Two-trait-locus linkage analysis: a powerful strategy for mapping complex genetic traits.

Recent advances in molecular biology have provided geneticists with ever-increasing numbers of highly polymorphic genetic markers that have made possible linkage mapping of loci responsible for many human diseases. However, nearly all diseases mapped to date follow clear Mendelian, single-locus segregation patterns. In contrast, many common familial diseases such as diabetes, psoriasis, several forms of cancer, and schizophrenia are familial and appear to have a genetic component but do not exhibit simple Mendelian transmission. More complex models are required to explain the genetics of these important diseases. In this paper, we explore two-trait-locus, two-marker-locus linkage analysis in which two trait loci are mapped simultaneously to separate genetic markers. We compare the utility of this approach to standard one-trait-locus, one-marker-locus linkage analysis with and without allowance for heterogeneity. We also compare the utility of the two-trait-locus, two-marker-locus analysis to two-trait-locus, one-marker-locus linkage analysis. For common diseases, pedigrees are often bilineal, with disease genes entering via two or more unrelated pedigree members. Since such pedigrees often are avoided in linkage studies, we also investigate the relative information content of unilineal and bilineal pedigrees. For the dominant-or-recessive and threshold models that we consider, we find that two-trait-locus, two-marker-locus linkage analysis can provide substantially more linkage information, as measured by expected maximum lod score, than standard one-trait-locus, one-marker-locus methods, even allowing for heterogeneity, while, for a dominant-or-dominant generating model, one-locus models that allow for heterogeneity extract essentially as much information as the two-trait-locus methods. For these three models, we also find that bilineal pedigrees provide sufficient linkage information to warrant their inclusion in such studies. We also discuss strategies for assessing the significance of the two linkages assumed in two-trait-locus, two-marker-locus models.     

Molecular and statistical approaches to the detection and correction of errors in genotype databases.

Errors in genotyping data have been shown to have a significant effect on the estimation of recombination fractions in high-resolution genetic maps. Previous estimates of errors in existing databases have been limited to the analysis of relatively few markers and have suggested rates in the range 0.5%-1.5%. The present study capitalizes on the fact that within the Centre d'Etude du Polymorphisme Humain (CEPH) collection of reference families, 21 individuals are members of more than one family, with separate DNA samples provided by CEPH for each appearance of these individuals. By comparing the genotypes of these individuals in each of the families in which they occur, an estimated error rate of 1.4% was calculated for all loci in the version 4.0 CEPH database. Removing those individuals who were clearly identified by CEPH as appearing in more than one family resulted in a 3.0% error rate for the remaining samples, suggesting that some error checking of the identified repeated individuals may occur prior to data submission. An error rate of 3.0% for version 4.0 data was also obtained for four chromosome 5 markers that were retyped through the entire CEPH collection. The effects of these errors on a multipoint map were significant, with a total sex-averaged length of 36.09 cM with the errors, and 19.47 cM with the errors corrected. Several statistical approaches to detect and allow for errors during linkage analysis are presented. One method, which identified families containing possible errors on the basis of the impact on the maximum lod score, showed particular promise, especially when combined with the limited retyping of the identified families. The impact of the demonstrated error rate in an established genotype database on high-resolution mapping is significant, raising the question of the overall value of incorporating such existing data into new genetic maps.     

Liming induced stimulation of the amino acid metabolism in mycorrhizal roots of Norway spruce (Picea abies [L.] Karst.)

Localization and activity of three enzymes involved in the amino acid metabolism of ectomycorrhizas were investigated within an interdisciplinary experiment performed in a mature Norway spruce stand in Southern Germany (Höglwald). The enzymes NAD-glutamate dehydrogenase and aspartate aminotransferase were present in root cells, whereas aminopeptidase was found in mycorrhizas of Norway spruce such as Piceirhiza nigra and those with the fungi Cenococcum geophilum, Elaphomyces sp., Russula ochroleuca and Tylospora sp. Mycorrhizas growing in the humus layer contained about double the amount of protein found in those taken from the upper mineral soil (0–5 cm).Acid irrigation of the soil had no effect on the activity of any of the investigated enzymes, soluble protein or total N-contents irrespective of whether roots were taken from the organic layer or from the upper mineral soil. Liming, however, stimulated the activity of the three enzymes in mycorrhizas of the organic layer (O_f+O_h) whereas it had no effect on the activity of the investigated enzymes of mycorrhizas in the upper mineral soil. This effect is attributed to increased contents of soluble organic nitrogen compounds in the soil of the limed plots as compared to the unlimed plots.     

Prevalence of Alzheimer's disease and vascular dementia: association with education. The Rotterdam study.

OBJECTIVE--To estimate the prevalence of dementia and its subtypes in the general population and examine the relation of the disease to education. DESIGN--Population based cross sectional study. SETTING--Ommoord, a suburb of Rotterdam. SUBJECTS--7528 participants of the Rotterdam study aged 55-106 years. RESULTS--474 cases of dementia were detected, giving an overall prevalence of 6.3%. Prevalence ranged from 0.4% (5/1181 subjects) at age 55-59 years to 43.2% (19/44) at 95 years and over. Alzheimer''s disease was the main subdiagnosis (339 cases; 72%); it was also the main cause of the pronounced increase in dementia with age. The relative proportion of vascular dementia (76 cases; 16%), Parkinson''s disease dementia (30; 6%), and other dementias (24; 5%) decreased with age. A substantially higher prevalence of dementia was found in subjects with a low level of education. The association with education was not due to confounding by cardiovascular disease. CONCLUSIONS--The prevalence of dementia increases exponentially with age. About one third of the population aged 85 and over has dementia. Three quarters of all dementia is due to Alzheimer''s disease. In this study an inverse dose-response relation was found between education and dementia--in particular, Alzheimer''s disease.     

Simulation model for gynecologic specimen classification in a high-resolution prescreening system

Presentation is made of the design of a statistical model for the generation of "artificial specimens" to be used in the development and testing of a high-resolution prescreening system for gynecologic specimen classification. The model is based on two considerations: (1) the nature of the biologic material to be examined and (2) the system to be studied, which in this case is the FAZYTAN cervical prescreening system. Since gynecologic specimens that belong to the same clinical class (Papanicolaou group) have similar compositions of the different cytologic cell types, the simulation model presented is based on the close relationship between the degree of cancer suspiciousness expressed in the clinical diagnostic group and the composition of the cellular samples on a specimen. Statistically, the model considered here is based on an analysis of the single-cell classification (SCC) output process, taking the inherent system properties into account. The statistical information obtained by evaluating large sets of labelled cells is then used to produce artificially generated point distributions in the SCC decision space ("artificial specimens"), which can be used for examination of system reactions under controlled conditions. False-positive and false-negative error rates and system operation characteristics can be measured, and the effects of varying cell compositions as well as the relative performance of different specimen classifiers can be investigated. Although the "artificial specimens" thus created allow the investigation of system reactions with respect to a great variety of input processes, they cannot replace experiments on thousands of original specimens in order to measure system quality under realistic conditions.     

Albumin extinction followed by de novo methylation of its gene in somatic hybrids of a rat hepatoma

We have previously identified an Msp I site at the 5′ end of the rat albumin gene whose undermethylation is necessary but not sufficient for stable albumin expression in rat hepatoma cells [1]. We have also shown that the extinction of albumin expression in somatic hybrids is not the result of methylation at this site, since for two different crosses, rapid extinction was found to occur in the absence of any de novo methylation of the previously active gene[2]. In the present study, we examine albumin expression and albumin gene methylation for independent hybrid clones isolated from crosses between albumin expressing rat hepatoma cells and cells of two different non-expressing lines. The cells from hybrid clones of both crosses are characterized by stable extinction of albumin expression. Moreover, we find that de novo methylation of the “extinguished” albumin gene can occur in somatic hybrids, but only some weeks after the gene has ceased to be expressed.     

The effect of short term calf removal in combination with GnRH treatment and the effect of limited nursing on reproductive performance of postpartum suckled beef cows administered PGF2alpha for ovulation control

Over a two year period, postpartum suckled Hereford and Angus Cows (n=213) were administered two injections of PGF(2)alpha (25 mg/injection) and divided into three groups. No additional treatments were administered to cows in Group I and calves were allowed to nurse their dams ad libitum. In Group II, calves were removed for 48 hours beginning on the third day following the initial PGF(2)alpha injection. These cows were given a subcutaneous injection of 250 mug GnRH dissolved in 2% carboxymethylcellulose midway through the 48 hour period. In Group III, calves were allowed to nurse their dams for only one hour per day for the first 7 days after the initial PGF(2)alpha injection. In year 1, PGF(2)alpha was administered 14 days apart whereas in year 2, PGF(2)alpha was administered 11 days apart. Cows were artificially inseminated at 72 and 96 hours after the second injection of PGF(2)alpha. In year 1, the numbers of cows that conceived to the timed inseminations were similar (P > .10) for the three groups. In year 2, a higher percentage of cows in groups II (P < .10) and III (P < .05) conceived to the timed inseminations than in group I. Other reproductive performance parameters were similar (P > .10) between groups for both years 1 and 2. In summary, limited nursing and short term calf removal in conjunction with GnRH treatment may improve the pregnancy rate in cows administered PGF(2)alpha for ovulation control.     

Maximum likelihood estimation by counting methods under polygenic and mixed models in human pedigrees.

For pedigree data, the maximum likelihood estimates of the parameters in polygenic and mixed models are derived analytically although not in closed form but in terms of "counting equations" allowing an iterative solution. Likelihood computations, tests of significance, and tests of goodness of fit are presented. Accelerating the (linear) rate of convergence by a very simple method is demonstrated.     

Wound complications after median sternotomy: A study of 61 patients from a consecutive series of 9,279

Among a consecutive series of 9,279 sternotomies performed during a period of 2(1/2) years, 61 (0.66%) patients developed significant wound complications. Of these, 58 (95.1%) survived. Sternal infection occurred in 36 patients (0.39%). Predisposing factors included chronic obstructive pulmonary disease, diabetes mellitus, obesity, closed chest massage, prolonged assisted ventilation, and excessive bleeding after operation. Positive end expiratory pressure (PEEP) did not, in itself, predispose to sternal dehiscence. Intermittent positive pressure breathing (IPPB) treatments caused excessive coughing, which may have increased the likelihood of dehiscence. Disposable drapes and expeditious surgery probably contributed to the low incidence of wound infection. Early diagnosis, surgical debridement, rewiring and primary closure with substernal drainage, without continuous antibiotic irrigation, resulted in satisfactory resolution in most patients.     

Ionescu-Shiley pericardial xenograft valve: Hemodynamic evaluation and early clinical follow-up of 326 patients

Dissatisfaction with the hemodynamic characteristics of available porcine valves prompted a clinical trial of the Ionescu-Shiley percardial xenograft (ISPX) valve. Three hundred fifty-six ISPX valves were implanted consecutively in 326 patients. Operative mortality was 2.6% (2/75) for aortic valve replacement alone and 7.7% (12/155) for aortic valve replacements that included reoperations and combined procedures such as mitral commissurotomy, annuloplasty, and coronary artery bypass. Operative mortality for all patients who underwent mitral valve replacement was 9.5% (14/147). The mean peak systolic gradient pressure in the aortic position was 5.4 mm Hg overall and 4.27 mm Hg with the size 19 mm valve. There were no embolic episodes in patients who received the ISPX valve in the aortic position. The available data indicate that the rate of peripheral embolism with the ISPX valve compares favorably with that of porcine valves. Considering its hemodynamic advantage, if the longterm durability of the full-orifice Ionescu-Shiley pericardial xenograft valve continues to be confirmed by follow-up studies, it is our opinion that it is the biologic valve of choice.