Chromosome Haplogroups Research Articles

Y chromosome haplogroups: a correlation with testicular dysgenesis syndrome?

Testicular dysgenesis syndrome encompasses low sperm quality, hypospadias, cryptorchidism and testicular cancer. Epidemiological studies and genetic data from familial cases suggest that testicular dysgenesis syndrome has a common etiology. The Y chromosome is known to encode genes that are involved in germ cell development or maintenance. We have therefore investigated if different classes of Y chromosomes in the general population (Y chromosome haplogroups) are associated with aspects of the testicular dysgenesis syndrome. We defined the Y chromosome haplogroups in individuals from different European counties who presented with either (i) oligo- or azoospermia associated with a Y chromosome microdeletion, (ii) unexplained reduced sperm counts (<20 x 10(6)/ml) or (iii) testicular cancer. We failed to find Y chromosome haplotype associations with either microdeletion formation or testicular cancer. However, in a study of the Danish population, we found that a specific Y chromosome haplogroup (hg26) is significantly overrepresented in men with unexplained reduced sperm counts compared with a Danish control population. The factors encoded by genes on this class of Y chromosome may be particularly susceptible to environmental influences that cause testicular dysgenesis syndrome. Our current data highlight the need for further analyses of clinically well-defined patient groups from a wide range of ethnic and geographic origins.

The Human Y Chromosome Haplogroup Tree: Nomenclature and Phylogeography of Its Major Divisions

▪ Abstract In this review we discuss the recent construction of a highly resolved tree of the nonrecombining portion of the Y chromosome (NRY), and the development of a cladistic nomenclatural system to name the resulting haplogroups. This phylogenetic gene tree comprises 18 major haplogroups that are defined by 48 binary polymorphisms. We also present results from a phylogeographic analysis of NRY haplogroups in a global sample of 2007 males, as well as from a regional study focusing on Siberia (n = 902). We use the following statistical techniques to explicate our presentation: analysis of molecular variance, multidimensional scaling, comparative measures of genetic diversity, and phylogeography-based frequency distributions. Our global results, based on the 18 major haplogroups, are similar to those from previous analyses employing additional markers and support the hypothesis of an African origin of human NRY diversity. Although Africa exhibits greater divergence among haplogroups, Asia contains the largest number of major haplogroups (N = 15). The multidimensional scaling analysis plot indicates that the Americas, Africa, and East Asia are outliers, whereas the rest of the world forms a large central cluster. According to our new global-level analysis of molecular variance, 43% of the total variance of NRY haplogroups is attributable to differences among populations (i.e., ΦST = 0.43). The Siberian regional analysis of 62 binary markers exhibits nonrandom associations between geographically restricted NRY haplogroups and language families. We conclude with a list of typing recommendations for laboratories that wish to use the Y chromosome as a tool to investigate questions of anthropological interest.

Y chromosome haplogroups in autistic subjects.

The male to female ratio in autism is 4:1 in the global autistic population, but increases to 23:1 in autistic subjects without physical or brain abnormalities.(1) Despite this well-recognised gender difference, male predisposition to autistic disorder remains unexplained and the role of sex chromosomes is still debated. Numerical and structural abnormalities of the sex chromosomes are among the most frequently reported chromosomal disorders associated with autism. However, genome scans have failed to detect linkage on the X chromosome(2,3,4) and this approach cannot study the non-recombining region of the Y chromosome. In this study, we searched for a specific Y chromosome effect in autistic subjects. Using informative Y-polymorphic markers, the Y chromosome haplotypes of 111 autistic subjects from France, Sweden and Norway were defined and compared with relevant control populations. No significant difference in Y-haplotype distribution between the affected and control groups was observed. Although this study cannot exclude the presence of a Y susceptibility gene, our results are not suggestive of a Y chromosome effect in autism.

Identification of a Y chromosome haplogroup associated with reduced sperm counts.

In man, infertility is associated with microdeletions of specific regions of the long arm of the Y chromosome. This indicates that factors encoded by the Y chromosome are necessary for spermatogenesis. However, the majority of men with either idiopathic azoospermia or oligozoospermia have grossly intact Y chromosomes and the underlying causes of their infertility are unknown. We hypothesized that some of these individuals may carry other rearrangements or sequence variants on the non-recombining region of the Y chromosome that may be associated with reduced spermatogenesis. To test this hypothesis, we typed the Y chromosome in a group of Danish men with known sperm counts and compared the haplotype distribution with that of a group of unselected Danish males. We found that one class of Y chromosome, referred to as haplogroup 26+, was significantly overrepresented (27.9%; P < 0.001) in the group of men with either idiopathic oligozoospermia (defined as <20 x 10(6 )sperm/ml) or azoospermia compared to the control Danish male population (4.6%). This study defines, for the first time, a class of Y chromosome that is at risk for infertility in a European population. This observation suggests that selection may be indeed active on the Y chromosome, at least in the Danish population, raising the possibility that it could alter the pattern of Y chromosome haplotype distribution in the general population.

The relationship between Y chromosome DNA haplotypes and Y chromosome deletions leading to male infertility.

Microdeletions on the short arm of the Y chromosome have defined three non-overlapping regions (AZFa, b, c) recurrently deleted among infertile males. These regions contain several genes or gene families involved in male germ-cell development and maintenance. Even though a meiotic origin for these microdeletions is assumed, the mechanisms and causes leading to microdeletion formation are largely unknown. In order to assess whether some Y chromosome groups (or haplogroups) are predisposed to, or protected against, deletion formation during male meiosis, we have defined and compared Y chromosome haplogroup distribution in a group of infertile/subfertile males harbouring Yq deletions and in a relevant Northwestern European control population. Our analyses suggest that Y chromosome deletion formation is, at least in the study populations, a stochastic event independent of the Y chromosome background on which they arise and may be caused by other genetic and/or environmental factors.

Y chromosome analysis reveals a sharp genetic boundary in the Carpathian region.

Nine single nucleotide (SNP) or indel binary polymorphisms were used to determine the frequencies and phylogenetic relationships of 12 Y chromosomal haplogroups in 289 males from Romania and the Republic of Moldova. Our data indicated a low but not null rate of the homoplasic appearance of the DYZ3 (-) allelic state. All other markers confirmed the previously proposed phylogeny. Based on the affinities between populations in terms of haplogroup frequencies, this work identified the geographical region of the Carpathians as a break point in the gene geography of Eastern Central Europe, providing a finer definition of one of the possible sharp genetic changes between Western and Eastern Europe.

Male Infertility and the Y Chromosome

Although it has been established since the 1970s thatdeletions of the long arm of the Y chromosome are as-sociated with spermatogenic failure, only in the last fewyears have these regions been described at the molecularlevel. In parallel, Y-linked genes and gene families thatmay explain the phenotypes of men carrying these de-letions have been identified. The first association be-tween spermatogenic failure and an underlying geneticcause was demonstrated by Tiepolo and Zuffardi (1976)in a report of six azoospermic patients carrying micro-scopically detectable deletions of the distal portion ofYq. In four patients, the deletion was de novo—that is,their fathers were tested and were found to carry intactY chromosomes. On this basis, Tiepolo and Zuffardi(1976) proposed the existence of a spermatogenesis fac-tor, called the “azoospermia factor” (AZF), encoded bya gene on distal Yq. However, the assumption that AZFrepresented a single Y-linked gene was overturned whenVogt et al. (1996) observed that Y chromosome micro-deletions follow a certain deletion pattern, with threerecurrently deleted nonoverlapping subregions in prox-imal, middle, and distal Yq11, designated “AZFa,”“AZFb,” and “AZFc,” respectively. In addition, it be-came clear that these deletions were not exclusively as-sociated with azoospermia (Reijo et al. 1996