Fast and accurate mutation detection in whole genome sequences of multiple isogenic samples with IsoMut.

BACKGROUND: Detection of somatic mutations is one of the main goals of next generation DNA sequencing. A wide range of experimental systems are available for the study of spontaneous or environmentally induced mutagenic processes. However, most of the routinely used mutation calling algorithms are not optimised for the simultaneous analysis of multiple samples, or for non-human experimental model systems with no reliable databases of common genetic variations. Most standard tools either require numerous in-house post filtering steps with scarce documentation or take an unpractically long time to run. To overcome these problems, we designed the streamlined IsoMut tool which can be readily adapted to experimental scenarios where the goal is the identification of experimentally induced mutations in multiple isogenic samples. METHODS: Using 30 isogenic samples, reliable cohorts of validated mutations were created for testing purposes. Optimal values of the filtering parameters of IsoMut were determined in a thorough and strict optimization procedure based on these test sets. RESULTS: We show that IsoMut, when tuned correctly, decreases the false positive rate compared to conventional tools in a 30 sample experimental setup; and detects not only single nucleotide variations, but short insertions and deletions as well. IsoMut can also be run more than a hundred times faster than the most precise state of art tool, due its straightforward and easily understandable filtering algorithm. CONCLUSIONS: IsoMut has already been successfully applied in multiple recent studies to find unique, treatment induced mutations in sets of isogenic samples with very low false positive rates. These types of studies provide an important contribution to determining the mutagenic effect of environmental agents or genetic defects, and IsoMut turned out to be an invaluable tool in the analysis of such data.

Predicting protein conformation by statistical methods.

The unique folded structure makes a polypeptide a functional protein. The number of known sequences is about a hundred times larger than the number of known structures and the gap is increasing rapidly. The primary goal of all structure prediction methods is to obtain structure-related information on proteins, whose structures have not been determined experimentally. Besides this goal, the development of accurate prediction methods helps to reveal principles of protein folding. Here we present a brief survey of protein structure predictions based on statistical analyses of known sequence and structure data. We discuss the background of these methods and attempt to elucidate principles, which govern structure formation of soluble and membrane proteins.

Principles governing amino acid composition of integral membrane proteins: application to topology prediction.

A new method is suggested here for topology prediction of helical transmembrane proteins. The method is based on the hypothesis that the localizations of the transmembrane segments and the topology are determined by the difference in the amino acid distributions in various structural parts of these proteins rather than by specific amino acid compositions of these parts. A hidden Markov model with special architecture was developed to search transmembrane topology corresponding to the maximum likelihood among all the possible topologies of a given protein. The prediction accuracy was tested on 158 proteins and was found to be higher than that found using prediction methods already available. The method successfully predicted all the transmembrane segments in 143 proteins out of the 158, and for 135 of these proteins both the membrane spanning regions and the topologies were predicted correctly. The observed level of accuracy is a strong argument in favor of our hypothesis.

Cold target competition analysis of the classical activation pathway of complement-mediated cytotoxicity: a non-interaction model for competing lysis.

A mathematical analysis of cold target competition experiments of complement-mediated lysis is presented, aimed at developing a minimal model of lysis where no interaction between the competing populations of sensitized blood group A and B erythrocytes is presumed. The model is able to predict the extent of lysis from the input values with remarkable accuracy suggesting that under the conditions used no stimulation and/or inhibition of the lysis of the sensitized erythrocytes occurs. The distribution of complement between the competing A and B erythrocyte populations is approximated by the model and found to be proportional to the 5th and 4th power of the ratios of the antibody and target cell concentrations, respectively. In accordance with earlier observations, suggesting that the interaction between the antibody and the C1q molecules is based on polar electrostatic charges, we propose that the sensitizing antibody provides an electrostatic field around the erythrocytes which attracts C1q molecules towards their membranes.

An indirect effect of an antibody on complement deposition and lysis of differently sensitized surrounding cells.

Lysis of papain-treated group A and B erythrocytes by human complement was studied by an anti-A (BRIC. 131) and an anti-B (BRIC. 30) IgM monoclonal antibody in 51Cr release assays. The indirect effect of membrane-bound antibody, i.e. its influence on complement binding to sensitized surrounding cells, was examined in a cold target competition test in which sensitized, non-labelled cells are present along with sensitized labelled cells and complement. The mode by which anti-A antibodies indirectly suppressed lysis of sensitized B cells up to 20-fold was studied by following C1q and C3b binding. C1q binding to both types of erythrocytes was not altered in mixed populations of erythrocytes in the presence of both antibodies. Binding of C3b to a mixture of both cell types was, however, suppressed, when both antibodies were present. C3b deposition in mixed cell populations did not reach a significantly higher extent than deposited to one type of erythrocyte alone. This was consistent with the results from competitive lysis and suggests that the anti-A captured most C3b at high anti-A concentrations and deprived the similarly sensitized B erythrocytes of complement. We think that this phenomenon is not due to an uneven removal of complement regulatory proteins from A and B erythrocytes by papain. Instead, the phenomenon might be due to an inherent property of anti-A mAb to better produce nucleation sites for C3 convertases which, upon binding factor B, better compete for the limiting factor D. A mathematical analysis of cold target competition experiment (containing 2430 individual measurements) also shows that the distribution of complement between the competing A and B erythrocyte population is uneven, since it predicts that in any given antibody combination the majority of complement is bound to A erythrocytes. This is consistent with the measured average percentage of lysis.

Membrane topology distinguishes a subfamily of the ATP-binding cassette (ABC) transporters.

A group of ATP-binding cassette (ABC) transporters, including the yeast cadmium transporter (YCF1), the mammalian multidrug resistance-associated protein (MRP), the multispecific organic anion transporter and its congener (MOAT and EBCR), as well as the sulfonylurea receptor (SUR), group into a subfamily by sequence comparison. We suggest that these MRP-related proteins are also characterized by a special, common membrane topology pattern. The most studied ABC transporters, the cystic fibrosis transmembrane conductance regulator (CFTR) and the multidrug resistance (MDR) proteins, were shown to contain a tandem repeat of six transmembrane helices, each set followed by an ATP-binding domain. According to the present study, in contrast to various membrane topology predictions proposed for the different MRP-related proteins, they all seem to have a CFTR/MDR-like core structure, and an additional, large, N-terminal hydrophobic region. This latter domain is predicted to contain 4-6 (most probably 5) transmembrane helices, and is occasionally glycosylated on the cell surface. Since all the MRP-related transporters were shown to interact with anionic compounds, the N-terminal membrane-bound domain may have a key role in these interactions.

Haemolysis mediated by anti-D monoclonal antibodies in direct and cold target competition ADCC assays.

Thirteen IgG anti-D human monoclonal antibodies (mAbs) were compared for their ability to mediate lysis of D-positive erythrocytes by PBMC in direct and cold target competition antibody-dependent cell-mediated cytotoxicity (ADCC) assays. In the latter assay, lysis of fluid-phase anti-D-sensitised O Rh D-positive papainised erythrocytes (E-IgG) was inhibited by A (or B) Rh D-negative papainised erythrocytes sensitised by fluid-phase anti-A (or anti-B) mAbs. The competitive and lytic activities of the anti-D mAbs were characterised by the equilibrium dilution (ED) values, which were the reciprocal of the dilution of anti-A (or anti-B) at which lysis of target E-IgG and competitor E-IgG were identical. There was a poor correlation between the number of erythrocyte-bound anti-D molecules and either the sensitivity of E-IgG anti-D to haemolysis in the direct ADCC assay, or to the ED values of the mAbs obtained in the cold target competition ADCC. The discriminatory power of the cold target competition ADCC was better than than of the direct ADCC to detect differences in the lytic potential of the anti-D mAbs.

Red-cell bound anti-A is more efficient than anti-B in competition for fluid phase complement.

Lysis of group A and B erythrocytes by human complement was studied by an anti-A (BRIC.131) and an anti-B (BRIC.30) IgM monoclonal antibody in a 51Cr-release assay. The relative concentration of membrane-bound immunoglobulins was detected by flow cytometric analysis, and the amount of C1q and C3 bound to the sensitized red cells was measured by using purified, 125I-labelled molecules. The direct haemolysis was identical with both reagents in the presence of excess and suboptimal complement over a wide range of antibody concentration (between 50 and 7000 ng/ml). The indirect effect of membrane-bound antibody, i.e. its influence on complement binding by sensitized bystander cells, was examined in a cold target competition assay in which sensitized, non-labelled cells are present when complement is incubated with sensitized labelled cells. We have found that the competitive capacity of sensitized erythrocytes correlated with the amount of membrane-bound immunoglobulins. In accordance with our earlier findings, an equal level of target and competitor cell lysis was obtained only if the fluid phase anti-B antibody concentration was 2 to 4 times higher than that of the anti-A antibodies. We demonstrate in this paper that the different competitive activity of IgM anti-A and anti-B monoclonal antibodies might be accounted for by differences in their C1q and C3 binding capacities.

Interactions in the complement-mediated lysis of blood group AB erythrocytes sensitized simultaneously with anti-A and anti-B monoclonal antibodies.

The lysis of group AB erythrocytes by human complement was studied by different anti-A and anti-B IgM monoclonal antibodies (mabs) in a 51Cr-release assay. The concentration of membrane-bound immunoglobulin was detected by ELISA, and the amount of C1q and C3 bound to sensitized red cells was measured by using purified, 125I-labelled molecules. We have demonstrated that there is an exponential relationship between the concentration of the sensitizing IgM mabs and C1q binding to the sensitized AB cell. The efficiency of binding was related to the number of antibodies bound; thus, anti-A sensitized cells bound 3-6 times more C1q than anti-B sensitized cells did. AB cells, on the other hand, bound similar amounts of C3 whether anti-A or anti-B was present. The lytic efficiencies of the various IgM mabs during short incubation times were different, suggesting that the complement activation rates vary widely with different antibodies on the AB cell membrane. The binding of C1q to an antibody-sensitized target activates a cascade, whose components may migrate away from the sensitizing antibody; interactions between the activation processes generated by the anti-A and anti-B antibodies may thus occur. Choosing appropriate pairs of anti-A and anti-B mabs for the simultaneous sensitization of AB cells has indeed resulted in stimulation in some and inhibition in other combinations of mabs. It is suggested that stimulation is observed when the activated intermediates are produced in excess, whereas inhibition occurs when a shortage of activated intermediates prevents mutual utilization.

Survival chance in papillary thyroid cancer in Hungary: individual survival probability estimation using the Markov method.

PURPOSE: The typically benign, but occasionally rapidly fatal clinical course of papillary thyroid cancer has raised the need for individual survival probability estimation, to tailor the treatment strategy exclusively to a given patient. MATERIALS AND METHODS: A retrospective study was performed on 400 papillary thyroid cancer patients with a median follow-up time of 7.1 years to establish a clinical database for uni- and multivariate analysis of the prognostic factors related to survival (Kaplan-Meier product limit method and Cox regression). For a more precise prognosis estimation, the effect of the most important clinical events were then investigated on the basis of a Markov renewal model. The basic concept of this approach is that each patient has an individual disease course which (besides the initial clinical categories) is affected by special events, e.g. internal covariates (local/regional/distant relapses). On the supposition that these events and the cause-specific death are influenced by the same biological processes, the parameters of transient survival probability characterizing the speed of the course of the disease for each clinical event and their sequence were determined. The individual survival curves for each patient were calculated by using these parameters and the independent significant clinical variables selected from multivariate studies, summation of which resulted in a mean cause-specific survival function valid for the entire group. On the basis of this Markov model, prediction of the cause-specific survival probability is possible for extrastudy cases, if it is supposed that the clinical events occur within new patients in the same manner and with the similar probability as within the study population. RESULTS: The patient's age, a distant metastasis at presentation, the extent of the surgical intervention, the primary tumor size and extent (pT), the external irradiation dosage and the degree of TSH suppression proved to be statistically significant and independent prognostic factors with regard to cause-specific survival in multivariate studies. During follow-up, 14, 14, 9 and 12% of the patients underwent local/regional/distant relapses or thyroid cancer-related death, respectively. Through use of the above six independent clinical variables and the parameters relating to the four clinical events and their interrelations, mean cause-specific survival probabilities of 88, 83 and 78% were determined at 10, 20 and 30 years, respectively. The survival-predicting software (PATHYPRE) written on the basis of the biostatistical model is available through Internet connections on the home page of the National Institute of Oncology, Budapest (www.oncol.hu). CONCLUSION: Prediction of the individual survival probability for extrastudy cases affords a rationale for individualization of the treatment of papillary thyroid cancer patients.

Ionizing radiation and genetic risks. V. Multifactorial diseases: a review of epidemiological and genetic aspects of congenital abnormalities in man and of models on maintenance of quantitative traits in populations.

This paper discusses (a) data on the epidemiological and etiological aspects of human congenital abnormalities, (b) the multifactorial threshold model and other models which have been proposed to explain their inheritance patterns and recurrence risks in families and (c) current concepts on mechanisms on the prevalence of heritable variation for quantitative traits in populations. Congenital abnormalities, which afflict an estimated 6% of all live births, are etiologically heterogeneous. The majority of these do not follow Mendelian transmission patterns, but do 'run' in families. The multifactorial threshold model is an extension of genetic principles developed for quantitative traits to all-or-none traits; in its simplest formulation, it assumes the existence in the population of an underlying normally distributed 'liability' (which is due to numerous genetic and environmental factors acting additively, each contributing a small amount of liability) and of a 'threshold' beyond which the individual is affected. For most congenital abnormalities, the nature of these factors remains unknown. Other models assume fewer causal factors although, again, these remain to be identified. The question of how considerable heritable variation for most quantitative/polygenic traits has come to exist is a long-standing one in evolutionary population genetics. Models postulating that its existence is consistent with a balance between recurrent mutation and stabilizing selection or suggesting the possible operation of other mechanisms have been published in the literature. In the absence of knowledge on mechanisms responsible for the stable prevalences of congenital abnormalities or other multifactorial conditions in the population (but which is required to predict the consequences of an increase in mutation rate on their prevalences) it is necessary (a) to adapt and use concepts derived from quantitative and evolutionary population genetics and (b) to examine how sensitive the predictions are to the assumptions used, and how consistent they are with biological realities.

[PATHYPRE: Pascal program for the estimation of the individual course of patients with papillary thyroid cancer]. / PATHYPRE: Pascal-program a papillaris pajzsmirigyrákos betegek individuális kórlefolyásának becslésére.

Individual survival probability estimation provided by mathematical models based on cases with a known clinical course is of great help as concerns the treatment strategy decision relating to malignant tumours. Data on four hundred Hungarian papillary thyroid cancer patients were used together with the Markov method to construct a survival model (Orv. Hetil. 1996 137: 1067-1078,) for prediction of the individual clinical course of newly diagnosed cases for 30 years following surgical intervention. Input data included the age, the primary tumour size and extent (pT), distant metastasis at presentation, the extent of the surgical intervention, the external irradiation dosage and the degree of TSH suppression. From the input data, the PATHYPRE program can estimate the individual local/regional/distant relapse-free survival probabilities and overall cause-specific survival probability. The survival probabilities may be predicted for variations in the treatment parameters, and thus the model helps in the selection of the most appropriate therapy for the patient. The PATHYPRE software is available through the Internet connections on the home page of the National Institute of Oncology, Budapest (www.oncol.hu).

[Malignant thyroid tumors in Hungary: morbidity and mortality]. / Malignus pajzsmirigytumorok Magyarországon: morbiditás és mortalitás.

In 1993, 181 new cases (36 men and 145 women) of thyroid cancer were diagnosed pathologically in Hungary, i.e. a morbidity of 1.8/100,000 for the total population, and of 0.7/100,000 and 2.7/100,000 for men and women, respectively. The distribution of the histological diagnoses: 61% papillary, 25% follicular, 5% medullary and 3% anaplastic carcinomas, and 6% others. In the same year, 125 patients (31 men and 94 women) died from thyroid cancer, i.e. a mortality rate of 1.2/100,000 for the total population, and of 0.6/100,000 and 1.8/100,000 for men and women, respectively. The relatively low morbidity reflects the fact that no new strong aetiological factor is operative in Hungary. The substantial mortality rate, however, is influenced by the geographically determined aggressivity of the disease, the inadequacy of the diagnostic procedures and therapeutic measures, and lack of the active follow-up. The latter facts are especially prominent in centres with a low patient turnover. In the field of health care, various measures must be introduced to prevent an increase in the morbidity and to diminish the mortality. Reduction of the iodine deficiency, rationalization of the medical use of ionizing irradiation, and implementation of the necessary hormonal medication for all patients operated by resection for thyroid diseases are needed for tumour prophylaxis. Before any medical decision-making, the achievement of complete diagnostic information, including the pathological revision of clinically questionable cases, is of paramount importance. The fundamental goals as concerns the treatment modalities are as follows: increased surgical skill and level of performance of external irradiation, the availability of radionuclide therapy, and guidance of all types of thyroxine medication by endocrine experts.

[Survival potentials of patients with papillary carcinoma of the thyroid gland in Hungary]. / A papillaris pajzsmirigyrákos betegek túlélési esélyei Magyarországon.

The typically benign, but occasionally rapid fatal clinical course of papillary thyroid cancer has raised the need for individual survival probability estimation, to tailor the treatment strategy exclusively to the given patient. A retrospective study was performed on 400 papillary thyroid cancer patients, with a mean follow-up time of 10.3 years, to establish a clinical database for uni- and multivariate analysis of the survival probability-related prognostic factors (Kaplan-Meier product limit method and Cox regression). For a more precise prognosis estimation, in the next step the most important clinical events were investigated and survival functions for each patient were calculated on the basis of a Markov renewal model. The basic concept of this approach is as follows: each patient has an individual disease course, which (besides the initial clinical categories) is affected by special events, e.g. internal covariates (local/regional/distant relapses), that a patient experiences throughout the course of the disease. On the supposition that these events and the cause-specific death are influenced by the same biological process, the parameters of transient survival probability characterizing the speed of the course of the disease for each sequence of clinical events were determined. The individual survival curves for each patients were calculated by using the former parameters and the independent, significant clinical variables, summation of which resulted in an overall cause-specific survival function valid for the entire group. The patient's age, a distant metastasis at presentation, the extent of the surgical intervention, the primary tumour size, the dosage of the external irradiation and the degree of the TSH suppression proved to be statistically significant (in that sequence) and independent prognostic factors as concerns cause-specific survival in multivariate studies. During follow-up 14%, 14%, 9% and 12% of the patients underwent local/regional/distant relapses and thyroid cancer-related death. Through use of the above six independent clinical variables and the parameters relating to the interrelations of the four clinical events, mean cause-specific survival probabilities of 88%, 83% and 78% were determined at 10, 20 and 30 years, respectively. The 30-year individual survival probability prediction for these study cases showed that no cancer-related death occurred > or = 92% (low-risk group), while the tumour-related deaths were considerable (31%) < or = 78% (high-risk group), and there were only 6% deaths in the intermediate-risk group. The constructed survival function permits a prediction of the individual survival probability of extra-study cases under the given treatment conditions and within the given population, and thus affords a rationale for individualization of the treatment of papillary thyroid cancer patients.