Evolutionary evidence of the effect of rare variants on disease etiology.

The common disease/common variant hypothesis has been popular for describing the genetic architecture of common human diseases for several years. According to the originally stated hypothesis, one or a few common genetic variants with a large effect size control the risk of common diseases. A growing body of evidence, however, suggests that rare single-nucleotide polymorphisms (SNPs), i.e. those with a minor allele frequency of less than 5%, are also an important component of the genetic architecture of common human diseases. In this study, we analyzed the relevance of rare SNPs to the risk of common diseases from an evolutionary perspective and found that rare SNPs are more likely than common SNPs to be functional and tend to have a stronger effect size than do common SNPs. This observation, and the fact that most of the SNPs in the human genome are rare, suggests that rare SNPs are a crucial element of the genetic architecture of common human diseases. We propose that the next generation of genomic studies should focus on analyzing rare SNPs. Further, targeting patients with a family history of the disease, an extreme phenotype, or early disease onset may facilitate the detection of risk-associated rare SNPs.

Usefulness of the top-scoring pairs of genes for prediction of prostate cancer progression.

Prediction of cancer progression after radical prostatectomy is one of the most challenging problems in the management of prostate cancer. Gene-expression profiling is widely used to identify genes associated with such progression. Usually candidate genes are identified according to a gene-by-gene comparison of expression. Recent reports suggested that relative expression of a gene pair more efficiently predicts cancer progression than single-gene analysis does. The top-scoring pair (TSP) algorithm classifies phenotypes according to the relative expression of a pair of genes. We applied the TSP approach to predict, which patients would experience systemic tumor progression after radical prostatectomy. Relative expression of TPD52L2/SQLE and CEACAM1/BRCA1 gene pairs identified those patients with more than 99% specificity but relatively low sensitivity (approximately 10%). These two gene pairs were validated in three independent data sets. In addition, combining two pairs of genes improved sensitivity without compromising specificity. Functional annotation of the TSP genes showed that they cluster by a limited number of biological functions and pathways, suggesting that relatively lower expression of genes from specific pathways can predict cancer progression. In conclusion, comparative analysis of the expression of two genes may be a simple and effective classifier for prediction of prostate cancer progression. In summary, the TSP approach can be used to identify patients whose prostate cancer will progress after they undergo radical prostatectomy. Two gene pairs can predict which men would experience progression to the metastatic form of the disease. However, because our analysis was based on a relatively small number of genes, a larger study will be needed to identify the best predictors of disease outcome overall.

Cost-benefit analysis of recombination and its application for understanding of chiasma interference.

A cost-benefit analysis of recombination was undertaken. The beneficial effects of crossing-over are proportional to the frequency of recombinant offspring, while its harmful effects (errors of crossing-over leading to mutations) are proportional to the number of crossover exchanges. An equilibrium point should exist where the beneficial effects of crossing-over are balanced by its harmful effects. It is suggested that natural selection sustains a number of crossover exchanges per meiosis at the level that provides highest benefit-cost difference. Chiasma interference prevents the arising of closely located exchanges which are less effective in the production of recombinants than exchanges separated by some "interference distance". Computer simulation shows that chiasma interference increases the recombination effectiveness of the multiple crossover exchanges as compared to the case without interference.

A transgenic insertion causing cryptorchidism in mice.

A distinctive feature of gonadal maturation in mammals is the movement to an extraabdominal location. Testicular descent is a complex, multistage process whereby the embryonic gonads migrate from their initial abdominal position to the scrotum. Failure in this process results in cryptorchidism, a frequent congenital birth defect in humans. We report here a new mouse transgenic insertional mutation, cryptorchidism with white spotting (crsp). Males homozygous for crsp exhibit a high intraabdominal position of the testes, associated with complete sterility. Heterozygous males have a wild-type phenotype, and homozygous females are fertile. Surgically descended testes in crsp/crsp males show normal spermatogenesis. Using FISH and genetic analyses, the transgenic insert causing the crsp mutation has been mapped to the distal part of mouse chromosome 5. Transgene integration resulted in a 550-kb deletion located upstream of the Brca2 gene. A candidate gene encoding a novel G protein-coupled receptor (Great) with an expression pattern suggesting involvement in testicular descent has been identified.

[Variation in the relative length of chromosomes in mammalian karyotypes. Hypothesis of equalizing selection]. / Izmenchivost' otnositel'nykh dlin khromosom v kariotipakh mlekopitaiushchikh. Gipoteza vyravnivaiushchego otbora.

A hypothesis on the selective neutrality of relative lengths of karyotype chromosomes was tested. Idiograms expected based on an assumption of selective neutrality of chromosome lengths were compared with actual idiograms in more than a hundred mammalian species. The observed idiograms differed from those expected in a similar manner: in the observed idiograms, the longest chromosomes were shorter, and the shortest were longer than expected. It is suggested that karyotype chromosome variation is limited by selection against chromosome rearrangements that produce very long or very short chromosomes. An analysis of reciprocal translocations in the mouse and Drosophila showed that translocations generating chromosomes of extreme lengths were more deleterious than those generating normal-sized chromosomes. A working hypothesis was advanced stating that within-karyotype variation of chromosome lengths is accounted for by two factors: chromosome rearrangements and natural selection. Chromosome rearrangements tend to randomize relative chromosome lengths in a karyotype, whereas natural selection acts to equalize them.

Staggered clines in a hybrid zone between two chromosome races of the harvestman Gagrellopsis nodulifera (Arachnida: Opiliones).

We analyzed a hybrid zone between two chromosome races (2n = 16 and 2n = 22) of a Japanese harvestman, Gagrellopsis nodulifera Sato and Suzuki (Arachnida: Opiliones: Phalangiidae). The hybrid zone is located in the eastern part of Tottori Prefecture, western Honshu. The width of the zone is approximately 5 to 15 km. Three independent tandem fusions/fissions seem to be the main cause of the karyotypic differences between the parental races. Ten karyotypic variants were found in the hybrid zone. They differed by numbers of diploid chromosomes and trivalents detected in meiosis. In most of the collecting sites, karyotypic heterozygotes were less common than expected. A positive correlation was found between number of trivalents in a karyotype and its deficiency rate. In some sites, the deficit of heterozygous individuals was accompanied by an excess of the intermediate homozygotes. One of the three transects across the zone was studied in detail. We found that three types of single heterozygotes (2n = 17, 2n = 19 and 2n = 21) formed a series of successive, spatially separated peaks along the transect. Two types of intermediate homozygotes (2n = 18 and 2n = 20) were also spatially separated. The most parsimonious explanation of such a structure is the staggering of clines of three tandem (or Robertsonian) fusion/fission variants that differentiate the parental races caused by selection against multiple heterozygotes. Analysis of nondisjunction in single heterozygotes demonstrated that there was a strong interindividual variation in nondisjunction rate. The mean frequency of aneuploid MII in single heterozygotes was 0.10 +/- 0.03. Crossover exchanges in some critical regions of trivalents result in abnormal chromosomal configurations: chromosomes with unequal chromatids and dicentric chromosomes. Frequency of crossover-induced chromosomal abnormalities was low in single heterozygotes (approximately equal to 4%), and was unexpectedly high in the double heterozygotes (approximately equal to 15%). Selection against karyotypic heterozygotes is considered as a main evolutionary force responsible for the structuring of the hybrid zone. A positive association between diploid chromosome number and altitude was found. The race 2n = 16 tended to occupy lower altitudes than the 2n = 22 parental race. Differences in ecological preferences may be a result of previous adaptations to different environments in allopatry. A hypothesis concerning the origin and evolution of the hybrid zone is proposed.

Analysis of the phenotypic effects of B chromosomes in a natural population of Metagagrella tenuipes (Arachnida: Opiliones).

Phenotypic effects of B chromosomes in a natural population of Metagagrella tenuipes (Arachnida: Opiliones) were studied. Mean number of Bs per individual in the population studied was 6.0, and remained stable during two successive summers of 1997 and 1998. In contrast to the number of B chromosomes, ratios between individuals possessing odd and those possessing even numbers of Bs changed during both collection seasons: the proportion of harvestmen with an even number of Bs decreased from June-July to October-November. A possible reason for this may be a difference in susceptibility to parasites between B-odd and B-even harvestmen. In the group of B-even individuals the percentage of infected harvestmen in the June-July samples was much higher compared to the B-odd group. In addition, the infection rate in the B-even group decreased more sharply than among B-odd harvestmen. In the group of B-even harvestmen infection was associated with reduced body size, whereas no such association was found among B-odd harvestmen. In the group of B-even individuals there was a U-shaped relationship between number of Bs and the probability of being infected by parasites, and an inverted-U-shaped relationship between body size and number of Bs. No such associations were found in the group of B-odd harvestmen. Seasonal selection is suggested to be a main factor contributing to the B-chromosome polymorphism in M. tenuipes.

Morphology and Meiotic/Mitotic Behavior of B Cromosomes in a Japanese Harvestman, Metagagrella tenuipes (Arachnida: Opiliones): No Evidence for B Accumulation Mechanisms.

Earlier, it has been demonstrated that wild populations of a Japanese harvestman Metagagrella tenuipes (Arachnida: Opiliones) are polymorphic for B chromosomes. In this paper, we present results of a study of the morphology and mitotic and meiotic behavior of the Bs. The B chromosomes varied considerably in size and proportion of eu- and heterochromatin. The single nucleolus organizing region, found in males, was located on a chromosome of the A complement. Some intercell variation in number of Bs may be explained by accidental chromosome losses during chromosome preparation. We also found no intertissue variation in number of Bs. There were also no differences in mean number of B chromosomes per individual among males and females, adult and subadult harvestmen. Segregation of Bs in mitotic and meiotic divisions was nonrandom; B chromosomes tended to segregate equally between daughter cells. The results obtained provide no support for the hypothesis of existence of B accumulation mechanism in this species.

Recombination in single and double heterozygotes for two partially overlapping inversions in chromosome 1 of the house mouse.

Recombination frequency, chiasmata and chromatid interference were studied by means of analysis of meiotic configurations in diakinesis and metaphase II in single and double heterozygotes for the partially overlapping inversions In(1)1Rk and In(1)12Rk in chromosome 1 of the house mouse. Recombination frequency in the inverted regions was decreased in single heterozygotes and increased in the double heterozygotes as compared to normal homozygotes. Chiasmata in the inverted regions in the double heterozygotes did not interfere with each other. A significant excess of 4-chromatid double exchanges in the inverted regions was detected in the double heterozygotes.

Sex differences in chiasma distribution along two marked mouse chromosomes: differences in chiasma distribution as a reason for sex differences in recombination frequency.

Chiasma distributions along bivalents 1 and 14 in female and male mice were studied. It was shown that the average chiasma number in both chromosomes show no sex difference. There are however, significant sex differences in chiasma distribution along 1 and 14 chromosomes. In males there are two terminal chiasma peaks in chromosome 1 and one subtelomeric peak of chiasmata in chromosome 14. In females chiasma distributions are more even. According to genetic data, females produce more recombinants between loci of chromosome 1 than males do. By means of a computer simulation it was demonstrated that the differences in the average recombination frequency result from differences in chiasma distribution.

[Meiotic crossing over--not the only source of recombinants in man]. / Meioticheskii krossingover--ne edinstvennyi istochnik rekombinantov u cheloveka.

On the basis of chiasma distributions along bivalents in human male meiosis, genetic lengths were counted for several chromosomal segments. These estimates appeared to be lower than the corresponding genetic lengths produced in the recombination analysis. When al so cytological distances and number of markers used in multilocus mapping were taken into account, the regression estimates of genetic lengths were shown to satisfactorily fit the observed values. This indicates that mitotic crossingover, genetic conversion, mutation and errors in allel's identification in addition to meiotic crossingover, appear to contribute to the observed genetic maps. It is suggested that these namely events, rather than the typing errors suggested by Morton (1991), seem observed over those predicted on the basis of chiasma counts.

Chiasma distribution in the first bivalent of mice carrying a double insertion of homogeneously-staining regions in homo- and heterozygous states.

An examination of the meiotic pattern of chromosome 1 isolated from a feral mouse population and containing a double insertion (Is) of homogeneously-staining regions (HSRs) was carried out. In a previous study is was shown that the region delineated by the proximal breakpoint of Is(HSR;1C5) 1Icg and the distal one of Is(HSR;1D)2Icg is unpaired during early pachytene and heterosynapsed at midpachytene. No synaptic disturbances were revealed in homozygotes in this study. Chiasmata number per first bivalent in heterozygous (1.87) and homozygous (1.88) males was shown to be higher than in normal ones (1.61). In normal males a single chiasma is located in the medial part of chromosome 1. In heterozygotes this segment is heterosynapsed and unavailable for recombination. This leads to a significant decrease in the frequency of bivalents bearing a single chiasma and an increase in the frequency of bivalents bearing double chiasmata located mostly at subcentromeric and subtelomeric regions of the chromosome. In homozygous males the frequency of double chiasmata is also increased, and even triple chiasmata become possible because of the increase in the physical length of the bivalents. Thus insertion of heterochromatic regions, which are inert with respect to recombination, leads to an increase in the length of the genetic map of the chromosome because of relaxation of interference restrictions.

[An unusual heteromorphic bivalent in the common vole (Microtus arvalis) from Byelarus]. / Neobychnyi geteromorfnyi bivalent u obyknovennykh polevok (Microtus arvalis) iz Belorussii.

Electron microscopic analysis was carried out on the synaptonemal complexes of ten male common voles (Microtus arvalis) caught of 1990 in Byelorussia. In the early pachytene stage of spermatocytes of four males heteromorphic bivalent has been found in one of five large autosomes. In the central region of the bivalent one of the lateral elements is in the form of a D-loop, characteristic of insertion/deletion heterozygotes. However, high-resolution G-band staining of mitotic chromosomes from fibroblasts showed no significant differences in the G-band patterns between homologues.

[Cytogenetic analysis of recombination interactions]. / Tsitogeneticheskii analiz rekombinatsionnykh vzaimodeistvii.

Chiasma interference between separate regions of chromosomes was studied in three phylogenetically distant species. All these species displayed the similar patterns of chiasma interference. Chiasma completely suppressed recombination in the regions next to chiasma within a chromosome's arm. The level of crossing-over suppression decreased non-linearly with increase in a distance between the chiasma and the region under analysis. Some kind of the threshold effect was observed. In some cases, negative interference between the regions rather remote from each other was noted. Polarity of interference was revealed: interstitial chiasma suppressed recombination in the proximal (in relation to the centromere) direction more effectively than in the distal direction. Some regions belonging to the different arms of the same chromosome were shown to be able to interfere.

Synaptic interrelationships between the segments of the heteromorphic bivalent in double heterozygotes for paracentric inversions in chromosome 1 of the house mouse.

Electron microscopic analysis of synaptonemal complexes in double heterozygotes for the partially overlapping inversions In(1)1Rk and In(1)12Rk in chromosome 1 of the house mouse was carried out. A great variety of synaptic configurations with complicated combinations of homologously and non-homologously paired segments was observed. Analysis of these configurations revealed at least five independent pairing regions in chromosome 1. Interrelationships between these regions with respect to their pairing ability were estimated. Pairings in the distal non-inverted segment and in inversions inhibit each other, while pairing in either inverted segment facilitates synapsis in the other. In other words, pairing initiations in different parts of the same bivalent are not independent events.

Unusual heteromorphic bivalents in the common vole (Microtus arvalis) from Belorussia.

Electron microscopic analysis was carried out on the synaptonemal complexes of 10 male common voles (Microtus arvalis) caught in 1990 in Belorussia. In the early pachytene stage of spermatocytes of four males, a heteromorphic bivalent has been found in one of five large autosomes. In the central region of the bivalent one of the lateral elements is in the form of a D-loop, characteristic of insertion/deletion heterozygotes. However, high-resolution G-band staining of mitotic chromosomes from fibroblasts shows no significant differences in the G-band pattern between homologs.

Chromosome pairing and recombination in mice heterozygous for different translocations in chromosomes 16 and 17.

In order to clarify the relationship between meiotic pairing and recombination, an electron microscopic (EM) study of synaptonemal complexes (SC) and an analysis of chiasma frequency and distribution were made in male mice singly and doubly heterozygous for Robertsonian [Rb(16.17)7Bnr] and reciprocal [T(16:17)43H] translocations and also in tertiary trisomics for the proximal region of chromosome 17. In all these genotypes an extensive zone of asynapsis/desynapsis around the breakpoints was revealed. At the same time a high frequency of non-homologous pairing was observed in precentromeric regions of acrocentric chromosomes. The presence in the proximal region of chromosome 17 of the t haplotype did not affect the synaptic behaviour of this region. Chiasma frequency in the proximal region of chromosome 17 in the T(16:17)43H heterozygotes and trisomics was increased when compared with that in Robertsonian heterozygotes.

Positional control of chiasma distribution in the house mouse. Chiasma distribution in mice homozygous and heterozygous for an inversion in chromosome 1.

An examination of the chiasma distribution in chromosome 1 of male mice homozygous and heterozygous for a distal inversion In(1) 12Rk and in normal males was carried out. No differences in chiasma distribution were found between homozygotes for the inversion and homozygotes for normal chromosome 1. A significant decrease in the frequency of bivalents bearing chiasmata in the pretelomeric region was found in heterozygotes. This, in its turn, produced a redistribution of chiasmata in the proximal non-inverted part of bivalent 1. These results could be interpreted as evidence for positional control of the chiasma distribution pattern: the distance of certain parts of the chromosome from the telomere and chiasmata interference are more important for determination of the chiasma frequency in a given region than its genetic content.

[Chromosomal control of chiasma distribution in house mice. Analysis of chiasma distribution in homo- and heterozygotes by inversion in chromosome 1]. / Khromosomnyi kontrol' raspredeleniia khiazm u domovoi myshi. Analiz raspredeleniia khizm u gomo- i geterozigot po inversii v 1-i khromosome.

Examination of chiasma distribution in the chromosome 1 in male mice homo- and heterozygous for distal inversion In(1)12Rk and in normal mice was carried out. No differences in chiasma distribution was found between homozygotes for the inversion and homozygotes for normal chromosome 1. A drastic change in this trait was revealed in heterozygous animals. In heterozygotes, the telomeric segments of SC were asynapsed and unavailable for recombination. This leads to significant decrease in the frequency of bivalents bearing chiasmata in pretelomeric region. In turn, it produced chiasma redistribution in proximal noninverted portion of the bivalent 1. These results could be interpreted as evidence for chromosomal control of chiasma distribution pattern: the distance of certain part of the chromosome from telomere and interference (which also operates at the chromosomal level) are more important for determination of the chiasmata frequency in the given region, than its genetic content.

[Chiasmata distribution in the normal karyotype of mice]. / Raspredelenie khiazm v normal'nom kariotipe myshi.

The number of chiasmata per cell and variance of chiasmata numbers were studied, as well as the recombinational interaction between different bivalents in CBA/Lac mice male line. No competition of bivalents for chiasmata was discovered in mice; at the same time, the chiasmata within one arm of the chromosome interfere with each other. The number of chiasmata per bivalent is estimated for each chromosome independently. The number of chiasmata per chromosome is limited both from below (minimum one chiasma independently of its size) and from above (positive interference of chiasmata).