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International Commission for Protection against Environmental Mutagens and Carcinogens. ICPEMC Working Paper 5/6. Perspectives in mutation epidemiology, 6. A 1983 view of sentinel phenotypes.

A sentinel phenotype is a clinical disorder or syndrome that (1) occurs sporadically as a consequence of a single, highly penetrant mutant gene, (2) is a dominant or X-linked trait of considerable frequency and low fitness, and (3) is uniformly expressed and accurately diagnosable with minimal effort at or near birth. Although 1828 autosomal dominant traits are known in human beings, 36 can be considered as candidate sentinel phenotypes, along with 5 X-linked disorders. Based on surveys of malformations in infants and children, 16 additional traits are proposed beyond previous lists. In Hungary, the 24 syndromes or defects with reliable manifestations in newborn infants occur with a frequency of 2.5-3.3 per 10 000 live births. As markers of human mutations, sentinel phenotypes have the advantage of representing germinal mutations that result in significant health problems. There are severe disadvantages that have, to date, prevented the launching of a field demonstration of the value of these phenotypes in mutation epidemiology. Agreement on a list of phenotypes has been delayed by continued recognition of two or more distinct genetic diseases within what was once thought to be a single disorder. For the same reason, most of the candidate sentinel phenotypes have not been assigned unique codes in the International Classification of Diseases. Each of the disorders is so rare and has features that overlap with so many other syndromes that highly trained clinical dysmorphologist and pediatric ophthalmologists would have to be engaged in any study. The sentinel phenotype approach, like other strategies in mutation epidemiology, would encounter problems with linkage among files of data, privacy, and access to sufficiently large populations. In contrast with the approach using multiple protein variants (as in the study of blood from offspring of survivors of the atomic bombs in Hiroshima and Nagasaki), the sentinel phenotype approach would likely be much less expensive and would encounter far fewer false attributions of paternity, but also would require a much larger study population. The best option for the present, in our opinion, is to broaden and sustain critical discussion of the approach. Perhaps the goal should be to plan a field demonstration by involving appropriate clinicians, epidemiologists, and public health officials. A pilot effort underway in Hungary may well give insight to applying the approach in a significantly larger population.

Chromosome Aberrations↗

Effects of dietary carbohydrate and phenotype on thyroid hormones and brown adipose tissue locularity in adult LA/N-cp rats.

1. Groups of lean and corpulent LA/N-cp rats were fed isoenergetic diets containing, 54% carbohydrate as maize starch (MS) or sucrose (SU), 20% protein, 16% mixed fats, plus other essential nutrients and fiber from 1.5-9 months of age. Final body weights of corpulent rats were 2-3 times those of their lean littermates, and were greater with SU than MS diet in both phenotypes. 2. Interscapular brown adipose tissue (IBAT) mass was greater in corpulent than lean and was greater with SU than MS diet in lean but not corpulent rats. IBAT cell diameters and adipocyte volumes were generally similar in both phenotypes, and were not markedly affected by dietary carbohydrate type. 3. Brown adipocyte locularity profiles were qualitatively similar in both phenotypes, and were morphologically indicative of thermogenic activity in both phenotypes. Locule profiles of corpulent animals contained a greater proportion of thermogenically less active types IV and V brown adipocytes than similarly fed lean animals, however, and locule distribution profiles were not influenced by diet. 4. Serum T3 concentrations were similar in both phenotypes, were greater in SU than MS lean rats and were not influenced by diet in the corpulent phenotype. In contrast, serum thyroxine concentrations and percent thyroxine uptake were not influenced by diet or phenotype. 5. These results are consistent with a partial impairment in BAT-mediated thermogenic activity in the corpulent phenotype and suggest that obesity in this strain may be due to factors other than biochemically defective brown adipose tissue thermogenesis.

Adipose Tissue, Brown↗

Effects of dietary carbohydrate and phenotype on adipose cellularity in female SHR/N-cp rats.

1. Adipose mass and cellularity were studied in congenic female SHR/N-cp rats fed iosenergetic diets containing 54% carbohydrate as sucrose (SU) or cooked cornstarch (CS), 20% protein, 16% mixed dietary fat plus vitamins, minerals, and non-nutritive fiber ad libitum from 5 weeks until 8.5 months of age. Measures of adipocyte lipid content, cell number per depot, and mass of principal white (WAT) and interscapular brown (IBAT) adipoe tissue depots were determined at the end of the study. 2. Final body weights (BW) of corpulent rats were more than twice those for their lean littermates, and were greater when fed the SU than the CS diet in both phenotypes. Phenotype effects (corpulent greater than lean) were present for fat pad weight, adipocyte number, and adipocyte lipid content in the dorsal (DOR) and retroperitoneal (RP) WAT depots. Diet effects were present for depot weight, adipocyte number, and adipocyte lipid content in both WAT depots, and were of qualitatively similar magnitude in both phenotypes. 3. IBAT weights, IBAT:BW ratios, and IBAT cell number of corpulent greater than lean, and were greater than with SU than CS diet in both phenotypes. 4. These results indicate that obesity in the corpulent phenotype of the SHR/N-cp rat occurs as the result of hypertrophy and hyperplasia of white adipose tissue, and that isoenergetic substitution of simple for complex carbohydrate resulted in greater fat accretion in both phenotypes. The greater diet and phenotype-associated adiposity occurred despite greater mass and cellularity of BAT. The results also indicate that sexual dimorphism occurs regarding effects of diet and phenotype on expression of adipose tissue development in this strain.

Adipose Tissue↗

Uncommon phenotypes of acute myelogenous leukemia: basophilic, mast cell, eosinophilic, and myeloid dendritic cell subtypes: a review.

The potential of the transformed (leukemic) multipotential hematopoietic cell to differentiate and mature along any myeloid lineage forms the basis for the phenotypic classification of acute and chronic myelogenous leukemia. Although most cases of leukemia can be classified phenotypically by the dominant lineage expressed, the genotype within each phenotype is heterogeneous. Thus, covert genetic factors, cryptic mutations, and/or polymorphisms may interact with the seminal transforming genetic mutations to determine phenotype. The phenotype usually is expressed sufficiently to determine the lineage that is dominant in the leukemic clone by light microscopic examination, by cytochemistry of blood and marrow cells, and by immunophenotyping. The basis for the frequency of the AML phenotypes is unclear, although there is a rough concordance with the frequency of marrow precursor cells of different lineages. The least common AML phenotypes are a reflection of the least common blood or marrow cell lineages: acute basophilic, acute mast cell, acute eosinophilic, and acute myeloid dendritic cell leukemia. We discuss the features of these uncommon phenotypes and review the criteria used for their diagnosis.

Basophils↗

Stat6(null phenotype) human lymphocytes exhibit increased apoptosis.

BACKGROUND: Inflammatory bowel disease (IBD) is associated with altered apoptosis and increased levels of Th1 cytokines (IL-12, TNF-alpha, and IFN-gamma). These proinflammatory events may result from dysfunctional IL-4/Stat6 signal transduction that normally promotes Th2 lymphocyte differentiation and consequential down-regulation of the immune response. The goal of the present study was to measure apoptosis, levels of relevant cytokines, and the effects of cytokine manipulation on apoptosis in cell lines derived from IBD patients that express dysfunctional Stat6 (Stat6(null phenotype)) and wild-type Stat6 (Stat6(high phenotype)). MATERIALS AND METHODS: Lymphocytes with Stat6(null phenotype) (n = 5) or wild-type (n = 5) status were cultured with and without the addition of exogenous cytokines or neutralizing antibodies (IL-12, TNF-alpha, and IFN-gamma). Apoptosis was determined by flow cytometry using Annexin V-PE dual staining. Cytokine levels were determined by ELISA. RESULTS: Stat6(null phenotype) cells exhibited increased apoptosis compared with wild-type cell lines (13.3% +/- 2.9 versus 4.5% +/- 0.4, P < 0.0001). Four of five Stat6(null phenotype) cell lines expressed 5- to 10-fold elevations in IL-12 and IFN-gamma. Addition of exogenous cytokines or neutralizing antibodies had no effect on apoptosis. CONCLUSIONS: Apoptotic cell death is elevated in Stat6(null phenotype) cell lines suggesting a role for Stat6 in apoptosis regulation, a previously unrecognized observation. Increased levels of IL-12 and IFN-gamma were found in the Stat6(null phenotype) cell lines; however, the apoptosis observed is not the consequence of increased IL-12, IFN-gamma, or TNF-alpha. Stat6(null phenotype) cell lines exhibit variably increased levels of these Th1 cytokines, consistent with their human source, and may be a valid source for investigations into IBD pathophysiology.

Antibodies↗

Genetic mapping of the cold-adapted phenotype of B/Ann Arbor/1/66, the master donor virus for live attenuated influenza vaccines (FluMist).

Cold adapted (ca) B/Ann Arbor/1/66 is the master donor virus for the influenza B (MDV-B) vaccine component of the live attenuated influenza vaccine (FluMist). The six internal genes contributed by MDV-B confer the characteristic cold-adapted (ca), temperature-sensitive (ts) and attenuated (att) phenotypes to the vaccine strains. Previously, it has been determined that the PA and NP segments of MDV-B control the ts phenotype while the att phenotype requires the M segment in addition to PA and NP. Here, we show that the PA, NP and PB2 segments are responsible for the ca phenotype of MDV-B when examined in chicken cell lines. Five loci in three RNA segments, R630 in PB2, M431 in PA and A114, H410 and T509 in NP, are sufficient to allow efficient virus growth at 25 degrees C. Substitution of these five amino acids with wt (wild type) residues completely reverted the MDV-B ca phenotype. Conversely, introduction of these five ca amino acids into B/Yamanashi/166/98 imparted the ca phenotype to this heterologous wt virus. In addition, we also found that the MDV-B M1 gene affected virus replication in chicken cells at 33 and 37 degrees C. Recombinant viruses containing the two MDV-B M1 residues (Q159, V183) replicated less efficiently than those containing wt M1 residues (H159, M183) at 33 and 37 degrees C, implicating the role of the MDV-B M segment to the att phenotype. The complexity of the multigenic signatures controlling the ca, ts and att phenotypes of MDV-B provides the molecular basis for the observed genetic stability of the FluMist vaccines.

Adaptation, Physiological↗

Phenotype definition in epilepsy.

Phenotype definition consists of the use of epidemiologic, biological, molecular, or computational methods to systematically select features of a disorder that might result from distinct genetic influences. By carefully defining the target phenotype, or dividing the sample by phenotypic characteristics, we can hope to narrow the range of genes that influence risk for the trait in the study population, thereby increasing the likelihood of finding them. In this article, fundamental issues that arise in phenotyping in epilepsy and other disorders are reviewed, and factors complicating genotype-phenotype correlation are discussed. Methods of data collection, analysis, and interpretation are addressed, focusing on epidemiologic studies. With this foundation in place, the epilepsy subtypes and clinical features that appear to have a genetic basis are described, and the epidemiologic studies that have provided evidence for the heritability of these phenotypic characteristics, supporting their use in future genetic investigations, are reviewed. Finally, several molecular approaches to phenotype definition are discussed, in which the molecular defect, rather than the clinical phenotype, is used as a starting point.

Epilepsy↗

Phenotypic heterogeneity in the presentation of D-2-hydroxyglutaric aciduria in monozygotic twins.

D-2-hydroxyglutaric aciduria (D-2-HGA) is a very rare autosomal recessive metabolic disorder that has recently been associated with mutations in the D-2-hydroxyglutarate dehydrogenase gene. The biochemical phenotype of D-2-HGA is defined by the accumulation of abnormal amounts of D-2-hydroxyglutarate in cerebrospinal fluid, blood, and urine while the clinical phenotype can vary from a severe epileptic encephalopathy to normal. The basis for this phenotypic variation is not well-defined. We report a set of 412-year-old monozygotic (MZ) female twins with D-2-hydroxyglutaric aciduria who are shown to be compound heterozygotes for c.326-327dupTC, p.Glu110ArgfsX19, and c.1123G-->T, p.Asp375Tyr mutations in the D-2-hydroxyglutarate dehydrogenase gene, but who have remarkably different clinical phenotypes. One twin presented with multiple congenital anomalies, severe developmental delay, and abnormal neuroradiological findings, while the other had normal neurocognitive and neuroradiological phenotypes, without concomitant congenital abnormalities. Monozygosity of these twins implies that the differences in the clinical phenotype arise from postzygotic genetic changes, epigenetic differences, or environmental factors that influence the phenotypic response to biochemical perturbation rather than allelic or locus heterogeneity. Though the mechanistic role of these factors in D-2-HGA is far from apparent, the discordance in the phenotypes of these siblings establishes that these factors are at least as important as the nature of the mutant alleles in influencing the progression of the disorder.

Base Sequence↗

Is the turbidimetric immunoassay of haptoglobin phenotype-dependent?

Comparison of the turbidimetric immunoassay of haptoglobin with a reference method (the RID technique with appropriate correction for phenotype) clearly showed the turbidimetric assay to be phenotype-dependent. Correction factors for the three main phenotypes were calculated and reference values determined. The observed overall reference range of haptoglobin, irrespective of the phenotype, was 0.56-3.76 g/L. After correction for phenotype, reference values for the three types were: Hp 1-1: 0.77-2.49; Hp 2-1: 0.86-4.76; and Hp 2-2: 0.48-3.15 g Hp/L. From our reference values for the several phenotypes of haptoglobin it may be argued that phenotyping is desirable only when the uncorrected haptoglobin value, determined by turbidimetry, is within the range 0.38-0.98 g/L. Limited to hemolytic diseases, phenotype determination can be omitted beyond this range.

Haptoglobins↗

Effect of apolipoprotein E3/4 phenotype on postprandial triglycerides and retinyl palmitate metabolism in plasma from hyperlipidemic subjects in Japan.

In a previous study it was shown that postprandial lipid metabolism is delayed in individuals with intra-abdominal visceral fat accumulation. Population studies have shown that as compared with individuals with apolipoprotein (apo) E3/3, those with phenotype apo E3/4 phenotype have higher plasma and low density lipoprotein (LDL)-cholesterol (C) concentration and increased susceptibility to coronary heart disease. The aim of the present study is to determine how apo E4 affects postprandial lipid metabolism by comparing individuals with apo E3/4 to those with apo E3/3 phenotype matched for abdominal visceral fat. Sixty-two Japanese subjects (41 male, 21 female) [average age 48+/-14 years; mean body mass index (BMI) 25+/-5.6 kg/m2] were recruited for this study. The subjects were divided into two groups: those with apo E3/3 (n=43) and those with apo E3/4 phenotype (n=19), as determined by isoelectric focusing (IEF). Visceral fat accumulation was analyzed as area of fat deposition by computerized tomography at the umbilicus level. After a 12-h overnight fasting, an oral vitamin A and a fatty meal were administered to these subjects. The plasma triglyceride (TG) increased significantly hours after fat loading in both groups but the levels of TG were significantly higher in apo E3/4 than in apo E3/3 phenotype at 2, 4 and 6 h after fat loading. Plasma retinyl palmitate (RP) levels were also significantly higher in individuals with apo E3/4 than in those with apo E3/3 phenotype at 2, 4 and 6 h after fat loading. This investigation was then conducted in both genders separately, and found that these associations were statistically significant in men. Furthermore, after matching men for fasting TG levels, these associations did not persist for plasma TG levels at any time point, while plasma RP levels were still significantly higher in apo E3/4 group at 2 and 6 h after fat loading. These results indicate that in Japanese population especially for men apo E phenotype E3/4 is associated with an impaired postprandial TG-rich lipoprotein metabolism relative to apo E3/3 phenotype when matched for intra-abdominal visceral fat accumulation, which has a substantial effect on the metabolism of plasma TG-rich lipoproteins.

Adult↗

Deciphering the genetic architecture of a multivariate phenotype.

A heritable multivariate quantitative phenotype comprises several correlated component phenotypes that are usually pleiotropically controlled by a set of major loci and environmental factors. One approach to decipher the genetic architecture of a multivariate phenotype, in particular to map the underlying loci, is to reduce the dimensionality of the data by means of a data reduction technique, such as principal component analysis. The extracted principal components are then analyzed in conjunction with marker data to map the underlying loci. We have examined the efficiency of this approach with and without taking into account the correlation structure of the multivariate phenotype when extracting principal components. We have assumed that genome-wide scan data on sibpairs are available for low-density (widely spaced) and high-density markers. Using extensive simulations, based on three models of the multivariate phenotype, we have shown that although ignoring the correlation structure of the multivariate phenotype does not have any serious impact on the efficiency of mapping the underlying trait loci in wide marker intervals, there is a significant adverse effect of this practice for fine-mapping. We, therefore, recommend that the correlation structure of the multivariate phenotype be carefully examined to decide on the strategy of extracting principal components for deciphering the genetic architecture of the multivariate phenotype.

Chromosome Mapping↗

Role of exopolysaccharide, the rugose phenotype and VpsR in the pathogenesis of epidemic Vibrio cholerae.

Vibrio cholerae, the causative agent of cholera can produce an exopolysaccharide (EPS). Some strains can also phenotypically switch from a smooth to a 'rugose' phenotype characterized by small wrinkled colonies, overproduction of EPS, increased biofilm formation in vitro and increased resistance to various stressful conditions. High frequency switching to the rugose phenotype is more common in epidemic strains than in non-pathogenic strains, suggesting EPS production and the rugose phenotype are important in cholera epidemiology. VpsR up-regulates Vibrio polysaccharide (VPS) genes and the synthesis of extracellular EPS (VPS). However, the function of VPS, the rugose phenotype and VpsR in pathogenesis is not well understood. We report that rugose strains of both classical and El Tor biotypes of epidemic V. cholerae are defective in the in vitro production of extracellular collagenase activity. In vivo studies in rabbit ileal loops suggest that VpsR mutants are attenuated in reactogenicity. Intestinal colonization studies in infant mice suggest that VPS production, the rugose phenotype and VpsR have a role in pathogenesis. Our results indicate that regulated VPS production is important for promoting in vivo biofilm formation and pathogenesis. Additionally, VpsR might regulate genes with roles in virulence. Rugose strains appear to be a subpopulation of cells that might act as a 'helper' phenotype promoting the pathogenesis of certain strains. Our studies provide new insight into the potential role of VPS, the rugose phenotype and VpsR in the pathogenesis of epidemic V. cholerae.

Animals↗

Relationships among Pasteurellaceae isolated from free ranging chickens and their animal contacts as determined by quantitative phenotyping, ribotyping and REA-typing.

One hundred and forty-three Pasteurella spp. strains and 10 unclassified strains obtained from free ranging poultry, dogs and cats were investigated by extended phenotypic characterization. One hundred and forty-nine of these strains were selected for further studies using ribotyping and REA-typing to evaluate the role of dogs and cats in Pasteurella multocida transmission. Seven and six type strains were included for comparison in phenotyping and genotyping, respectively. Eleven clusters and six unclustered strains were revealed by phenotyping. Ribotyping outlined 12 clusters and six unclustered strains. A correlation between clusters obtained by phenotyping and ribotyping was demonstrated which indicated that a genetic basis exists for clusters outlined by quantitative evaluation of phenotypic data. Similarities and differences in hosts, phenotype, ribotype, and zone of isolation were demonstrated among Pasteurella strains investigated. Isolates of P. multocida from ducks were shown to be clonal by both phenotyping and ribotyping. These strains were identical to one of the chickens strains. REA-typing, however, showed that the chicken strain was different underlining that exchange of clones of P. multocida between avian species rarely happens under village conditions. Management practise in the villages suggest the potential for exchange of P. multocida between poultry and animals kept in contact. The present findings, however, did not indicate that clones of P. multocida are widely exchanged between poultry and other animal species, even though close contact exists. In the present investigation exchange of clones of P. multocida was only demonstrated among animals belonging to the same species. Caution is drawn to the use of ribotyping as the sole method for epidemiological typing and tracing of P. multocida. The present results also underline the importance of proper phenotyping in the identification of P. multocida and related species.

Animals↗

Colonisation phenotype and colonisation potential differences in Campylobacter jejuni strains in chickens before and after passage in vivo.

Campylobacter jejuni strains isolated from chicken faeces and from humans suffering from gastroenteritis were used to determine the colonisation phenotypes and colonisation potential of these strains in chickens. Five different colonisation types were observed ranging from immediate and sustained colonisation to completely non-colonising. Phenotype one showed immediate colonisation with prolonged excretion of viable C. jejuni bacteria. Phenotype two showed delayed colonisation with prolonged excretion of viable C. jejuni bacteria. Phenotype three showed immediate colonisation and delayed clearing of viable C. jejuni bacteria. Phenotype four showed delayed colonisation and delayed clearing of viable C. jejuni bacteria. Strains of phenotype five could not colonise chickens. Inoculum levels to obtain maximum caecal colonisation for each phenotype for strains cultured in vitro and in vivo was also determined. Following passage in vivo through a chicken, the minimum inoculum required for sustained colonisation dropped approximately 1000-fold, however, the colonisation phenotype remained unchanged before and after a passage in vivo.

Animals↗

Susceptibility and modifier genes in cutaneous basal cell carcinomas and their associations with clinical phenotype.

While ultraviolet radiation (UV) is critical in the pathogenesis of basal cell carcinomas (BCC), its role in determining the phenotypic variation shown by patients is unknown. Thus, patients manifest variation in BCC numbers, patterns of presentation and tumour site. We have used this diversity to classify patients into subgroups that are associated with different risks of developing tumours. Two phenotypes are particularly interesting. Firstly, presentation with clusters of BCC. These patients, termed multiple presentation phenotype (MPP), had two to five BCC at one presentation, suggesting rapid accrual over short periods of time. They comprised 15% of our 1200 BCC patients. A minority of patients demonstrated multiple clustering events, a phenomenon that is associated with a genetic pre-disposition. The second risk phenotype, characterised by tumours on the trunk, is also associated with a pre-disposition. Both phenotypes were characterised by a susceptibility to develop numerous BCC. Thus, all our patients with more than five BCC had one or both of these phenotypes. We are using a candidate gene approach to identify loci associated with risk of these phenotypes (susceptibility genes) and tumour numbers in them (modifier genes). Interestingly, we did not identify differences in UV exposure between patients with high- and low-risk phenotypes.

Basal Cell Carcinoma↗

Haptoglobin phenotype correlates with development of cardiac transplant vasculopathy.

OBJECTIVES: The purpose of this study was to investigate the association between haptoglobin phenotypic variation and development of cardiac transplant vasculopathy. BACKGROUND: The development of coronary vasculopathy determines long-term survival after cardiac transplantation. Serum haptoglobin levels are associated with non-transplant atherosclerosis. In addition to free hemoglobin binding, haptoglobin influences free radical formation, prostaglandin synthesis and angiogenesis. Three phenotypes of haptoglobin exist in humans, which have both quantitative and qualitative differences. METHODS: Coronary disease was diagnosed at post-transplant routine surveillance angiography. Hemoglobin (10%) was added to recipient plasma to form a haptoglobin-hemoglobin complex. Sample aliquots were applied to acid hemoglobin plates and electrophoretically separated. Phenotypes were recognized by comparing the electrophoretic pattern with that of established standards. Haptoglobin concentrations were measured using an immunoturbidimetric technique with polyethylene glycol (PEG)-enhanced precipitation. RESULTS: Ninety-three patients were independently studied. Phenotype 1-1 was found in 20.4%, 2-1 in 41.9% and 2-2 in 37.6%. Haptoglobin levels were highest in 1-1 recipients (2.1 +/- 0.58 g/liter) compared with 1.78 +/- 0.88 g/liter and 1.3 +/- 0.81 g/liter in 2-1 and 2-2 individuals, respectively (p = 0.001). Haptoglobin phenotype was significantly related to the development of vasculopathy; recipients with a 2-1 phenotype were more likely to develop angiographic disease (p = 0.0084). No differences were found among the 3 groups according to univariate analysis. Multivariate analysis identified 3 risk factors for vasculopathy development: age of donor (hazard ratio 1.056 [95% confidence interval 1.02 to 1.094], p = 0.0023); pre-transplant recipient body mass index (hazard ratio 1.116 [95% confidence interval 1.015 to 1.23], p = 0.024), and haptoglobin phenotype (hazard ratio 2.725 [95% confidence interval 1.031 to 7.19], p = 0.012). CONCLUSIONS: Haptoglobin, through phenotype-dependent mechanisms, correlates with the development of coronary vasculopathy. This finding furthers our understanding of the disease, opens up new areas of research, and may lead to novel therapies.

Adult↗

Clustering expressed genes on the basis of their association with a quantitative phenotype.

Cluster analyses of gene expression data are usually conducted based on their associations with the phenotype of a particular disease. Many disease traits have a clearly defined binary phenotype (presence or absence), so that genes can be clustered based on the differences of expression levels between the two contrasting phenotypic groups. For example, cluster analysis based on binary phenotype has been successfully used in tumour research. Some complex diseases have phenotypes that vary in a continuous manner and the method developed for a binary trait is not immediately applicable to a continuous trait. However, understanding the role of gene expression in these complex traits is of fundamental importance. Therefore, it is necessary to develop a new statistical method to cluster expressed genes based on their association with a quantitative trait phenotype. We developed a model-based clustering method to classify genes based on their association with a continuous phenotype. We used a linear model to describe the relationship between gene expression and the phenotypic value. The model effects of the linear model (linear regression coefficients) represent the strength of the association. We assumed that the model effects of each gene follow a mixture of several multivariate Gaussian distributions. Parameter estimation and cluster assignment were accomplished via an Expectation-Maximization (EM) algorithm. The method was verified by analysing two simulated datasets, and further demonstrated using real data generated in a microarray experiment for the study of gene expression associated with Alzheimer's disease.

Algorithms↗

Phenotypes and randomly amplified polymorphic DNA profiles of Candida albicans isolates from root canal infections in a Finnish population.

A total of thirty-seven Candida albicans isolates from root canal infections in a Finnish population were subtyped using phenotypic and genotypic methods. A previously described biotyping method based on the presence of five different enzymes, assimilation of eleven different carbohydrates and boric acid sensitivity of the yeasts was used to determine the phenotype. Commercially available API ZYM and API 20 C test kits were used to determine the presence of enzymes and assimilation of carbohydrates. The sensitivity of the isolates to boric acid was tested by their ability to grow on yeast-nitrogen-agar with incorporated boric acid (1.8 mg. ml(-1)). Combination of the tests revealed a total of 14 different phenotypes. The majority of the isolates, 26 strains, were classifiable into three major phenotypes: 16 isolates (43.2%) belonged to phenotype A1R, six (16.2%) to A1S and four (10.8%) to B1S. The remaining 11 phenotypes represented only a single isolate each. The randomly amplified polymorphic DNA profiles were used to determine the genotypes. For this purpose two different primers, RSD6 and RSD12 were used to develop a combination randomly amplified polymorphic DNA profile for each isolate. Altogether 31 genotypes were noted among the 37 isolates, of which only three pairs of isolates presented with congruent phenotypic and genotypic profiles. The heterogeneity of both the phenotypic and randomly amplified polymorphic DNA profiles of C. albicans isolates from root canal infections is akin to previous reports from other oral and non-oral sources in different geographic locales.

Bacterial Typing Techniques↗