N-Band polymorphism of human acrocentric chromosomes and its relevance to satellite association

Summary With the aid of Q- and N-banding techniques we investigated the relationship between the length of satellite stalks, the appearance of N-bands and the frequency of satellite association of individual acrocentric chromosomes in the cells of seven individuals, including one male with a satellited and small Y-chromosome. The appearance of N-bands seemed to be a constant and characteristic property of individual acrocentric chromosomes, independent of the status of concentration of the chromosomes at metaphase. The homolog with longer satellite stalks had larger N-bands and participated in satellite association at a higher frequency than the one with shorter stalks. It appeared that N-bands were present along the whole length of the satellite stalk, the size of which could possibly reflect the amount of rDNA present in the nucleolar organizers in human chromosomes.     

Additional evidence for fragile X activity in heterozygous carriers.

The result of a previous study showing an association between mental development and fragile X activity in heterozygous females is given further support by similar investigations of three additional kindreds. The increased frequency of demonstrable fragile X chromosomes in mentally retarded females appears to be due to an increase in the active fragile X while the inactive marker X remains at a similar low frequency in all heterozygotes whether retarded or not. The frequencies of the active fragile X separated the normal and abnormal subjects into two distinct populations. The suggested inverse correlation between the number of lymphocytes with detectable fragile X chromosomes and advancing age can be attributed to ascertainment biases.     

Possible origin of a small bisatellited additional chromosome

Summary The possible derivation of a small supernumerary marker chromosome was investigated by means of different staining techniques and the frequency of satellite associations. It could be demonstrated that the marker chromosome participates at satellite association more than randomly. The marker chromosome is supposed to derive from 2 of chromosomes 13, 14, 21, or 22.Who died accidentally in 1978     

Association of nucleolus organizer chromosomes in domestic sheep (Ovis aries) shown by silver staining.

The nucleolus organizer regions of domestic sheep (Ovis aries), as shown by silver staining, are located terminally on chromosomes 1, 2, 3, 4, and 25. Significant differences between individuals in the number of Ag-NORs per cell were found. The frequency of involvement of individual chromosome pairs in nucleolar organization was found to be a characteristic of individual animals. Association frequencies of individual chromosomes were accounted for by their frequency of participation in nucleolar organization. No evidence for nonrandom association of chromosome pairs was found.     

Telomeric associations in cigarette smokers exposed to low levels of X-rays

Telomeric association (TA), i.e. fusion of chromosomes by their telomeres, predisposes a cell to genetic instability. Because of this we investigated the effect of X-rays exposure and cigarette smoking on the frequency of TA in peripheral blood lymphocytes of exposed individuals, in order to determine if TA can be a chromosomal marker in populations exposed to these carcinogens and if there is an synergistic effect between both agents. We found that the exposed groups show a greater percentage of TA when compared with the control group (P<0.001). However, although the percentage of metaphases with TA in the group with combined exposure (12.6%) was greater than in the others exposed groups (P<0.05), this value was less than the sum of the two individual effects (15.1%). Our results suggest that probably there is not an additive or synergistic effect between X-rays and smoking, and that TA may be a useful cytogenetic marker for evaluating populations exposed to mutagens.     

Autonomy of association frequencies of telomeric regions in salivary gland chromosomes during interspecific hybridization]

The study of association frequency and combination of salivary gland chromosomes participating in telomeric associations in interspecific hybrids between related species of "virilis" group of Drosophila (D. virilis, D. texana and D. imeretensis Sokolov) enables to conclude that each homologous chromosome behaves as an individual unit in the process. Besides, it is shown that the frequency of association of an autonomous property of telomere, i. e. it is not changed in interspecific hybrids in comparison with parental species.     

Mitomycin C-induced meiotic crossing-over on the interstitial segments in the Chinese hamster heterozygous for a reciprocal translocation

Using Chinese hamsters heterozygous for T(2;10)3Idr and T(1;3)8Idr reciprocal translocations, the authors studied mitomycin C (MMC)-induced crossing-over on the interstitial segments. Marker chromosomes with unequal-length chromatids resulting from crossing-over were clearly detectable, and the frequencies of such marker chromosomes were constant among individual males which were heterozygous for the same reciprocal translocation. The frequency of MMC-induced crossing-over on the interstitial segments increased roughly with increase in dose. These findings, therefore, indicated that marker chromosomes with unequal-length chromatids in translocation heterozygotes may be a useful indicator for detection of the cytogenetic effects of environmental mutagens on germ cells.     

Variation in pattern and frequency of acrocentric association in normal and trisomy-21 individuals

Summary Chromosomally normal and trisomy-21 individuals were studied for the ability of their nucleolus-organising chromosomes to form satellite associations in G-banded lymphocyte metaphases. Two types of parameter, absolute association frequency and relative association frequency, were used. There was no significant difference between females and males or between Caucasoids and Mongoloids for either type of association parameter in the controls, nor was there significant correlation between age (17–40 years) and either type of parameter in the controls.The pattern of two chromosome associations is accounted for by two related models in both normal and trisomic individuals. These models imply that there is an extensive polymorphism for associating ability and that this ability may be zero in individual chromosomes. Homologous do not associate preferentially with each other. The absolute frequency of acrocentric association is lower in trisomy 21 individuals than disomic controls, but the relative involvement of chromosome 21 (after correction for the trisomic state) is higher than in the controls.     

Aneuploidy in human sperm: a review of the frequency and distribution of aneuploidy, effects of donor age and lifestyle factors

Application of fluorescence in situ hybridization (FISH) analysis has opened the way for comprehensive studies on numerical chromosome abnormalities in human sperm. During the last decade, more than five million sperm from approximately 500 normal men were analyzed by a number of laboratories from around the world by this approach. Except for chromosome 19 which has been analyzed in only one study, all other chromosomes have been examined by two or more studies with considerable differences in disomy frequency for an individual chromosome among studies. The mean disomy frequency is 0.15% for each of the autosomes and 0.26% for the sex chromosomes. Most chromosomes analyzed have an equal distribution of disomy with the exception of chromosomes 14, 21, 22 and the sex chromosomes, which display significantly higher disomy frequencies. Slight but significant increases in disomy frequency with advancing paternal age were observed for some chromosomes, in particular for the sex chromosomes. Some lifestyle factors such as smoking, alcohol drinking and caffeine consumption have been investigated and no consistent association between disomy frequency and any type of lifestyle factors has been established. The question of whether different geographic and ethnic groups of men have inherent differences in frequency of disomic sperm has been investigated by two studies with conflicting results.     

Analysis of replication patterns in chromosomes of normal Chinese hamster and its cell lines

Replication patterns of the normal male Chinese hamster chromosomes and the three cell lines CHW, 1102 and 1103, were determined using fluorescent, plus Giemsa or acridine orange, techniques. The individual chromosomes or chromosomal segments were consistent in the replication patterns of normal Chinese hamster chromosomes and all the transformed cell lines. Late DNA replication was regularly identified in the long arm of the X chromosome, the entire Y chromosome, the short arms of chromosomes 6 and 7, and the paracentromeric regions of chromosomes 8, 9 and 10. A similar consistency was demonstrated in the large late replicating areas of chromosomes X and Y. Each cell line had specific marker chromosomes by which the cell line was identified and their replication patterns have been described. The chromosome analysis in cell line 1103 indicated that chromosomes 2, 3, 8 and 9 were more stable than others, of which chromosome 2 was extremely stable. The markers M4 and M5 in cell line 1103 are very interesting. The cytogenetic behaviour of marker M4 indicated a new phenomenon of translocation by simple association. The marker chromosome M5 indicated that inactivation spread to the early replicating distal region. These cell lines are very useful tools for studying replication patterns and providing a basic understanding of mammalian cytogenetics.     

Quantitative studies on the arrangment of human metaphase chromosomes

Summary The pattern of association of acrocentric chromosomes was examined in ten and five carriers of a 15/21 and a 13/14 Robertsonian translocation, respectively, and was compared with that of the same numbers of relatives with normal karyotypes. In the carriers of 15/21 translocation, the number of large associations (involving more than two acrocentrics) and the association frequencies for individual acrocentric chromosomes, were significantly higher than in the control group. The mean number of associations of the single homologs of the translocation chromosomes was much higher than that of the other acrocentrics. In the carriers of 13/14 translocations, only the association frequency for chromosome 13 was higher than in the normal relatives. The uninvolved chromosomes homologous to those involved in translocations showed an insignificant increase in associations in comparison with the other acrocentrics. These results suggest that some mechanism within the cells compensates for the effect of missing acrocentrics or of acrocentrics lacking NORs on the number of associations. The possible relations of this phenomenon to the activity of the nucleolus organizing regions are discussed.     

Distribution patterns of the ΔF508 mutation in the CFTR gene on CF-linked marker haplotypes in the German population

Summary We have measured the frequency of the ΔF508 mutation in the cystic fibrosis transmembrane conductance regulator (CFTR) gene and its association with cystic fibrosis (CF)-linked marker haplotypes in the German population. Based on the analysis of 400 CF chromosomes, the frequency of the ΔF508 mutation is estimated to be 77.3%, the vast majority being associated with marker haplotype KM19-XV2c 2 1. Our data further suggest the presence of another frequent CF mutation associated with this marker haplotype.     

Detection of marker associations with a dominant disease gene in genetically complex and heterogeneous diseases.

Linkage disequilibrium of a marker allele with disease may characterize a chromosomal region containing the disease gene. In several diseases, only a limited number of pedigrees are linked to a particular region, because of linkage heterogeneity. Disequilibrium in this situation is more easily detected when the association is positive (an infrequent marker allele associated with disease mutation), and sampling is conditional on presence or absence of illness in individuals or gametes. Defining H as the marker frequency in illness-transmitting gametes, and Q the marker frequency in normal chromosomes, we compute the power of a given sample (of ill persons/gametes) to detect association in a disease that is genetically heterogeneous, with a dominantly transmitted form linked to a marker. The estimation of Q and the effects of linkage heterogeneity (when unrelated individuals are examined) are also analyzed. Two linked pedigrees give acceptable power to detect association when the allele is frequent enough in illness gametes (H greater than or equal to .6) and infrequent enough in normals (Q less than or equal to .01). If H greater than or equal to .2, 14 pedigrees are needed to give the same power. From the analysis of different values of Q and H, it appears that even in the presence of considerable genetic heterogeneity and complex inheritance (where some normals carry the disease mutation), association may be detected with clinically feasible sample sizes.     

Acrocentric chromosome associations in man.

Heterogeneity among chromosomes was found to be a highly significant source of variation for association proportions, while culture, slide, and observer were negligible sources of variation for association proportions although important for numbers of associations. The consequences of these results for tests of group differences are discussed. It seems evident that each pair of acrocentric chromosomes has its own characteristic probability of entering into association. This is presumably a combination of the probability for each individual member of the pair, a proposition easily tested utilizing acrocentric chromosomes carrying polymorphisms which allow each member of the pair to be individually recognized. A mathematical theory for pairwise satellite association was developed and shown to fit observations on banded chromosomes. While we found very significant heterogeneity among individuals in the frequency with which different chromosomes entered into associations, there was no significant evidence for preferential association between any particular chromosomes, either heterologous or homologous. This finding in our material of apparently random associations between different chromosomes is contrary to claims made by other investigators and should be tested on other material. No correlation was found between the phenotype of the chromosome, as judged by cytogenetic polymorphisms, and its probability of association.     

The integration of canine genetic maps with the canine karyotype using specific gene amplification of chromosome-specific DNA

We have used a rapid approach to place markers that are already represented in current genetic maps onto individual chromosomes in species for which chromosome paints exist. PCR-based techniques are used to look for the presence of individual marker genes within each chromosome-specific DNA pool. The presence of a given marker within a DNA pool allows assignment of the complete radiation hybrid group, or linkage group from which the marker is drawn, to an individual chromosome. We have used this method with a new set of canine chromosome paints (Yang et al., 1999). In this way, we have assigned 39 of 44 published RH or syntenic RH groups to canine chromosomes, together with 33 of 40 canine linkage groups in a recently published map (Neff et al., 1999).     

Large-scale detection of rare variants via pooled multiplexed next-generation sequencing: towards next-generation Ecotilling

Common variants, such as those identified by genome-wide association scans, explain only a small proportion of trait variation. Growing evidence suggests that rare functional variants, which are usually missed by genome-wide association scans, play an important role in determining the phenotype. We used pooled multiplexed next-generation sequencing and a customized analysis workflow to detect mutations in five candidate genes for lignin biosynthesis in 768 pooled Populus nigra accessions. We identified a total of 36 non-synonymous single nucleotide polymorphisms, one of which causes a premature stop codon. The most common variant was estimated to be present in 672 of the 1536 tested chromosomes, while the rarest was estimated to occur only once in 1536 chromosomes. Comparison with individual Sanger sequencing in a selected sub-sample confirmed that variants are identified with high sensitivity and specificity, and that the variant frequency was estimated accurately. This proposed method for identification of rare polymorphisms allows accurate detection of variation in many individuals, and is cost-effective compared to individual sequencing.     

Preferential association of nucleolar organizing human chromosomes as revealed by silver staining technique at mitosis

Summary The frequency of different types of satellite associations of nucleolar organizing human chromosomes (i.e. acrocentric chromosomes; 13, 14, 15, 21, and 22) is reported using 10 normal individuals by Ag-staining technique. The preferential involvement of acrocentric chromosomes in satellite association is suggested. Only acrocentric chromosomes with active NORs (i.e. Ag-stained) were found in association while unstained (inactive NORs) chromosomes were never seen in satellite association. In general as number of NORs expression increase, the frequency of association per cell was also increased. A possible mechanism and the clinical consequences of such an unusual phenophenon is described.     

The frequency of aneuploidy among individual chromosomes in 6,821 human sperm chromosome complements

The human sperm/hamster egg fusion technique has been used to analyse 6,821 human sperm chromosome complements from 98 men to determine if all chromosomes are equally likely to be involved in aneuploid events or if some chromosomes are particularly susceptible to nondisjunction. The frequency of hypohaploidy and hyperhaploidy was compared among different chromosome groups and individual chromosomes. In general, hypohaploid sperm complements were more frequent than hyperhaploid complements. The distribution of chromosome loss in the hypohaploid complements indicated that significantly fewer of the large chromosomes and significantly more of the small chromosomes were lost, suggesting that technical loss predominantly affects small chromosomes. Among the autosomes, the observed frequency of hyperhaploid sperm equalled the expected frequency (assuming an equal frequency of nondisjunction for all chromosomes) for all chromosome groups. Among individual autosomes, only chromosome 9 showed an increased frequency of hyperhaploidy. The sex chromosomes also showed a significant increase in the frequency of hyperhaploidy. These results are consistent with studies of spontaneous abortions and liveborns demonstrating that aneuploidy for the sex chromosomes is caused by paternal meiotic error more commonly than aneuploidy for the autosomes.     

Karyotypic characteristics of the murine myeloma line sp2/0-Ag14

Using methods of G- and C-banding, a study was made of the karyotype of mouse myeloma cell line sp2/0-Ag14. The number of chromosomes varies from 58 to 65, the modal class being 61-62. 50 per cent of chromosomes are rearranged. Normal chromosomes 6, 12 and X were not detected in either examined cell of this line. Among the marker chromosomes there are an isochromosome (19/19), three dicentric markers and one marker with two interstitial C-bands. There is a specific marker t (12; 15) of mouse plasmacytomas in the karyotype sp2/0-Ag14. A possible association of specific translocations and segregations of the normal chromosomes with the phenotype of line sp2/0-Ag14 is discussed. The results obtained may be useful for cytogenetic analysis of hybridomas.     

In silico analysis of disease-association mapping strategies using the coalescent process and incorporating ascertainment and selection

We present a new method for simulating samples of marker haplotypes, genotypes, or diplotypes in case-control studies in which the markers are linked to a disease locus in any specified region of the genome. The method allows realistic features to be incorporated into the simulations, including selection acting on disease alleles, sample ascertainment of disease chromosomes and polymorphic markers, a genetic dominance model of disease expression that allows incomplete penetrance and phenocopies, and an accurate genetic map of recombination rates and hotspots for recombination in the human genome (or, alternatively, an improved method for simulating the distribution of hotspots). The new method uses an approach that combines simulation of the coalescent process for the sampled chromosomes with a diffusion process used to model the evolution of the disease-mutation frequency over time. Examples illustrate how the method may be used to study the expected power of a marker-disease association study.