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PubMed2004

The C-terminal basic tail of RhoG assists the guanine nucleotide exchange factor trio in binding to phospholipids.

The multidomain protein Trio regulates among others neuronal outgrowth and axonal guidance in vertebrates and invertebrates. Trio contains two Dbl-homology/pleckstrin homology (DH/PH) tandem domains that activate several RhoGTPases. Here, we present the x-ray structure of the N-terminal DH/PH, hereafter TrioN, refined to 1.7-A resolution. We show that the relative orientations of the DH and PH domains of TrioN and free Dbs are similar. However, this relative orientation is dissimilar to Dbs in the Dbs/Cdc42 structure. In vitro nucleotide exchange experiments catalyzed by TrioN show that RhoG is approximately 3x more efficiently exchanged than Rac and support the conclusion that RhoG is likely the downstream target of TrioN. Residues 54 and 69, which are not conserved between the two GTPases, are responsible for this specificity. Dot-blot assay reveals that the TrioN-PH domain does not detectably bind phosphatidylinositol 3,4-bisphosphate, PtdIns(3,4)P(2), or other phospholipids. This finding is supported by our three-dimensional structure and affinity binding experiments. Interestingly, the presence of RhoG but not Rac or a C-terminal-truncated RhoG mutant allows TrioN to bind PtdIns(3,4)P(2) with a micromolar affinity constant. We conclude the variable C-terminal basic tail of RhoG specifically assists the recruitment of the TrioN-PH domain to specific membrane-bound phospholipids. Our data suggest a role for the phosphoinositide 3-kinase, PI 3-kinase, in modulating the Trio/RhoG signaling pathway.

Amino Acid Sequence↗

PubMed2001

Multipoint linkage-disequilibrium-mapping approach based on the case-parent trio design.

In the present study we propose a multipoint approach, for the mapping of genes, that is based on the case-parent trio design. We first derive an expression for the expected preferential-allele-transmission statistics for transmission, from either parent to an affected child, for an arbitrary location within a chromosomal region demarcated by several genetic markers. No assumption about genetic mechanism is needed in this derivation, beyond the assumption that no more than one disease gene lies in the region framed by the markers. When one builds on this representation, the way in which one may maximize the genetic information from multiple markers becomes obvious. This proposed method differs from the popular transmission/disequilibrium test (TDT) approach for fine mapping, in the following ways: First, in contrast with the TDT approach, all markers contribute information, regardless of whether the parents are heterozygous at any one marker, and incomplete trio data can be utilized in our approach. Second, rather than performing the TDT at each marker separately, we propose a single test statistic that follows a chi(2) distribution with 1 df, under the null hypothesis of no linkage or linkage disequilibrium to the region. Third, in the presence of linkage evidence, we offer a means to estimate the location of the disease locus along with its sampling uncertainty. We illustrate the proposed method with data from a family study of asthma, conducted in Barbados.

Alleles↗

PubMed2005

SOP3v2: web-based selection of oligonucleotide primer trios for genotyping of human and mouse polymorphisms.

SOP3v2 is a database-driven graphical web-based application for facilitating genotyping assay design. SOP3v2 accepts data input in numerous forms, including gene names, reference sequence numbers and physical location. For each entry, the application presents a set of recommended forward and reverse PCR primers, along with a sequencing primer, which is optimized for sequence-based genotyping assays. SOP3v2-generated oligonucleotide primer trios enable analysis of single nucleotide polymorphisms (SNPs) as well as insertion/deletion polymorphisms found in genomic DNA. The application's database was generated by warehousing information from the National Center for Biotechnology Information (NCBI) dbSNP database, genomic DNA sequences from human and mouse, and LocusLink gene attribute information. Query results can be sorted by their biological relevance, such as nonsynonymous coding changes or physical location. Human polymorphism queries may specify ethnicity, haplotype and validation status. Primers are developed using SOP3v2's core algorithm for evaluating primer candidates through stability tests and are suitable for use with sequence-based genotyping methods requiring locus-specific amplification. The method has undergone laboratory validation. Of the SOP3v2-designed primer trios that were tested, a majority (>80%) have successfully produced genotyping data. The application may be accessed via the web at http://imgen.ccbb.pitt.edu/sop3v2.

Animals↗

PubMed1985

Tracheal insufflation of O2 (TRIO) at low flow rates sustains life for several hours.

The emergency management of respiratory arrest can be a difficult problem. The authors hypothesized that tracheal insufflation of O2 (TRIO) at low flows could provide adequate oxygenation and sufficient CO2 elimination to sustain life until more definitive (but more difficult to implement) measures could be applied. Therefore, 10 anesthetized, paralyzed dogs (15.9-48.2 kg), initially ventilated with conventional mechanical ventilation (CMV) using room air, were studied. CMV was stopped and a 1- or 5-mm id catheter with a constant flow (V) of O2 ranging from 0.2 to 3.0 l/min was inserted to within 1 cm of the carina. With all flow rates, PaO2 and PaCO2 initially increased with time; the rate of increase of PaO2 was greater and that of PaCO2 was less, with increasing V. In three dogs studied at flow rates of 2.0 or 3.0 l/min, arterial blood gases reached a plateau after about 2 h: pH = 6.87; PCO2 = 164 mmHg; and PO2 = 363 mmHg (mean values). These studies were stopped at between 4 and 5 h, with no dogs showing any signs of cardiovascular or other decompensation. Results in which catheter position was studied indicated that as long as the catheter tip was at or past the carina, gas transport was similar to that observed when the catheter tip was 1 cm proximal to the carina. The authors conclude that TRIO at low flow rates can produce sufficient gas exchange to support life for prolonged periods in apneic dogs.

Animals↗

PubMed2003

Crystallization and initial crystal characterization of the N-terminal DH/PH domain of Trio.

Trio is a multidomain signaling protein that plays an important role in neurite outgrowth, axon guidance and skeletal muscle development. Trio contains two DH/PH tandem domains that respectively activate the small GTPases RhoG/Rac and RhoA. The N-terminal DH/PH domain, TrioN, crystallizes in space group P3(1)21, with one TrioN molecule in the asymmetric unit and diffracts to 1.7 A resolution. The unit-cell parameters are a = b = 99.5, c = 98.3 A, alpha = beta = 90, gamma = 120 degrees. A greater than 90% complete native data set has been collected and structure determination using the multiple isomorphous replacement (MIR) method is ongoing.

Crystallization↗

PubMed2006

Solo/Trio8, a membrane-associated short isoform of Trio, modulates endosome dynamics and neurite elongation.

With DNA microarrays, we identified a gene, termed Solo, that is downregulated in the cerebellum of Purkinje cell degeneration mutant mice. Solo is a mouse homologue of rat Trio8-one of multiple Trio isoforms recently identified in rat brain. Solo/Trio8 contains N-terminal sec14-like and spectrin-like repeat domains followed by a single guanine nucleotide exchange factor 1 (GEF1) domain, but it lacks the C-terminal GEF2, immunoglobulin-like, and kinase domains that are typical of Trio. Solo/Trio8 is predominantly expressed in Purkinje neurons of the mouse brain, and expression begins following birth and increases during Purkinje neuron maturation. We identified a novel C-terminal membrane-anchoring domain in Solo/Trio8 that is required for enhanced green fluorescent protein-Solo/Trio8 localization to early endosomes (positive for both early-endosome antigen 1 [EEA1] and Rab5) in COS-7 cells and primary cultured neurons. Solo/Trio8 overexpression in COS-7 cells augmented the EEA1-positive early-endosome pool, and this effect was abolished via mutation and inactivation of the GEF domain or deletion of the C-terminal membrane-anchoring domain. Moreover, primary cultured neurons transfected with Solo/Trio8 showed increased neurite elongation that was dependent on these domains. These results suggest that Solo/Trio8 acts as an early-endosome-specific upstream activator of Rho family GTPases for neurite elongation of developing Purkinje neurons.

Animals↗

PubMed1994

Trio learning: a new strategy for building hybrid neural trees.

Neural trees are constructive algorithms which build decision trees whose nodes are binary neurons. We propose a new learning scheme, "trio-learning," which leads to a significant reduction in the tree complexity. In this strategy, each node of the tree is optimized by taking into account the knowledge that it will be followed by two son nodes. Moreover, trio-learning can be used to build hybrid trees, with internal nodes and terminal nodes of different nature, for solving any standard tasks (e.g. classification, regression, density estimation). Significant results on a handwritten character classification are presented.

Artificial Intelligence↗

PubMed2005

Expectation maximization algorithm based haplotype relative risk (EM-HRR): test of linkage disequilibrium using incomplete case-parents trios.

The Haplotype Relative Risk (HRR) was first proposed [Falk et al., Ann Hum Genet 1987] to test for Linkage Disequilibrium (LD) between a marker and a putative disease locus using case-parent trios. Spurious association does not appear in such family-based studies under population admixture. In this paper, we extend the HRR to accommodate incomplete trios via the Expectation-Maximization (EM) algorithm [Dempster et al., J R Stat Soc Ser B, 1977]. In addition to triads and dyads (parent-offspring pair), the EM-HRR easily incorporates individuals with no parental genotype information available, which is excluded from the one parent Transmission/Disequilibrium Test (1-TDT) [Sun et al., Am J Epidemiol 1999]. Due to the data structure of EM-HRR, transmitted alleles are always available regardless of the number of missing parental genotypes. As a result of having a larger sample size, computer simulations reveal that the EM-HRR is more powerful in detecting LD than the 1-TDT in a population under Hardy-Weinberg Equilibirum (HWE). If admixture is not extreme, the EM-HRR remains more powerful. When a large degree of admixture exists, the EM-HRR performs better the 1-TDT when the association is strong, though not as well when the association is weak. We illustrate the proposed method with an application to the Framingham Heart Study.

Algorithms↗

PubMed1976

Matching with a trio of concurrent variable-interval schedules of reinforcement.

A trio of concurrent variable-interval schedules of reinforcement was arranged according to a changeover-key procedure, including a changeover delay of 1.5 sec. The three schedules provided a combined maximum reinforcement rate of 45 reinforcements per hour. With that restriction, the nine experimental conditions included several combinations of variable-interval schedules, sometimes including extinction. The pigeons matched relative response rate and relative time to relative reinforcement rate. Relative time appeared to match some-what better than relative response rate. Performance adjusted rapidly from one experimental condition to the next, whether the change involved two or all three schedules of the concurrent trio.

Journal Article↗

PubMed2000

Analysis of parent-offspring trios provides evidence for linkage and association between the insulin gene and type 2 diabetes mediated exclusively through paternally transmitted class III variable number tandem repeat alleles.

Variation at the variable number tandem repeat (VNTR) minisatellite 5' of the insulin gene (INS) is associated with several phenotypes, including type 1 diabetes, polycystic ovary syndrome, and birth weight. Case-control studies have suggested that class III VNTR alleles are also associated with type 2 diabetes, but results have been inconsistent and may reflect population stratification. To explore further the role of the INS-VNTR in type 2 diabetes susceptibility, we used family-based association methods in 155 parent-offspring trios from the British Diabetic Association-Warren Trios repository, each ascertained via a Europid proband with type 2 diabetes. Overall, there was no significant association between diabetes and the INS-VNTR genotype, with 65 of 119 heterozygous parents (55%) transmitting class III and 54 class I (P = 0.16, one-sided). However, whereas maternal transmissions followed Mendelian expectation, there was a marked excess of class III transmission from the 49 heterozygous fathers (34 [69%] vs. 15, P = 0.003 vs. 50% expectation, P = 0.003 vs. maternal transmission). These results confirm that variation within the TH-INS-IGF2 locus, most plausibly at the VNTR itself, influences type 2 diabetes susceptibility. By demonstrating that this effect is mediated exclusively by the paternally derived allele, these findings implicate imprinted genes in the pathogenesis of type 2 diabetes.

Adult↗

PubMed2026

Comprehensive analysis of de novo variants across 2,497 orofacial cleft trios reveals novel genetic drivers of disease.

BACKGROUND: Orofacial clefts (OFCs) and other palate abnormalities (PAs) are among the most common birth defects worldwide and are characterized by the abnormal formation of the lip and/or palate. Genetic studies have traditionally classified OFC cases as either syndromic, involving OFCs alongside other congenital anomalies, or nonsyndromic, which represent the majority of cases and occur in isolation. Emerging genomic evidence indicates that genes traditionally associated with syndromic forms of OFC can also harbor variants contributing to isolated cases, challenging the notion of a strict dichotomy between these categories and supporting their integration for gene discovery. METHODS: In this study, we applied multiple analytic approaches to characterize the genetic architecture of OFC and PAs by integrating genomic data from 2,497 trios with probands diagnosed with an OFC (n=2,080) or PA (n=417). We compared these findings across OFC subtypes and syndromic status with those from 5,515 control trios to identify enriched biological pathways and mechanisms and to prioritize candidate genes using variant burden testing. RESULTS: We observed a significant enrichment of de novo protein-truncating and damaging missense variants in cases compared to controls (OR = 2.17, p = 1.21×10-32), with particularly strong signals in biologically relevant gene sets involving OFC-associated, constrained, Mendelian disorder, and mouse candidate genes. Variant burden testing identified 39 OFC risk genes at FDR ≤ 0.05, which we then integrated with 593 established OFC genes to interrogate the functional underpinnings of OFC via network analysis. This analysis revealed 309 high-order interactor genes not previously associated with OFC. Notably, this OFC network clustered into ten distinct biological pathways, with nucleosome-associated genes showing significant enrichment among cases in our cohort (OR = 14.8, p = 8.1×10-4). In a final integrative step, we combined evidence across all analyses to nominate 231 candidate genes, 32 of which contained at least two deleterious de novo variants in our cohort. CONCLUSIONS: These findings underscore the value of integrating diverse OFC and PA subtypes, syndromic status, and variant classes to elucidate the genetic architecture of these disorders, highlighting both phenotypic expansion of known disease genes and the emergence of novel gene-phenotype associations.

De Novo Variant Enrichment↗

PubMed1993

Paternity investigation among known false trios: ABO, Rh, MNSs, Kell, Duffy, Kidd, and HLA systems.

This paternity study was performed with trios in which the putative father was not the biological father (NBF), in order to evaluate adjustment of genetic markers employed to disclose non biological fathers for the population, and the biological meaning of likelihood of paternity in casework. All 923 generated trios had ABO, Rh, MNS, Kell and HLA systems tested; 372 of them also had Duffy and Kidd systems tested. The most powerful exclusion system was HLA, followed, in this order, by ABO, Rh, Duffy, MNSs, Kidd, and Kell. Taking into account the Indian/black/white historical miscegenation background in the population, an improvement in the performance of red blood cells as disclosers of non biological fathers could be achieved, if particular additional sera were used. In the group tested with seven different systems, direct exclusions were observed in 90.31%, and they were single system exclusions in 26.61%. In order to avoid the remote possibility of mutation, it is suggested that the number of used systems be increased. Indirect exclusions were verified in 8.87% and only 0.81% of NBF were not excluded at all. In this last group, probabilities of paternity were calculated and two values greater than 95% were obtained. To be able to accomplish the "visum et repertum" duty and to assist the court, the expert should equally emphasize: a) the probability of paternity of the alleged father and the possibility of finding an unexcluded NBF; b) the actual performance of systems used to uncover NBF, together with the probabilities of paternity of those who were not discovered; c) the previous referenced trend of probabilities of paternity of true and of non-biological fathers to cluster in distinct class intervals of likelihood of paternity.

ABO Blood-Group System↗

PubMed2026

Trio-based GWAS reveals loci associated with different forms of isolated cleft lip.

Orofacial clefts (OFCs) are the most common craniofacial birth defect and comprise a diverse group of traits with complex and heterogeneous etiologies. Genetic studies of OFCs typically approach this diversity by stratifying cases into broad diagnostic classes, including cleft lip (CL), cleft palate (CP), and cleft lip with palate (CLP). Although this strategy has yielded important insights into OFC risk, it ignores the phenotypic heterogeneity within each subtype. CL exhibits marked phenotypic variability, involving differences in alveolar involvement, laterality, and sidedness that may reflect distinct etiologies. Given this phenotypic diversity within CL, we assembled a multi-ancestry cohort of 837 nonsyndromic CL case-parent trios with whole-genome sequencing and detailed phenotyping. We performed genome-wide association scans (GWAS) via transmission disequilibrium tests for CL overall and for 14 CL subtypes defined by involvement of the alveolus (with and without), laterality (uni- and bilateral), and sidedness (left and right). We identified four genome-wide significant loci. Two loci, IRF6 and 8q24.21, were both detected in the overall CL GWAS. PLCB1/PLCB4 and MAFB were detected in GWASs of alveolar cleft involvement and CL left sidedness, respectively. These subtype-specific associations were followed by case-only comparisons that reflect the presence or absence of alveolus cleft or left-sided bias of CL to confirm the specificity of the association signal to the particular subtype. Our results provide evidence of within-class CL subtype-specific genetic links for loci previously discussed in the context of primary OFC classes and demonstrate the value of granular OFC subtype characterization to capture trait-specific associations.

Alveolus Cleft↗

PubMed2001

Expression of kalirin, a neuronal GDP/GTP exchange factor of the trio family, in the central nervous system of the adult rat.

Kalirin is a multifunctional protein identified by its interaction with peptidylglycine alpha-amidating monooxygenase, an enzyme essential for neuropeptide biosynthesis. Several forms of Kalirin exist, all containing spectrin-like repeats, a Dbl homology (DH) domain, and an adjacent pleckstrin homology (PH) domain; several different COOH-termini provide additional DH/PH domains and a putative protein kinase. Kalirin binds Rac1 and affects cytoskeletal organization, neuropeptide secretion, and iNOS activity. By in situ hybridization, the highest levels of Kalirin mRNA were found in the cerebral cortex, hippocampal formation, and Purkinje cells, with high levels also in thalamus, caudate putamen, septal nucleus, nucleus accumbens, amygdala, and anterior olfactory nucleus. Low levels of Kalirin mRNA were detected in the paraventricular, supraoptic, and reticular thalamic nuclei and in the ventromedial hypothalamic nucleus. Brain areas with high levels of Kalirin mRNA showed strong Kalirin-like immunoreactivity. Pyramidal neurons with strongly staining soma and long dendrites were observed primarily in layer 5 of the cerebral cortex. In the hippocampus, a uniform distribution of neurons with fine dendritic staining was observed in the pyramidal cell layer, in the granule cell layer, and in the hilar cells of the dentate gyrus as well as in isolated interneurons. Cerebellar Purkinje neurons exhibited intense staining in the soma and in extensive dendritic arbors extending to the surface of the molecular layer. During embryonic development, Trio, the Drosophila orthologue of Kalirin, plays an essential role in axon guidance; localization of Kalirin to the somatodendritic region of adult neurons provides the basis for future studies of regulation and function.

Animals↗

PubMed2002

Investigation of linkage and association/linkage disequilibrium of HLA A-, DQA1-, DQB1-, and DRB1-alleles in 69 sib-pair- and 89 trio-families with schizophrenia.

The hypothesis that HLA antigens confer susceptibility to schizophrenic disorders has been tested by studying linkage and association in a family sample with 69 sib-pair families. Suggestive evidence for linkage was obtained by nonparametric multipoint LOD score analysis with a maximum around DQB CAR (P = 0.0004), a microsatellite marker that is in linkage disequilibrium with the HLA antigen DQB1. Spurious evidence for negative association as calculated by the transmission disequilibrium test was found for HLA- DRB1*11 (chi-square = 11.72, corrected P value = 0.03) and for the haplotype DQB1*301-DQA1*501-DRB1*11 (chi-square = 11.3, corrected P value = 0.043). No evidence of association with these alleles was obtained in a sample of 89 trios with schizophrenic offspring and parents. Our results are not in favor of a direct involvement of the HLA system in development of schizophrenia, but are compatible with the possible existence of a susceptibility gene in the MHC region at chromosome 6p 21.31.

Alleles↗

PubMed2004

Family-based association study between autism and glutamate receptor 6 gene in Chinese Han trios.

The glutamate pathways are involved in diverse processes such as learning and memory, epilepsy, and they play important roles in neural plasticity, neural development, and neurodegeneration. It has been proposed that autism could be a hypoglutamatergic disorder. Recently, Jamain et al. reported that the glutamate receptor 6 (GluR6 or GRIK2) is in linkage disequilibrium with autism. In the present study, the transmission disequilibrium test (TDT) and the haplotype transmission were performed to analyze the four SNPs (SNP1: rs995640; SNP2: rs2227281; SNP3: rs2227283; SNP4: rs2235076) of GluR6 in 174 Chinese Han parent-offspring trios. The TDT demonstrated that the two SNPs (SNP2 and SNP3) showed preferential transmission (TDT P = 0.032). The global chi(2) test for haplotype transmission also revealed an association between GluR6 and autism (chi(2) = 10.78, df = 3, P = 0.013). Our results suggested that GluR6 is in linkage disequilibrium with autism.

Alleles↗

PubMed2003

Candidate gene association analysis for a quantitative trait, using parent-offspring trios.

With the increasing availability of genetic data, many studies of quantitative traits focus on hypotheses related to candidate genes, and also gene-environment (G x E) and gene-gene (G x G) interactions. In a population-based sample, estimates and tests of candidate gene effects can be biased by ethnic confounding, also known as population stratification bias. This paper demonstrates that even a modest degree of ethnic confounding can lead to unacceptably high type I error rates for tests of genetic effects. The parent-offspring trio design is reviewed, and several forms of the quantitative transmission disequilibrium test (QTDT) are summarized. A variation of the QTDT (QTDTM) is described that is based on a linear regression model with multiple intercepts, one per parental mating type. This and other models are expanded to allow testing of G x E and G x G interactions. A method for computing required sample sizes using direct computations is described. Sample size requirements for tests of genetic main effects and G x E and G x G interactions are compared across various QTDT approaches to infer their efficiencies relative to one another. The QTDTM is found to meet or exceed the efficiency of other QTDT approaches. For example, the QTDTM is approximately 3% more efficient than the QTDT of Rabinowitz ([1997] Hum. Hered. 47:342-350) for testing a genetic main effect, but can be as much as twice as efficient for testing G x E interaction, and three times more efficient for testing G x G interaction.

Algorithms↗

PubMed2004

Bayesian trio models for association in the presence of genotyping errors.

Errors in genotyping can greatly affect family-based association studies. If a mendelian inconsistency is detected, the family is usually removed from the analysis. This reduces power, and may introduce bias. In addition, a large proportion of genotyping errors remain undetected, and these also reduce power. We present a Bayesian framework for performing association studies with SNP data on samples of trios consisting of parents with an affected offspring, while allowing for the presence of both detectable and undetectable genotyping errors. This framework also allows for the inclusion of missing genotypes. Associations between the SNP and disease were modelled in terms of the genotypic relative risks. The performances of the analysis methods were investigated under a variety of models for disease association and genotype error, looking at both power to detect association and precision of genotypic relative risk estimates. As expected, power to detect association decreased as genotyping error probability increased. Importantly, however, analyses allowing for genotyping error had similar power to standard analyses when applied to data without genotyping error. Furthermore, allowing for genotyping error yielded relative risk estimates that were approximately unbiased, together with 95% credible intervals giving approximately correct coverage. The methods were also applied to a real dataset: a sample of schizophrenia cases and their parents genotyped at SNPs in the dysbindin gene. The analysis methods presented here require no prior information on the genotyping error probabilities, and may be fitted in WinBUGS.

Alleles↗