Repeat Sequences and Base Correlations in Human Y Chromosome Palindromes

On the basis of information theory and statistical methods, we use mutual information, n- tuple entropy and conditional entropy, combined with biological characteristics, to analyze the long range correlation and short range correlation in human Y chromosome palindromes. The magnitude distribution of the long range correlation which can be reflected by the mutual information is PS〉PSa〉PSb （P5a and P5b are the sequences that replace solely Alu repeats and all interspersed repeats with random uneorrelated sequences in human Y chromosome palindrome 5, respectively）; and the magnitude distribution of the short range correlation which can be reflected by the n-tuple entropy and the conditional entropy is PS〉P5a〉PSb〉random uncorrelated sequence. In other words, when the Alu repeats and all interspersed repeats replace with random uneorrelated sequence, the long range and short range correlation decrease gradually. However, the random nncorrelated sequence has no correlation. This research indicates that more repeat sequences result in stronger correlation between bases in human Y chromosome. The analyses may be helpful to understand the special structures of human Y chromosome palindromes profoundly.

Frequency of Y chromosome microdeletions and chromosomal abnormalities in infertile Thai men with oligozoospermia and azoospermia

Aim： To investigate the possible causes of oligozoospermia and azoospermia in infertile Thai men, and to find the frequencies of Y chromosome microdeletions and cytogenetic abnormalities in this group. Methods： From June 2003 to November 2005, 50 azoospermic and 80 oligozoospermic men were enrolled in the study. A detailed history was taken for each man, followed by general and genital examinations. Y chromosome microdeletions were detected by multiplex polymerase chain reaction （PCR） using 11 gene-specific primers that covered all three regions of the azoospermic factor （AZFa, AZFb and AZFc）. Fifty men with normal semen analysis were also studied. Karyotyping was done with the standard G- and Q-banding. Serum concentrations of follicle stimulating hormone （FSH）, luteinizing hormone （LH）, prolactin （PRL） and testosterone were measured by electrochemiluminescence immunoassays （ECLIA）. Results： Azoospermia and oligozoospermia could be explained by previous orchitis in 22.3%, former bilateral cryptorchidism in 19.2%, abnormal karyotypes in 4.6% and Y chromosome microdeletions in 3.8% of the subjects. The most frequent deletions were in the AZFc region （50%）, followed by AZFb （33%） and AZFbc （17%）. No significant difference was detected in hormonal profiles of infertile men, with or without microdeletions. Conclusion： The frequencies of Y chromosome microdeletions and cytogenetic abnormalities in oligozoospermic and azoospermic Thai men are comparable with similarly infertile men from other Asian and Western countries.

Routine screening for classical azoospermia factor deletions of the Y chromosome in azoospermic patients with Klinefelter syndrome

Aim： To evaluate the occurrence of classical azoospermia factor （AZF） deletions of the Y chromosome as a routine examination in azoospermic subjects with Klinefelter syndrome （KS）. Methods： Blood samples were collected from 95 azoospermic subjects with KS （91 subjects had a 47,XXY karyotype and four subjects had a mosaic 47,XXY/46, XY karyotype） and a control group of 93 fertile men. The values of testosterone, follicle stimulating hormone （FSH） and luteinizing hormone （LH） were measured. To determine the presence of Y chromosome microdeletions, polymerase chain reaction （PCR） of five sequence-tagged site primers （sY84, sY 129, sY 134, sY254, sY255） spanning the AZF region, was performed on isolated genomic DNA. Results： Y chromosome microdeletions were not found in any of the 95 azoosperrnic subjects with KS. In addition, using similar conditions of PCR, no microdeletions were observed in the 93 fertile men evaluated. The level of FSH in KS subjects was higher than that in fertile men （38.2 ± 10.3 mIU/mL vs. 5.4 ±2.9 mIU/mL, P 〈 0.001） and the testosterone level was lower than that in the control group （1.7 ±0.3 ng/mL vs. 4.3 ± 1.3 ng/mL, P 〈 0.001）. Conclusion： Our data and review of the published literature suggest that classical AZF deletions might not play a role in predisposing genetic background for the phenotype of azoospermic KS subjects with a 47,XXY karyotype. In addition, routine screening for the classical AZF deletions might not be required for these subjects. Further studies including partial AZFc deletions （e.g. gr/gr or b2/b3） are necessary to establish other mechanism underlying severe spermatogenesis impairment in KS.

The prevalence of azoospermia factor microdeletion on the Y chromosome of Chinese infertile men detected by multi-analyte suspension array technology

Aim： To develop a high-throughput multiplex, fast and simple assay to scan azoospermia factor （AZF） region microdeletions on the Y chromosome and establish the prevalence of Y chromosomal microdeletions in Chinese infertile males with azoospermia or oligozoospermia. Methods： In total, 178 infertile patients with azoospermia （nonobstructed）, 134 infertile patients with oligozoospermia as well as 40 fertile man controls were included in the present study. The samples were screened for AZF microdeletion using optimized multi-analyte suspension array （MASA） technology. Results： Of the 312 patients, 36 （11.5%） were found to have deletions in the AZF region. The rnicrodeletion frequency was 14% （25/178） in the azoospermia group and 8.2% （11/134） in the oligospermia group. Among 36 patients with microdeletions, 19 had deletions in the AZFc region, seven had deletions in AZFa and six had deletions in AZFb. In addition, four patients had both AZFb and AZFc deletions. No deletion in the AZF region was found in the 40 fertile controls. Conclusion： There is a high prevalence of Y chromosomal microdeletions in Chinese infertile males with azoospermia or oligozoospermia. The MASA technology, which has been established in the present study, provides a sensitive and high-throughput method for detecting the deletion of the Y chromosome. And the results suggest that genetic screening should be advised to infertile men before starting assisted reproductive treatments.

Clinical and pathological correlation of the microdeletion of Y chromosome for the 30 patients with azoospermia and severe oligoasthenospermia

Aim: To review the accumulated 30 patients with different area of Y chromosome microdeletions, focusing on their correlation with the clinical and pathological findings. Methods: A total of 334 consecutive infertile men with azoospermia (218 patients) and severe oligoasthenospermia (116 patients) were screened. Complete physical and endocrinological examinations, general chromosome study and multiplex polymerase chain reaction assay to evaluate the Y chromosome microdeletion were performed. Ten patients received testicular biopsy. Then the clinical and pathological findings were analyzed with reference to the areas of Y chromosome microdeletion. Results: There is a decline of the percentage of sperm appearing in semen in the group that the gene deletion region from AZFc to AZFb. The clinical evidence of the impairment (decreased testicular size and elevated serum FSH) is also relevantly aggravated in this group. However, the pathology of testicular biopsy specimen was poorly correlated with the different deletion areas of the Y chromosome, which may be due to the limited number of specimens. Conclusion: The clinical correlation of spermatogenic impairment to the different AZF deletion regions may provide the information for the infertile couples in pre-treatment counseling.

Y chromosome microdeletions in azoospermic patients with Klinefelter's syndrome

Aim： To study the occurrence of Y chromosome microdeletions in azoospermic patients with Klinefelter＇s syndrome （KFS）. Methods： Blood and semen samples were collected from azoospermic patients with KFS （n = 14） and a control group of men of proven fertility （n = 13）. Semen analysis was done according to World Health Organization （WHO） guidelines. Blood samples were processed for karyotyping, fluorescent in situ hybridization （FISH） and measurement of plasma follicle stimulating hormone （FSH） by radioimmunoassay. To determine Y chromosome microdeletions, polymerase chain reaction （PCR） of 16 sequence tagged sites （STS） and three genes （DFFRY, XKRY and RBM1 Y） was performed on isolated genomic DNA. Testicular fine needle aspiration cytology （FNAC） was done in selected cases. Results： Y chromosome microdeletions spanning the azoospermia factor （AZF）a and AZFb loci were found in four of the 14 azoospermic patients with KFS. Karyotype and FISH analysis revealed that, of the four cases showing Y chromosome microdeletion, three cases had a 47,XXY/46,XY chromosomal pattern and one case had a 46,XY/47,XXY/48,XXXY/48,XXYY chromosomal pattern. The testicular FNAC of one sample with Y chromosome microdeletion revealed Sertoli cell-only type of morphology. However, no Y chromosome microdeletions were observed in any of the 13 fertile men. All patients with KFS had elevated plasma FSH levels. Conclusion： Patients with KFS may harbor Y chromosome microdeletions and screening for these should be a part of their diagnostic work-up, particularly in those considering assisted reproductive techniques. （Asian JAndrol 2006 Jan; 8： 81-88）

"Micro-deletions" of the human Y chromosome and their relationship with male infertility

The Y chromosome evolves from an autochromosome and accumulates male-related genes including sex-determining region of Y-chromosome （SRY） and several spermatogenesis-related genes. The human Y chromosome （60 Mb long） is largely composed of repetitive sequences that give it a heterochromatic appearance, and it consists of pseudoautosomal, euchromatic, and heterochromatic regions. Located on the two extremities of the Y chromosome, pseudoautosomal regions 1 and 2 （PAR1 and PAR2, 2.6 Mb and 320 bp long, respectively） are homologs with the termini of the X chromosome. The euchromatic region and some of the repeat-rich heterochromatic parts of the Y chromosome are called ＂male-specific Y＂ （MSY）, which occupy more than 95% of the whole Y chromosome. After evolution, the Y chromosome becomes the smallest in size with the least number of genes but with the most number of copies of genes that are mostly spermatogenesis-related. The Y chromosome is characterized by highly repetitive sequences （including direct repeats, inverted repeats, and palindromes） and high polymorphism. Several gene rearrangements on the Y chromosome occur during evolution owing to its specific gene structure. The consequences of such rearrangements are not only loss but also gain of specific genes. One hundred and fifty three haplotypes have been discovered in the human Y chromosome. The structure of the Y chromosome in the GenBank belongs to haplotype R1. There are 220 genes （104 coding genes, 111 pseudogenes, and 5 other uncategorized genes） according to the most recent count. The 104 coding genes encode a total of about 48 proteins/protein families （including putative proteins/protein families）. Among them, 16 gene products have been discovered in the azoospermia factor region （AZF） and are related to spermatogenesis. It has been discovered that one subset of gene rearrangements on the Y chromosome, ＂micro-deletions＂, is a major cause of male infertility in some populations. However, controversies exist about different Y chromosome haplotypes. Six AZFs of the Y chromosome have been discovered including AZFa, AZFb, AZFc, and their combinations AZFbc, AZFabc, and partial AZFc called AZFc/gr/gr. Different deletions in AZF lead to different content spermatogenesis loss from teratozoospermia to infertility in different populations depending on their Y haplotypes. This article describes the structure of the human Y chromosome and investigates the causes of micro-deletions and their relationship with male infertility from the view of chromosome evolution. After analysis of the relationship between AZFc and male infertility, we concluded that spermatogenesis is controlled by a network of genes, which may locate on the Y chromosome, the autochromosomes, or even on the X chromosome. Further investigation of the molecular mechanisms underlying male fertility/infertility will facilitate our knowledge of functional genomics.

Gonadal dysgenesis in Turner syndrome with Y-chromosome mosaicism:Two case reports

BACKGROUND Turner syndrome(TS)has a variety of different karyotypes,with a wide range of phenotypic features,but the specific karyotype may not always predict the phenotype.TS with Y chromosome mosaicism may have mixed gonadal dysgenesis,and the mosaicism is related to the potential for gonadoblastoma.CASE SUMMARY In this case report,we report two cases of TS with different karyotypes and gonadal dysgenesis.Patient 1 had obvious virilization,and was positive for the SRY gene,but her karyotype in peripheral blood lymphocytes was 45X.Patient 2 had a mosaic karyotype,45X/46X,dic(Y:Y)(p11.3:p11.2),and the proportion of Y-bearing cells was 50%in peripheral blood lymphocytes,but the patient had normal female external genitalia and streaky gonads,with no genital virilism.Different tissues in the same TS individual may exhibit different ratios of mosaicism.The gonadal determination and differentiation of mosaic TS are primarily dependent on the predominant cell line in the gonads.CONCLUSION In TS patients with virilization,it is necessary to test at least two to three tissues to search for cryptic Y material.

Identification of cultured male epidermaI allografts by detecting Y chromosome DNA fragments in female burn victims

The existence of cultured male epidermal allografts in 14 bioptic samples of 9 female burned cases was identified by detecting Y chromosome DNA fragments with polymerase chain reaction (PCR). Y chromosome DNA fragments were found in all the samples and the longest case of allograft survival was detected in a 92nd-day sample. This suggests that the survival time of cultured human epidermal allografts on the wounds is longer than those of non-cultured ones.

Multiplex PCR Screening of Y Chromosome Microdeletions in Azoospermic Patients

Objective To develop a multiplex PCR protocol for routine screening of microdeletions on the Y chromosome Methods Five multiplex sets were established and Y chromosome microdeletions screening were carried out in 26 azoospermic men who undertook ICSI and 30 azoospermic men who undertook testicular biopsy. Results In 56 azoospermic men, 5 patients were found with AZFc/DAZ microdeletions, 2 patients were accompanied by AZFc/DAZ and AZFb/RBM1 double microdeletion, and 1 patient had only single sY153 microdeletion. Conclusion The multiplex PCR protocol presented in this study is an easy and reliable method for detecting microdeletions on the Y chromosome. Routine screening for microdeletions on the Y chromosome in azoospermic patients is essential.

SRY in an XX male does not influence random chromosome X inactivation: Cytogenetic evidence. Definition of the boundaries of the translocated Y segment through FISH and PCR-RT in a case report and review of the literature

We report a case of an SRY positive XX male. The phenotype was completely masculinised except for the reduced facial hair;testes were small, and azoospermia was present. The patient’s metaphases, coloured with acridine-orange to reveal the late replicating X chromosome, were sequentially hybridised with SRY and X centromeric probes: a random X chromosome inactivation pattern (XCIP) was present, with SRY present about half the time on both the active X and the inactive X. The most likely hypothesis is that the translocated SRY gene escaped inactivation as part of the entire X Pseudo Autosomal telomeric Region 1 (PAR 1). This hypothesis can explain the masculine phenotype, which would be incompatible with a halved expression of SRY. Review of the literature about the association of 46, XX males with a specific XCI pattern is made. The analysis of region AZF and QF-PCR for Y polymorphic loci allowed us to define the boundaries of the translocated Y segment as restricted to the region around the SRY locus. Chromosomal fragility analysis, using SCE (Sister Chromatid Exchanges), ruled out chromosomal fragility as a predisposing factor in the proband’s father;in addition, no chromosome Y polymorphic variant (inversion, Y qh +/﹣), was present in the proband’s father. However, like the AZF region c microdeletions and PRKX/PRKY translocation XX males, a particular Y haplotype could be also in this case a predisposing factor.

LYMPHOCYTE CHROMOSOME SURVEY IN 80 PATIENTS WITH RETINOBLASTOMA

Cytogenetic analysis of eight cases of retinoblastoma patients was carried out to determine the occurrence of chromosome aberrations and to identify consistently associated clinical abnormalities. Among the 80 cases, 55 cases were unilateral,25 cases were bilateral, seventy patients had a positive family history of Rb in 10 families. Normal chromosomes Were found in 70 patients. Ten patients showed abnormal karyotypes: two cases of 13q deletion, one case of mosaicism of 13q deletion, one case of translocation between chromosomes 13 and 15 with the interstitial deletion of 13q, one case of 47, xxy, three cases of pericentric inversion of heteromorphic region of chromosome 9, two cases of pericentirc inversion of chromosome Y. The patient who had the translocation between 13 and 5 with 13q deletion was found to have the characteristic midfacial appearance associated with 13q-deletion syndrome.

Genetic Structure of Cartagena de Indias Population Using Hypervariable Markers of Y Chromosome

Ethnicity has been associated with the incidence of diseases and consequently it is a cornerstone in medical genetic studies. It is mainly important in admixture populations, where the population stratification can produce spurious results that lead to erroneous conclusions. Consequently, population stratification has become one of the most important confounding factors in population-based genetic association studies, especially in Latino populations. Cartagena de Indias is a cosmopolitan city with dissimilar ancestry proportions due to recent miscegenation. This population mainly exhibits African and Amerindian matrilineal ancestries. Nevertheless, important asymmetries in the paternal genetic history related to the complex patterns of migration in the colonial period increase the male genetic diversity in this population. As a result of this recent admixture, population stratification has arisen, where each subpopulation is not equally represented. Consequently, the allele differences between cases and controls could be related with different frequencies among different population strata rather than the association of the genes with the disease. In order to define the patrilineal substructure of the Cartagena’s population, a total of 130 unrelated men were ancestrally studied using 15 Y-STR loci routinely employed in anthropological, forensic and population genetics. Our results show that Cartagena is an admixture population consisting of European (80%), Amerindian (10%) and African ancestries (10%), which are represented by haplogroups R1b and I2a (xI2a1), Q-M242/Q-M3, and E1b1a/E1b1b, respectively. Complex genetic patterns found in Cartagena’s population emphasize the importance to know the genetic variation in order to diminish the inconsistence for future genetic association studies. In addition, our findings illustrate the complex genetic background of Cartagena population and reinforce the need to encompass more geographic regions to generate more robust data for anthropological and forensic applications.

Presence of G84E Allelic Heterogeneity of the European Prostate Cancer SNP Mutation of HOX13B-G84E Associated with the European R-Haplogroup of Y-Chromosome and Absence of Gene Flow into Moroccans Patients

SNP mutations in the HOXB13 gene associated with prostate cancer were determined in Moroccans prostate cancer patients (PCa). All PCa SNP mutations were new and belong to the SNP point-mutations located on the stop codon of HOXB13 exon 1 and 2 located in chromosome 17. The five mutations and their frequencies were as follows: rs1197613952 (12%), rs1597934612 (4%), rs1597933874 (4%), rs1597933837 (4%) and rs867793282 (4%). The European HOXB13-G84E (rs138213197) PCa mutation was not detected among Moroccan patients. The Y-chromosome genealogical haplotypes of the Western European (R1b1b2-M2G9) and the Eastern European (R191a-M-17) were not observed in Moroccans PCa patients. The patients have their own haplotypes E1b1 and J with a frequency of 55 and 35%, respectively. The results of the SNP mutations in the HOXB13, the absence of the HOXB13-G84E of the European in the Moroccans PCa patients, the absence of the European-lineage haplogroups (R1a1a-M17 and R1b1b2-M269) and the presence of E1b1b and J in Moroccans PCa patients would clearly indicate the absence of gene flow from European to Moroccans gene pool.

等臂双着丝粒Y染色体胎儿的产前诊断、遗传咨询与随访

目的分析5例等臂双着丝粒Y染色体[idic(Y)]胎儿的产前诊断、遗传咨询与随访结果,为idic(Y)胎儿的临床处理提供参考依据。方法选择2018年1月至2022年8月7347例有产前诊断指征的孕妇,采用常规G显带核型及染色体微阵列分析(CMA)技术检测胎儿羊水,并用荧光原位杂交(FISH)技术验证,亲代染色体核型溯源检测。遗传咨询后跟踪随访妊娠结局。结果共诊断新发的idic(Y)胎儿5例,其中例1胎儿为单纯的idic(Yq),例2~5均为idic(Yq)与X单体的嵌合体。产前超声提示5例胎儿均为男性,除例1胎儿伴双侧马蹄内翻足可能外,其余4例均未见明显结构畸形。结合超声结果并予以个性化咨询后,例1~2选择继续妊娠,例3~5均终止妊娠。随访例1患儿至4周岁,足内翻手术效果良好,轻度发育迟缓经康复训练后好转;随访例2患儿至2周岁,暂未见异常表型;例3已再次受孕并分娩1名健康女婴;例4~5仍在备孕中。结论细胞与分子遗传学技术的联合应用有助于产前诊断idic(Y)胎儿,合理的遗传咨询及长期随访可为其后续的临床诊疗提供重要依据。

Y染色体微缺失检测试剂盒行业标准的建立

目的建立Y染色体微缺失检测试剂盒行业标准。方法选择9个厂家的Y染色体微缺失检测试剂盒,统一发放Y染色体微缺失检测参考品,按照拟定的行业标准,对外观、检测限、阳性参考品符合率、阴性参考品符合率和重复性项目进行验证。结果8个试剂盒的全部项目的检测结果均满足要求。检测限和阳性参考品符合率项目中,仅试剂盒8未检出AZFa微缺失,不满足要求。结论大部分验证结果均能满足拟定行标中的要求,表明行业标准各指标具有一定的合理性,可操作性强。Y染色体微缺失检测试剂盒行业标准的建立将有助于规范这类试剂盒发展,提升质量,并为监管提供技术支持。

贵州苗族非梗阻性无精男性3例的Y染色体微缺失及致病候选基因

目的研究贵州苗族无精症男性的Y染色体微缺失和致病候选基因突变。方法本研究招募苗族非梗阻性无精症男性3人,使用目标区域捕获测序及全外显子测序,分析注释到相关基因区域,解析苗族无精症男性的Y染色体微缺失及致病候选位点。结果3例苗族非梗阻性无精症患者中未发现Y染色体微缺失位点。全外显子测序结果发现USP9Y、CFTR、ZMYND15、DNAH1的突变位点,可能是苗族非梗阻性无精症的候选致病突变。结论贵州苗族男性Y染色体微缺失阴性的非梗阻性无精症可能具有特异的基因致病突变位点,在男性不育研究及临床中应引起关注。

Y-chromosomal microdeletions and partial deletions of the Azoospermia Factor c(AZFc)region in normozoospermic,severe oligozoospermic and azoospermic men in Sri Lanka

Aim： To assess for the first time the occurrence of Y chromosomal microdeletions and partial deletions of the Azoospermia Factor c （AZFc） region in Sri Lankan men and to correlate them with clinical parameters. Methods： In a retrospective study, we analyzed 96 infertile men （78 with non-obstructive azoospermia） and 87 controls with normal spermatogenesis. AZFa, AZFb, AZFc and partial deletions within the AZFc region were analyzed by multiplex polymerase chain reaction （PCR） according to established protocols. Results： No AZFa, AZFb or AZFc deletions were found in the control group. Seven patients in the group of infertile men were found to have deletions as following： one AZFa, two AZFc, two AZFbc and two AZFabc. The relative distribution of these patterns was significantly different compared with that found in the German population. Extension analysis confirmed that the deletions occurred according to the current pathogenic model, gr/gr deletions were found to be equally present both in the patients （n = 4） and in the control group （n = 4）. One b2/b3 deletion was found in the patient group. Conclusion： These results suggest that the frequency and pattern of microdeletions of the Y chromosome in Sri Lankan men are similar to those found in other populations and confirm that gr/gr deletions are not sufficient to cause spermatogenetic failure. （Asian J Androl 2006 Jan; 8： 39-44）

Chromosomal disorders and male infertility

Infertility in humans is surprisingly common occurring in approximately 15% of the population wishing to start a family. Despite this, the molecular and genetic factors underlying the cause of infertility remain largely undiscovered. Nevertheless, more and more genetic factors associated with infertility are being identified. This review will focus on our current understanding of the chromosomal basis of male infertility specifically： chromosomal aneuploidy, structural and numerical karyotype abnormalities and Y chromosomal microdeletions. Chromosomal aneuploidy is the leading cause of pregnancy loss and developmental disabilities in humans. Aneuploidy is predominantly maternal in origin, but concerns have been raised regarding the safety of intracytoplasmic sperm injection as infertile men have significantly higher levels of sperm aneuploidy compared to their fertile counterparts. Males with numerical or structural karyotype abnormalities are also at an increased risk of producing aneuploid sperm. Our current understanding of how sperm aneuploidy translates to embryo aneuploidy will be reviewed, as well as the application of preimplantation genetic diagnosis （PGD） in such cases. Clinical recommendations where possible will be made, as well as discussion of the use of emerging array technology in PGD and its potential applications in male infertility.