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Complex Etiology (complex + etiology)
Selected AbstractsEvaluating the Ability of Tree-Based Methods and Logistic Regression for the Detection of SNP-SNP InteractionANNALS OF HUMAN GENETICS, Issue 3 2009M. García-Magariños Summary Most common human diseases are likely to have complex etiologies. Methods of analysis that allow for the phenomenon of epistasis are of growing interest in the genetic dissection of complex diseases. By allowing for epistatic interactions between potential disease loci, we may succeed in identifying genetic variants that might otherwise have remained undetected. Here we aimed to analyze the ability of logistic regression (LR) and two tree-based supervised learning methods, classification and regression trees (CART) and random forest (RF), to detect epistasis. Multifactor-dimensionality reduction (MDR) was also used for comparison. Our approach involves first the simulation of datasets of autosomal biallelic unphased and unlinked single nucleotide polymorphisms (SNPs), each containing a two-loci interaction (causal SNPs) and 98 ,noise' SNPs. We modelled interactions under different scenarios of sample size, missing data, minor allele frequencies (MAF) and several penetrance models: three involving both (indistinguishable) marginal effects and interaction, and two simulating pure interaction effects. In total, we have simulated 99 different scenarios. Although CART, RF, and LR yield similar results in terms of detection of true association, CART and RF perform better than LR with respect to classification error. MAF, penetrance model, and sample size are greater determining factors than percentage of missing data in the ability of the different techniques to detect true association. In pure interaction models, only RF detects association. In conclusion, tree-based methods and LR are important statistical tools for the detection of unknown interactions among true risk-associated SNPs with marginal effects and in the presence of a significant number of noise SNPs. In pure interaction models, RF performs reasonably well in the presence of large sample sizes and low percentages of missing data. However, when the study design is suboptimal (unfavourable to detect interaction in terms of e.g. sample size and MAF) there is a high chance of detecting false, spurious associations. [source] Multiplex primer extension analysis for rapid detection of major European mitochondrial haplogroupsELECTROPHORESIS, Issue 19 2006Martina Wiesbauer Abstract The evolution of the human mitochondrial genome is reflected in the existence of ethnically distinct lineages or haplogroups. Alterations of mitochondrial DNA (mtDNA) have been instrumental in studies of human phylogeny, in population genetics, and in molecular medicine to link pathological mutations to a variety of human diseases of complex etiology. For each of these applications, rapid and cost effective assays for mtDNA haplogrouping are invaluable. Here we describe a hierarchical system for mtDNA haplogrouping that combines multiplex PCR amplifications, multiplex single-base primer extensions, and CE for analyzing ten haplogroup-diagnostic mitochondrial single nucleotide polymorphisms. Using this rapid and cost-effective mtDNA genotyping method, we were able to show that within a large, randomly selected cohort of healthy Austrians (n,=,1172), mtDNAs could be assigned to all nine major European haplogroups. Forty-four percent belonged to haplogroup H, the most frequent haplogroup in European Caucasian populations. The other major haplogroups identified were U (15.4%), J (11.8%), T (8.2%) and K (5.1%). The frequencies of haplogroups in Austria is within the range observed for other European countries. Our method may be suitable for mitochondrial genotyping of samples from large-scale epidemiology studies and for identifying markers of genetic susceptibility. [source] A locus for an auditory processing deficit and language impairment in an extended pedigree maps to 12p13.31-q14.3GENES, BRAIN AND BEHAVIOR, Issue 6 2010L. Addis Despite the apparent robustness of language learning in humans, a large number of children still fail to develop appropriate language skills despite adequate means and opportunity. Most cases of language impairment have a complex etiology, with genetic and environmental influences. In contrast, we describe a three-generation German family who present with an apparently simple segregation of language impairment. Investigations of the family indicate auditory processing difficulties as a core deficit. Affected members performed poorly on a nonword repetition task and present with communication impairments. The brain activation pattern for syllable duration as measured by event-related brain potentials showed clear differences between affected family members and controls, with only affected members displaying a late discrimination negativity. In conjunction with psychoacoustic data showing deficiencies in auditory duration discrimination, the present results indicate increased processing demands in discriminating syllables of different duration. This, we argue, forms the cognitive basis of the observed language impairment in this family. Genome-wide linkage analysis showed a haplotype in the central region of chromosome 12 which reaches the maximum possible logarithm of odds ratio (LOD) score and fully co-segregates with the language impairment, consistent with an autosomal dominant, fully penetrant mode of inheritance. Whole genome analysis yielded no novel inherited copy number variants strengthening the case for a simple inheritance pattern. Several genes in this region of chromosome 12 which are potentially implicated in language impairment did not contain polymorphisms likely to be the causative mutation, which is as yet unknown. [source] Mutation frequencies of X-linked mental retardation genes in families from the EuroMRX consortium,,HUMAN MUTATION, Issue 2 2007Arjan P.M. de Brouwer Abstract The EuroMRX family cohort consists of about 400 families with non-syndromic and 200 families with syndromic X-linked mental retardation (XLMR). After exclusion of Fragile X (Fra X) syndrome, probands from these families were tested for mutations in the coding sequence of 90 known and candidate XLMR genes. In total, 73 causative mutations were identified in 21 genes. For 42% of the families with obligate female carriers, the mental retardation phenotype could be explained by a mutation. There was no difference between families with (lod score >2) or without (lod score <2) significant linkage to the X chromosome. For families with two to five affected brothers (brother pair=BP families) only 17% of the MR could be explained. This is significantly lower (P=0.0067) than in families with obligate carrier females and indicates that the MR in about 40% (17/42) of the BP families is due to a single genetic defect on the X chromosome. The mutation frequency of XLMR genes in BP families is lower than can be expected on basis of the male to female ratio of patients with MR or observed recurrence risks. This might be explained by genetic risk factors on the X chromosome, resulting in a more complex etiology in a substantial portion of XLMR patients. The EuroMRX effort is the first attempt to unravel the molecular basis of cognitive dysfunction by large-scale approaches in a large patient cohort. Our results show that it is now possible to identify 42% of the genetic defects in non-syndromic and syndromic XLMR families with obligate female carriers. © 2007 Wiley-Liss, Inc. [source] Association chain graphs: modelling etiological pathwaysINTERNATIONAL JOURNAL OF METHODS IN PSYCHIATRIC RESEARCH, Issue 2 2003Michael Höfler Abstract Multiple time-dynamic and interrelated risk factors are usually involved in the complex etiology of disorders. This paper presents a strategy to explore and display visually the relative importance of different association pathways for the onset of disorder over time. The approach is based on graphical chain models, a tool that is powerful but still under-utilized in most fields. Usually, the results of these models are displayed using directed acyclic graphs (DAGs). These draw an edge between a pair of variables whenever the assumption of conditional independence given variables on an earlier or equal temporal footing is violated to a statistically significant extent. In the present paper, the graphs are modified in that confidence intervals for the strengths of associations (statistical main effects) are visualized. These new graphs are called association chain graphs (ACGs). Statistical interactions cause ,edges' between the respective variables within the DAG framework (because the assumption of conditional independence is violated). In contrast they are represented as separate graphs within the subsample where the different association chains may work within the ACG framework. With this new type of graph, more specific information can be displayed whenever the data are essentially described only with statistical main- and two-way interaction effects. Copyright © 2003 Whurr Publishers Ltd. [source] Advances in mechanisms of postsurgical gastroparesis syndrome and its diagnosis and treatmentJOURNAL OF DIGESTIVE DISEASES, Issue 2 2006Ke DONG Postsurgical gastroparesis syndrome (PGS) is a complex disorder characterized by post-prandial nausea and vomiting, and gastric atony in the absence of mechanical gastric outlet obstruction, and is often caused by operation at the upper abdomen, especially by gastric or pancreatic resection, and sometimes also by operation at the lower abdomen, such as gynecological or obstetrical procedures. PGS occurs easily with oral intake of food or change in the form of food after operation. These symptoms can be disabling and often fail to be alleviated by drug therapy, and gastric reoperations usually prove unsuccessful. The cause of PGS has not been identified, nor has its mechanism quite been clarified. PGS after gastrectomy has been reported in many previous studies, with an incidence of approximately 0.4,5.0%. PGS is also a frequent complication of pylorus-preserving pancreatoduodenectomy (PPPD), and the complication occurs in the early postoperative period in 20,50% of patients. PGS caused by pancreatic cancer cryoablation (PCC) has been reported about in 50,70% of patients. Therefore, PGS has a complex etiology and might be caused by multiple factors and mechanisms. The frequency of this complication varies directly with the type and number of gastric operations performed. The loss of gastric parasympathetic control resulting from vagotomy contributes to PGS via several mechanisms. It has been reported that the interstitial cells of Cajal (ICC) may play a role in the pathogenesis of PGS. Recent studies in animal models of diabetes suggest specific molecular changes in the enteric nervous system may result in delayed gastric emptying. The absence of the duodenum, and hence gastric phase III, may be a cause of gastric stasis. It was thought that PGS after PPPD might be attributable, at least in part, to delayed recovery of gastric phase III, due to lowered concentrations of plasma motilin after resection of the duodenum. The damage to ICC might play a role in the pathogenesis of PGS after PCC, for which multiple factors are possibly responsible, including ischemic and neural injury to the antropyloric muscle and the duodenum after freezing of the pancreatoduodenal regions or reduction of circulating levels of motilin. As the treatment of gastroparesis is far from ideal, non-conventional approaches and non-standard medications might be of use. Multiple treatments are better than single treatment. This article reviews almost all the papers related to PGS from various journals published in English and Chinese in recent years in order to facilitate a better understanding of PGS. [source] Familial essential tremor with apparent autosomal dominant inheritance: Should we also consider other inheritance modes?MOVEMENT DISORDERS, Issue 9 2006Shaochun Ma MD Abstract A positive family history is present in many patients with essential tremor (ET), but twin studies and segregation analysis have suggested that ET is not entirely a genetic disorder. Two genetic loci have been identified in autosomal dominant (AD) ET and polymorphisms in the DRD3 and HS1-BP3 genes have been proposed as the possible susceptibility factors for ET. There is also evidence for further genetic heterogeneity. We evaluated 4 unrelated large kindreds with ET with an apparent AD mode of transmission. Each kindred spanned at least 3 generations and contained at least 13 living affected subjects who met criteria for definitive ET. None of the pedigrees had evidence for inheritance of ET from both parents. Known genetic ET loci were excluded in these families. We detected a preferential transmission of ET in every kindred and the proportion of affected offspring varied from 75% to 90% (P < 0.05) in the generations with complete ascertainment. Our data indicate that non-Mendelian preferential transmission of an affected allele is a feature in many ET kindreds with multiple affected members and an apparent AD mode of inheritance. ET may have a complex etiology. Additional genetic models need to be considered, including an interaction of susceptibility genes and environmental risk factors. © 2006 Movement Disorder Society [source] Trans Fatty Acids, Insulin Resistance, and Type 2 DiabetesNUTRITION REVIEWS, Issue 8 2006Andrew O. Odegaard BA Type 2 diabetes, a growing global health problem, has a complex etiology involving many interactions between genetic and environmental factors. Essential to the development of the disease is insulin resistance of the peripheral tissues. Insulin resistance may be partly modified by the specific types of dietary fatty acids. Trans fatty acids (TFAs), created through the transformation of polyunsaturated fatty acids from their natural cis form to the trans form, are abundant in the Western diet. TFAs take on similar properties as saturated fats, and appear to be more atherogenic. High intakes of saturated fats may promote insulin resistance. It is therefore reasonable to hypothesize that high intakes of TFAs would have similar, or stronger, effects. In this review, all current evidence on the topic of TFAs, insulin resistance, and type 2 diabetes is summarized and interpreted. Although there is some support from observational and experimental studies for the hypothesis that high intakes of TFAs may increase the risk for type 2 diabetes, inconsistencies across studies and methodological problems make it premature to draw definitive conclusions at this time. More experimental research in humans is needed to further address this question. [source] Disease complex in coffee involving Meloidogyne arabicida and Fusarium oxysporumPLANT PATHOLOGY, Issue 3 2000B. Bertrand Coffee corky-root disease, also called corchosis, was first detected in 1974 in a small area of Costa Rica where the root-knot nematode Meloidogyne arabicida is the dominant species. An epidemiological study revealed a constant association between Meloidogyne spp. and Fusarium sp. in cases of corky root. No corky root appears to have been reported in association with Meloidogyne exigua, which is the prevalent root-knot nematode on coffee in Costa Rica. Fusarium spp. are often cited as components of disease complexes in association with nematodes. Combined inoculations using M. arabicida or M. exigua with Fusarium oxysporum under controlled conditions showed that only the combination with M. arabicida produced corky-root symptoms on Coffea arabica cvs Caturra or Catuai. Fusarium oxysporum alone was nonpathogenic. Meloidogyne exigua or M. arabicida alone caused galls and reduction in shoot height, but no corky-root symptoms. When cultivars susceptible and resistant to M. arabicida were studied under field conditions for 5 years, all the susceptible cultivars exhibited corky-root symptoms on 40,80% of their root systems. Cultivars that were resistant to M. arabicida but not to M. exigua showed no corky root. These observations lead to the conclusion that corky-root disease has a complex etiology, and emphasize the dominant role of M. arabicida as a predisposing agent to subsequent invasion by F. oxysporum. Consequently, genetic resistance to M. arabicida appears to provide an effective strategy against the disease. [source] Comparative morphometrics of embryonic facial morphogenesis: Implications for cleft-lip etiologyTHE ANATOMICAL RECORD : ADVANCES IN INTEGRATIVE ANATOMY AND EVOLUTIONARY BIOLOGY, Issue 1 2007Nathan M. Young Abstract Cleft lip (CL) with or without cleft palate (CL[P]) has a complex etiology but is thought to be due to either genetic or environmentally induced disruptions of developmental processes affecting the shape and size of the facial prominences (medial nasal, lateral nasal, and maxilla). Recent advances in landmark-based morphometrics enable a rigorous reanalysis of phenotypic shape variation associated with facial clefting. Here we use geometric morphometric (GM) tools to characterize embryonic shape variation in the midface and head of six strains of mice that are both cleft-liable (A, A/WySn, CL/Fr) and normal (BALB/cBy, C57BL, CD1). Data were comprised of two-dimensional landmarks taken from frontal and lateral photographs of embryos spanning the time period in which the facial prominences fuse (GD10-12). Results indicate that A/- strain mice, and particularly A/WySn, have overall smaller midfaces compared to other strains. The A/WySn strain also has significant differences in facial shape related to retarded development. Overall, CL/Fr strain mice are normal-sized, but tend to have undersized maxillary prominences that do not project anteriorly and have a small nasal contact area. These results suggest that the etiology of clefting differs in A/WySn and CL/Fr strains, with the former strain suffering disruptions to developmental processes affecting overall size (e.g., neural crest migration deficiencies and lower mitotic activity), while the latter strain has defects restricted to the shape and size of the maxilla. A combination of molecular experimentation and phenotypic analysis of shape is required to test these hypotheses further. Anat Rec, 290:123,139, 2007. © 2006 Wiley-Liss, Inc. [source] ORIGINAL ARTICLE: Genetic Predisposition to Idiopathic Recurrent Spontaneous Abortion: Contribution of Genetic Variations in IGF-2 and H19 Imprinted GenesAMERICAN JOURNAL OF REPRODUCTIVE IMMUNOLOGY, Issue 2 2008a Ostoji Problem, Recurrent spontaneous abortion (RSA) is a common clinical problem with a complex etiology of genetic and non-genetic causes, which remains to be fully determined. IGF-2 stimulates trophoblast invasion, proliferation and maturation of placenta, while H19 RNA suppresses growth. As genomic imprinting plays a critical role in the development of placenta and embryo, our aim was to evaluate the possible role of variations in IGF-2 and H19 imprinted genes as factors of predisposition for RSA. Method of study, A case,control study was conducted to determine the association between IGF-2 and H19 gene polymorphisms and the susceptibility to RSA in 113 couples with RSA and 226 controls. PCR/RFLP were performed to analyze IGF-2 ApaI and H19 HhaI polymorphisms. Results, We found a statistically significant difference in the genotype frequency distribution of IGF-2 ApaI polymorphism between males from couples with RSA and healthy males (,2(2) = 45.12; P < 0.0001). There were no differences in the genotype and allele distribution of H19 polymorphism frequencies, or for the IGF-2 ApaI polymorphism between female groups. Conclusion, The presence of IGF-2 ApaI polymorphism in partners of RSA women could affect IGF-2 level of expression in placenta and embryo and represent a risk factor for RSA susceptibility. [source] High-density genotyping of STAT4 reveals multiple haplotypic associations with systemic lupus erythematosus in different racial groupsARTHRITIS & RHEUMATISM, Issue 4 2009Bahram Namjou Objective Systemic lupus erythematosus (SLE) is the prototypical systemic autoimmune disorder, with complex etiology and a strong genetic component. Recently, gene products involved in the interferon pathway have been under intense investigation in terms of the pathogenesis of SLE. STAT-1 and STAT-4 are transcription factors that play key roles in the interferon and Th1 signaling pathways, making them attractive candidates for involvement in SLE susceptibility. Methods Fifty-six single-nucleotide polymorphisms (SNPs) across STAT1 and STAT4 on chromosome 2 were genotyped using the Illumina platform, as part of an extensive association study in a large collection of 9,923 lupus patients and control subjects from different racial groups. DNA samples were obtained from the peripheral blood of patients with SLE and control subjects. Principal components analyses and population-based case,control association analyses were performed, and the P values, false discovery rate q values, and odds ratios with 95% confidence intervals were calculated. Results We observed strong genetic associations with SLE and multiple SNPs located within STAT4 in different ethnic groups (Fisher's combined P = 7.02 × 10,25). In addition to strongly confirming the previously reported association in the third intronic region of this gene, we identified additional haplotypic association across STAT4 and, in particular, a common risk haplotype that is found in multiple racial groups. In contrast, only a relatively weak suggestive association was observed with STAT1, probably due to its proximity to STAT4. Conclusion Our findings indicate that STAT4 is likely to be a crucial component in SLE pathogenesis in multiple racial groups. Knowledge of the functional effects of this association, when they are revealed, might improve our understanding of the disease and provide new therapeutic targets. [source] | |||||||||||||