On the use of dense SNP marker data for the identification of distant relative pairs.

There has been recent interest in the exploitation of readily available dense genome scan marker data for the identification of relatives. However, there are conflicting findings on how informative these data are in practical situations and, in particular, sets of thinned markers are often used with no concrete justification for the chosen spacing. We explore the potential usefulness of dense single nucleotide polymorphism (SNP) arrays for this application with a focus on inferring distant relative pairs. We distinguish between relationship estimation, as defined by a pedigree connecting the two individuals of interest, and estimation of general relatedness as would be provided by a kinship coefficient or a coefficient of relatedness. Since our primary interest is in the former case, we adopt a pedigree likelihood approach. We consider the effect of additional SNPs and data on an additional typed relative, together with choice of that relative, on relationship inference. We also consider the effect of linkage disequilibrium. When overall relatedness, rather than the specific relationship, would suffice, we propose an approximate approach that is easy to implement and appears to compete well with a popular moment-based estimator and a recent maximum likelihood approach based on chromosomal sharing. We conclude that denser marker data are more informative for distant relatives. However, linkage disequilibrium cannot be ignored and will be the main limiting factor for applications to real data.

Isolation and characterization of a candidate gene for Norrie disease.

Previous analysis has refined the location of the gene for Norrie disease, a severe, X-linked, recessive neurodevelopmental disorder, to a yeast artificial chromosome subfragment of 160 kilobases (kb). This fragment was used to screen cDNA libraries from human fetal and adult retina. As a result, we have identified an evolutionarily conserved cDNA, which is expressed in fetal and adult brain and encodes a predicted protein of 133 amino acids. The cDNA detects genomic sequences which span a maximum of 50 kb, and which are partly deleted in several typical Norrie disease patients. An EcoRI polymorphism with a calculated heterozygosity value of 43% was observed. The locus identified is a strong candidate for the Norrie disease gene.

Localization of DNA sequences required for human centromere function through an analysis of rearranged Y chromosomes.

We have localized the DNA sequences required for mitotic centromere function on the human Y chromosome. Analysis of 33 rearranged Y chromosomes allowed the centromere to be placed in interval 8 of a 24-interval deletion map. Although this interval is polymorphic in size, it can be as small as approximately 500kb. It contains alphoid satellite DNA and approximately 300kb of adjacent Yp sequences. Chromosomes with rearrangements in this region were analysed in detail. Two translocation chromosomes and one monocentric isochromosome had breakpoints within the alphoid array. Of 12 suppressed Y centromeres on translocation chromosomes and dicentric isochromosomes that were also analysed two showed deletions one of which only removed alphoid DNA. These results indicate that alphoid DNA is a functional part of the Y chromosome centromere.

Copy number variation on the human Y chromosome.

The Y chromosome is unusual in being constitutively haploid and escaping recombination for most of its length. This has led to a correspondingly unusual genomic landscape, rich in segmental duplications, which provide a potent environment for the generation of copy number variation (CNV). Interest in the chromosome comes from diverse fields, including infertility research, population genetics, forensics, and genealogy. Together with inclusion in more systematic surveys, this has led to the ascertainment of a variety of CNVs. Assessment in the context of the well-resolved Y phylogeny allows their mutational history to be deciphered and an estimation of mutation rate. The functional consequences of variants are moderated by the specialization of the chromosome and the presence of functionally equivalent X-chromosomal homologues for some genes. However, deletions of the AZFa, b, and c regions cause impaired spermatogenesis, while partial deletions and duplications within these regions, and deletions and duplications elsewhere, may be selectively neutral or have subtle phenotypes.

A selective difference between human Y-chromosomal DNA haplotypes.

DNA analysis is making a valuable contribution to the understanding of human evolution [1]. Much attention has focused on mitochondrial DNA (mtDNA) [2] and the Y chromosome [3] [4], both of which escape recombination and so provide information on maternal and paternal lineages, respectively. It is often assumed that the polymorphisms observed at loci on mtDNA and the Y chromosome are selectively neutral and, therefore, that existing patterns of molecular variation can be used to deduce the histories of populations in terms of drift, population movements, and cultural practices. The coalescence of the molecular phylogenies of mtDNA and the Y chromosome to recent common ancestors in Africa [5] [6], for example, has been taken to reflect a recent origin of modern human populations in Africa. An alternative explanation, though, could be the recent selective spread of mtDNA and Y chromosome haplotypes from Africa in a population with a more complex history [7]. It is therefore important to establish whether there are selective differences between classes (haplotypes) of mtDNA and Y chromosomes and, if so, whether these differences could have been sufficient to influence the distributions of haplotypes in existing populations. A precedent for this hypothesis has been established for mtDNA in that one mtDNA background increases susceptibility to Leber hereditary optic neuropathy [8]. Although studies of nucleotide diversity in global samples of Y chromosomes have suggested an absence of recent selective sweeps or bottlenecks [9], selection may, in principle, be very important for the Y chromosome because it carries several loci affecting male fertility [10] [11] and as many as 5% of males are infertile [11] [12]. Here, we show that one class of infertile males, PRKX/PRKY translocation XX males, arises predominantly on a particular Y haplotypic background. Selection is, therefore, acting on Y haplotype distributions in the population.

In the name of the father: surnames and genetics.

Hereditary surnames contain information about relatedness within populations. They have been used as crude indicators of population structure and migration events, and to subdivide samples for epidemiological purposes. In societies that use patrilineal surnames, a surname should correlate with a type of Y chromosome, provided certain assumptions are met. Recent studies involving Y-chromosomal haplotyping and surname analysis are promising and indicate that genealogists of the future could be turning to records written in DNA, as well as in paper archives, to solve their problems.

Fathers and sons: the Y chromosome and human evolution.

It should be possible to use Y chromosome DNA polymorphisms to trace paternal lineages for evolutionary and other studies, but progress in these areas has been slow because it has been difficult to find suitable markers. However, it is now possible to use selected, slowly evolving polymorphisms to draw a rudimentary Y chromosome tree, while more rapidly evolving polymorphisms allow most independent Y chromosomes to be distinguished. Different populations often have characteristically different Y chromosomes, and Y chromosome studies are soon likely to make a major contribution to our understanding of the origins of modern humans.

New uses for new haplotypes the human Y chromosome, disease and selection.

Recent discoveries of many new genes have made it clear that there is more to the human Y chromosome than a heap of evolutionary debris, hooked up to a sequence that happens to endow its bearer with testes. Coupled with the recent development of new polymorphic markers on the Y, making it the best-characterized haplotypic system in the genome, this gives us new opportunities to assess its role in disease and selection, through association studies with phenotypes such as infertility and cancers. However, the peculiar genetics of this bizarre chromosome means that we should interpret such studies particularly cautiously.

Divergent outcomes of intrachromosomal recombination on the human Y chromosome: male infertility and recurrent polymorphism.

The Y chromosome provides a unique opportunity to study mutational processes within the human genome, decoupled from the confounding effects of interchromosomal recombination. It has been suggested that the increased density of certain dispersed repeats on the Y could account for the high frequency of causative microdeletions relative to single nucleotide mutations in infertile males. Previously we localised breakpoints of an AZFa microdeletion close to two highly homologous complete human endogenous retroviral sequences (HERV), separated by 700 kb. Here we show, by sequencing across the breakpoint, that the microdeletion occurs in register within a highly homologous segment between the HERVs. Furthermore, we show that recurrent double crossovers have occurred between the HERVs, resulting in the loss of a 1.5 kb insertion from one HERV, an event underlying the first ever Y chromosomal polymorphism described, the 12f2 deletion. This event produces a substantially longer segment of absolute homology and as such may result in increased predisposition to further intrachromosomal recombination. Intrachromosomal crosstalk between these two HERV sequences can thus result in either homogenizing sequence conversion or a microdeletion causing male infertility. This represents a major subclass of AZFa deletions.

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.

Patterns of inter- and intra-group genetic diversity in the Vlax Roma as revealed by Y chromosome and mitochondrial DNA lineages.

Previous genetic studies, supported by linguistic and historical data, suggest that the European Roma, comprising a large number of socially divergent endogamous groups, may be a complex conglomerate of founder populations. The boundaries and characteristics of such founder populations and their relationship to the currently existing social stratification of the Roma have not been investigated. This study is an attempt to address the issues of common vs independent origins and the history of population fissioning in three Romani groups that are well defined and strictly endogamous relative to each other. According to linguistic classifications, these groups belong to the Vlax Roma, who account for a large proportion of the European Romani population. The analysis of mtDNA sequence variation has shown that a large proportion of maternal lineages are common to the three groups. The study of a set of Y chromosome markers of different mutability has revealed that over 70% of males belong to a single lineage that appears unique to the Roma and presents with closely related microsatellite haplotypes and MSY1 codes. The study unambiguously points to the common origins of the three Vlax groups and the recent nature of the population fissions, and provides preliminary evidence of limited genetic diversity in this young founder population.

Y-chromosomal SNP haplotype diversity in forensic analysis.

Many Y-chromosomal single nucleotide polymorphisms (SNPs) are now available. The haplogroups which they define are highly non-randomly distributed among populations, and could contribute much to population-of-origin prediction from DNA. If this potential is to be exploited in forensic analysis, high-throughput, parallel methods are required for Y-SNP typing.

DNA Commission of the International Society of Forensic Genetics: recommendations on forensic analysis using Y-chromosome STRs.

During the past few years, the DNA Commission of the International Society of Forensic Genetics has published a series of documents providing guidelines and recommendations concerning the application of DNA polymorphisms to the problems of human identification. This latest report addresses a relatively new area - namely, Y-chromosome polymorphisms, with particular emphasis on short tandem repeats (STRs). This report addresses nomenclature, use of allelic ladders, population genetics and reporting methods.

Online reference database of European Y-chromosomal short tandem repeat (STR) haplotypes.

The reference database of highly informative Y-chromosomal short tandem repeat (STR) haplotypes (YHRD), available online at http://ystr.charite.de, represents the largest collection of male-specific genetic profiles currently available for European populations. By September 2000, YHRD contained 4688 9-locus (so-called "minimal") haplotypes, 40% of which have been extended further to include two additional loci. Establishment of YHRD has been facilitated by the joint efforts of 31 forensic and anthropological institutions. All contributing laboratories have agreed to standardize their Y-STR haplotyping protocols and to participate in a quality assurance exercise prior to the inclusion of any data. In view of its collaborative character, and in order to put YHRD to its intended use, viz. the support of forensic caseworkers in their routine decision-making process, the database has been made publicly available via the Internet in February 2000. Online searches for complete or partial Y-STR haplotypes from evidentiary or non-probative material can be performed on a non-commercial basis, and yield observed haplotype counts as well as extrapolated population frequency estimates. In addition, the YHRD website provides information about the quality control test, genotyping protocols, haplotype formats and informativity, population genetic analysis, literature references, and a list of contact addresses of the contributing laboratories.

A survey of long-range DNA polymorphisms on the human Y chromosome.

The human Y chromosome is poor in conventional DNA polymorphisms, and this has hindered studies of the paternal lineage. However, three large hypervariable arrays exist, and haplotyping at these loci defines two groups in Caucasian and Asian populations, reflecting the existence of two ancestral Y chromosomes. In this study, the Y was systematically surveyed for further long-range polymorphisms, by the hybridization of 33 probes to SfiI digests of DNA from males of different ethnic origins and from the two groups. Five novel polymorphisms were identified, all showing variability consistent with a changing number of tandem repeats within an array. A search for conventional polymorphisms was also done, using 41 probes and the enzyme TaqI; three novel variants and one polymorphism with a frequency of 18% (n = 66) were found. The novel polymorphisms were typed in 66 Y chromosomes, including the set of 42 in which the two groups were originally defined. Known long-range and conventional polymorphisms were also extended to cover the whole set, yielding compound haplotypes comprising the states of twelve polymorphisms. This haplotyping distinguishes between all 66 chromosomes, and should distinguish between most in the population. The existence of the two groups is supported, and a third group can be defined; six of the eight members of this group are known to be from India. Twelve chromosomes do not fall into any of these groups, and are likely to be representatives of further groups.

Haploid chromosomes in molecular ecology: lessons from the human Y.

We review the potential use of haploid chromosomes in molecular ecology, using recent work on the human Y chromosome as a paradigm. Chromosomal sex-determination systems, and hence constitutively haploid chromosomes, which escape from recombination over much of their length, have evolved multiple times in the animal kingdom. In mammals, where males are the heterogametic sex, the patrilineal Y chromosome represents a paternal counterpart to mitochondrial DNA. Work on the human Y chromosome has shown it to contain the same range of polymorphic markers as the rest of the nuclear genome and these have rendered it the most informative haplotypic system in the human genome. Examples from research on the human Y chromosome are used to illustrate the common interests of anthropologists and ecologists in investigating the genetic impact of sex-specific behaviours and dispersals, as well as patterns of global diversity. We present some methodologies for extracting information from these uniquely informative yet under-utilized loci.

The Y chromosome in forensic analysis and paternity testing.

The male specificity of the human Y chromosome makes it potentially useful in forensic studies and paternity testing, and markers are now available which will allow its usefulness to be assessed in practice. However, while it can be used confidently for exclusions, the unusual properties of the Y mean that inclusions will be very difficult to make: haplotypes are confined within lineages, so population sub-structuring is a major problem, and many male relatives of a suspect will share his Y chromosome. Y haplotyping is most likely to find application in special instances, such as deficiency cases in paternity testing and in the analysis of mixtures of male and female DNA, or in combination with autosomal markers.

Hypervariable digital DNA codes for human paternal lineages: MVR-PCR at the Y-specific minisatellite, MSY1 (DYF155S1).

We describe the first haploid minisatellite, the human Y chromosome-specific locus, MSY1. It consists of an array of 48-114 AT-rich 25 bp repeats of at least five different variant types. A minisatellite variant repeat PCR (MVR-PCR) system gives Y-specific DNA codes, with a virtual heterozygosity of 99.9%, making MSY1 by far the single most variable locus on the Y. African populations contain the most diverged MSY1 structures. MSY1 is the only Y-chromosomal system where the characteristics of large numbers of mutations can be studied in detail: it provides a uniquely powerful tool both for the investigation of mutation in a haploid system, and for the dating of paternal lineages.

Y-chromosome-specific microsatellite mutation rates re-examined using a minisatellite, MSY1.

Polymorphic Y-chromosome-specific microsatellites are becoming increasingly used in evolutionary and forensic studies and, in particular, in dating the origins of Y-chromosomal lineages. Previously, haplotyping of Y chromosomes from males belonging to a set of deep-rooting pedigrees was used to estimate a conservative average Y-chromosomal microsatellite mutation rate of 2.1 x 10(-3)per locus per generation. A number of males showed multiple differences in haplotypes compared with other males within their pedigrees, and these were excluded from the calculation of this estimate, on the grounds that non-paternity was a more probable explanation than multiple mutation within a lineage. Here we reanalyse the pedigrees using an independent highly polymorphic system, the Y-specific minisatellite, MSY1. This supports the hypothesis of non-paternity where more than one microsatellite difference was observed, provides further support for the previously deduced microsatellite mutation rate and throws light on the mutation dynamics of MSY1 itself, suggesting that single-step changes are not the only mode of mutation.