RESUMEN

Nitroreductase (NR) from Enterobacter cloacae reduces diverse nitroaromatics including herbicides, explosives, and prodrugs, and holds promise for bioremediation, prodrug activation, and enzyme-assisted synthesis. We solved crystal structures of NR complexes with bound substrate or analog for each of its two half-reactions. We complemented these with kinetic isotope effect (KIE) measurements elucidating H-transfer steps essential to each half-reaction. KIEs indicate hydride transfer from NADH to the flavin consistent with our structure of NR with the NADH analog nicotinic acid adenine dinucleotide (NAAD). The KIE on reduction of p-nitrobenzoic acid (p-NBA) also indicates hydride transfer, and requires revision of prior computational mechanisms. Our mechanistic information provided a structural restraint for the orientation of bound substrate, placing the nitro group closer to the flavin N5 in the pocket that binds the amide of NADH. KIEs show that solvent provides a proton, enabling accommodation of different nitro group placements, consistent with the broad repertoire of NR.

Asunto(s)

Proteínas Bacterianas/química , Nitrorreductasas/química , Proteínas Bacterianas/metabolismo , Sitios de Unión , Enterobacter cloacae/enzimología , Flavinas/metabolismo , NAD/metabolismo , Nitrobenzoatos/metabolismo , Nitrorreductasas/metabolismo , Unión Proteica , Especificidad por Sustrato

RESUMEN

If methane, the main component of natural gas, can be efficiently converted to liquid fuels, world reserves of methane could satisfy the demand for transportation fuels in addition to use in other sectors. However, the direct activation of strong C-H bonds in methane and conversion to desired products remains a difficult technological challenge. This perspective reveals an opportunity to rethink the logic of biological methane activation and conversion to liquid fuels. We formulate a vision for a new foundation for methane bioconversion and suggest paths to develop technologies for the production of liquid transportation fuels from methane at high carbon yield and high energy efficiency and with low CO2 emissions. These technologies could support natural gas bioconversion facilities with a low capital cost and at small scales, which in turn could monetize the use of natural gas resources that are frequently flared, vented or emitted.

Asunto(s)

Biocombustibles , Metano/metabolismo , Aerobiosis , Anaerobiosis , Biotransformación , Oxidación-Reducción

RESUMEN

Proton uptake accompanies the reduction of all known substrates by nitrogenase. As a consequence, a higher pH should limit the availability of protons as a substrate essential for turnover, thereby increasing the proportion of more highly reduced forms of the enzyme for further study. The utility of the high-pH approach would appear to be problematic in view of the observation reported by Pham and Burgess [(1993) Biochemistry 32, 13725-13731] that the MoFe-protein undergoes irreversible protein denaturation above pH 8.65. In contrast, we found by both enzyme activity and crystallographic analyses that the MoFe-protein is stable when incubated at pH 9.5. We did observe, however, that at higher pHs and under turnover conditions, the MoFe-protein is slowly inactivated. While a normal, albeit low, level of substrate reduction occurs under these conditions, the MoFe-protein undergoes a complex transformation; initially, the enzyme is reversibly inhibited for substrate reduction at pH 9.5, yet in a second, slower process, the MoFe-protein becomes irreversibly inactivated as measured by substrate reduction activity at the optimal pH of 7.8. The final inactivated MoFe-protein has an increased hydrodynamic radius compared to that of the native MoFe-protein, yet it has a full complement of iron and molybdenum. Significantly, the modified MoFe-protein retains the ability to specifically interact with its nitrogenase partner, the Fe-protein, as judged by the support of ATP hydrolysis and by formation of a tight complex with the Fe-protein in the presence of ATP and aluminum fluoride. The turnover-dependent inactivation coupled to conformational change suggests a mechanism-based transformation that may provide a new probe of nitrogenase catalysis.

Asunto(s)

Molibdoferredoxina/antagonistas & inhibidores , Molibdoferredoxina/metabolismo , Nitrogenasa/antagonistas & inhibidores , Nitrogenasa/metabolismo , Adenosina Trifosfato/metabolismo , Azotobacter vinelandii/química , Cristalografía por Rayos X , Concentración de Iones de Hidrógeno , Hidrólisis , Modelos Moleculares , Molibdoferredoxina/química , Nitrogenasa/química , Factores de Tiempo

RESUMEN

The effects of disease mutations on protein structure and function have been extensively investigated, and many predictors of the functional impact of single amino acid substitutions are publicly available. The majority of these predictors are based on protein structure and evolutionary conservation, following the assumption that disease mutations predominantly affect folded and conserved protein regions. However, the prevalence of the intrinsically disordered proteins (IDPs) and regions (IDRs) in the human proteome together with their lack of fixed structure and low sequence conservation raise a question about the impact of disease mutations in IDRs. Here, we investigate annotated missense disease mutations and show that 21.7% of them are located within such intrinsically disordered regions. We further demonstrate that 20% of disease mutations in IDRs cause local disorder-to-order transitions, which represents a 1.7-2.7 fold increase compared to annotated polymorphisms and neutral evolutionary substitutions, respectively. Secondary structure predictions show elevated rates of transition from helices and strands into loops and vice versa in the disease mutations dataset. Disease disorder-to-order mutations also influence predicted molecular recognition features (MoRFs) more often than the control mutations. The repertoire of disorder-to-order transition mutations is limited, with five most frequent mutations (R→W, R→C, E→K, R→H, R→Q) collectively accounting for 44% of all deleterious disorder-to-order transitions. As a proof of concept, we performed accelerated molecular dynamics simulations on a deleterious disorder-to-order transition mutation of tumor protein p63 and, in agreement with our predictions, observed an increased α-helical propensity of the region harboring the mutation. Our findings highlight the importance of mutations in IDRs and refine the traditional structure-centric view of disease mutations. The results of this study offer a new perspective on the role of mutations in disease, with implications for improving predictors of the functional impact of missense mutations.

Asunto(s)

Enfermedad/genética , Modelos Genéticos , Mutación , Proteínas/genética , Arginina/genética , Análisis por Conglomerados , Biología Computacional , Humanos , Simulación de Dinámica Molecular , Conformación Proteica , Proteínas/química , Proteínas/metabolismo , Análisis de Secuencia de ADN , Factores de Transcripción , Proteínas Supresoras de Tumor

RESUMEN

BACKGROUND/AIMS: There is a growing interest regarding the effect of differential misclassification on power and type I error rate in genome-wide association studies. We present an extension of a previously published test statistic: the likelihood ratio test allowing for errors (LRTAE). This test uses double-sample information on a subset of individuals to increase power for genetic association in the presence of nondifferential misclassification. METHODS: We extend the original LRTAE by allowing for differential genotype misclassification between case and control populations. We label this new statistic as LRT(D)A(M)E . We test the performance of this statistic with data simulated under differential misclassification specifications and two different types of genetic models: null and power. For simulations using the null model, we specify that there is no difference between case and control genotype frequencies before the introduction of errors. For simulations under power, we consider three modes of inheritance: dominant, multiplicative, and recessive. RESULTS: We show that the LRT(D)A(M)E , with p values computed using permutation, maintains a correct type I error rate under the null model after the introduction of differential genotyping errors. Also, we find that as little as 10 to 15% of double-sampled genotype data is needed to achieve this effect. Aside from a few situations (particularly recessive mode of inheritance simulations) the LRT(D)A(M)E version that calculates p values through permutation requires 15 to 20% double sampling to maintain an 80% power for a 0.05 significance level and approximately 20% double sampling for a 0.01 significance level.

Asunto(s)

Análisis Costo-Beneficio , Estudio de Asociación del Genoma Completo/economía , Estudio de Asociación del Genoma Completo/métodos , Modelos Estadísticos , Estudios de Casos y Controles , Simulación por Computador , Genotipo , Humanos , Modelos Genéticos

RESUMEN

Ubiquitination plays an important role in many cellular processes and is implicated in many diseases. Experimental identification of ubiquitination sites is challenging due to rapid turnover of ubiquitinated proteins and the large size of the ubiquitin modifier. We identified 141 new ubiquitination sites using a combination of liquid chromatography, mass spectrometry, and mutant yeast strains. Investigation of the sequence biases and structural preferences around known ubiquitination sites indicated that their properties were similar to those of intrinsically disordered protein regions. Using a combined set of new and previously known ubiquitination sites, we developed a random forest predictor of ubiquitination sites, UbPred. The class-balanced accuracy of UbPred reached 72%, with the area under the ROC curve at 80%. The application of UbPred showed that high confidence Rsp5 ubiquitin ligase substrates and proteins with very short half-lives were significantly enriched in the number of predicted ubiquitination sites. Proteome-wide prediction of ubiquitination sites in Saccharomyces cerevisiae indicated that highly ubiquitinated substrates were prevalent among transcription/enzyme regulators and proteins involved in cell cycle control. In the human proteome, cytoskeletal, cell cycle, regulatory, and cancer-associated proteins display higher extent of ubiquitination than proteins from other functional categories. We show that gain and loss of predicted ubiquitination sites may likely represent a molecular mechanism behind a number of disease-associatedmutations. UbPred is available at http://www.ubpred.org.

Asunto(s)

Proteoma/análisis , Proteínas de Saccharomyces cerevisiae/análisis , Saccharomyces cerevisiae/metabolismo , Proteínas Ubiquitinadas/análisis , Secuencia de Aminoácidos , Bases de Datos de Proteínas , Complejos de Clasificación Endosomal Requeridos para el Transporte/metabolismo , Humanos , Espectrometría de Masas , Datos de Secuencia Molecular , Proteoma/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Análisis de Secuencia de Proteína , Complejos de Ubiquitina-Proteína Ligasa/metabolismo , Proteínas Ubiquitinadas/metabolismo , Ubiquitinación

RESUMEN

Individuals are frequently observed to have long segments of uninterrupted sequences of homozygous markers. One of the major mechanisms that gives rise to such long homozygous segments is consanguineous marriages, where parents pass shared chromosomal segments to their child. Such chromosomal segments are also known as autozygous segments. The clinical evidence that progeny from inbred individuals may have reduced health and fitness because of homozygosity of recessive alleles is well known. As the length of such homozygous segments depends on the degree of parental consanguinity, it would be logical to observe shorter homozygous segments in more outbred populations. However, a recent study identified long homozygous regions, thus likely to be autozygous segments in the HapMap populations. While an abundance of homozygous segments may significantly reduce the ability to fine map disease genes using association studies, detecting tracts of extended homozygosity related to disease status seems the natural next step in genome-wide association studies beyond allele, genotype and haplotype association analyses. In this study, we propose a new algorithm to map disease-related segments based on autozygosity using case-control data. The underlying rationale for the proposed method is that shared autozygosity regions that differ between diseased and healthy individuals may harbor mutations underlying diseases. Specifically, our algorithm uses a sliding-window framework and employs a logarithm of the odds score measure of autozygosity coupled with permutation-based methods to identify disease-related regions. We illustrate the advantage of the algorithm with its application to a genome-wide association study on Parkinson's disease.

Asunto(s)

Mapeo Cromosómico/estadística & datos numéricos , Genoma Humano , Estudio de Asociación del Genoma Completo/estadística & datos numéricos , Algoritmos , Alelos , Cromosomas Humanos Par 20/genética , Consanguinidad , Femenino , Frecuencia de los Genes , Genética Médica/estadística & datos numéricos , Homocigoto , Humanos , Escala de Lod , Masculino , Epidemiología Molecular/estadística & datos numéricos , Enfermedad de Parkinson/genética , Polimorfismo de Nucleótido Simple

RESUMEN

While there have been significant advances in understanding the genetic etiology of human hair loss over the previous decade, there remain a number of hereditary disorders for which a causative gene has yet to be identified. We studied a large, consanguineous Brazilian family that presented with woolly hair at birth that progressed to severe hypotrichosis by the age of 5, in which 6 of the 14 offspring were affected. After exclusion of known candidate genes, a genome-wide scan was performed to identify the disease locus. Autozygosity mapping revealed a highly significant region of extended homozygosity (lod score of 10.41) that contained a haplotype with a linkage lod score of 3.28. Results of these two methods defined a 9-Mb region on chromosome 13q14.11-q14.2. The interval contains the P2RY5 gene, in which we recently identified pathogenic mutations in several families of Pakistani origin affected with autosomal recessive woolly and sparse hair. After the exclusion of several other candidate genes, we sequenced the P2RY5 gene and identified a homozygous mutation (C278Y) in all affected individuals in this family. Our findings show that mutations in P2RY5 display variable expressivity, underlying both hypotrichosis and woolly hair, and underscore the essential role of P2RY5 in the tissue integrity and maintenance of the hair follicle.

Asunto(s)

Genes Recesivos , Predisposición Genética a la Enfermedad , Hipotricosis/genética , Mutación , Receptores Purinérgicos P2/genética , Secuencia de Aminoácidos , Animales , Brasil , Mapeo Cromosómico , Cromosomas Humanos Par 13/genética , Femenino , Ligamiento Genético , Humanos , Escala de Lod , Masculino , Ratones , Modelos Moleculares , Datos de Secuencia Molecular , Linaje , Polimorfismo de Nucleótido Simple , Análisis de Secuencia de ADN

RESUMEN

Genome-wide association studies are now widely used tools to identify genes and/or regions which may contribute to the development of various diseases. With case-control data a 2x3 contingency table can be constructed for each SNP to perform genotype-based tests of association. An increasingly common technique to increase the power to detect an association is to collapse each 2x3 table into a table assuming either a dominant or recessive mode of inheritance (2x2 table). We consider three different methods of determining which genetic model to choose and show that each of these methods of collapsing genotypes increases the type I error rate (i.e., the rate of false positives). However, one of these methods does lead to an increase in power compared with the usual genotype- and allele-based tests for most genetic models.

Asunto(s)

Estudios de Casos y Controles , Predisposición Genética a la Enfermedad , Genotipo , Modelos Genéticos , Análisis de Secuencia por Matrices de Oligonucleótidos/estadística & datos numéricos , Polimorfismo de Nucleótido Simple , Alelos , Análisis de Varianza , Distribución de Chi-Cuadrado , Genes Dominantes , Genes Recesivos , Humanos , Proyectos de Investigación

RESUMEN

BACKGROUND: Studies of association methods using DNA pooling of single nucleotide polymorphisms (SNPs) have focused primarily on the effects of "machine-error", number of replicates, and the size of the pool. We use the non-centrality parameter (NCP) for the analysis of variance test to compute the approximate power for genetic association tests with DNA pooling data on cases and controls. We incorporate genetic model parameters into the computation of the NCP. Parameters involved in the power calculation are disease allele frequency, frequency of the marker SNP allele in coupling with the disease locus, disease prevalence, genotype relative risk, sample size, genetic model, number of pools, number of replicates of each pool, and the proportion of variance of the pooled frequency estimate due to machine variability. We compute power for different settings of number of replicates and total number of genotypings when the genetic model parameters are fixed. Several significance levels are considered, including stringent significance levels (due to the increasing popularity of 100 K and 500 K SNP "chip" data). We use a factorial design with two to four settings of each parameter and multiple regression analysis to assess which parameters most significantly affect power. RESULTS: The power can increase substantially as the genotyping number increases. For a fixed number of genotypings, the power is a function of the number of replicates of each pool such that there is a setting with maximum power. The four most significant parameters affecting power for association are: (1) genotype relative risk, (2) genetic model, (3) sample size, and (4) the interaction term between disease and SNP marker allele probabilities. CONCLUSION: For a fixed number of genotypings, there is an optimal number of replicates of each pool that increases as the number of genotypings increases. Power is not substantially reduced when the number of replicates is close to but not equal to the optimal setting.

Asunto(s)

Análisis Mutacional de ADN/métodos , Predisposición Genética a la Enfermedad , Genética de Población/economía , Modelos Genéticos , Proyectos de Investigación , Manejo de Especímenes , Estudios de Casos y Controles , Análisis Costo-Beneficio , Análisis Mutacional de ADN/economía , Frecuencia de los Genes , Genética de Población/métodos , Genotipo , Humanos , Desequilibrio de Ligamiento , Polimorfismo de Nucleótido Simple , Análisis de Regresión

RESUMEN

The purpose of this work is the development of linear trend tests that allow for error (LTT ae), specifically incorporating double-sampling information on phenotypes and/or genotypes. We use a likelihood framework. Misclassification errors are estimated via double sampling. Unbiased estimates of penetrances and genotype frequencies are determined through application of the Expectation-Maximization algorithm. We perform simulation studies to evaluate false-positive rates for various genotype classification weights (recessive, dominant, additive). We compare simulated power between the LTT ae and its genotypic test equivalent, the LRT ae, in the presence of phenotype and genotype misclassification, to evaluate power gains of the LTT ae for multi-locus haplotype association with a dominant mode of inheritance. Finally, we apply LTT ae and a method without double-sample information (LTT std) to double-sampled phenotype data for an actual Alzheimer's disease (AD) case-control study with ApoE genotypes. Simulation results suggest that the LTT ae maintains correct false-positive rates in the presence of misclassification. For power simulations, the LTT ae method is at least as powerful as LRT ae method, with a maximum power gain of 0.42 over the LRT ae method for certain parameter settings. For AD data, LTT ae provides more significant evidence for association (permutation p=0.0522) than LTT std (permutation p=0.1684). This is due to observed phenotype misclassification. The LTT ae statistic enables researchers to apply linear trend tests to case-control genetic data, increasing power to detect association in the presence of misclassification. If the disease MOI is known, LTT ae methods are usually more powerful due to the fact that the statistic has fewer degrees of freedom.

Asunto(s)

Enfermedad de Alzheimer/genética , Estudios de Casos y Controles , Estadística como Asunto , Algoritmos , Apolipoproteínas E/genética , Simulación por Computador , Interpretación Estadística de Datos , Genotipo , Haplotipos , Humanos , Funciones de Verosimilitud , Fenotipo

RESUMEN

The Biology of Addictive Diseases-Database (BiolAD-DB) system is a research bioinformatics system for archiving, analyzing, and processing of complex clinical and genetic data. The database schema employs design principles for handling complex clinical information, such as response items in genetic questionnaires. Data access and validation is provided by the BiolAD-DB client application, which features a data validation engine tightly coupled to a graphical user interface. Data integrity is provided by the password-protected BiolAD-DB SQL compliant server and database. BiolAD-DB tools further provide functionalities for generating customized reports and views. The BiolAD-DB system schema, client, and installation instructions are freely available at http://www.rockefeller.edu/biolad-db/.

Asunto(s)

Informática Médica/métodos , Biología Computacional/métodos , Gráficos por Computador , Sistemas de Administración de Bases de Datos , Bases de Datos Factuales , Bases de Datos Genéticas , Procesamiento Automatizado de Datos , Humanos , Internet , Proyectos de Investigación , Programas Informáticos

RESUMEN

Alopecia areata (AA) is a genetically determined, immune-mediated disorder of the hair follicle that affects 1%-2% of the U.S. population. It is defined by a spectrum of severity that ranges from patchy localized hair loss on the scalp to the complete absence of hair everywhere on the body. In an effort to define the genetic basis of AA, we performed a genomewide search for linkage in 20 families with AA consisting of 102 affected and 118 unaffected individuals from the United States and Israel. Our analysis revealed evidence of at least four susceptibility loci on chromosomes 6, 10, 16 and 18, by use of several different statistical approaches. Fine-mapping analysis with additional families yielded a maximum multipoint LOD score of 3.93 on chromosome 18, a two-point affected sib pair (ASP) LOD score of 3.11 on chromosome 16, several ASP LOD scores >2.00 on chromosome 6q, and a haplotype-based relative risk LOD of 2.00 on chromosome 6p (in the major histocompatibility complex locus). Our findings confirm previous studies of association of the human leukocyte antigen locus with human AA, as well as the C3H-HeJ mouse model for AA. Interestingly, the major loci on chromosomes 16 and 18 coincide with loci for psoriasis reported elsewhere. These results suggest that these regions may harbor gene(s) involved in a number of different skin and hair disorders.

Asunto(s)

Alopecia Areata/genética , Cromosomas Humanos/genética , Ligamiento Genético , Genoma Humano , Mapeo Cromosómico , Femenino , Predisposición Genética a la Enfermedad , Humanos , Masculino , Linaje

RESUMEN

The questions addressed in this paper are: What single nucleotide polymorphism (SNP) genotyping errors are most costly, in terms of minimum sample size necessary (MSSN) to maintain constant asymptotic power and significance level, when performing case-control studies of genetic association applying the Cochran-Armitage trend test? And which trend test or chi2 test is more powerful under standard genetic models with genotyping errors? Our strategy is to expand the non-centrality parameter of the asymptotic distribution of the trend test to approximate the MSSN using a Taylor series linear in the genotyping error rates. We apply our strategy to example scenarios that assume recessive, dominant, additive, or over-dominant disease models. The most costly errors are recording the more common homozygote as the less common homozygote, and the more common homozygote as the heterozygote, with MSSN that become indefinitely large as the minor SNP allele frequency approaches zero. Misclassifying the heterozygote as the less common homozygote is costly when using the recessive trend test on data from a recessive model. The chi2 test has power close to, but less than, the optimal trend test and is never dominated over all genetic models studied by any specific trend test.

Asunto(s)

Genotipo , Modelos Genéticos , Polimorfismo de Nucleótido Simple , Estudios de Casos y Controles , Genética Médica/estadística & datos numéricos , Humanos , Modelos Lineales , Tamaño de la Muestra

RESUMEN

PURPOSE: To investigate further the genetic contribution to age-related macular degeneration (AMD), increasing the power of a previous analysis and reproducing the original findings. METHODS: A large cohort of families with this condition was assembled, and an expanded genome scan was performed with 556 microsatellite markers. In 2003, the results were reported of a genome-wide linkage analysis of 70 of these pedigrees. Members of 51 new families have now been ascertained and many of the original pedigrees expanded. Parametric and nonparametric linkage analyses were performed with a denser map of markers. In addition, analyses were performed with the sample stratified by age at ascertainment and by two major advanced phenotypes for the disease: neovascular AMD (choroidal neovascularization) and geographic atrophy. RESULTS: The results corroborate the macular degeneration-susceptibility loci consistently reported by the authors and others in genome-wide scans. New loci were identified, including the finding of a two-point HLOD of 3.70 at 6q25.2. CONCLUSIONS: The results suggest that the use of families enriched in predisposition to AMD has legitimacy. Genetic analyses of a genome-wide scan performed on our large cohort of families add further confirmatory evidence that susceptibility loci lie on 1q, 3p, 9q, and 10q. Furthermore, new loci have been identified, including a locus on 6q.

Asunto(s)

Mapeo Cromosómico , Predisposición Genética a la Enfermedad , Genoma Humano , Degeneración Macular/genética , Anciano , Cromosomas Humanos Par 1/genética , Cromosomas Humanos Par 10/genética , Cromosomas Humanos Par 3/genética , Cromosomas Humanos Par 9/genética , Salud de la Familia , Ligamiento Genético , Humanos , Escala de Lod , Repeticiones de Microsatélite , Linaje

RESUMEN

Recent proteome-wide screening approaches have provided a wealth of information about interacting proteins in various organisms. To test for a potential association between protein connectivity and the amount of predicted structural disorder, the disorder propensities of proteins with various numbers of interacting partners from four eukaryotic organisms (Caenorhabditis elegans, Saccharomyces cerevisiae, Drosophila melanogaster, and Homo sapiens) were investigated. The results of PONDR VL-XT disorder analysis show that for all four studied organisms, hub proteins, defined here as those that interact with > or = 10 partners, are significantly more disordered than end proteins, defined here as those that interact with just one partner. The proportion of predicted disordered residues, the average disorder score, and the number of predicted disordered regions of various lengths were higher overall in hubs than in ends. A binary classification of hubs and ends into ordered and disordered subclasses using the consensus prediction method showed a significant enrichment of wholly disordered proteins and a significant depletion of wholly ordered proteins in hubs relative to ends in worm, fly, and human. The functional annotation of yeast hubs and ends using GO categories and the correlation of these annotations with disorder predictions demonstrate that proteins with regulation, transcription, and development annotations are enriched in disorder, whereas proteins with catalytic activity, transport, and membrane localization annotations are depleted in disorder. The results of this study demonstrate that intrinsic structural disorder is a distinctive and common characteristic of eukaryotic hub proteins, and that disorder may serve as a determinant of protein interactivity.

Asunto(s)

Proteínas de Caenorhabditis elegans/metabolismo , Proteínas Portadoras/metabolismo , Proteínas de Drosophila/metabolismo , Proteínas ELAV/metabolismo , Ligasas/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Aminoácidos/química , Animales , Caenorhabditis elegans/química , Caenorhabditis elegans/genética , Caenorhabditis elegans/metabolismo , Proteínas de Caenorhabditis elegans/química , Proteínas de Caenorhabditis elegans/clasificación , Proteínas de Caenorhabditis elegans/genética , Proteínas Portadoras/química , Proteínas Portadoras/clasificación , Proteínas Portadoras/genética , Biología Computacional , Proteínas de Drosophila/química , Proteínas de Drosophila/clasificación , Proteínas de Drosophila/genética , Drosophila melanogaster/química , Drosophila melanogaster/genética , Drosophila melanogaster/metabolismo , Proteínas ELAV/química , Proteínas ELAV/clasificación , Proteínas ELAV/genética , Proteína 2 Similar a ELAV , Humanos , Ligasas/química , Ligasas/clasificación , Ligasas/genética , Modelos Moleculares , Unión Proteica , Estructura Terciaria de Proteína , Saccharomyces cerevisiae/química , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/química , Proteínas de Saccharomyces cerevisiae/clasificación , Proteínas de Saccharomyces cerevisiae/genética

RESUMEN

Patients diagnosed with a standard clinical method (subject to misclassification error) are often combined with patients diagnosed with a gold-standard method (with zero or very small misclassification error) in family-based studies of complex disease. For example, non-autopsied patients (NAP) are often included along with autopsy-proven (AP) patients in family-based studies of complex diseases, such as Alzheimer's disease (AD). Theoretical and simulation studies suggest that certain misclassification errors can result in severe reduction of power in genetic linkage and association analyses and that phenotype (or diagnostic) error can produce misleading results. Morton's test for heterogeneity can identify genomic regions where error may have led to loss in power. We applied this test to pedigree data from the NIMH Alzheimer's Disease Genetics Initiative Database separated into AP and NAP pedigrees. Morton's test identified one highly significant region of heterogeneity on chromosome 2. The source of the heterogeneity was due to significant indication of linkage in the AP pedigrees at position 109 cM (p value = 6.68 x 10(-5)) with no indication in the NAP pedigrees. Furthermore, Morton's test showed no evidence for heterogeneity on chromosome 19 in early-onset pedigrees that showed highly significant evidence for linkage in other published reports. These results suggest that supplementing linkage analysis with Morton's test can be usefully applied to genetic data sets that have AP and NAP samples, or other sample mixtures that include a 'gold standard' subgroup with reduced error rate, to increase power to detect linkage in the presence of diagnostic misclassification.

Asunto(s)

Enfermedad de Alzheimer/genética , Ligamiento Genético , Mapeo Cromosómico , Bases de Datos Genéticas , Salud de la Familia , Marcadores Genéticos , Humanos , Desequilibrio de Ligamiento , Modelos Genéticos , National Institute of Mental Health (U.S.) , Linaje , Proyectos de Investigación , Estados Unidos

RESUMEN

BACKGROUND: In the field of statistical genetics, phenotype and genotype misclassification errors can substantially reduce power to detect association with genetic case/control studies. Misclassification also can bias population frequency parameters such as genotype, haplotype, or multi-locus genotype frequencies. These problems are of particular concern in case/control designs because, short of repeated sampling, there is no way to detect misclassification errors. We developed a double-sampling procedure for case/control genetic association using a likelihood ratio test framework. Different approaches have been proposed to deal with misclassification errors. We have chosen the likelihood framework because of the ease with which misclassification probabilities may be incorporated into in the statistical framework and hypothesis testing. The statistic is called the Likelihood Ratio Test allowing for errors (LRTae) and is freely available via software download. RESULTS: We applied our procedure to 10,000 replicates of simulated case/control data in which we introduced phenotype misclassification errors. The phenotype considered is Ankylosing Spondylitis (AS). The LRTae method power was always greater than LRTstd power for the significance levels considered (5%, 1%, 0.1%, 0.01%). Power gains for the LRTae method over the LRTstd method increased as the significance level became more stringent. Multi-locus genotype frequency estimates using LRTae method were more accurate than estimates using LRTstd method. CONCLUSION: The LRTae method can be applied to single-locus genotypes, multi-locus genotypes, or multi-locus haplotypes in a case/control framework and can be more powerful to detect association in case/control studies when both genotype and/or phenotype errors are present. Furthermore, the LRTae method provides asymptotically unbiased estimates of case and control genotype frequencies, as well as estimates of phenotype and/or genotype misclassification rates.

Asunto(s)

Interpretación Estadística de Datos , Proyectos de Investigación , Estudios de Casos y Controles , Genética de Población , Genotipo , Humanos , Modelos Genéticos , Modelos Estadísticos , Fenotipo , Reproducibilidad de los Resultados

RESUMEN

Serine/arginine-rich (SR) splicing factors play an important role in constitutive and alternative splicing as well as during several steps of RNA metabolism. Despite the wealth of functional information about SR proteins accumulated to-date, structural knowledge about the members of this family is very limited. To gain a better insight into structure-function relationships of SR proteins, we performed extensive sequence analysis of SR protein family members and combined it with ordered/disordered structure predictions. We found that SR proteins have properties characteristic of intrinsically disordered (ID) proteins. The amino acid composition and sequence complexity of SR proteins were very similar to those of the disordered protein regions. More detailed analysis showed that the SR proteins, and their RS domains in particular, are enriched in the disorder-promoting residues and are depleted in the order-promoting residues as compared to the entire human proteome. Moreover, disorder predictions indicated that RS domains of SR proteins were completely unstructured. Two different classification methods, the charge-hydropathy measure and the cumulative distribution function (CDF) of the disorder scores, were in agreement with each other, and they both strongly predicted members of the SR protein family to be disordered. This study emphasizes the importance of the disordered structure for several functions of SR proteins, such as for spliceosome assembly and for interaction with multiple partners. In addition, it demonstrates the usefulness of order/disorder predictions for inferring protein structure from sequence.

Asunto(s)

Empalme del ARN , Proteínas de Unión al ARN/química , Proteínas de Unión al ARN/clasificación , Aminoácidos/análisis , Arginina/análisis , Humanos , Estructura Terciaria de Proteína , Análisis de Secuencia de Proteína , Serina/análisis

RESUMEN

UNLABELLED: A website that plots power and sample size calculations over a range of up to eight parameters (including diagnostic misclassification error parameters) for two commonly used statistical tests of genetic association, the linear trend test and the genotypic test of association. AVAILABILITY: This method is made available via the website http://linkage.rockefeller.edu/pawe3d/ CONTACT: pawe3d@linkage.rockefeller.edu.

Asunto(s)

Predisposición Genética a la Enfermedad/genética , Pruebas Genéticas/métodos , Genética de Población/métodos , Imagenología Tridimensional/métodos , Carácter Cuantitativo Heredable , Programas Informáticos , Interfaz Usuario-Computador , Algoritmos , Estudios de Casos y Controles , Humanos