Genetic causes of male infertility

Current Progress in Stem Cell Therapy for Male Infertility

Infertility has become one of the most common issues worldwide, which has negatively affected society and infertile couples. Meanwhile, male infertility is responsible for about 50% of infertility. Accordingly, a great number of researchers have focused on its treatment during the last few years; however, current therapies such as assisted reproductive technology (ART) are not effective enough in treating male infertility. Because of their self-renewal and differentiation capabilities and unlimited sources, stem cells have recently raised great hope in the treatment of reproductive system disorders. Stem cells are undifferentiated cells that can induce different numbers of specific cells, such as male and female gametes, demonstrating their potential application in the treatment of infertility. The present review aimed at identifying the causes and potential factors that influence male fertility. Besides, we highlighted the recent studies that investigated the efficiency of stem cells such as spermatogonial stem cells (SSCs), embryonic stem cells (ESCs), very small embryonic-like stem cells (VSELs), induced pluripotent stem cells (iPSCs), and mesenchymal stem cells (MSCs) in the treatment of various types of male infertility.

[AZF gene microdeletions in azoospermic-oligozoospermic males]

BACKGROUND AND OBJECTIVE

The presence of microdeletions in the Y-chromosome azoospermia factor (AZF) region (YCMs) is considered the most frequent genetic cause of male infertility along with Klinefelter syndrome. The objective of this study was to investigate the frequencies and type of YCMs in infertile men in Aragon and to analyze the relationship between sex hormones, sperm count and microdeletions in them.

PATIENTS AND METHODS

Retrospective descriptive study of 644 men who during 2006-2019 were screened for YCMs using YChromStrip (Operón, Spain) by PCR+reverse hybridization, spermiogram, karyotype and quantification of sex hormones.

RESULTS

The frequency of YCMs was 3.88% (25/644), not being detected in any patient with mild or normospermic oligozoospermia, that is, in sperm counts higher than 5×10⁶/mL. The group of azoospermic patients was the one that presented a higher frequency of YCMs (14.58%, 14/96). Deletions in the AZFc region were the most frequent (68%). 20% (5/25) of patients with YCMs also presented some type of karyotype abnormality that included aneuploidies, deletions, duplications and/or translocations. Sperm count was significantly lower and FSH and LH concentrations significantly higher in the group of patients with YCMs.

CONCLUSIONS

YCMs screening is a key test in the diagnostic approach to male infertility. Obtaining an adequate result allows choosing suitable assisted reproduction techniques, preventing unnecessary treatments and the transmission of genetic defects to offspring.

The Association of Soluble VEGFR-1 Serum Level and Genetic (rs7993418) Polymorphism with In Vitro Fertilization and Embryo Transfer Outcome in the Population of Northern Iran

Background

Vascular endothelial growth factor receptors (VEGFRS) play an important role in embryo implantation. The aim of the present study was to examine the association of VEGFR1 circulating level and gene polymorphism with in vitro fertilization and embryo transfer (IVF-ET) outcome.

Methods

In this case-control study, 120 women who had unsuccessful IVF (IVF-) history and 120 women who had successful IVF outcome (IVF+) as controls were included. Genomic DNA was extracted from blood samples. Genotyping was performed using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). The serum levels of soluble VEGFR1 (sVEGFR1) were measured by ELISA. ANOVA test was used for statistical analysis.

Results

The frequency of T and C alleles in IVF+ individuals were 87.5%, 12.5% and among IVF- were 75.5%, 24.5%, respectively (p=0.0006). The minor allele (C) was associated with an increased risk of IVF failure based on results from co-dominant (OR=3.86, 95%CI 1.19-12.47), dominant (OR=2.32, 95%CI 1.31-4.10), recessive (OR=3.22, 95%CI 1.00-10.29), and allele models (OR=2.28, 95%CI 1.40-3.69). We also showed that there is a significant decrease in serum sVEGFR1 levels in IVF as compared to IVF+ (p=0.006) groups. Moreover, TT genotype is significantly associated with increased serum sVEGFR1 concentration in IVF group (TT, CT, and CC serum levels were 106.55±11.04, 94.33±10.75, and 83.33±9.13 ng/ml, and in IVF+ group were 156.11±18.08, 120.66±16.51, and 84.66±20.31 ng/ml, respectively).

Conclusion

The results of this study indicate that VEGFR1 polymorphism and sVEGFR1 circulating levels are associated with IVF-ET outcome. Moreover, CC genotype is associated with decreased sVEGFR-1 serum concentration and IVF-ET failure.

Screening by single-molecule molecular inversion probes targeted sequencing panel of candidate genes of infertility in azoospermic infertile Jordanian males

Infertility is a common health problem that affects around 1 in 6 couples in the United States, where half of these cases are attributed to male factors. Genetics play an important role in infertility and it is estimated that up to 50% of cases are due to genetic factors. Despite this, many male infertility cases are still idiopathic. This study aimed to identify the presence of possibly pathogenic rare variants in a set of candidate genes related to azoospermia in 69 Jordanian men using a next-generation sequencing-based panel covering more than a hundred male infertility related genes. A total of 9 variants were found and validated. Among them, two variants included reported pathogenic variants in CFTR and one novel pathogenic variant in the USP9Y gene. We also report the detection of 6 other variants with uncertain significance in other genes. Interestingly, male cases with CFTR variants did not show the expected cystic fibrosis phenotypes except for infertility. This work helps to uncover the contribution of additional genetic factors to the aetiology of male infertility and highlights the importance to obtain more reliable information about the presence of genetic variation in the Jordanian population.

Does ICSI outcome in obstructive azoospermia differ according to the origin of retrieved spermatozoa or the cause of epididymal obstruction? A comparative study

Purpose

To determine whether ICSI outcomes are affected by sperm source or genital tract inflammatory status.

Methods

A retrospective cohort study was conducted in all consecutive obstructive azoospermia patients who underwent testicular sperm aspiration (TESA) or percutaneous epididymal sperm aspiration (PESA) and ICSI between February 1, 2017, and December 31, 2020. Couples were excluded if they were diagnosed with monogenic disease, abnormal karyotype, or had female uterine malformation. The primary objective was to determine whether ICSI outcomes are affected by the use of testicular or epididymal spermatozoa, and the secondary objective was to explore the effect of granulocyte elastase on ICSI outcomes using epididymal spermatozoa.

Results

Compared with TESA, inflammatory and non-inflammatory PESA patients exhibited a better high-quality embryo rate, with significant differences among the three groups (49.43 vs. 55.39% and 56.03%; odds ratio, 6.345 and 6.631; 95% confidence interval, 0.340–12.350, and 1.712–11.550; P = 0.038 and P = 0.008, respectively). The fertilization rate, clinical pregnancy rate, live birth delivery rate, and congenital anomaly birth rate were similar in patients who underwent TESA or PESA (with or without inflammation).

Conclusions

The high-quality embryo rate in PESA patients was higher than that in TESA patients. After successful pregnancy, ICSI outcomes did not differ between patients with obstructive azoospermia who experienced TESA or PESA and those with or without genital tract inflammation.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11255-022-03350-x.

Abnormal Y chromosome detection in infertile males using multiplex ligation-dependent probe amplification

Y chromosome abnormalities are the leading cause of male infertility. The clinical detection of abnormalities is necessary for appropriate genetic counselling. This study describes the prevalence, distribution and characteristics of Y chromosome abnormalities, which should be considered in the clinical management of infertile males. A total of 121 patients with oligozoospermia, 120 with azoospermia and 88 normal individuals were recruited between June 2019 and July 2021. Y chromosome microdeletions were assessed using multiplex ligation-dependent probe amplification (MLPA). The abnormal Y chromosome prevalence was 30.70%, and it was most common in patients aged 26-40 years. The frequencies of azoospermia factor (AZF) deletion, duplication and deletions/duplications were 19.76%, 9.42% and 1.52% respectively. The most common abnormalities were AZFc deletion (19.80%), AZFc partial deletion (40.59%) and AZFc partial duplication (17.82%). Oligozoospermia was associated with an increased incidence of AZF deletion. In the subgroup analysis, patients <30 years old with azoospermia exhibited elevated follicle-stimulating hormone levels and oestradiol. Moreover, the incidence of AZF deletion was higher in those with azoospermia (OR: 2.12; 95% CI: 1.05-5.28; p = 0.023) or oligozoospermia (OR: 2.54; 95% CI: 1.13-5.79; p = 0.008) than in normal individuals for ages ≥30 years.

Oxidative Stress and Male Fertility: Role of Antioxidants and Inositols

Infertility is defined as a couple’s inability to conceive after at least one year of regular unprotected intercourse. This condition has become a global health problem affecting approximately 187 million couples worldwide and about half of the cases are attributable to male factors. Oxidative stress is a common reason for several conditions associated with male infertility. High levels of reactive oxygen species (ROS) impair sperm quality by decreasing motility and increasing the oxidation of DNA, of protein and of lipids. Multi-antioxidant supplementation is considered effective for male fertility parameters due to the synergistic effects of antioxidants. Most of them act by decreasing ROS concentration, thus improving sperm quality. In addition, other natural molecules, myo-inositol (MI) and d-chiro–inositol (DCI), ameliorate sperm quality. In sperm cells, MI is involved in many transduction mechanisms that regulate cytoplasmic calcium levels, capacitation and mitochondrial function. On the other hand, DCI is involved in the downregulation of steroidogenic enzyme aromatase, which produces testosterone. In this review, we analyze the processes involving oxidative stress in male fertility and the mechanisms of action of different molecules.

A novel frameshift mutation in ubiquitin-specific protease 26 gene in a patient with severe oligozoospermia

Ubiquitin-specific protease 26 (USP26) encodes a predicted protein containing his- and cys- domains that are conserved among deubiquitinating enzymes. USP26 is specifically expressed in testis tissue and is a potential infertility gene. In the present study, we performed genetic testing related to spermatogenesis impairment in a patient with idiopathic severe oligozoospermia to identify the cause. The patient underwent clinical examination and reproductive hormone testing. Genes associated with male infertility, including USP26, were assessed by targeted exome sequencing. A novel frameshift mutation, c.2195delT (p.Phe732Serfs*14), was identified in USP26. This frameshift mutation was located in residue 732 of USP26 gene, leading to loss of the conserved deubiquitinating enzyme His-domain and producing a truncated protein of 744 amino acids. Bioinformatics analysis revealed this mutation to be pathogenic. A novel framshift mutation c.2195delT (p.Phe732Serfs*14) in USP26 gene was reported to be associated with male infertility in a Chinese patient with severe oligozoospermia.

De novo mutations in idiopathic male infertility-A pilot study

STUDY QUESTION

Are de novo mutations in the human genome associated with male infertility?

SUMMARY ANSWER

We identified de novo mutations in five candidate genes: SEMA5A, NEURL4, BRD2, CD1D, and CD63.

WHAT IS KNOWN ALREADY

Epidemiological and genetic studies have consistently indicated contribution of genetic factors to the etiology of male infertility, suggesting that more than 1500 genes are involved in spermatogenesis.

STUDY DESIGN, SIZE, DURATION

First, we searched for de novo mutations in patients with idiopathic azoospermia with whole-exome sequencing (WES). To evaluate the potential functional impact of de novo identified mutations, we analyzed their expression differences on independent testis samples with normal and impaired spermatogenesis. In the next step, we tested additional group of azoospermic patients for mutations in identified genes with de novo mutations. In addition to the analysis of de novo mutations in patients with idiopathic azoospermia, we considered other models of inheritance and searched for candidate genes harboring rare maternally inherited variants and biallelic autosomal and X-chromosome hemizygous variants.

PARTICIPANTS/MATERIALS, SETTING, METHODS

We performed WES in 13 infertile males with idiopathic azoospermia and their parents. Potential functional impact of de novo identified mutations was evaluated by global gene expression profiling on 20 independent testis samples. To replicate the results, we performed WES in further 16 independent azoospermic males, which were screened for the variants in the same genes. Library preparation was performed with Nextera Coding Exome Capture Kit (Illumina), with subsequent sequencing on Illumina HiSeq 2500 platform.

MAIN RESULTS AND THE ROLE OF CHANCE

We identified 11 de novo mutations in 10 genes of which 5 were considered potentially associated with azoospermia: SEMA5A, NEURL4, BRD2, CD1D, and CD63. All candidate genes showed significant differential expression in testis samples composed of patients with severely impaired and normal spermatogenesis. Additionally, we identified rare, potentially pathogenic mutations in the genes previously implicated in male infertility-a maternally inherited heterozygous frameshift variant in FKBPL gene and inframe deletion in UPF2 gene, homozygous frameshift variant in CLCA4 gene, and a heterozygous missense variant NR0B1 gene, which represent promising candidates for further clinical implication.

LIMITATIONS OF THE STUDY, REASONS FOR CAUTION

We provided limited functional support for involvement of de novo identified genes in pathogenesis of male infertility, based on expression analysis. Additionally, the sample size was limited.

WIDER IMPLICATIONS OF THE FINDINGS

We provide support that de novo mutations might contribute to male infertility and propose five genes as potentially implicated in its pathogenesis.

Genetic contribution of HIST1H1T regulatory region alternations to human nonobstructive azoospermia

HIST1H1T encodes H1T, a testicular variant of histone H1, which is expressed during spermatogenesis especially in primary spermatocytes and facilitates histone to protamine exchanges during maturation of spermatozoa. The goal of the conducted research was to evaluate four genetic variations of HIST1H1T in men with nonobstructive azoospermia. This case-control study was conducted among a total number of 200 men, including 100 nonobstructive azoospermic (NOA) infertile men. In this study, three single-nucleotide polymorphisms, including c.-54C>T (rs72834678), c.-912A>C (rs707892) and c.-947A>G (rs74293938) in regulatory region as well as one SNP c.40G>C (rs198844) in coding region were identified using PCR sequencing. According to statistical analysis, none of those SNPs in regulatory regions showed significant differences in case and control groups. For SNP (c.40G>C), a significantly higher frequency of C allele in the case group was observed compared to the control group (p-value: .044). In conclusion, according to statistical analysis it seems that the polymorphism of c.40G>C is not associated with nonobstructive azoospermia.

Evaluation of chromosomal abnormalities and Y-chromosome microdeletions in 1696 Turkish cases with primary male infertility: A single-center study

OBJECTIVE

The aim of this study was to determine the frequencies of chromosomal abnormalities and Y-chromosome microdeletions in Turkish cases with primary male infertility in a single center.

MATERIAL AND METHODS

Chromosomal abnormalities and Y-chromosome microdeletions were investigated in 1696 cases with primary male infertility between 2012 and 2017. Karyotype analyzes and Y-chromosome microdeletions analyzes [azoospermia factor (AZF) regions] were performed in all cases by using standard cytogenetic methods and the multiplex polymerase chain reaction method, respectively.

RESULTS

Chromosomal abnormalities were found in 142 cases (8.4%; 142/1696). Y-chromosome microdeletions were detected in 46 cases (2.7%; 46/1696). Y-chromosome microdeletions in the AZFc region were found in 20 of 46 cases (43%).

CONCLUSION

This study is one of the few were a large number of cases was studied in Turkey. It indicates that cytogenetic and Y-chromosome microdeletion studies should be conducted in cases with primary male infertility prior to selecting assisted reproductive techniques.

A different look at genetic factors in individuals with non-obstructive azoospermia or oligospermia in our research study: To whom, which threshold, when, in what way?

INTRODUCTION

In our study, we sought answers to many questions about male infertility from a different perspective. The first step in male infertility is anamnesis, physical examination and sperm count. The European Academy of Andrology recommends examination of genetic causes in individuals with fewer than 5million/ml semen counts. The American Urological Association and American Society for Reproductive Medicine have guidelines recommending performing karyotype and AZF subgroup deletion testing in azoospermia and fewer than 5 million sperm total count. Klinefelter syndrome and Y chromosome microdeletions are still very important in male infertility. Based on patients with Klinefelter syndrome or Y microdeletion, we sought answers to many questions in male infertility.

MATERIALS AND METHODS

In the presented study 327 male patients with having fewer than 15millionsperm/ml detected in at least two consecutive sperm analysis were examined. Patients were divided into sub-groups according to the presence of semen count, chromosomal anomaly and Y microdeletion. In addition, FSH, LH and testosterone levels were analyzed.

RESULTS

Numerical chromosomal anomalies were observed in 34 (10.4%) of 327 patients, and all of these anomalies were found as 47, XXY. Individuals with no AZF microdeletion constituted 95.1% (n=311) of the study group. The overall frequency of AZF microdeletions was 4.9% (16/327). No AZF microdeletions were detected for the patients who have sperm counts above 2million/ml. FSH, LH and testosterone levels were found significantly different between the groups.

DISCUSSION

The results of our study provide another layer of evidence to demonstrate the controversial threshold value of the EAA. In light of our data and current literature, we recommend to set the threshold value at 2million/ml for semen analysis. Further studies conducted in different ethnic groups and larger patient groups would contribute to clarify what exact value should be used to apply genetic tests.

The Association of PON1 192 Q/R Polymorphism with the Risk of Idiopathic Male Infertility in Northern Iran

BACKGROUND

Infertility is defined as the inability to achieve pregnancy after 12 months of regular unprotected sexual intercourse. Environmental and genetic factors are involved in male infertility. The polymorphism studies have a crucial role in disease recognition. Paraoxonase (PON) is an oxidant enzyme which is associated with inflammation, oxidative stress and lipid metabolism. The present study aimed to evaluate the relationship between PON1 192 Q/R polymorphism and the susceptibility to idiopathic male infertility.

METHODS

Samples were collected from 220 patients diagnosed with male infertility and 230 controls genotyped by Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP).

RESULTS

A significant difference in genotype distributions of PON1 192 Q/R polymorphism was observed between patients and controls (p=0.001). Our findings revealed that individuals with the variant QR had a significant decreased risk of idiopathic male infertility (OR=0.49, 95%CI=0.33-0.73, p=0.0004). Moreover, analyses showed that R allele may have a protective effect on susceptibility of idiopathic male infertility (OR=0.31, 95%CI=0.21-0.47, p=0.0001).

CONCLUSION

The data from this study indicates that the PON1 192 Q/R polymorphism is associated with decreased risk of idiopathic male infertility. However, more studies should be considered with larger number of patients and control subjects to confirm our results.

STAT6, PBX2, and PBRM1 Emerge as Predicted Regulators of 452 Differentially Expressed Genes Associated With Puberty in Brahman Heifers

The liver plays a central role in metabolism and produces important hormones. Hepatic estrogen receptors and the release of insulin-like growth factor 1 (IGF1) are critical links between liver function and the reproductive system. However, the role of liver in pubertal development is not fully understood. To explore this question, we applied transcriptomic analyses to liver samples of pre- and post-pubertal Brahman heifers and identified differentially expressed (DE) genes and genes encoding transcription factors (TFs). Differential expression of genes suggests potential biological mechanisms and pathways linking liver function to puberty. The analyses identified 452 DE genes and 82 TF with significant contribution to differential gene expression by using a regulatory impact factor metric. Brain-derived neurotrophic factor was observed as the most down-regulated gene (P = 0.003) in post-pubertal heifers and we propose this gene influences pubertal development in Brahman heifers. Additionally, co-expression network analysis provided evidence for three TF as key regulators of liver function during pubertal development: the signal transducer and activator of transcription 6, PBX homeobox 2, and polybromo 1. Pathway enrichment analysis identified transforming growth factor-beta and Wnt signaling pathways as significant annotation terms for the list of DE genes and TF in the co-expression network. Molecular information regarding genes and pathways described in this work are important to further our understanding of puberty onset in Brahman heifers.

Computational Analysis of High-Risk SNPs in Human DBY Gene Responsible for Male Infertility: A Functional and Structural Impact

BACKGROUND

DEAD-box helicase 3, Y-linked (DBY) is a candidate gene of the AZF region which is involved in spermatogenesis process. Mutations in the DBY gene may disrupt the spermatogenesis and lead to infertility in men. Identification of functionally neutral mutation from the disease-causing mutation is the biggest challenge in human genetic variation analysis. Owing to the importance of DBY in male infertility, functional analysis was carried out to reveal the association between genetic mutation and phenotypic variation through various in silico approaches.

METHODS

The present study analyzed the functional consequences of the nsSNPs in human DBY gene using SIFT, PolyPhen 2, PROVEAN, SNAP2, PMut, nsSNPAnalyzer, PhD-SNP and SNPs&GO along with stability analysis through I-Mutant2.0, MuPro and iPTREE-STAB. The conservational analysis of amino acid residues, biophysical properties and conserved domains of the DBY protein was analyzed using various computational tools. The 3D structure of the protein was generated using SPARKS-X and validated using RAMPAGE.

RESULTS

Out of 1130 SNPs reported in dbSNP, only one nsSNP (G300D) was found to have a functional effect on stability as well as the function of the DBY protein. The results showed the presence of G300 in the putative structure of DBY domain.

CONCLUSION

To the best of our knowledge, this is the first study to detect pathologically significant nsSNPs (G300D) through a computational approach in the DBY which can be useful for development in potent drug discovery studies.

The frequencies of Y chromosome microdeletions in infertile males

OBJECTIVE

To determine the frequencies and the characteristics of Y chromosome microdeletions in infertile males.

MATERIAL AND METHODS

The records of 1616 infertile males were included in the study. The cases were divided into groups according to the infertility etiology and semen analysis. The frequencies and the characteristics of Y chromosome microdeletions were investigated in groups.

RESULTS

Y chromosome microdeletion was detected in 54 (3.3%) of 1616 cases. Microdeletions in the azoospermia factor (AZF) region were the most common (48.1%). When the cases were grouped according to causes of infertility that could be detected, no Y chromosome microdeletions were detected in some groups (cases with Klinefelter Syndrome, hypogonadotropic hypogonadism, congenital absence of vas deferens, and 47, XYY karyotype).

CONCLUSION

Y chromosome microdeletions were detected quite frequently in certain infertility subgroups. Therefore, detailed evaluation of an infertile man by physical examination, semen analysis, hormonal evaluations and when required, karyotype analysis may predict the patients for whom Y chromosome microdeletion analysis is necessary and also prevent cost increases.

Association and meta-analysis of HLA and non-obstructive azoospermia in the Han Chinese population

The exact aetiology and pathogenesis of most non-obstructive azoospermia (NOA) are still unknown. The previous two genomewide association studies (GWASs) have identified three different loci within the HLA region for NOA in the Han Chinese population, including rs3129878, rs498422 and rs7194. To further validate the risk of three GWAS-linked loci for NOA, we conducted a case-control study of these three risk loci in an independent Han Chinese male population, with 603 NOA patients and 610 controls. Furthermore, we also performed a meta-analysis of five studies on these three NOA-risk loci. The case-control study strongly suggested a significant association between loci rs3129878, rs498422 and rs7194 and NOA (P = 6.75 × 10^-21 (OR = 2.2586), P = 0.0060 (OR = 1.4013) and P = 0.0128 (OR = 1.2626) respectively). Our meta-analyses also supported the susceptibility of these three risk loci to NOA (P < 0.01). The risk variants within the HLA region potentially have a strong effect on males at risk of NOA, and may serve as diagnostic markers for male infertility. However, considering genetic difference between different populations, future validating studies in larger independent samples and animal experiments are suggested.

Association of 370-371insACA, 494T>C, and 1423C>T haplotype in ubiquitin-specific protease 26 gene and male infertility: a meta-analysis

Whether the 370-371insACA, 494T>C, and 1423C>T haplotype in ubiquitin-specific protease 26 (USP26) gene is associated with male infertility is controversial. To clarify this issue, we conducted a meta-analysis based on the most recent studies. Eligible studies were screened by using PubMed and Embase. Pooled odd ratio (OR) with 95% confidence interval (CI) was calculated with fixed effect models. Ten studies with 1603 patients and 2505 controls were included. Overall, the results indicated that there was an association between the haplotype and male infertile risk (OR = 1.74, 95% CI: 1.09–2.77). The OR calculated based on the five studies in Asia and three in Europe was 1.96 (95% CI: 1.05–3.67) and 1.54 (95% CI: 0.75–3.16) respectively, however, the OR was 0.86 (95% CI: 0.05–15.29) based on the two investigations in America. In addition, the data from the patients with azoospermia (AZO) showed an increased pooled OR of 2.35 (95% CI: 1.22–4.50). In contrast, the studies with oligoasthenoteratozoospermia (OAT) exhibited that the pooled OR was 0.97 (95% CI: 0.43–2.16). Our analyses indicate that there is an association of alteration in USP26 with male infertility, especially in AZO and Asian population.

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.

The association of ApE1 -656T>G and 1349T>G polymorphisms and idiopathic male infertility risk

PURPOSE

In spite of variety studies in understanding of human reproductive and fertility, the underlying causes of male infertility remains undefined in about 50 % of cases. The polymorphism studies have a crucial role in diseases recognizing. Human apurinic/apyrimidinic endonuclease 1 (ApE1) is a multifunctional protein that has an important role in the base excision repair pathway. The present study was aimed to evaluate whether two polymorphisms -656T>G and 1349T>G ApE1 are related with the susceptibility to idiopathic male infertility.

METHODS

Samples were collected from 180 patients diagnosed with idiopathic male infertility and 120 control subjects and genotyped by tetra-primer amplification refractory mutation system PCR.

RESULTS

We observed a significant difference in genotype distributions of -656T>G ApE1 polymorphism between infertile patients and controls (P = 0.0001). Our findings indicated individuals with the variant TG genotypes had a significant increased risk of idiopathic male infertility (OR 1.84, 95 % CI 1.09-3.11, P = 0.021), whereas the significant association between the 1349T>G polymorphism and idiopathic male infertility risk was not observed (P = 0.2).

CONCLUSIONS

Our data suggest that the -656T>G ApE1 polymorphism may be associated with increased risk of idiopathic male infertility. Larger studies with more patients and controls are needed to confirm the results.

Study of Three Single Nucleotide Polymorphisms in the SLC6A14 Gene in Association with Male Infertility

Although several genetic causes of male infertility are known, the condition in around 60.0–75.0% of infertile male patients appears to be idiopathic. In some, genetic causes may be polygenic and require several low-penetrance genes to produce a phenotype outcome. In others, pleiotropy, when a gene can produce several phenotypic traits, may be involved. We have investigated whether single nucleotide polymorphisms (SNPs) in the SLC6A14 [solute carrier family 6 (amino acid transporter), member 14] gene are associated with male infertility. This gene has previously been linked with obesity and cystic fibrosis, which are associated with male infertility. It has a role in the transport of tryptophan and synthesis of serotonin that are important for normal spermatogenesis and testicular function. We have analyzed three SNPs (rs2312054, rs2071877 and rs2011162) in 370 infertile men and 241 fertile controls from two different populations (Macedonian and Slovenian). We found that the rs2011162(G) allele and rs2312054(A)-rs2071877(C)-rs2011162(G) haplotype are present at lower frequencies in the infertile rather than the fertile men (p = 0.044 and p = 0.0144, respectively).

We concluded that the SLC6A14 gene may be a population-specific, low-penetrance locus which confers susceptibility to male infertility/subfertility. Additional follow-up studies of a large number of infertile men of different ethnic backgrounds are needed to confirm such a susceptibility.