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PubMed2002

[Genetic analysis and estimation of genetic diversity in east-European breeds of swift hounds (Canis familiaris L.) based on the data of genomic studies using RAPD markers].

The method of polymerase chain reaction with a set of arbitrary primers (RAPD-PCR) was used to describe genetic variation and to estimate genetic diversity in East-European swift hounds, Russian Psovyi and Hortyi Borzois. For comparison, swift hounds of two West-European breeds (Whippet and Greyhound) and single dogs of other breed groups (shepherd, terriers, mastiffs, and bird dogs) were examined. For all dog groups, their closest related species, the wolf Canis lupus, was used as an outgroup. Variation of RAPD markers was studied at several hierarchic levels: intra- and interfamily (for individual families of Russian Psovyi and Hortyi Borzois), intra- and interbreed (for ten dog breeds), and interspecific (C. familiaris-C. lupus). In total, 57 dogs and 4 wolfs were studied. Using RAPD-PCR with three primers, 93 DNA fragments with a length of 150-1500 bp were detected in several Borzoi families with known filiation. These fragments were found to be inherited as dominant markers and to be applicable for estimation of genetic differences between parents and their offspring and for comparison of individuals and families with different level of inbreeding. A high level of intra- and interbreed variation was found in Russian Psovyi and Hortyi Borzois. In these dog groups, genetic similarity indices varied in a range of 72.2 to 93.4% (parents-offspring) and 68.0 to 94.5 (sibs). Based on the patterns of RAPD markers obtained using six primers, a dendrogram of genetic similarity between the wolf and different dog breeds was constructed, and indices of intragroup diversity were calculated. All studied breeds were found to fall into two clusters, swift hounds (Borzoi-like dogs) and other dogs. Russian Borzois represent a very heterogeneous group, in which the Russian Psovyi Borzoi is closer to Greyhound than the Russian Hortyi Borzoi. All studied wolfs constituted a separate cluster. Significant differences were found between the wolf and dogs by the number of RAPD markers (92.8 and 86.1, respectively) and by the indices of genetic diversity (54.3 and 64.8%, respectively). The reasons for the high intraspecific variation of dogs (including Russian Borzois) and the prospects of using the studied group of markers for genetic analysis and differentiation in C. familiaris are discussed.

Animals↗
PubMed2003

Genetic analysis of phenotypes derived from longitudinal data: Presentation Group 1 of Genetic Analysis Workshop 13.

The participants of Presentation Group 1 used the GAW13 data to derive new phenotypes, which were then analyzed for linkage and, in one case, for association to the genetic markers. Since the trait measurements ranged over longer time periods, the participants looked at the time dependence of particular traits in addition to the trait itself. The phenotypes analyzed with the Framingham data can be roughly divided into 1) body weight-related traits, which also include a type 2 diabetes progression trait, and 2) traits related to systolic blood pressure. Both trait classes are associated with metabolic syndrome. For traits related to body weight, linkage was consistently identified by at least two participating groups to genetic regions on chromosomes 4, 8, 11, and 18. For systolic blood pressure, or its derivatives, at least two groups obtained linkage for regions on chromosomes 4, 6, 8, 11, 14, 16, and 19. Five of the 13 participating groups focused on the simulated data. Due to the rather sparse grid of microsatellite markers, an association analysis for several traits was not successful. Linkage analysis of hypertension and body mass index using LODs and heterogeneity LODs (HLODs) had low power. For the glucose phenotype, a combination of random coefficient regression models and variance component linkage analysis turned out to be strikingly powerful in the identification of a trait locus simulated on chromosome 5. Haseman-Elston regression methods, applied to the same phenotype, had low power, but the above-mentioned chromosome 5 locus was not included in this analysis.

Cardiovascular Diseases↗
PubMed2001

Male infertility, genetic analysis of the DAZ genes on the human Y chromosome and genetic analysis of DNA repair.

Many genes that are required for fertility have been identified in model organisms (). Mutations in these genes cause infertility due to defects in development of the germ cell lineage, but the organism is otherwise healthy. Although human reproduction is undoubtedly as complex as that of other organisms, very few fertility loci have been mapped (). This is in spite of the prevalence of human infertility, the lack of effective treatments to remedy germ cell defects, and the cost to couples and society of assisted reproductive techniques. Fifteen percent of couples are infertile and half of all cases can be traced to the male partner. Aside from defects in sperm production, most infertile men are otherwise healthy. This review is divided into two distinct parts to discuss work that: (i) led to the identification of several genes on the Y chromosome that likely function in sperm production; and (ii) implicates DNA repair in male infertility via increased frequency of mutations in DNA from men with meiotic arrest.

Animals↗
PubMed1988

Toward a population genetic analysis of Salmonella: genetic diversity and relationships among strains of serotypes S. choleraesuis, S. derby, S. dublin, S. enteritidis, S. heidelberg, S. infantis, S. newport, and S. typhimurium.

Variation in the chromosomal genomes of 1527 isolates of eight common serotypes (O and H antigen profiles) of Salmonella was assessed by analysis of electrophoretically demonstrable allelic polymorphism at 23 metabolic enzyme loci. Seventy-one distinctive electrophoretic types, representing multilocus genotypes, were identified. A basically clonal population structure was indicated by the presence of strong linkage disequilibrium among enzyme loci, the association of each serotype with a relatively small number of multilocus enzyme genotypes, and the global distribution of certain genotypes. For each of six of the serotypes, 83-96% of isolates were members of a single clone. The occurrence of each of four serotypes (S. derby, S. enteritidis, S. infantis, and S. newport) in isolates of clones belonging to several evolutionary lineages, some of which are distantly related, suggests that the horizontal transfer and recombination of chromosomal genes mediating expression of cell-surface antigens has been a significant process in the evolution of the salmonellae. Two divergent clone clusters of S. derby differ in the relative frequency with which they cause disease in birds versus mammals, and two major lineages of S. newport differ in the frequency with which their clones are associated with disease in humans versus animals.

Alleles↗
PubMed2006

Genetic analysis of anger: genetic dominance or competitive sibling interaction.

The knowledge of the causes and development of anger is still scarce. Previous studies on the sources of variance on Type A Behavior Pattern (TABP) related measures found variable heritability estimates ranging from 0.12 to 0.68, and large differences between MZ and DZ correlations. Some authors considered dominance genetic effects, competitive sibling interaction and sex differences as possible mechanisms to explain the results, but most studies lacked power. The present study uses a large sample of more than 2,500 families, with longitudinal data from MZ and DZ pairs as well as their parents, to disentangle the sources of variance on anger. Model Fitting results showed that the sources of variance differ across sexes. For males 23% of the variance is due to additive genetic effects, and 26% to dominance genetic effects. For females 34% of the variance is due to additive genetic effects, and no dominance effects are found. There was no consistent evidence to confirm the presence of competitive sibling interaction as an alternative explanation for the low correlations in DZ males. The focus of research on the prediction of coronary heart disease (CHD) risk through psychological characteristics has recently changed from the multidimensional TABP to its emotional component: Anger. Understanding the sources of individual differences on anger can help to clarify the mechanisms that link it with CHD and its possible implications for treatment and prevention.

Adolescent↗
PubMed2001

Preliminary implementation of new data mining techniques for the analysis of simulation data from Genetic Analysis Workshop 12: problem 2.

We introduce a new data mining method applicable to complex disease genetics. Our approach is suited to a broad spectrum of diseases, identifying the noteworthy sharing of combinations of alleles in unrelated affected individuals. Furthermore, this approach may be extended to comprise the common types of genotype data, including single-nucleotide polymorphisms, candidate-gene sequences, etc. Using a method derived from data-mining computer algorithms, we analyze a data set of unrelated affected individuals chosen from the simulated pedigrees of problem 2 of the Genetics Analysis Workshop 12. We observe that most marker subsets containing a flanking marker for each of six or seven of the disease-gene loci yield significant numbers of individuals manifesting substantially similar genotypes. However, initial attempts (blind to the generating model) to identify the predisposing loci have not been successful. Refining our methods so that such loci may routinely be found and validated is underway.

Algorithms↗
PubMed2001

[First attempts in preimplantation genetic diagnosis: genetic analysis].

Preimplantation genetic diagnosis is a new approach for the prevention of genetic disorders, which provides a healthy pregnancy avoiding the need for its possible termination. The combination of in vitro fertilization techniques and single cell molecular genetic diagnosis allows only unaffected embryos to be selected for transfer to the uterus. It is an acceptable alternative of prenatal diagnosis for certain couples. Here we report our first attempts in the application of fluorescent PCR for sex determination and the detection of the delta-F508 mutation in human blastomeres. We modelled clinical PGD situations as we performed sex determination on 23 preembryos. Sex determination was successful is 20 preembryos (83%). We performed the detection of the delta-F508 mutation on 23 preembryos, which was successful in 20 preembryos (87%). Our experience suggests, that the established fluorescent PCR analysis is a reliable method for PGD, which enables us to apply it for clinical preimplantation genetic diagnosis.

Blastomeres↗
PubMed2006

Linkage Group Selection--a fast approach to the genetic analysis of malaria parasites.

Genetic analysis of malaria parasites has shown that the mechanisms of inheritance in these organisms are classically Mendelian. In other words, alleles of genes at different loci recombine, and alleles at the same gene locus segregate, in the progeny of a genetic cross between two genetically distinct lines of malaria parasite. Importantly, such progeny are haploid in the first filial generation following genetic crossing. Consequently, genetic analysis, including linkage analysis, can be done directly upon the cloned cross progeny. Linkage analysis conducted upon the progeny of genetic crosses between malaria parasites can lead to the location of a single gene controlling a specific phenotype, as has been achieved to identify the gene for chloroquine resistance in Plasmodium falciparum. The work involved, however, is extremely labour intensive. It involves the generation of many hundreds, to a thousand or so, of independent recombinant clones from the cross progeny and the biological characterisation, and genetic typing for hundreds of molecular genetic markers of each such clone. We discuss here a fast-track method for identifying genes controlling specific phenotypes, e.g. drug resistance/sensitivity. It involves the mass screening with quantitative molecular genetic markers of the uncloned progeny of a genetic cross following its growth under a selection pressure representing the phenotype of interest. We have called the method Linkage Group Selection.

Animals↗
PubMedDate not supplied

[Saccharomyces bayanus var. Uvarum comb.nov., a new variety established by genetic analysis].

Partial genetic isolation of two Saccharomyces bayanus varieties, S. bayanus var. bayanus and S. bayanus var. uvarum comb. nov., was established by hybridological analysis. The hybrids of these two varieties were semisterile: their ascospores were characterized by low survival. Earlier, the new variety was described as a group of cryophilic wine yeast cultivars capable of fermenting melibiose.

DNA, Fungal↗
PubMed2002

Chloroplast and nuclear DNA studies in a few members of the Brassica oleracea L. group using PCR-RFLP and ISSR-PCR markers: a population genetic analysis.

A population genetic analysis of chloroplast and nuclear DNA was performed covering nine wild populations of Brassica oleracea. Three members of the n = 9 group, all close to B. oleracea, Brassica alboglabra Bailey, Brassica bourgeaui (Webb) O. Kuntze and Brassica montana Pourret, were also studied to better understand their relationship with B. oleracea. Chloroplast DNA was analysed using the PCR-RFLP (polymerase chain reaction - restriction fragment length polymorphism) method. The ISSR-PCR (inter-simple sequence repeat - polymerase chain reaction) technique was adopted to study nuclear DNA. Twelve primer pairs of chloroplast DNA showed very good amplification. The amplified product of each primer pair, digested by three restriction enzymes, revealed no variation of cpDNA among the taxa studied. This indicates they may have the same chloroplast genotype. Seven selected ISSR primers have detected genetic variation, both within and among the populations/taxa surveyed. The information obtained on the intra- and inter-populational genetic diversity of wild populations of B. oleracea neatly defined the individual plants. It could provide important guidelines for backing management and conservation strategies in this species. The study confirms a close relationship between B. alboglabra, B. bourgeaui and B. montana, which is parallel to their morphological similitude.

Brassica↗
PubMed2004

Global genetic analysis.

The introduction of molecular markers in genetic analysis has revolutionized medicine. These molecular markers are genetic variations associated with a predisposition to common diseases and individual variations in drug responses. Identification and genotyping a vast number of genetic polymorphisms in large populations are increasingly important for disease gene identification, pharmacogenetics and population-based studies. Among variations being analyzed, single nucleotide polymorphisms seem to be most useful in large-scale genetic analysis. This review discusses approaches for genetic analysis, use of different markers, and emerging technologies for large-scale genetic analysis where millions of genotyping need to be performed.

Animals↗
PubMed1995

[Genetic analysis for hereditary disorders].

Many genetic abnormalities responsible for hereditary disorders has been localized on chromosomes by positional cloning. Identification of RFLP and VNTR markers facilitated the process. Once mutations have been fully characterized, prenatal or presymptomatic diagnosis can be easily made by using polymerase chain reaction (PCR). Since no curable treatments are available for most of hereditary disorders, the following premises should be well understood when performing genetic analysis; 1) association of the mutation to look at and the hereditary disorder must be clearly demonstrated, 2) patients and their families must have opportunities to have counseling on the disease by experts in the field. 3) everybody must respect the will of patients and families to have or not to have genetic analyses, 4) every information should be securely kept and privacy of patients and families must be fully protected, and 5) genetic analysis procedures must be accurate and reliable. Recently, we characterized dysfibrinogenemia Matsumoto I. The proband was asymptomatic and only screening coagulation tests revealed mild prolongation of prothrombin time. Its functional level was as low as 5% of its immunologically determined level. Genetic analysis identified an amino acid substitution of gamma 364Asp-->His. Living-related liver transplantation performed to treat a patient with familial amyloid polyneuropathy is briefly described in this article.

Afibrinogenemia↗
PubMed2004

Breed relationships and definition in British cattle: a genetic analysis.

The genetic diversity of eight British cattle breeds was quantified in this study. In all, 30 microsatellites from the FAO panel of markers were used to characterise the DNA samples from nearly 400 individuals. A variety of methods were applied to analyse the data in order to look at diversity within and between breeds. The relationships between breeds were not highly resolved and breed clusters were not associated with geographical distribution. Analyses also defined the cohesiveness or definition of the various breeds, with Highland, Guernsey and Jersey as the best defined and most distinctive of the breeds.

Animals↗
PubMed2001

Familial and sporadic renal oncocytomas--a comparative molecular-genetic analysis.

OBJECTIVES: Genetic causes of sporadic and familial renal oncocytomas are not known. We analyzed these tumors genetically in order to detect tumor-specific chromosome alterations. METHODS: DNA from 26 sporadic and 31 familial renal oncocytomas were screened by comparative genomic hybridization according to standard protocols including degenerate oligonucleotide-primed PCR. RESULTS: Chromosome alterations were detected in 19/26 sporadic (73%) and in 4/31 familial renal oncocytomas (13%). Partial or complete losses of chromosome 1 were most frequently found in both sporadic (15/26) and familial tumors (2/4). Less frequently, loss of chromosome 14 (3/26) was detected in sporadic renal oncocytomas as well as losses of 2p, 2q, 4q, 10 and 18 and gains of 1q and 17q in individual sporadic tumors. Inter-tumor variation of chromosome aberrations was prominent in 1 patient, where 1 tumor showed gains of chromosomes 5, 6q, 7, 10p, 12 and 13q, whereas the second tumor exhibited gains of chromosomes 5 and 7 and loss of 10q. In contrast to sporadic renal oncocytomas, most familial tumors (87%) were devoid of chromosome instabilities. CONCLUSION: Our results demonstrate that partial or complete loss of chromosome 1 is the most common alteration in renal oncocytomas, sporadic and familial. However, chromosome changes are much rarer in familial than in sporadic renal oncocytomas.

Adenoma, Oxyphilic↗
PubMed1995

Analysis of familial breast cancer in genetic analysis workshop 9: summary of findings.

As part of the 9th Genetic Analysis Workshop held in Val Morin, Quebec, October 16-18, 1994, four workshop participants analyzed a large breast cancer data set. This data set consisted of phenotype and genetic marker data on 3884 individuals in 214 families with at least four cases of breast cancer contributed by members of an international breast cancer consortium. Two of the four papers [Barrett and Rigby; Commenges; this issue] utilized variants of affected pair methods to assess linkage of breast/ovarian cancer to the 17q markers in the data set. The third paper by Bansal et al. used a Monte-Carlo approach to examine the question of intrafamilial clustering of breast and ovarian cancer. The last paper in the series [Leal and Ott] described a method of computing support intervals for risk estimates when there are uncertainties associated with the parameter estimates used to compute these risks.

Breast Neoplasms↗