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.

Genetic Polymorphism of 38 Y-chromosome Short Tandem Repeats in Beijing Han Population from China

Objective:To investigate 38 Y-chromosome short tandem repeat(Y-STR)genetic polymorphisms in Beijing Han and analyze the genetic distance with neighboring or linguistically similar populations.Materials and Methods:In the study,we selected 531 unrelated male individuals of Beijing Han,and the results were statistically analyzed by testing with GSTAR™41Y reagents.Results:The allele peak heights were balanced among the Y loci,the amplified fragment ranged from 100 to 500 bps.A total of 531 haplotypes were detected in 531 samples.Eight null genotypes were observed on locus DYS448.One and three double alleles were observed on single-copy locus DYS576 and DYS19,respectively.DYS385 a/b,DYF387S1 a/b,and DYS527 a/b were more common in double copies,but 3,13,and 11 triple alleles were detected,respectively.The gene diversity values of Y-STRs except DYS391,DYS438,and DYS645 were>0.5.Twenty-seven Y-STRs of Beijing Han population were selected for genetic distance comparison with 17 populations including Changchun Han,with Rst values ranging from 0.0002 to 0.1703.Conclusion:The 38 Y-STRs in this study have strong male lineage identification ability and have great potential for individual identification,kinship identification,Y-STR database construction,and genetic relationship research.

Y-chromosome evidence for no independent origin of modern human in China

East Asia is one of the few regions in the world where a large number of human fossils have been unearthed. The continuity of hominid fossils in East Asia, particularly in China has been presented as strong evidence supporting an independent origin of modern humans in this area. To search for such evidence of a possible independent origin of modern humans in China, a total of 9988 male individuals were sampled across China. Three Y-chromosome biallelic markers (M89, M130 and YAP), which were located at the non-re-combinant region of Y-chromosome, were typed among the samples. Our result showed that all the individuals carry a mutation at one of the three loci. The three mutations (M89T, M130T, YAP+) coalesce to another mutation (M168T), which was originally derived from Africa about 31000 to 79000 years ago. In other words, all Y-chromosome samples from China, with no exception, were originally derived from a lineage of African origin. Hence, we conclude that even a very minor contribution of in situ hominid origin in China cannot be supported by the Y-chromosome evidence.

Y-chromosome haplotype distribution in Han Chinese populations and modern human origin in East Asians

We investigated the distribution of Y-chromosome haplotype using 19 Y-SNPs in Han Chinese populations from 22 provinces of China. Our data indicate distinctive patterns of Y chromosome between southern and northern Han Chinese populations. The southern populations are much more polymorphic than northern populations. The latter has only a subset of the southern haplotypes. This result confirms the genetic difference observed between southern and northern ethnic populations in East Asia. It supports the hypothesis that the first settlement of modern hu-mans of African origin occurred in the southern part of East Asia during the last Ice Age, and a northward migration led to the peopling of northern China.

Y-chromosome microdeletions in nonobstructive azoospermia and severe oligozoospermia

The aim of the present work was to present the outcomes of the patients with Y-chromosome microdeletions treated by intracytoplasmic sperm injection （ICSI）, either using fresh （TESE） or frozen-thawed （TESE-C） testicular sperm and ejaculated sperm （EJAC）. The originality of this work resides in the comparisons between the different types of Y-microdeletions （AZFa, AZFb, and AZFc） and treatments, with detailed demographic, stimulation, embryological, clinical, and newborn （NB） outcomes. Of 125 patients with Y-microdeletions, 33 patients presented severe oligozoospermia （18 performed ICSI with ejaculated sperm） and 92 secretory azoospermia （65 went for TESE with 40 having successful sperm retrieval and performed ICSI）. There were 51 TESE treatment cycles and 43 TESE-C treatment cycles, with a birth of 19 NB （2 in AZFa/TESE-C, 12 in AZFc/TESE, and 5 in AZFc/TESE-C）. Of the 29 EJAC cycles, there was a birth of 8 NB （in AZFc）. In TESE and EJAC cycles, there were no significant differences in embryological and clinical parameters. In TESE-C cycles, there was a significant lower oocyte maturity rate, embryo cleavage rate and mean number of embryos transferred in AZFb, and a higher mean number of oocytes and lower fertilization rate in AZFc. In conclusion, although patients with AZFc microdeletions presented a high testicular sperm recovery rate and acceptable clinical outcomes, cases with AZFa and AZFb microdeletions presented a poor prognosis. Due to the reported heredity of microdeletions, patients should be informed about the infertile consequences on NB and the possibility of using preimplantation genetic diagnosis for female sex selection.

Mutation Studies of 31 Highly Mutated Y-chromosomal Short Tandem Repeat Systems in the Han Population of Northern China

A six-color fluorescent multiplex amplification system for 31 Y-chromosomal short tandem repeats(Y-STRs)(DYS19,DYS390,DYS391,DYF399S1,DYF404S1,DYS439,DYS444,DYS449,DYS452,DYS456,DYS458,DYS460,DYS481,DYS508,DYS513,DYS516,DYS518,DYS543,DYS547,DYS549,DYS552,DYS557,DYS570,DYS576,DYS612,DYS622,DYS626,DYS627,DYS630,DYS635,and Y-GATA-A10)was developed for investigating the mutation rates of 31 highly mutated Y-STR genes in the Han population of northern China.The mutation rates of the 31 highly mutated Y-STRs were calculated using the father-son pair study method after typing 526 Northern Han father-son pairs with this system.Statistically,148 Y-STR mutations were found,with mutation rates ranging from 0(95%confidence interval[CI]0 to 9.0×10^(−3),DYS622)to 7.0×10^(−2)(95%CI 5.1×10^(−2)to 9.7×10^(−2),DYF399S1).Out of these,126 father-son pairs were successfully identified,with a distinction rate of 24.0%(95%CI 20.4%-27.9%).The ability of the 31 highly mutated Y-STRs to distinguish closely related males from the same paternal lineage in the Northern Han population is extremely valuable for criminal investigations and other purposes.

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.

"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.

Outcomes for offspring of men having ICSI for male factor infertility

Since the introduction of intracytoplasmic sperm injection （ICSI） using single sperm isolated from testicular tissue in men with obstructive and non-obstructive azoospermia, or using ejaculated sperm in those with poor semen quality, there have been concerns that this might have adverse effects on the offspring compared to conventional in vitrofertilisation （IVF） and natural conceptions. ICSI is done for reasons other than male factor infertility, and on the whole has not been shown to have any more negative effects than those seen with IVF. There have however, been very few studies of ICSI with a focus on, or large enough numbers to examine, the specific outcomes associated with male factor infertility. From the limited information available in relation to the source of the sperm and aetiology of infertility in the presence of ICSI, there appears to be no increased risk of congenital malformations. There is, however, a small increase in both de novoand inherited chromosome abnormalities. In terms of growth and neurodevelopment, there are very few studies, and so far, no adverse outcomes have been found in young children whose fathers have a sperm defect. The origin of the sperm used in ICSI does not have a major influence on the early life outcomes for the offspring, but transgenerational and epigenetic effects remain unknown. When the male factor infertility is known or thought to be due to a Y-chromosome deletion, this information should be given to the young male offspring at a time that will ensure his own reproductive health and plans are optimized.

Studies on microdeletion of genes relevant to spermatoge nesis in infertile men

Objective: To study the relationship between relevant gene micro-deletion and spermatogenesis in infertile men. Methods: To analyze the relevant genes of the Y-chromosome and the karyotype of peripheral blood chromosome in 149 azoospermic/sever oligo-spermic infertile men and 100 normal controls by multipolymerase chain reaction (PCR). Results: Microdeletions in different gene segments of the Y-chromosome were present in 11 cases of the infertile group (7.38 %). No microdeletion in the corresponding areas was found in the controls. The incidence of abnormal karyotype in the infertile group was 14.09 % and in the controls, 2 %. In the 11 infertiles with microdeletion in different gene segments, only one had abnormal karyotype, indicating no relativity between the two. Conclusion: Microdeletion of Y-chromosome may be an important cause of male infertility.

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.

Y‑STR Kits and Y‑STR Diversity in the South African Population: A Review

The South African population consists of four ethnic groups,i.e.,Blacks,Coloreds,Indians,and Whites,and is considered the most diverse conglomeration of humans.In addition to autosomal short tandem repeat(STR)variation,an important tool to study population diversity is Y-chromosome(Y)-STR analysis.Y-STRs aid in forensic investigations and provide essential data about paternal lineage origins.Y-STR kits consisting of an array of stable and rapidly mutating markers offer crucial information on a given population’s genetic and haplotype diversity.This review discusses the development of Y-STR kits over the years and highlights some prominent Y-STR studies conducted on the South African population.The earliest Y-STR kit developed was the Y-PLEX™6,with the most recent being the UniQTyper™Y-10 Multiplex.The South African population studies show varying data,with the“minimal haplotype”having low discrimination capacity among the ethnic groups and the UniQTyper™Y-10 showing high genetic diversity among the ethnic groups of the country.There is a dearth of Y-STR studies on the South African population.With the advent of new Y-STR kits with increased discriminatory markers,additional studies are required to represent the South African population in the Y-STR databases.Considering the diversity of the South African population,establishment of a local/regional population database would be beneficial.In addition,data on the origins and prevalence of mutations and silent alleles should be obtained from STR datasets generated during kinship investigations(specifically,parentage tests)so that detailed information about the frequencies of mutations,silent alleles,and uniparental disomy in the South African population at Y STR loci can be estimated.