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At least 55 records · Page 3Linked to original sources
PubMed2005

An EM algorithm for mapping quantitative resistance loci.

Many disease resistance traits in plants have a polygenic background and the disease phenotypes are modified by environmental factors. As a consequence, the phenotypic values usually show a quantitative variation. The phenotypes of such disease traits, however, are often measured in discrete but ordered categories. These traits are called ordinal traits. In terms of disease resistance, they are called quantitative resistance traits, as opposed to qualitative resistance traits, and are controlled by the quantitative resistance loci (QRL). Classical quantitative trait locus mapping methods are not optimal for ordinal trait analysis because the assumption of normal distribution is violated. Methods for mapping binary trait loci are not suitable either because there are more than two categories in ordinal traits. We developed a maximum likelihood method to map these QRL. The method is implemented via a multicycle expectation-conditional-maximization (ECM) algorithm under the threshold model, where we can estimate both the QRL effects and the thresholds that link the disease liability and the categorical phenotype. The method is verified in simulated data under various combinations of the parameters. An SAS program is available to implement the multicycle ECM algorithm. The program can be downloaded from our website at www.statgen.ucr.edu.

Algorithms↗
PubMed2003

Congenital talipes equinovarus (clubfoot): a disorder of the foot but not the hand.

Idiopathic (non-syndromic) congenital talipes equinovarus, or clubfoot, is a poorly understood but common developmental disorder of the lower limb, which affects at least 2 per 1000 Scottish births (ISD data). It is defined as a fixation of the foot in a hand-like orientation--in adduction, supination and varus--with concomitant soft tissue abnormalities. Despite advances in treatment, disability often persists. The aetiology of the condition has been little studied and is poorly understood. Neurological, muscular, bony, connective tissue and vascular mechanisms have been proposed, but the only firm evidence is that the mildest cases appear to be associated with intra-uterine posture. There is evidence for a genetic contribution to congenital talipes equinovarus aetiology. Its incidence varies with ethnic group, and we found that a family history is present in 24-50% of cases, depending on the population studied. Complex segregation analysis suggests that the most likely inheritance pattern is a single gene of major effect operating against a polygenic background. Possible mechanisms for congenital talipes equinovarus are discussed.

Amniocentesis↗
PubMed2005

Possible association of the human KCNE1 (minK) gene and QT interval in healthy subjects: evidence from association and linkage analyses in Israeli families.

QT interval prolongation is associated with increased risk of sudden and non-sudden cardiac death. Potassium channel gene variants are associated with inherited long QT syndromes. Using linkage and association analyses, we investigated whether variants in the potassium channel subunit KCNE1 are associated with QTc intervals in an unselected population sample of 80 kindreds living in kibbutz settlements in Israel. Variance-component linkage analysis revealed weak evidence of linkage of KCNE1 polymorphisms with QTc intervals. Family-based association analysis showed a significant association between the G38S polymorphism and QTc interval. Further quantitative trait association analysis demonstrated a significant residual heritability component (h(2)= 0.33), and that the effect of the G38S variant allele is modified by gender. Estimated maximum likelihood parameters from these models indicated that male gender, age, hypertension, diabetes, hypercholesterolemia, fibrinogen and BMI were positively associated with QTc interval; level of education and cigarette smoking showed an inverse association. Both erythrocyte membrane n-6 and n-3 fatty acids showed a significant inverse association with QTc interval. While more than 15.8% of QTc variability was contributed by covariates, another 4.7% was explained by dietary factors, the G38S polymorphism explained 2.2%, and approximately 36% was explained by polygenes. An in silico analysis showed also that the novel V80 SNP, another KCNE1 synonymous variant, abolishes the recognition for a splicing enhancer, which may lead to an increased effect of the G38S mutation. These results demonstrate that, in addition to polygenic background, dietary factors and other covariables, the KCNE1 G38S variant is involved in determining QTc levels in this population-based sample of families.

Adult↗
PubMedDate not supplied

Millennium fat-cell lipolysis reveals unsuspected novel tracks.

Adipose tissue lipolysis, i.e., the catabolic process leading to the breakdown of triglycerides into fatty acids and glycerol, is often considered as a simple and well-understood metabolic pathway. However, progress on the hormonal regulation and molecular mechanism of fat-cell lipolysis is opening new avenues and points to a number of unanswered questions. Recent studies on the lipolytic beta- and antilipolytic alpha2-adrenergic control of lipolysis has allowed a better understanding of the relative contribution of the two types of receptors and provide strong evidence for the in vivo implication of alpha2-adrenoceptors in the physiological control of subcutaneous adipose-tissue lipolysis. A novel lipolytic system has been characterized in human fat cells. Natriuretic peptides stimulate lipolysis through a cGMP-dependent pathway. The molecular details of the lipolytic reaction are not fully understood. Translocation of hormone-sensitive lipase, the rate-limiting enzyme of lipolysis, to the lipid droplet seems to be an important step during lipolytic activation. Reorganization of the lipid droplet coating by perilipins may also facilitate the access of the enzyme. Unexpectedly, hormone-sensitive lipase-deficient mice are not obese and show residual adipose-tissue lipolysis, which suggests the existence of another triglyceride lipase. Whether the expression of this uncharacterized neutral lipase is compensatory for the lack of hormone-sensitive lipase is an important question yet to be resolved. In humans, alterations of hormone-sensitive lipase expression are associated with changes in lipolysis in various physiological and pathological states. Genetic studies show that beta2-adrenoceptor and hormone-sensitive lipase genes may participate in the polygenic background of obesity.

Adipose Tissue↗
PubMed2006

Segregation analysis of blood oxygen saturation in broilers suggests a major gene influence on ascites.

1. Blood oxygen saturation (SaO) is a potential indicator trait for resistance to ascites in chickens. 2. The objective of the study was to investigate the genetic architecture of SaO in a meat-type chicken line reared in commercial conditions. 3. Data were collected over 15 generations of selection and were divided into two data sets on the basis of a change in recording age from 6 to 5 weeks of age, approximately halfway through the period. The resulting pedigrees comprised in excess of 90,000 birds each and, on average, 12% of these birds had SaO records. 4. Segregation analyses of SaO were carried out assuming a mixed inheritance model that included a major locus segregating in a polygenic background. 5. The analyses suggest that a major gene is involved in the genetic control of SaO in this line. The putative gene acts in a dominant fashion and has an additive effect of around 0.90 sigma(p), equivalent to a predicted difference in SaO between the two homozygous classes of more than 10%. The frequency of the allele that increases SaO changed from 0.53 to 0.65 from the first to the second set of data, consistent with selection on SaO scores. 6. Using estimated genotype probabilities at the putative major locus, we inferred that it acts in an overdominant fashion on body weight and fleshing score. If the low SaO allele leads to susceptibility to ascites, its combined effects are consistent with it being maintained in the population by a balance of natural selection on fitness nad artificial selection on growth and carcase traits. 7. Even with selection on both SaO and growth traits, the combined genotypic effects would make it difficult to remove the unfavourable low-SaO allele by means of traditional selection without the use of genetic markers.

Animals↗
PubMed2000

After BRCA1 and BRCA2-what next? Multifactorial segregation analyses of three-generation, population-based Australian families affected by female breast cancer.

Mutations in BRCA1 and BRCA2 that cause a dominantly inherited high risk of female breast cancer seem to explain only a small proportion of the aggregation of the disease. To study the possible additional genetic components, we conducted single-locus and two-locus segregation analyses, with and without a polygenic background, using three-generation families ascertained through 858 women with breast cancer diagnosed at age <40 years, ascertained through population cancer registries in Melbourne and Sydney, Australia. Extensive testing for deleterious mutations in BRCA1 and BRCA2, to date, has identified 34 carriers. Our analysis suggested that, after other possible unmeasured familial factors are adjusted for and the known BRCA1 and BRCA2 mutation carriers are excluded, there appears to be a residual dominantly inherited risk of female breast cancer in addition to that derived from mutations in BRCA1 and BRCA2. This study also suggests that there is a substantial recessively inherited risk of early-onset breast cancer. According to the best-fitting model, after excluding known carriers of mutations in BRCA1 and BRCA2, about 1/250 (95% confidence interval [CI] 1/500 to 1/125) women have a recessive risk of 86% (95% CI 69%-100%) by age 50 years and of almost 100% by age 60 years. Possible reasons that our study has implicated a novel strong recessive effect include our inclusion of data on lineal aunts and grandmothers, study of families ascertained through women with early-onset breast cancer, allowance for multiple familial factors in the analysis, and removal of families for whom the cause (i.e., BRCA1 or BRCA2) is known. Our findings may have implications for attempts to identify new breast cancer-susceptibility genes.

Age Factors↗
PubMed1984

Inheritance of adrenal phenylethanolamine N-methyltransferase activity in the rat.

Phenylethanolamine N-methyltransferase (PNMT) is the enzyme that catalyzes the S-adenosyl-L-methionine-dependent methylation of (-)norepinephrine to (-)epinephrine in the adrenal medulla. Adrenal PNMT activity is markedly different in two highly inbred rat strains; enzyme activity in the F344 strain is more than fivefold greater than that in the Buf strain. Initial characterization of the enzyme in the two inbred strains reveals evidence for catalytic and structural differences, as reflected in dissimilar Km values for the cosubstrate (S-adenosyl-L-methionine) and prominent differences in thermal inactivation curves. To assess adrenal PNMT activity in an F344 X Buf pedigree, we employed a statistical procedure to test for one- and two-locus hypotheses in the presence of within-class correlations due to cage or litter effects. The PNMT data in the pedigree are best accounted for by segregation at a simple major locus superimposed upon a polygenic background; data obtained from the biochemical studies suggest that the major locus is a structural gene locus.

Adrenal Medulla↗
PubMed1996

Maximum likelihood analysis of rare binary traits under different modes of inheritance.

Maximum likelihood methodology was applied to determine the mode of inheritance of rare binary traits with data structures typical for swine populations. The genetic models considered included a monogenic, a digenic, a polygenic, and three mixed polygenic and major gene models. The main emphasis was on the detection of major genes acting on a polygenic background. Deterministic algorithms were employed to integrate and maximize likelihoods. A simulation study was conducted to evaluate model selection and parameter estimation. Three designs were simulated that differed in the number of sires/number of dams within sires (10/10, 30/30, 100/30). Major gene effects of at least one SD of the liability were detected with satisfactory power under the mixed model of inheritance, except for the smallest design. Parameter estimates were empirically unbiased with acceptable standard errors, except for the smallest design, and allowed to distinguish clearly between the genetic models. Distributions of the likelihood ratio statistic were evaluated empirically, because asymptotic theory did not hold. For each simulation model, the Average Information Criterion was computed for all models of analysis. The model with the smallest value was chosen as the best model and was equal to the true model in almost every case studied.

Algorithms↗
PubMed1997

Bayesian statistical analyses for presence of single genes affecting meat quality traits in a crossed pig population.

Presence of single genes affecting meat quality traits was investigated in F2 individuals of a cross between Chinese Meishan and Western pig lines using phenotypic measurements on 11 traits. A Bayesian approach was used for inference about a mixed model of inheritance, postulating effects of polygenic background genes, action of a biallelic autosomal single gene and various nongenetic effects. Cooking loss, drip loss, two pH measurements, intramuscular fat, shearforce and back-fat thickness were traits found to be likely influenced by a single gene. In all cases, a recessive allele was found, which likely originates from the Meishan breed and is absent in the Western founder lines. By studying associations between genotypes assigned-to individuals based on phenotypic measurements for various traits, it was concluded that cooking loss, two pH measurements and possibly backfat thickness are influenced by one gene, and that a second gene influences intramuscular fat and possibly shearforce and drip loss. Statistical findings were supported by demonstrating marked differences in variances of families of fathers inferred as carriers and those inferred as noncarriers. It is concluded that further molecular genetic research effort to map single genes affecting these traits based on the same experimental data has a high probability of success.

Animals↗
PubMed2001

Statistical issues in the analysis of quantitative traits in combined crosses.

We consider some practical statistical issues in QTL analysis where several crosses originate in multiple inbred parents. Our results show that ignoring background polygenic variation in different crosses may lead to biased interval mapping estimates of QTL effects or loss of efficiency. Threshold and power approximations are derived by extending earlier results based on the Ornstein-Uhlenbeck diffusion process. The results are useful in the design and analysis of genome screen experiments. Several common designs are evaluated in terms of their power to detect QTL.

Crosses, Genetic↗
PubMed2004

Haplotypes and SNPs in 13 lipid-relevant genes explain most of the genetic variance in high-density lipoprotein and low-density lipoprotein cholesterol.

Single nucleotide polymorphisms (SNPs) and derived haplotypes within multiple genes may explain genetic variance in complex traits; however, this hypothesis has not been rigorously tested. In an earlier study we analyzed six genes and have now expanded this investigation to include 13. We studied 250 families including 1054 individuals and measured lipid phenotypes. We focused on low-density cholesterol (LDL), high-density cholesterol (HDL) and their ratio (LDL/HDL). A component analysis of the phenotypic variance relying on a standard genetic model' showed that the genetic variance on LDL explained 26%, on HDL explained 38% and on LDL/HDL explained 28% of the total variance, respectively. Genotyping of 93 SNPs in 13 lipid-relevant genes generated 230 haplotypes. The association of haplotypes in all the genes tested explained a major fraction of the genetic phenotypic variance component. For LDL, the association with haplotypes explained 67% and for HDL 58% of the genetic variance relative to the polygenic background. We conclude that these haplotypes explain most of the genetic variance in LDL, HDL and LDL/HDL in these representative German families. An analysis of the contribution to the genetic variance at each locus showed that APOE (50%), CETP (28%), LIPC (9%), APOB (8%) and LDLR (5%) influenced variation in LDL. LIPC (53%), CETP (25%), ABCA1 (10%), LPL (6%) and LDLR (6%) influenced the HDL variance. The LDL/HDL ratio was primarily influenced by APOE (36%), CETP (27%) and LIPC (31%). This expanded analysis substantially increases the explanation of genetic variance on these complex traits.

Cholesterol, HDL↗
PubMed1999

No mutations found in candidate genes for dystocia.

Dystocia is a disorder characterized by prolonged or dysfunctional labour. Delivery that starts late or not at all, leads to an increased risk for Caesarean section, infant morbidity and mortality. Familial aggregations of dystocia suggest a polygenic background. We have studied three candidate genes for dystocia, i.e. the genes for testosterone 5-alpha reductase type 1, prostaglandin F2alpha receptor and endothelin 1 and performed mutational screening in 23 women with dystocia, of which 12 have affected relatives. No mutations were found, making it unlikely that any of these genes represent a major cause of dystocia in man.

3-Oxo-5-alpha-Steroid 4-Dehydrogenase↗
PubMed1989

Current knowledge regarding the genetics of human hypertension.

Observations over 11 years from the University of Utah Cardiovascular Genetics Research Clinic and published data from other studies are reviewed to illustrate research approaches, developing results and prospects for future studies. Strong associations with hypertension have been found for several biochemical tests that show substantial genetic determination. Suggestions of recessive major gene effects and significant polygenic background determinations have been found for several variables, including urinary kallikrein excretion, intracellular sodium concentration, sodium-lithium countertransport and sodium-potassium cotransport. Each of these variables is related in some way to sodium or potassium metabolism, or both, and may help to improve the understanding of a possibly inherited susceptibility to hypertension that is related to dietary electrolyte intake. A second major group of factors involving familial predisposition to hypertension include lipid abnormalities (increased very-low- and low-density lipoprotein cholesterol and decreased high-density lipoprotein cholesterol); increased fasting insulin levels or insulin resistance, or both; obesity (especially central or upper body obesity); and multiple environmental factors influencing these metabolic systems, including dietary fat, carbohydrate and calorie intake; physical exercise; and certain antihypertensive medications that adversely affect lipid metabolism and glucose tolerance. Some studies even suggest a possible link between these two large groups of factors (electrolyte metabolism and lipid-insulin metabolism). Hypertriglyceridaemia and hyperinsulinaemia are both significantly correlated with increased levels of several cation-flux tests. It is recommended that studies of human hypertension apply these biochemical profiles to study sibships with two or more hypertensive siblings as a cost-effective initial approach.(ABSTRACT TRUNCATED AT 250 WORDS)

Diabetes Mellitus↗
PubMed2001

A maximum likelihood-based method for mining major genes affecting a quantitative character.

In this article, we present a maximum likelihood-based analytical approach for detecting a major gene of large effect on a quantitative trait in a progeny population derived from a mating design. Our analysis is based on a mixed genetic model specifying both major gene and background polygenic inheritance. The likelihood of the data is formulated by combining the information about population behaviors of the major gene during hybridization and its phenotypic distribution densities. The EM algorithm is implemented to obtain maximum likelihood estimates for population and quantitative genetic parameters of the major locus. This approach is applied to detect an overdominant gene governing stem volume growth in a factorial mating design of aspen trees. It is suggested that further molecular genetic research toward mapping single genes affecting aspen growth and production based on the same experimental data has a high probability of success.

Algorithms↗
PubMed1994

Genetic analysis of atopy and asthma as quantitative traits and ordered polychotomies.

Traits related to atopy and asthma were defined in a random cohort of 131 families with three or more children. Correlation analysis provides no evidence of imprinting, maternal effect, or a major role of environment shared by sibs. Commingling analysis favours more than one distribution, the upper one being common for asthma and very common for atopy. Segregation analysis of rank-transformed variables provides only equivocal evidence of major genes against a polygenic background but suggests that such genes (if present) are individually common and not of large effect. Segregation analysis under a two-locus model gives consistent results with minimal distributional assumptions. To enter combined segregation analysis we favour a restricted model in which the major locus is additive on the liability scale and the pseudopolygenic modifier locus accounts for at least half the genetic variance. Total IgE and bronchial reactivity are proposed for meta-analysis of atopy and asthma respectively. Genetic analysis of complex inheritance is discussed and it is shown that allelic association with random loci is not a feasible approach.

Adolescent↗
PubMed2006

Genetic and epigenetic risks of intracytoplasmic sperm injection method.

Pregnancies achieved by assisted reproduction technologies, particularly by intracytoplasmic sperm injection (ICSI) procedures, are susceptible to genetic risks inherent to the male population treated with ICSI and additional risks inherent to this innovative procedure. The documented, as well as the theoretical, risks are discussed in the present review study. These risks mainly represent that consequences of the genetic abnormalities underlying male subfertility (or infertility) and might become stimulators for the development of novel approaches and applications in the treatment of infertility. In addition, risks with a polygenic background appearing at birth as congenital anomalies and other theoretical or stochastic risks are discussed. Recent data suggest that assisted reproductive technology might also affect epigenetic characteristics of the male gamete, the female gamete, or might have an impact on early embryogenesis. It might be also associated with an increased risk for genomic imprinting abnormalities.

Animals↗
PubMed1990

Evidence of a rare gene for low systolic blood pressure in the Framingham Heart Study.

A major risk factor for coronary heart disease in both men and women is elevated systolic blood pressure (SBP). We performed segregation analysis on age, sex-adjusted, and transformed systolic blood pressure data on 1,141 families from the Framingham cohort-offspring study using the segregation analysis program POINTER. The results of hypothesis testing revealed: (1) these data are consistent with familial transmission; (2) there is evidence for the transmission of a rare, major gene for low SBP with a gene frequency of q = 0.02; and (3) most of the transmissible component to SBP can be attributed to the polygenic background with H = 0.31.

Adult↗
PubMedDate not supplied

Population studies in northern Sweden. 18. Geographical covariation between hypercholesterolemia and Finnish genetic influence.

The population of northern Sweden shows a marked ethnic heterogeneity and a unique distribution of disorders with a monogenic or polygenic background, among them cardiovascular diseases. We have studied variations between 23 North Swedish subpopulations (regions) with respect to hypercholesterolemia and its possible determinants including dietary factors, obesity and the degree of Finnish genetic influence. A significant regional heterogeneity was found concerning hypercholesterolemia, obesity and high consumption of 'boiled' coffee. Hypercholesterolemia showed significant geographical covariations with Finnish genetic influence and consumption of 'boiled' coffee. The results are consistent with the hypothesis that in addition to environmental factors Finnish genetic influence contributes to the development of hypercholesterolemia and thereby to the increased rate of cardiovascular disease found in northern Sweden.

Adult↗