Y chromosome polymorphisms in medicine

High incidence of AZF duplications in clan-structured Iranian populations detected through Y chromosome sequencing read depth analysis

The ampliconic region of the human Y chromosome consists of large duplicated sequences that can undergo non-allelic homologous recombination (NAHR), resulting in structural rearrangements that may cause infertility, especially when they occur in the azoospermia factor b/c (AZFb/c) region. Although AZF duplications have long been neglected due to the technical limitations of STS-based studies that focused mainly on deletions, recent next generation sequencing (NGS) technologies provided evidence for their importance in fertility. In this study, a NGS read depth approach was used to detect AZFb/c rearrangements in 87 Iranians from different ethnic groups. The duplication frequency in Iran proved to be twice as high as in the "1000 Genomes" dataset. Interestingly, most duplications were found in patrilineal ethnic groups, possibly as a consequence of their lower male effective population size which can counteract negative selection. Moreover, we found a large 8.0 Mb duplication, resulting in a fourfold increase in the copy number of AZFc genes, which to our knowledge is the largest duplication ever reported in this region. Overall, our results suggest that it is important to consider not only AZF deletions but also duplications to investigate the causes of male infertility, especially in patrilineal clan-based populations.

Unlocking the mystery associated with infertility and prostate cancer: an update

Male-specific reproductive disorders and cancers have increased intensely in recent years, making them a significant public health problem. Prostate cancer (PC) is the most often diagnosed cancer in men and is one of the leading causes of cancer-related mortality. Both genetic and epigenetic modifications contribute to the development and progression of PC, even though the exact underlying processes causing this disease have yet to be identified. Male infertility is also a complex and poorly understood phenomenon believed to afflict a significant portion of the male population. Chromosomal abnormalities, compromised DNA repair systems, and Y chromosome alterations are just a few of the proposed explanations. It is becoming widely accepted that infertility shares a link with PC. Much of the link between infertility and PC is probably attributable to common genetic defects. This article provides an overview of PC and spermatogenic abnormalities. This study also investigates the link between male infertility and PC and uncovers the underlying reasons, risk factors, and biological mechanisms contributing to this association.

Association of MSY haplotype background with nonobstructive azoospermia is AZF-dependent: A case-control study

Identifying causal genes of spermatogenic failure on the male-specific region of Y chromosome (MSY) has been a challenging process. Due to the nonrecombining nature of MSY, haplotype-based approaches have recently been shown to be promising in identifying associated MSY haplogroups. We conducted an MSY analysis of nonobstructive azoospermia (NOA) patients in a case-control setting (N = 278 and 105 respectively) to identify modal haplogroups strongly associated with NOA. Patients with AZF deletions (AZF+) and no AZF deletions (AZF-) were compared with the control group. Given the larger sample set of AZF- NOA patients, we further investigated the association based on histopathological severity, namely Sertoli cell-only syndrome and maturation arrest subtypes. We observed no significant enrichment of MSY haplogroups in AZF- azoospermic patients (or its subtypes). However, we observed a strongly significant association between haplogroup J2a* and AZF+ patients (FDR-corrected p = .0056; OR = 7.02, 95%CI 1.89 to 39.20), a haplogroup which also showed significant enrichment for AZFa/b deletions (p = 4x10^-4 ). We conclude that unlike AZF+ patients, AZF- NOA are less likely to have an MSY causative factor with large effect size, thus indicating that the aetiology of AZF- NOA, and to some extent AZFc NOA, is more likely to be based on non-MSY factors.

Do partial AZFc deletions affect the sperm retrieval rate in non-mosaic Klinefelter patients undergoing microdissection testicular sperm extraction?

BACKGROUND

The purpose of this study is to evaluate the prognostic factors for sperm retrieval and determine if Y chromosome deletion is associated with deleterious effects on spermatogenesis in non-mosaic Klinefelter patients. Whether Y chromosome deletion determines the sperm retrieval rate in non-mosaic Klinefelter patients has not yet been addressed.

METHODS

We retrospectively collected medical records of azoospermic patients from Sep 2009 to Dec 2018, and enrolled 66 non-mosaic 47, XXY patients who were receiving mTESE. The predictive values of patients age, serum follicle-stimulating hormone (FSH), luteinizing hormone (LH), testosterone, prolactin, estradiol and Y chromosome deletion were assessed for successful sperm recovery.

RESULTS

Testicular sperm recovery was successful in 24 (36.4%) of 66 men. The mean age (36.0 vs. 36.6 years), and levels of FSH (30.0 vs 36.9 IU/L), LH (17.7 vs 21.9 IU/L), testosterone (2.4 vs. 2.1 ng/ml), prolactin (9.1 vs. 8.8 ng/ml), and estradiol (19.4 vs. 22.3 pg/ml) did not show any significant difference when comparing patients with and without successful sperm retrieval. Partial deletion of azoospermic factor c (AZFc) was noted in 5 (20.8%) of 24 patients with successful sperm retrieval, including three b2/b3 and two gr/gr deletion cases, whereas 4 (9.5%) of 42 patients with unsuccessful sperm retrieval were noted to have AZFc partial deletion (one b2/b3, one sY1206 and two gr/gr deletion), though the difference was not statistically significant (p = 0.27).

CONCLUSION

According to present results, age and AZFc partial deletion status should not be a deterrent for azoospermic males with non-mosaic Klinefelter syndrome to undergo mTESE.

Ancestry and different rates of suicide and homicide in European countries: A study with population-level data

INTRODUCTION

There are large differences in suicide rates across Europe. The current study investigated the relationship of suicide and homicide rates in different countries of Europe with ancestry as it is defined with the haplotype frequencies of Y-DNA and mtDNA.

MATERIAL AND METHODS

The mortality data were retrieved from the WHO online database. The genetic data were retrieved from http://www.eupedia.com. The statistical analysis included Forward Stepwise Multiple Linear Regression analysis and Pearson Correlation Coefficient (R).

RESULTS

In males, N and R1a Y-DNA haplotypes were positively related to both homicidal and suicidal behaviors while I1 was negatively related. The Q was positively related to the homicidal rate. Overall, 60-75% of the observed variance was explained. L, J and X mtDNA haplogroups were negatively related with suicide in females alone, with 82-85% of the observed variance described.

DISCUSSION

The current study should not be considered as a study of genetic markers but rather a study of human ancestry. Its results could mean that research on suicidality has a strong biological but locally restricted component and could be limited by the study population; generalizability of the results at an international level might not be possible. Further research with patient-level data are needed to verify whether these haplotypes could serve as biological markers to identify persons at risk to commit suicide or homicide and whether biologically-determined ancestry could serve as an intermediate grouping method or even as an endophenotype in suicide research.

Using Y-Chromosomal Haplogroups in Genetic Association Studies and Suggested Implications

Y-chromosomal (Y-DNA) haplogroups are more widely used in population genetics than in genetic epidemiology, although associations between Y-DNA haplogroups and several traits, including cardiometabolic traits, have been reported. In apparently homogeneous populations defined by principal component analyses, there is still Y-DNA haplogroup variation which will result from population history. Therefore, hidden stratification and/or differential phenotypic effects by Y-DNA haplogroups could exist. To test this, we hypothesised that stratifying individuals according to their Y-DNA haplogroups before testing for associations between autosomal single nucleotide polymorphisms (SNPs) and phenotypes will yield difference in association. For proof of concept, we derived Y-DNA haplogroups from 6537 males from two epidemiological cohorts, Avon Longitudinal Study of Parents and Children (ALSPAC) (n = 5080; 816 Y-DNA SNPs) and the 1958 Birth Cohort (n = 1457; 1849 Y-DNA SNPs), and studied the robust associations between 32 SNPs and body mass index (BMI), including SNPs in or near Fat Mass and Obesity-associated protein (FTO) which yield the strongest effects. Overall, no association was replicated in both cohorts when Y-DNA haplogroups were considered and this suggests that, for BMI at least, there is little evidence of differences in phenotype or SNP association by Y-DNA structure. Further studies using other traits, phenome-wide association studies (PheWAS), other haplogroups and/or autosomal SNPs are required to test the generalisability and utility of this approach.

Patterns of Inter-Chromosomal Gene Conversion on the Male-Specific Region of the Human Y Chromosome

The male-specific region of the human Y chromosome (MSY) is characterized by the lack of meiotic recombination and it has long been considered an evolutionary independent region of the human genome. In recent years, however, the idea that human MSY did not have an independent evolutionary history begun to emerge with the discovery that inter-chromosomal gene conversion (ICGC) can modulate the genetic diversity of some portions of this genomic region. Despite the study of the dynamics of this molecular mechanism in humans is still in its infancy, some peculiar features and consequences of it can be summarized. The main effect of ICGC is to increase the allelic diversity of MSY by generating a significant excess of clustered single nucleotide polymorphisms (SNPs) (defined as groups of two or more SNPs occurring in close proximity and on the same branch of the Y phylogeny). On the human MSY, 13 inter-chromosomal gene conversion hotspots (GCHs) have been identified so far, involving donor sequences mainly from the X-chromosome and, to a lesser extent, from autosomes. Most of the GCHs are evolutionary conserved and overlap with regions involved in aberrant X–Y crossing-over. This review mainly focuses on the dynamics and the current knowledge concerning the recombinational landscape of the human MSY in the form of ICGC, on how this molecular mechanism may influence the evolution of the MSY, and on how it could affect the information enclosed within a genomic region which, until recently, appeared to be an evolutionary independent unit.

Spermatogenic failure and the Y chromosome

The Y chromosome harbors a number of genes essential for testis development and function. Its highly repetitive structure predisposes this chromosome to deletion/duplication events and is responsible for Y-linked copy-number variations (CNVs) with clinical relevance. The AZF deletions remove genes with predicted spermatogenic function en block and are the most frequent known molecular causes of impaired spermatogenesis (5-10% of azoospermic and 2-5% of severe oligozoospermic men). Testing for this deletion has both diagnostic and prognostic value for testicular sperm retrieval in azoospermic men. The most dynamic region on the Yq is the AZFc region, presenting numerous NAHR hotspots leading to partial losses or gains of the AZFc genes. The gr/gr deletion (a partial AZFc deletion) negatively affects spermatogenic efficiency and it is a validated, population-dependent risk factor for oligozoospermia. In certain populations, the Y background may play a role in the phenotypic expression of partial AZFc rearrangements and similarly it may affect the predisposition to specific deletions/duplication events. Also, the Yp contains a gene array, TSPY1, with potential effect on germ cell proliferation. Despite intensive investigations during the last 20 years on the role of this sex chromosome in spermatogenesis, a number of clinical and basic questions remain to be answered. This review is aimed at providing an overview of the role of Y chromosome-linked genes, CNVs, and Y background in spermatogenesis.

Human Chromosome Y and Haplogroups; introducing YDHS Database

BACKGROUND

As the high throughput sequencing efforts generate more biological information, scientists from different disciplines are interpreting the polymorphisms that make us unique. In addition, there is an increasing trend in general public to research their own genealogy, find distant relatives and to know more about their biological background. Commercial vendors are providing analyses of mitochondrial and Y-chromosomal markers for such purposes. Clearly, an easy-to-use free interface to the existing data on the identified variants would be in the interest of general public and professionals less familiar with the field. Here we introduce a novel metadatabase YDHS that aims to provide such an interface for Y-chromosomal DNA (Y-DNA) haplogroups and sequence variants.

METHODS

The database uses ISOGG Y-DNA tree as the source of mutations and haplogroups and by using genomic positions of the mutations the database links them to genes and other biological entities. YDHS contains analysis tools for deeper Y-SNP analysis.

RESULTS

YDHS addresses the shortage of Y-DNA related databases. We have tested our database using a set of different cases from literature ranging from infertility to autism. The database is at http://www.semanticgen.net/ydhs

CONCLUSIONS

Y-chromosomal DNA (Y-DNA) haplogroups and sequence variants have not been in the scientific limelight, excluding certain specialized fields like forensics, mainly because there is not much freely available information or it is scattered in different sources. However, as we have demonstrated Y-SNPs do play a role in various cases on the haplogroup level and it is possible to create a free Y-DNA dedicated bioinformatics resource.

Male reproductive cancers and infertility: a mutual relationship

Reproductive dysfunction and malignancies related to the male gender represent a serious health concern, whose incidence has significantly risen over the past years. Prior to treatment, testicular or prostate cancer patients often display poor semen characteristics similar to subfertile or infertile patients. This fact is underscored by cases where the malignancy is often diagnosed in males who undergo a general fertility screening. This review aims to examine the associations between male infertility and reproductive cancers focusing on common etiologies and biological mechanisms underlining these pathologies. Furthermore, we discuss compelling epidemiological data hypothesizing that male reproductive failure may act as a precursor of future andrological malignancies, including testicular or prostate cancer, thus providing a stimulus for a more specific research in male reproductive health and emphasizing the importance of this relation for physicians taking care of male patients with a reproductive disease.

Inter- and intraspecies phylogenetic analyses reveal extensive X-Y gene conversion in the evolution of gametologous sequences of human sex chromosomes

It has long been believed that the male-specific region of the human Y chromosome (MSY) is genetically independent from the X chromosome. This idea has been recently dismissed due to the discovery that X–Y gametologous gene conversion may occur. However, the pervasiveness of this molecular process in the evolution of sex chromosomes has yet to be exhaustively analyzed. In this study, we explored how pervasive X–Y gene conversion has been during the evolution of the youngest stratum of the human sex chromosomes. By comparing about 0.5 Mb of human–chimpanzee gametologous sequences, we identified 19 regions in which extensive gene conversion has occurred. From our analysis, two major features of these emerged: 1) Several of them are evolutionarily conserved between the two species and 2) almost all of the 19 hotspots overlap with regions where X–Y crossing-over has been previously reported to be involved in sex reversal. Furthermore, in order to explore the dynamics of X–Y gametologous conversion in recent human evolution, we resequenced these 19 hotspots in 68 widely divergent Y haplogroups and used publicly available single nucleotide polymorphism data for the X chromosome. We found that at least ten hotspots are still active in humans. Hence, the results of the interspecific analysis are consistent with the hypothesis of widespread reticulate evolution within gametologous sequences in the differentiation of hominini sex chromosomes. In turn, intraspecific analysis demonstrates that X–Y gene conversion may modulate human sex-chromosome-sequence evolution to a greater extent than previously thought.

The Y-located gonadoblastoma gene TSPY amplifies its own expression through a positive feedback loop in prostate cancer cells

The testis-specific protein Y-encoded (TSPY) is a repetitive gene located on the gonadoblastoma region of the Y chromosome, and has been considered to be the putative gene for this oncogenic locus on the male-only chromosome. It is expressed in spermatogonial cells and spermatocytes in normal human testis, but abundantly in gonadoblastoma, testicular germ cell tumors and a variety of somatic cancers, including melanoma, hepatocellular carcinoma and prostate cancer. Various studies suggest that TSPY accelerates cell proliferation and growth, and promotes tumorigenesis. In this report, we show that TSPY could bind directly to the chromatin/DNA at exon 1 of its own gene, and greatly enhance the transcriptional activities of the endogenous gene in the LNCaP prostate cancer cells. Domain mapping analyses of TSPY have localized the critical and sufficient domain to the SET/NAP-domain. These results suggest that TSPY could efficiently amplify its expression and oncogenic functions through a positive feedback loop, and contribute to the overall tumorigenic processes when it is expressed in various human cancers.

Seeing the wood for the trees: a minimal reference phylogeny for the human Y chromosome

During the last few decades, a wealth of studies dedicated to the human Y chromosome and its DNA variation, in particular Y-chromosome single-nucleotide polymorphisms (Y-SNPs), has led to the construction of a well-established Y-chromosome phylogeny. Since the recent advent of new sequencing technologies, the discovery of additional Y-SNPs is exploding and their continuous incorporation in the phylogenetic tree is leading to an ever higher resolution. However, the large and increasing amount of information included in the "complete" Y-chromosome phylogeny, which now already includes many thousands of identified Y-SNPs, can be overwhelming and complicates its understanding as well as the task of selecting suitable markers for genotyping purposes in evolutionary, demographic, anthropological, genealogical, medical, and forensic studies. As a solution, we introduce a concise reference phylogeny whereby we do not aim to provide an exhaustive tree that includes all known Y-SNPs but, rather, a quite stable reference tree aiming for optimal global discrimination capacity based on a strongly reduced set that includes only the most resolving Y-SNPs. Furthermore, with this reference tree, we wish to propose a common standard for Y-marker as well as Y-haplogroup nomenclature. The current version of our tree is based on a core set of 417 branch-defining Y-SNPs and is available online at http://www.phylotree.org/Y.

AMY-tree: an algorithm to use whole genome SNP calling for Y chromosomal phylogenetic applications

Background

Due to the rapid progress of next-generation sequencing (NGS) facilities, an explosion of human whole genome data will become available in the coming years. These data can be used to optimize and to increase the resolution of the phylogenetic Y chromosomal tree. Moreover, the exponential growth of known Y chromosomal lineages will require an automatic determination of the phylogenetic position of an individual based on whole genome SNP calling data and an up to date Y chromosomal tree.

Results

We present an automated approach, ‘AMY-tree’, which is able to determine the phylogenetic position of a Y chromosome using a whole genome SNP profile, independently from the NGS platform and SNP calling program, whereby mistakes in the SNP calling or phylogenetic Y chromosomal tree are taken into account. Moreover, AMY-tree indicates ambiguities within the present phylogenetic tree and points out new Y-SNPs which may be phylogenetically relevant. The AMY-tree software package was validated successfully on 118 whole genome SNP profiles of 109 males with different origins. Moreover, support was found for an unknown recurrent mutation, wrong reported mutation conversions and a large amount of new interesting Y-SNPs.

Conclusions

Therefore, AMY-tree is a useful tool to determine the Y lineage of a sample based on SNP calling, to identify Y-SNPs with yet unknown phylogenetic position and to optimize the Y chromosomal phylogenetic tree in the future. AMY-tree will not add lineages to the existing phylogenetic tree of the Y-chromosome but it is the first step to analyse whole genome SNP profiles in a phylogenetic framework.

Role of deoxyribonucleic acid technology in forensic dentistry

In the last few years, Deoxyribonucleic Acid (DNA) analysis methods have been applied to forensic cases. Forensic dental record comparison has been used for human identification in cases where destruction of bodily tissues or prolonged exposure to the environment has made other means of identification impractical, that is, after fire exposure or mass disaster. Teeth play an important role in identification and criminology, due to their unique characteristics and relatively high degree of physical and chemical resistance. The use of a DNA profile test in forensic dentistry offers a new perspective in human identification. The DNA is responsible for storing all the genetic material and is unique to each individual. The currently available DNA tests have high reliability and are accepted as legal proofs in courts. This article gives an overview of the evolution of DNA technology in the last few years, highlighting its importance in cases of forensic investigation.

Extinction conditions for Y-linked mutant-alleles through two-sex branching processes with blind-mating structure

A new two-sex bidimensional branching process is introduced to model the evolution of the number of carriers of an allele and its mutations of a Y-linked gene. A population is assumed in which females and males coexist and mate without the gene influencing the mating process. It is deduced from the model that the key determining conditions for the extinction or survival of the allele are given by the probability that an offspring is female, the rate of mutation, and the mean number of offspring per mating unit. It is also proved that the destiny of the allele's mutations in the population also depends on the survival or extinction of the original allele.

Admixture and population structure in Mexican-Mestizos based on paternal lineages

In the nonrecombining region of the Y-chromosome, there are single-nucleotide polymorphisms (Y-SNPs) that establish haplogroups with particular geographical origins (European, African, Native American, etc.). The complex process of admixture that gave rise to the majority of the current Mexican population (~93%), known as Mestizos, can be examined with Y-SNPs to establish their paternal ancestry and population structure. We analyzed 18 Y-SNPs in 659 individuals from 10 Mexican-Mestizo populations from different regions of the country. In the total population sample, paternal ancestry was predominately European (64.9%), followed by Native American (30.8%) and African (4.2%). However, the European ancestry was prevalent in the north and west (66.7-95%) and, conversely, Native American ancestry increased in the center and southeast (37-50%), whereas the African ancestry was low and relatively homogeneous (0-8.8%). Although this paternal landscape concurs with previous studies based on genome-wide SNPs and autosomal short tandem repeats (STRs), this pattern contrasts with the maternal ancestry, mainly of Native American origin, based on maternal lineages haplogroups. In agreement with historical records, these results confirm a strong gender-biased admixture history between European males and Native American females that gave rise to Mexican-Mestizos. Finally, pairwise comparisons and analysis of molecular variance tests demonstrated significant population structure (F(ST)=4.68%; P<0.00005), delimiting clusters that were geographically defined as the following: north-west, center-south and southeast.

Male reproductive health and prostate cancer risk

PURPOSE OF REVIEW

Male infertility impacts a substantial proportion of men and has serious implication for a man's quality of life. Advances in reproductive technology may allow men to bypass urologic care in order to achieve their family planning goals. Recent data suggests that male reproductive failure may be a harbinger of future urologic diseases, including prostate cancer (CaP), thus emphasizing the importance of dedicated urologic evaluation and care for all male infertility patients.

RECENT FINDINGS

We will review the epidemiologic data that explores an association between male reproductive health and CaP. We will review the potential biologic mechanisms that may underlie this association, and explore possible reasons for inconsistencies in study findings.

SUMMARY

Studies of the association between male infertility and CaP are inconsistent. Despite this, the association between reproductive health in a man's fourth decade (30s) and his development of aggressive CaP in his sixth decade (50s) should not be ignored. These findings, combined with the robustness of the potential common underlying mechanisms, provide a foundation for future studies of male reproductive health that are more specific in their approach to answering questions about the association between male reproductive failure and future systemic disease.

Examination of disease-based selection, demographic history and population structure in European Y-chromosome haplogroup I

We attempted to refine the understanding of an association of Y-chromosomal haplogroup I (hg-I) with enhanced AIDS progression that had been previously reported. First, we compared the progression phenotype between hg-I and its phylogenetically closest haplogroup J (hg-J). Then, we took a candidate gene approach resequencing DDX3Y, a crucial autoimmunity gene, in hg-I and other common European Y- chromosome haplogroups looking for functional variants. We extended the genetic analyses to CD24L4 and compared and contrasted the roles of disease based selection, demographic history, and population structure shaping the contemporary genetic landscape of hg-I chromosomes. Our results confirmed and refined the AIDS progression signal to hg-I, though no gene variant was identified that can explain the disease association. Molecular evolutionary and genetic analyses of the examined loci suggested a unique evolutionary history in hg-I, probably shaped by complex interactions of selection, demographic history, and high geographical differentiation leading to the formation of distinct hg-I subhaplogroups that today are associated with HIV/AIDS onset. Clearly, further studies on Y chromosome candidate loci sequencing to discover functional variants and discern the roles of evolutionary factors are warranted.

Y Chromosome Single Nucleotide Polymorphisms Typing by SNaPshot MINISEQUENCING

Analysis of Y chromosome haplogroups, defined by single nucleotide polymorphisms (SNPs), is now a standard approach for study of the origin of human populations and measurement of the variability among them. It is also a new forensic tool, because it may allow determination of the origin of any male sample of interest. We have used a strategy for rapid, simple and inexpensive Y chromosome SNP typing of 343 male DNA samples, of which 211 were Macedonians, 111 Albanians and 21 Roma, Serbs or Turks. Using multiplex polymerase chain reaction (mPCR) and a SNaPshot multiplex kit for single nucleotide extension reaction, 28 markers were grouped into five multiplexes. Twenty different Y haplogroups were found in these samples. The most common Y haplogroups in Macedonians were I2a-P37b (27.5%), E1b1b1a-M78 (15.6%), R1a1-SRY1532 (14.2%) and R1b1-P25 (11.4%). In the Albanians E1b1b1a-M78 accounted for 28.8%, R1b1-P25 for 18.0%, J2b2-M241 for 13.5% and R1a1-SRY1532 for 12.6%. We conclude that five haplogroups (E1b1b1a-M78, I2a-P37b, J2b2-M241, R1a1-SRY1532 and R1b1-P25) comprised 72.6% of the Y chromosomes, this being characteristic of the typical European Y chromosome gene pool.

TSPY1 copy number variation influences spermatogenesis and shows differences among Y lineages

CONTEXT

TSPY1 is a tandemly-repeated gene on the human Y chromosome forming an array of approximately 21-35 copies. The testicular expression pattern and the inferred function of the TSPY1 protein suggest possible involvement in spermatogenesis. However, data are scarce on TSPY1 copy number variation in different Y lineages and its role in spermatogenesis.

OBJECTIVES

We sought to define: 1) the extent of TSPY1 copy number variation within and among Y chromosome haplogroups; and 2) the role of TSPY1 dosage in spermatogenic efficiency.

MATERIALS AND METHODS

A total of 154 idiopathic infertile men and 130 normozoospermic controls from Central Italy were analyzed. We used a quantitative PCR assay to measure TSPY1 copy number and also defined Y haplogroups in all subjects.

RESULTS

We provide evidence that TSPY1 copy number shows substantial variation among Y haplogroups and thus that population stratification does represent a potential bias in case-control association studies. We also found: 1) a significant positive correlation between TSPY1 copy number and sperm count (P < 0.001); 2) a significant difference in mean TSPY1 copy number between patients and controls (28.4 +/- 8.3 vs. 33.9 +/- 10.7; P < 0.001); and 3) a 1.5-fold increased risk of abnormal sperm parameters in men with less than 33 copies (P < 0.001).

CONCLUSIONS

TSPY copy number variation significantly influences spermatogenic efficiency. Low TSPY1 copy number is a new risk factor for male infertility with potential clinical consequences.

Y chromosome variation in Europe: Continental and local processes in the formation of the extant gene pool

The polymorphism of the male-specific portion of the Y chromosome has been increasingly used to describe the composition of the European gene pool and to reconstruct its formation. Here the theoretical grounds and the limitations of this approach are presented, together with the different views on debated issues. The emerging picture for the composition of the male gene pool of the continent is illustrated, but local peculiarities that represent departures from the main trends are also highlighted, in order to illustrate the main unifying feature, i.e. the overlay of recent patterns onto more ancient ones. A synopsis of the main findings and conclusions obtained in regional studies has also been compiled.

Bisexual branching processes to model extinction conditions for Y-linked genes

In a two-sex monogamic population, the evolution of the number of carriers of the two alleles of a Y-linked gene is considered. To this end, a multitype bisexual branching model is presented in which it is assumed that the gene has no influence on the mating process. It is deduced from this model that the average numbers of female and male descendants per mating unit constitute the key to determining the extinction or survival of each allele. Moreover, the destiny of each allele in the population is found not to depend on the behavior of the other.

Association of Y chromosome haplogroup I with HIV progression, and HAART outcome

The host genetic basis of differential outcomes in HIV infection, progression, viral load set point and highly active retroviral therapy (HAART) responses was examined for the common Y haplogroups in European Americans and African Americans. Accelerated progression to acquired immune deficiency syndrome (AIDS) and related death in European Americans among Y chromosome haplogroup I (Y-I) subjects was discovered. Additionally, Y-I haplogroup subjects on HAART took a longer time to HIV-1 viral suppression and were more likely to fail HAART. Both the accelerated progression and longer time to viral suppression results observed in haplogroup Y-I were significant after false-discovery-rate corrections. A higher frequency of AIDS-defining illnesses was also observed in haplogroup Y-I. These effects were independent of the previously identified autosomal AIDS restriction genes. When the Y-I haplogroup subjects were further subdivided into six I subhaplogroups, no one subhaplogroup accounted for the effects on HIV progression, viral load or HAART response. Adjustment of the analyses for population stratification found significant and concordant haplogroup Y-I results. The Y chromosome haplogroup analyses of HIV infection and progression in African Americans were not significant. Our results suggest that one or more loci on the Y chromosome found on haplogroup Y-I have an effect on AIDS progression and treatment responses in European Americans.

Environment, testicular dysgenesis and carcinoma in situ testis

The testicular dysgenesis syndrome (TDS) hypothesis proposes that a proportion of the male reproductive disorders-cryptorchidism, hypospadias, infertility and testicular cancer-may be symptoms of one underlying developmental disease, TDS, which is most likely a result of disturbed gonadal development in the embryo. TDS may be caused by genetic factors, environmental/life-style factors, or a combination of both. Some rare disorders of sex development of genetic origin are among the best-known examples of severe TDS. Among the environmental and life-style factors that are suspected to influence the hormonal milieu of the developing gonad are the endocrine disrupters. A prenatal exposure to commonly used chemicals, e.g. phthalates, may result in a TDS-like phenotype in rats. Currently, this animal model is the best model for TDS. In humans the situation is much more complex, and TDS exists in a wide range of phenotypes: from the mildest and most common form, in which impaired spermatogenesis is the only symptom, to the most severe cases, in which the patient may develop testicular cancer. It is of great importance that clinicians in different specialties treating patients with TDS are aware of the association between the different symptoms.

Genetic risk factors in male infertility

The etiopathogenesis of testicular failure remains unknown in about half of the cases and is referred to as "idiopathic infertility". "Idiopathic" testicular failure is of probable genetic origin since the number of genes involved in human spermatogenesis is likely thousands and only a small proportion of them have been identified and screened in infertile men. In parallel with studies aimed to identify mutations with a clear cause-effect relationship in spermatogenesis candidate genes, there is an increasing interest towards genetic susceptibility factors to male infertility. Despite many efforts, only a few clinically relevant polymorphisms have been identified. This is mainly related to the multifactorial nature of male infertility and to the inappropriate study design of the majority of the studies. The most promising polymorphisms are in genes involved in the endocrine regulation of spermatogenesis and on the Y chromosome, the "gr/gr" deletions. Polymorphisms are generally considered as co-factors. Their final effect on testis function and fertility is probably modulated by the genetic background of each individual and/or by the presence of certain environmental factors. In this review, recent findings concerning some of the most widely studied polymorphisms and male infertility will be discussed.

Useful marker for the estimation of a recombination pair in the partial azoospermia factor c (gr/gr) deletion using quantitative real-time polymerase chain reaction

Background and aims:  Azoospermia factor c (AZFc) microdeletions are associated with male infertility and are caused by intrachromosal recombination between homologous repetitive sequence segments. Partial AZFc deletion (gr/gr) has been reported in male factor infertility. In the present study, we established detecting the copy number using quantitative real-time polymerase chain reaction (qRT-PCR) with the genome DNA, and assessed the association of the recombination pair set of gr/gr deletion and deleted in azoospermia copies. Furthermore, we determined the clinical significance of differential recombination patterns of gr/gr deletion, and compared them with azoospermia and proven fertile volunteers, with both groups having gr/gr deleted Japanese subjects. Materials and methods:  A total of 16 Japanese subjects with idiopathic azoospermia, and 13 proven fertile men with gr/gr deletion, were studied. qRT-PCR was used for the estimation of an identical site number. Results:  The g1/g2 deletion was found in 69.2% (9/13) in proven fertile men and in 75% (12/16) of idiopathic infertile men. The gr/gr deletion could result in the recombination of g1/g2 segments. Furthermore, there was no difference in the position of deletion between azoospermic patients and controls (P = 0.59). Conclusion:  There was no association between the loss of DAZ cluster and azoospermia in gr/gr deletion. This suggests that most of the partial deletions are neutral variants.

Prostate cancer in fathers with fewer male offspring: the Jerusalem Perinatal Study cohort

Recent studies have suggested the involvement of loci on the Y chromosome in prostate cancer. We studied the relative risk (RR) of prostate cancer in relation to sex ratio of offspring in a cohort of 38,934 Israeli men who were followed from the birth of their offspring (in 1964 through 1976) until 2005. Cox models were used to adjust for changes in incidence over time, age, the man's year of birth, and social and ethnic variables. A total of 712 men were diagnosed with prostate cancer. Compared with men who had at least one son, men with only daughters had an increased risk of prostate cancer (adjusted RR = 1.40, 95% confidence interval [CI] = 1.20 to 1.64, P<.0001). In men with one, two, or three or more offspring, the relative risks associated with absence of sons were 1.25 (95% CI = 1.00 to 1.56), 1.41 (95% CI = 1.04 to 1.91), and 1.60 (95% CI = 1.05 to 2.43), respectively. Men with no daughters showed no statistically significantly altered risk, compared with men who had offspring of both sexes. The relative risk of prostate cancer decreased as the number of sons increased (P(trend)<.0001) but did not change with the number of daughters. These findings suggest that a Y chromosome locus may be involved in prostate cancer risk in this population.

Y-chromosome haplogroups and susceptibility to azoospermia factor c microdeletion in an Italian population

BACKGROUND

A limited number of studies aimed at investigating the possible association of Y-chromosome haplogroups with microdeletions of the azoospermia factors (AZFs) or with particular infertile phenotypes, but definitive conclusions have not been attained. The main confounding elements in these association studies are the small sample sizes and the lack of homogeneity in the geographical origin of studied populations, affecting, respectively, the statistical power and the haplogroup distribution.

MATERIALS AND METHODS

To assess whether some Y-chromosome haplogroups are predisposing to, or protecting against, azoospermia factor c (AZFc; b2/b4) deletions, 31 north Italian patients carrying the AZFc b2/b4 microdeletion were characterised for 8 Y-chromosome haplogroups, and compared with the haplogroup frequency shown by a north Italian population without the microdeletion (n = 93).

RESULTS AND DISCUSSION

A significant difference was observed between the two populations, patients with microdeletions showing a higher frequency of the E haplogroup (29.3% vs 9.7%, p<0.01). The geographical homogeneity of the microdeleted samples and of the control population, controlled at microgeographical level, allows the possibility that the geographical structure of the Y genetic variability has affected our results to be excluded.

CONCLUSION

Thus, it is concluded that in the north Italian population Y-chromosome background affects the occurrence of AZFc b2/b4 deletions.

How the gene content of human sex chromosomes evolved

The X and Y chromosomes of humans and other mammals both have very atypical gene contents. The degenerate Y bears only a handful of genes that are specialized for male sex and reproduction. Now it seems that the X over-represents genes controlling reproductive traits and intelligence. This is hard to explain in terms of function but makes excellent sense in terms of evolution. Comparisons between the gene content of the X and Y in humans, distantly related mammals, and other vertebrates, define the evolutionary past of our sex chromosomes and suggest how special selective forces act on the X and Y.

Developmental model for the pathogenesis of testicular carcinoma in situ: genetic and environmental aspects

Carcinoma in situ testis (CIS), also known as intratubular germ cell neoplasia (ITGCN), is a pre-invasive precursor of testicular germ cell tumours, the commonest cancer type of male adolescents and young adults. In this review, evidence supporting the hypothesis of developmental origin of testicular germ cell cancer is summarized, and the current concepts regarding aetiology and pathogenesis of this disease are critically discussed. Comparative studies of cell surface proteins (e.g. PLAP and KIT), some of the germ cell-specific markers (e.g. MAGEA4, VASA, TSPY and NY-ESO-1), supported by studies of regulatory elements of the cell cycle (e.g. p53, CHK2 and p19-INK4d) demonstrated a close similarity of CIS to primordial germ cells and gonocytes, consistent with the pre-meiotic origin of CIS. Recent gene expression profiling studies showed that CIS cells closely resemble embryonic stem cells (ESCs). The abundance of factors associated with pluripotency (NANOG and OCT-3/4) and undifferentiated state (AP-2gamma) may explain the remarkable pluripotency of germ cell neoplasms, which are capable of differentiating to various somatic tissue components of teratomas. Impaired gonadal development resulting in the arrest of gonocyte differentiation and retention of its embryonic features, associated with an increasing genomic instability, is the most probable model for the pathogenesis of CIS. Genomic amplification of certain chromosomal regions, e.g. 12p, may facilitate survival of CIS and further invasive progression. Genetic studies, have so far not identified gene polymorphisms predisposing to the most common non-familial testicular cancer, but this research has only recently begun. Association of CIS with other disorders, such as congenital genital malformations and some forms of impaired spermatogenesis, all rising in incidence in a synchronous manner, led to the hypothesis that CIS might be a manifestation of testicular dysgenesis syndrome (TDS). The aetiology of TDS including testicular cancer remains to be elucidated, but epidemiological trends suggest a primary role for environmental factors, probably combined with genetic susceptibility.

Estrogen receptor α promoter polymorphism: stronger estrogen action is coupled with lower sperm count

BACKGROUND

Although the importance of estrogens in male reproduction is indisputable, little attention has been paid to the role of estrogen receptor (ER) gene mutations in male infertility. Significant correlation between (TA)n repeat allelic variants and lumbar bone mineral density was previously observed in the promoter region of the ERalpha gene, indicating that allelic combinations with higher number of (TA)n repeats are functionally more active genetic variants.

METHODS

We studied the (TA)n repeat polymorphism situated in the promoter region of the ERalpha gene in a large group of infertile and normospermic men (n = 347).

RESULTS

Although the (TA)n polymorphism failed to show a significant association with male infertility, we found a significant effect of this polymorphism on sperm count. In the group of infertile men, the mean TA repeat number and sperm concentration (P = 0.022) and total sperm number (P = 0.043) were inversely correlated, showing an association between higher TA repeat number (genotype A) and lower sperm production. In line with this observation, normospermic subjects with genotype A had a significantly lower mean sperm concentration with respect to men bearing genotype B with shorter TA alleles (P < 0.05) and a lower total sperm count (P < 0.01).

CONCLUSIONS

Our data indicate that specific allelic combinations of the ERalpha, which confer a stronger estrogen effect, may negatively influence human spermatogenesis.

Rapid and/or high-throughput genotyping for human red blood cell, platelet and leukocyte antigens, and forensic applications

BACKGROUND

Traditionally, transfusion medicine, platelet and human leukocyte antigen (HLA) typing, and forensic medicine relied on serologic studies.

METHODS

In recent years, molecular testing on nucleic acids has been increasingly applied to these areas. Although conventional molecular diagnostic methods such as PCR-sequence-specific priming, PCR-restriction fragment-length polymorphism, PCR-single-strand conformation polymorphism, sequence-based typing, and DNA fingerprinting have been shown to perform well, their use is limited by long turnaround times, high cost, labor-intensiveness, the need for special technical skills, and/or the high risk of amplicon contamination. With advance of fast and/or high-throughput methods and platforms that often combine amplification and detection, a new era of molecular genotyping is emerging in these fields dominated by serology for a century. As new targets, short tandem repeats, mitochondrial DNA and Y-chromosome sequences were introduced for forensic applications. This article reviews the current status of the application of rapid and/or high-throughput genotyping methods to these areas.

RESULTS

The results are already promising with real-time PCR, pyrosequencing, microarrays, and mass spectrometry and show high concordance rates with classic serologic and earlier manual molecular diagnostic methods. Exploration of other emerging methodologies will likely further enhance the diagnostic utility of molecular testing in these areas.

Fertility Among Brothers of Patients with Testicular Cancer

OBJECTIVE

Patients with testicular cancer have decreased fertility prior to the diagnosis of cancer, although it is not clear whether the subfertility is the result of an emerging tumor, or whether subfertility and testicular cancer share causes. To test if they share causes, we assessed fertility among brothers of patients with testicular cancer.

METHODS

We compared 5,613 siblings (2,878 brothers) of patients with germ-cell testicular cancer, diagnosed in Sweden from 1960 to 2002, with 6,151 population controls (3,202 men). Using the Swedish Multi-Generation Register, we obtained information on the number of children born (until December 2003) from cases (n = 9,480) and controls (n = 10,739). Fertility was measured using two indicators, (a) offspring twinning rates, as dizygotic twinning is reduced by male subfertility, and (b) number of children. We used unconditional logistic regression, and analyzed brothers and sisters separately. Analyses on the number of children were restricted to subjects (39%) born prior to 1954, for whom information on reproductive life until age 50 was available.

RESULTS

Brothers, but not sisters, of patients with testicular cancer were less likely to have unlike-sex twins than controls (for unlike-sex twins, the odds ratio for the father being a sibling of testicular cancer patient was 0.53; 95% confidence interval, 0.26-1.09). The likelihood of being a brother of a patient with testicular cancer decreased monotonically with increasing number of children (P = 0.05), whereas no association was observed for the sisters.

CONCLUSION

The decreased fertility found among brothers of patients with testicular cancer argues in favor of shared causes between cancer-associated subfertility and testicular cancer. Genetic links and shared environment could explain the association.