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PubMed1989

Estimation of segregation and linkage parameters in simulated data. I. Segregation analyses with different ascertainment schemes.

We report the results of a simulation study designed to assess the capability of segregation analysis to detect Mendelian transmission and to estimate genetic model parameters for complex qualitative traits, characterized by heritability in the range 0.20-0.45 and low heterozygote penetrance. The pedigree analysis package, PAP, was used to perform the analyses. For all data sets, models of no transmission could be rejected. In most cases, models of Mendelian transmission could not be rejected; however, several samples approached significance levels. When Mendelian transmission was assumed, reasonably good parameter estimates were obtained, although heterozygote penetrances were often overestimated. Different sampling schemes were imposed on the simulated data in order to examine the extent of information loss with the reduction in sample size. One of these strategies (a sequential sampling scheme) appears to have resulted in critical loss of information in some cases.

Alleles↗
PubMed1985

Human gene therapy: scientific and ethical considerations.

The term "gene therapy" encompasses at least four types of application of genetic engineering for the insertion of genes into humans. The scientific requirements and the ethical issues associated with each type are discussed. Somatic cell gene therapy is technically the simplest and ethically the least controversial. The first clinical trials will probably be undertaken within the next year. Germ line gene therapy will require major advances in our present knowledge and it raises ethical issues that are now being debated. In order to provide guidelines for determining when germ line gene therapy would be ethical, the author presents three criteria which should be satisfied prior to the time that a clinical protocol is attempted in humans. Enhancement genetic engineering presents significant, and troubling, ethical concerns. Except where this type of therapy can be justified on the grounds of preventive medicine, enhancement engineering should not be performed. The fourth type, eugenic genetic engineering, is impossible at present and will probably remain so for the foreseeable future, despite the widespread media attention it has received. There are four potential levels of the application of genetic engineering for the insertion of gene into a human being. Somatic cell therapy: this would result in correcting a genetic defect in the somatic (i.e.,body) cells of a patient. Germ line gene therapy: this would require the insertion of the gene into the reproductive tissue of the patient in such a way that the disorder in his or her offspring would also be corrected. Enhancement genetic engineering: this would involve the insertion of a gene to try to "enhance" a known characteristic; for example, the placing of an additional growth hormone gene into a normal child. Eugenic genetic engineering: this is defined as the attempt to alter or "improve" complex human traits each of which is coded by a large number of genes; for example, personality, intelligence, character, formation of body organs, and so on.

Adenosine Deaminase↗
PubMedDate not supplied

[Genetic determination and the spectrum of the hemolytic activity of Vibrio cholerae: their significance in the complex of biovar-specific traits].

A collection of 363 V. cholerae strains isolated from different sources were studied by the spectrum of their hemolytic activity in combination with biovar-associated properties. The strains were analyzed for the presence of the cholera toxin (CT) gene (vct) and the hemolysin gene (hly) with the use of the CT probe and a previously cloned 6.56 kb fragment of V. eltor DNA coding the synthesis of hemolysin. The study revealed that all V. cholerae strains had the hly gene irrespective of the spectrum of their hemolytic activity, biovar, 01 agglutinability and the presence of the vct gene in their genome, while other species of the genus Vibrio and related groups contained no hly gene sequence. The results of the comparative study of the hemolytic activity of V. cholerae and V. eltor are discussed.

Animals↗
PubMed1993

Two-hit model for sporadic congenital anomalies in mice with the disorganization mutation.

Congenital anomalies have complex etiologies involving both genetic and nongenetic components. Many are sporadic, without obvious evidence for heritability. An important model for these anomalies is a mutation in laboratory mice that is called "disorganization" (Ds), which functions as a variable autosomal dominant and leads to a wide variety of congenital anomalies involving many developmental processes and systems. Variable expressivity, asymmetrical manifestations, and low penetrance suggest that somatic events determine the location and nature of these anomalies. A statistical analysis suggests that occurrence of anomalies in mice with the Ds mutation follows a Poisson distribution. These results suggest that congenital anomalies in mice with the Ds mutation occur independently of each other. We propose that Ds causes a heritable predisposition to congenital anomalies and that Ds and appropriate somatic events combine to compromise normal development. We also propose that some sporadic, nonheritable congenital anomalies involve somatic mutations at Ds-like loci. Ds may therefore serve not only as a model for developmental anomalies in cell fate and pattern formation but also for complex developmental traits showing variable expressivity, low penetrance, and sporadic occurrence in mice and humans.

Abnormalities, Multiple↗
PubMed1996

Polygenic inheritance of predisposition to lung cancer.

Inherited predisposition to lung tumor development appears to be a complex genetic trait, in humans as well as in experimental animals. In humans, tobacco smoking represents the main risk factor for lung tumors. Familial clusterings of lung cancer cases are rare, although affected sib pairs are reported. However, several studies have reported an increased risk of lung cancer in first degree relatives of lung cancer patients, as compared with appropriate controls. Inheritence of particular alleles of genes or phenotypes for drug metabolizing enzymes are also associated with an increased lung cancer risk. In experimental models, murine inbred strains with high genetic predisposition to lung cancer are available, as well as resistant strains. A major locus affecting inherited predisposition to lung cancer in mice has been mapped on chromosome 6, near the Kras2 gene. The locus, pulmonary adenoma susceptibility 1 (Pas1) derives from the A/J strain. Additional "minor" loci have also been mapped. Dominant lung tumor resistance loci have also demonstrated in the mouse genome. Therefore, evidence for polygenic inheritance of predisposition to lung cancer is demonstrated in the mouse model, and it is strongly suggested for human lung cancer.

Adenocarcinoma↗
PubMed1996

Transgenics and essential hypertension.

Primary or "essential' hypertension is generally perceived to be a multifactorial or complex genetic trait. An individual's susceptibility to high blood pressure (BP) is influenced not only by the many genetic factors, which effect control through biochemical and physiological mechanisms, but also by environmental determinants. In a small proportion of human hypertensives the cause is a single genetic defect, exhibiting Mendelian characteristics. The vast heterogeneous majority, however, result from a multitude of contributing factors, making identification of the underlying etiology very difficult. We will briefly review a number of strategies which have helped to identify genetic factors involved in hypertension. These include the search for genetic defects in Mendelian forms of hypertension, intensive study of classical animal models such as the spontaneously hypertensive rat, and linkage analyses in animal models and hypertensive patients. We will then discuss the role which transgenesis can play in complementing and extending such analyses.

Animals↗
PubMed1997

Genetic influences determining progenitor cell mobilization and leukocytosis induced by granulocyte colony-stimulating factor.

The mechanisms involved in the mobilization of progenitor cells into the blood by granulocyte colony-stimulating factor (G-CSF) and other cytokines are poorly understood. To identify important influences on this complex process, in vivo murine models were used. Granulocyte-macrophage colony-stimulating factor (GM-CSF) transgenic, Max41 transgenic, W/Wv, Mpl-null, GM-CSF receptor (beta chain)-null mice, wild-type littermate controls, and six inbred strains of mice were injected with 200 microg/kg/d G-CSF for 5 days. Three parameters of response were monitored: white blood cell count (WCC), peripheral blood progenitor cell (PBPC) numbers, and spleen weight. In all genotypes studied, G-CSF induced increases in these three parameters. However, PBPC mobilization in W/Wv and Mpl-null mice was only 30% and 9%, respectively, of that observed in wild-type mice. In contrast, perturbations of GM-CSF signalling had no demonstrable effect on in vivo responses to G-CSF. Broad variability was evident between inbred strains for each parameter of the response to G-CSF. A 10-fold range in response was observed for circulating progenitor cell numbers, similar to that observed for normal human subjects receiving G-CSF. The interstrain differences were in the distribution of mature and progenitor cells between peripheral blood, bone marrow, and spleen rather than in the total numbers of these cells in the body. Results of an F2 intercross of low-responding C57BL/6 and intermediate-responding SJL mice indicated that regulation of progenitor cell mobilization is a complex genetic trait, that there is a correlation between this trait and WCC response (r2 = .5), and that this approach may serve as a useful model for the identification of genes involved in the mobilization process.

Animals↗
PubMedDate not supplied

A newly discovered role of transcription factors involved in pancreas development and the pathogenesis of diabetes mellitus.

The prevalence of diabetes mellitus is increasing worldwide, averaging 5% to 15% in various population groups. Diabetes predisposes to premature morbidity and death. The underlying metabolic cause of diabetes is a failure of the beta-cells of the pancreas to provide insulin in amounts sufficient to meet the body's needs, leading to hyperglycemia. Juvenile (type 1) diabetes results from immune destruction of the beta-cells. Adult onset (type 2) diabetes, which accounts for 90% of all forms of diabetes, is a complex polygenic disease manifested in a dysregulation of insulin secretion. Environmental influences and complex genetic traits contribute to the pathogenesis of both types of diabetes. However, a subpopulation of type 2 diabetes is monogenic and due to inactivating mutations in genes that are critical for normal beta-cell function. Heterozygous carriers of the mutant genes develop early-onset diabetes known as MODY (mature onset diabetes of the young). Notably, three MODY genes encode transcription factors implicated in the regulation of insulin gene transcription: hepatocyte nuclear factors 1 alpha and 4 alpha, and islet duodenum homeobox-1 (IDX-1, also known as IPF-1). The fourth gene encodes glucokinase, the rate-limiting enzyme required for glucose metabolism in beta-cells. Further, an individual born without a pancreas (agenesis) is homozygous for an inactivating mutation of the IDX-1 gene, recapitulating the phenotype of the IDX-1 knockout mouse and demonstrating that expression of IDX-1 is critical for pancreas development. Recently, mouse knockouts of the transcription factors Pax4, Pax6, beta 2/neuroD, and Isl-1 result in severe anomalies in the development of the endocrine pancreas. Gene mutations for these factors are possible candidates for additional MODY genes.

Amino Acid Sequence↗
PubMed1997

Issues in mapping genes for eating disorders.

Recent twin studies show that both genetic and environmental factors contribute to the development of eating disorders. As in many other fields, there is much enthusiasm regarding the possibility of locating the specific genes that influence the risk of eating disorders. Advances in molecular and statistical technology have made this task more feasible than it was in the past, and continued enhancements in new technology are expected in the future. Despite these advances, the resources required to map a gene for traits as complex as eating disorders are likely to be enormous. Researchers considering such an undertaking may wish to look for ways to reduce this demand, such as (1) using multivariate analyses, (2) studying intermediate quantitative phenotypes, (3) using large sibships, (4) analytic enhancements (e.g., multipoint analyses), (5) reconceptualizing power, (6) data pooling, and (7) disequilibrium mapping.

Chromosome Mapping↗
PubMed1998

Insertional mutagenesis in transgenic mice generated by the pronuclear microinjection procedure.

Insertional mutagenesis in transgenic mice is a powerful method to study structure/function relationships between individual genes and complex developmental traits in the whole organism. Unlike spontaneous or chemical-induced mutations, insertional mutations have the advantage that the mutant locus is "tagged" with the transgene and, therefore, readily accessible at the molecular level. Starting with the work on the limb deformity locus, we describe here the characterization of several mouse mutants generated by insertional mutagenesis with the pronuclear microinjection procedure. These transgenic lines have proven to be ideal as models for human disease and for studying the function of novel genes during development. We also describe the unique features of insertional mutations that arise in transgenic mice produced with the pronuclear microinjection procedure and provide recommendations on how to clone and characterize these mutations at the molecular level. Finally, we discuss future prospects for the use of this unique form of germline mutagenesis in the mouse.

Animals↗
PubMed1990

Association of class I bovine lymphocyte antigen complex alleles with health and production traits in dairy cattle.

Ninety-eight Holstein cows from the I-O-State breeding research herd were serologically typed for class I bovine lymphocyte antigens. After exclusion of animals carrying alleles that occurred at frequencies lower than 4%, records from 82 cows that had 161 lactations remained for analysis of major histocompatibility complex allelic effects. A gene substitution model was used to evaluate the additive effects of nine alleles (frequencies of 4 to 20%) at the bovine lymphocyte antigen complex A locus on general health, udder health, and production traits. Allele w14(w8) was associated with decreased quarter milk sample California Mastitis Test scores, composite milk sample California Mastitis Test and Wisconsin Mastitis Test scores, decreased total health costs, and with increased milk yield, fat yield, fat percentage, and income over feed costs. Allele w11 was associated with decreased clinical mastitis, discarded milk, and udder health costs but was also associated with decreased fat yield, fat percentage, and income over feed costs. Allele w31(w30) was associated with decreased fat percentage. These relationships suggest that alleles at the bovine lymphocyte antigen complex A locus may serve as markers for health and production traits. Thus, the potential may exist for enhancement of disease resistance or production in cattle via marker-assisted selection and genetic manipulation techniques using class I genes of the bovine major histocompatibility complex.

Alleles↗
PubMed1989

The chicken major histocompatibility complex in disease resistance and poultry breeding.

Numerous studies confirm that genes in the chicken major histocompatibility complex exert major genetic control over host resistance to autoimmune, viral, bacterial, and parasitic diseases. Examples of major histocompatibility complex associations with traits of growth and reproduction in the chicken are also available. Thus, the major effects of the major histocompatibility complex on the economically important traits of disease resistance, growth, and reproduction make the major histocompatibility complex a valuable subject for intensive analysis in agricultural species. This paper examines, as a model for integration of genetics and immunology, the research on the chicken major histocompatibility complex, which confirmed its role in genetic control of disease resistance, focusing on Marek's disease, a virally induced cancer. Current knowledge of associations of the chicken major histocompatibility complex with specific disease resistance, immune response, and other economic traits are selectively reviewed. Use of major histocompatibility complex typing in the poultry industry, including speculation about future applications, is presented.

Animals↗
PubMed2006

Bayesian method for gene detection and mapping, using a case and control design and DNA pooling.

Association mapping studies aim to determine the genetic basis of a trait. A common experimental design uses a sample of unrelated individuals classified into 2 groups, for example cases and controls. If the trait has a complex genetic basis, consisting of many quantitative trait loci (QTLs), each group needs to be large. Each group must be genotyped at marker loci covering the region of interest; for dense coverage of a large candidate region, or a whole-genome scan, the number of markers will be very large. The total amount of genotyping required for such a study is formidable. A laboratory effort efficient technique called DNA pooling could reduce the amount of genotyping required, but the data generated are less informative and require novel methods for efficient analysis. In this paper, a Bayesian statistical analysis of the classic model of McPeek and Strahs is proposed. In contrast to previous work on this model, I assume that data are collected using DNA pooling, so individual genotypes are not directly observed, and also account for experimental errors. A complete analysis can be performed using analytical integration, a propagation algorithm for a hidden Markov model, and quadrature. The method developed here is both statistically and computationally efficient. It allows simultaneous detection and mapping of a QTL, in a large-scale association mapping study, using data from pooled DNA. The method is shown to perform well on data sets simulated under a realistic coalescent-with-recombination model, and is shown to outperform classical single-point methods. The method is illustrated on data consisting of 27 markers in an 880-kb region around the CYP2D6 gene.

Alleles↗
PubMed2001

Parallel evolution of histophagy in ciliates of the genus Tetrahymena.

BACKGROUND: Species of Tetrahymena were grouped into three complexes based on morphological and life history traits: the pyriformis complex of microstomatous forms; the patula complex of microstome-macrostome transformers; and the rostrata complex of facultative and obligate histophages. We tested whether these three complexes are paraphyletic using the complete sequence of the small subunit rDNA (SSrDNA). RESULTS: In addition to the 16 species of Tetrahymena whose SSrDNA sequences are known, we sequenced the complete SSrDNA from the following histophagous Tetrahymena species; Tetrahymena bergeri, Tetrahymena mobilis, Tetrahymena rostrata, and Tetrahymena setosa as well as the macrostome species Tetrahymena vorax. We also included a ciliate tentatively identified as Lambornella sp., a parasite of the mosquito Aedes sp. We confirmed earlier results using SSrDNA, which showed two distinct clusters of Tetrahymena species: the australis group and borealis group. The genetic distances among Tetrahymena are in general very small. However, all nodes were supported by high bootstrap values. With the exception of T. bergeri and T. corlissi, which are both histophagous and group as sister species, all other histophagous Tetrahymena species are most closely related to a bacterivorous species. Furthermore, Lambornella sp. and T. empidokyrea, both mosquito parasites, are sister species, although there is a considerable genetic distance between them. CONCLUSIONS: There has been parallel evolution of histophagy in the genus Tetrahymena and the three classical species complexes are paraphyletic. As the genus Lambornella arises within the Tetrahymena clade, it is not likely a defensible one.

Animals↗
PubMed1999

Associations of the bovine major histocompatibility complex DRB3 (BoLA-DRB3) with production traits in Canadian dairy cattle.

Associations of two alleles of the bovine major histocompatibility complex DRB3 gene (BoLA-DRB3) with lowered somatic cell score (SCS) and occurrence of disease (BoLA-DRB3.2* 16 and *23, respectively) have previously been documented. The objective of this study was to evaluate potential relationships between BoLA-DRB3 alleles with production traits, namely 305-day milk, milk fat and milk protein yield, in a population of Canadian dairy cattle (Holstein, n = 835 and Jersey, n = 66) over the course of two lactations. No significant associations were detected between BoLA alleles and production traits in Jerseys. In Holsteins, alleles *16 and *23 also did not show associations with production traits but allele *8 was significantly associated with increased 305-day milk, fat and protein yields in the previous lactation (the lactation prior to immunization with a gram negative core antigen vaccine), and with increased protein production in the subsequent (with reference to the time of immunization) lactation. Allele *22 was associated with decreased milk and protein yield in both previous and subsequent lactations. Therefore, it can be concluded that increasing or decreasing the frequency of BoLA alleles *16 and *23 to reduce SCS or increase resistance to mastitis in this population would not have adverse effects on production in this population, and that certain BoLA alleles (*8 and *22) are associated with altered production traits in Canadian Holsteins.

Alleles↗
PubMed2005

The landscape of genetic complexity across 5,700 gene expression traits in yeast.

Many studies have identified quantitative trait loci (QTLs) that contribute to continuous variation in heritable traits of interest. However, general principles regarding the distribution of QTL numbers, effect sizes, and combined effects of multiple QTLs remain to be elucidated. Here, we characterize complex genetics underlying inheritance of thousands of transcript levels in a cross between two strains of Saccharomyces cerevisiae. Most detected QTLs have weak effects, with a median variance explained of 27% for highly heritable transcripts. Despite the high statistical power of the study, no QTLs were detected for 40% of highly heritable transcripts, indicating extensive genetic complexity. Modeling of QTL detection showed that only 3% of highly heritable transcripts are consistent with single-locus inheritance, 17-18% are consistent with control by one or two loci, and half require more than five loci under additive models. Strikingly, analysis of parent and progeny trait distributions showed that a majority of transcripts exhibit transgressive segregation. Sixteen percent of highly heritable transcripts exhibit evidence of interacting loci. Our results will aid design of future QTL mapping studies and may shed light on the evolution of quantitative traits.

Computer Simulation↗
PubMedDate not supplied

Complex segregation analysis of quantitative dermatoglyphic traits in five Indian populations.

OBJECTIVE: Dermatoglyphics is widely used as a genetically determined trait in anthropogenetics although the genetic nature of its inheritance is still inconclusive, due to the lack of any established genetic model to resolve the existing inconsistencies in the literature. However, advanced statistical packages for complex segregation analyses are available and the aim of the present study is to determine the mode of dermatoglyphic trait inheritance in five different ethnic populations. METHODS: Five hundred families (2435 individuals) of two generations were used for principal component analysis, familial correlation and segregation analysis (package MAN-5). RESULTS: The similarity of three factors suggests a common internal structure. Significant familial correlation (except spouse) indicates the involvement of a familial component in the variation of dermatoglyphic traits. Segregation analyses suggest the transmission of a genetic effect in the families which follows the Mendelian model and confirms a major gene effect on factor 1 and factor 2 with two co-dominant alleles. There is no evidence of a major gene effect or environmental effect on factor 3 (a-b ridge counts). The nature of transmission and trait variance (H2) strongly supports the existence of a common nature of dermatoglyphic trait inheritance in populations, irrespective of ethnic and geographic area. CONCLUSION: Major gene involvement in finger dermatoglyphics according to Mendelian models is confirmed.

Analysis of Variance↗
PubMed2005

Non-lactational traits of importance in dairy cows and applications for emerging biotechnologies.

Dairy cattle have traditionally been selected for their ability to produce milk and milk components. The traditional single-minded approach to selection of dairy cattle has now changed and secondary traits are being included in selection indices by decreasing the emphasis on production. Greater emphasis on non-production traits reflects the industry's desire for functional dairy cattle. Six broad categories of non-lactational traits are discussed in this review. They are: type; growth, body size and composition; efficiency of feed utilisation; disease resistance, e.g. udder health as measured by somatic cell score; reproduction; and management. Most of these traits can be found within selection indices worldwide, although relative emphasis varies. The non-lactational traits mentioned above are quantitative, meaning that the phenotype in the whole animal represents the sum of lesser traits that cannot be easily measured. The physiological mechanisms that underlie quantitative traits are extremely complex. Genetic selection can be applied to quantitative traits but it is difficult to link successful genetic selection with the underlying physiological mechanisms. The importance that the bovine genome sequence will play in the future of the genetics of dairy cattle cannot be understated. Completing the bovine genome sequence is the first step towards modernising our approach to the genetics of dairy cattle. Finding genes in the genome is difficult and scanning billions of base pairs of DNA is an imperfect task. The function of most genes is either unknown or incompletely understood. Combining all of the information into a useable format is known as bioinformatics. At the present time, our capacity to generate information is great but our capacity to understand the information is small. The important information resides within subtle changes in gene expression and within the cumulative effect that these have. Traditional methods of genetic selection in dairy cattle will be used for the foreseeable future. Most non-lactational traits are heritable and will be included in selection indices if the traits have value. The long-term prognosis for genome science is good but advances will take time. Genetic selection in the genome era will be different because DNA sequence analysis may replace traditional methods of genetic selection.

Animals↗