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - M Yoshida
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - H Noma
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - S Hamada
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - M Morikawa
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Y Uno
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - T Okada
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - T Iidaka
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - S Iritani
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - T Yamamoto
- Department of Legal Medicine and Bioethics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - M Miyashita
- Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - A Kobori
- Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - M Arai
- Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - M Itokawa
- Center for Medical Cooperation, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - M-C Cheng
- Department of Psychiatry, Yuli Mental Health Research Center, Yuli Branch, Taipei Veterans General Hospital, Hualien, Taiwan
| | - Y-A Chuang
- Department of Psychiatry, Yuli Mental Health Research Center, Yuli Branch, Taipei Veterans General Hospital, Hualien, Taiwan
| | - C-H Chen
- Department of Psychiatry, Chang Gung Memorial Hospital-Linkou, Taoyuan, Taiwan.,Department and Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - M Suzuki
- Department of Neuropsychiatry, University of Toyama Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan
| | - T Takahashi
- Department of Neuropsychiatry, University of Toyama Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan
| | - R Hashimoto
- Molecular Research Center for Children's Mental Development, United Graduate School of Child Development, Osaka University, Suita, Japan.,Department of Psychiatry, Osaka University Graduate School of Medicine, Suita, Japan
| | - H Yamamori
- Department of Psychiatry, Osaka University Graduate School of Medicine, Suita, Japan
| | - Y Yasuda
- Department of Psychiatry, Osaka University Graduate School of Medicine, Suita, Japan
| | - Y Watanabe
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - A Nunokawa
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - T Someya
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - M Ikeda
- Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Japan
| | - T Toyota
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Wako, Japan
| | - T Yoshikawa
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Wako, Japan
| | - S Numata
- Department of Psychiatry, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - T Ohmori
- Department of Psychiatry, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - S Kunimoto
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - D Mori
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Brain and Mind Research Center, Nagoya University, Nagoya, Japan
| | - N Iwata
- Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Japan
| | - N Ozaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
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The Y chromosome as the most popular marker in genetic genealogy benefits interdisciplinary research. Hum Genet 2016; 136:559-573. [DOI: 10.1007/s00439-016-1740-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 10/16/2016] [Indexed: 01/01/2023]
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