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At least 127 records · Page 7Linked to original sources
PubMed1997

Huntingtin-associated protein 1 (HAP1) binds to a Trio-like polypeptide, with a rac1 guanine nucleotide exchange factor domain.

Huntington's disease (HD) occurs when the widely expressed protein huntingtin contains an expanded glutamine repeat. The selective degeneration and neuronal morphologic abnormalities of HD may involve interactions with proteins that bind to huntingtin, such as HAP1. The biological significance of this interaction is unclear because neither HAP1 nor huntingtin have significant homology to known proteins. Therefore, we sought to identify HAP1-binding proteins. Using the yeast two-hybrid system, we isolated a rat cDNA encoding part of a protein that interacts with HAP1, and we confirmed the specificity of this interaction using an in vitro protein-binding assay. We called the protein Duo because it is closely related to the human protein Trio but is shorter. Northern blot analysis indicates brain-specific expression of Duo. Human Duo contains a guanine nucleotide exchange factor (GEF) domain that is likely to be rac1-specific, a pleckstrin homology (PH) domain and spectrin-like repeat units. These data support the hypothesis that huntingtin is involved in vesicle trafficking and cytoskeletal functions, and raise the possibility of a role for huntingtin in the regulation of a ras-related signaling pathway.

Amino Acid Sequence↗
PubMed2005

Suggestive evidence for association of D2S2188 marker (2q31.1) with autism in 143 Sicilian (Italian) TRIO families.

We have screened 143 Sicilian (Italian) families with one autistic child to verify, by a linkage disequilibrium approach, the involvement of the 2q31.1 region in the cause of the disease in these families. Our study design includes the use of intrafamilial association to prevent a population stratification bias and ethnic homogeneity of the sample. The results of our analysis provided suggestive evidence of the occurrence of transmission disequilibrium between autism and the D2S2188 polymorphism in Sicilian TRIO families, a finding which provides further and independent support to the hypothesis of the existence of a susceptibility gene (or genes) for autism on chromosome 2q.

Autistic Disorder↗
PubMed1995

Evaluation of a new agar in Uricult-Trio for rapid detection of Escherichia coli in urine.

A new commercial agar (Uricult-Trio) with 8-hydroxyquinoline-beta-glucuronide was used to assess 2,536 uropathogens for beta-glucuronidase activity typical of Escherichia coli. Included in the study were 1,807 strains of the family Enterobacteriaceae, 284 strains of nonfermentative bacilli, 345 strains of gram-positive cocci, and 100 yeast strains. In identifying E. coli, the test agar gave a sensitivity of 95.5% and a specificity of 97.2%. Fifty E. coli isolates gave negative reactions; 31 non-E. coli strains produced black colonies characteristic of E. coli. No growth of gram-positive cocci and no false-positive reactions from yeasts were observed. The recovery rate for E. coli on this agar was at least 10% higher than that on blood agar.

Agar↗
PubMed2002

Detection rates for genotyping errors in SNPs using the trio design.

One well-known approach for the analysis of transmission-disequilibrium is the investigation of single nucleotide polymorphisms (SNPs) in trios consisting of an affected child and its parents. Results may be biased by erroneously given genotypes. Various reasons, among them sample swap or wrong pedigree structure, represent a possible source for biased results. As these can be partly ruled out by good study conditions together with checks for correct pedigree structure by a series of independent markers, the remaining main cause for errors is genotyping errors. Some of the errors can be detected by Mendelian checks whilst others are compatible with the pedigree structure. The extent of genotyping errors can be estimated by investigating the rate of detected genotyping errors by Mendelian checks. In many studies only one SNP of a specific genomic region is investigated by TDT which leaves Mendelian checks as the only tool to control genotyping errors. From the rate of detected errors the true error rate can be estimated. Gordon et al. [Hum Hered 1999;49:65-70] considered the case of genotyping errors that occur randomly and independently with some fixed probability for the wrong ascertainment of an allele. In practice, instead of single alleles, SNP genotypes are determined. Therefore, we study the proportion of detected errors (detection rate) based on genotypes. In contrast to Gordon et al., who reported detection rates between 25 and 30%, we obtain higher detection rates ranging from 39 up to 61% considering likely error structures in the data. We conclude that detection rates are probably substantially higher than those reported by Gordon et al.

Genotype↗
PubMed2002

Confidence intervals for genotype relative risks and allele frequencies from the case parent trio design for candidate-gene studies.

OBJECTIVES: Confidence intervals for genotype relative risks, for allele frequencies and for the attributable risk in the case parent trio design for candidate-gene studies are proposed which can be easily calculated from the observed familial genotype frequencies. METHODS: Likelihood theory and the delta method were used to derive point estimates and confidence internals. We used Monte Carlo simulations to show the validity of the formulae for a variety of given modes of inheritance and allele frequencies and illustrated their usefulness by applying them to real data. RESULTS: Generally these formulae were found to be valid for 'sufficiently large' sample sizes. For smaller sample sizes the estimators for genotype relative risks tended to be conservative whereas the estimator for attributable risk was found to be anti-conservative for moderate to high allele frequencies. CONCLUSIONS: Since the proposed formulae provide quantitative information on the individual and epidemiological relevance of a genetic variant they might be a useful addition to the traditional statistical significance level of TDT results.

Alleles↗
PubMed2005

On confidence intervals for genotype relative risks and attributable risks from case parent trio designs for candidate-gene studies.

Scherag et al. [Hum Hered 2002;54:210-217] recently proposed point estimates and asymptotic as well as exact confidence intervals for genotype relative risks (GRRs) and the attributable risk (AR) in case parent trio designs using single nucleotide polymorphism (SNP) data. The aim of this study was the investigation of coverage probabilities and bias in estimates if the marker locus is not identical to the disease locus. Using a variety of parameter constellations, including marker allele frequencies identical to and different from the SNP at the disease locus, we performed an analytical study to quantify the bias and a Monte-Carlo simulation study for quantifying both bias and coverage probabilities. No bias was observed if marker and trait locus coincided. Two parameters had a strong impact on coverage probabilities of confidence intervals and bias in point estimates if they did not coincide: the linkage disequilibrium (LD) parameter delta and the allele frequency at the marker SNP. If marker allele frequencies were different from the allele frequencies at the functional SNP, substantial biases occurred. Further, if delta between the marker and the disease locus was lower than the maximum possible delta, estimates were also biased. In general, biases were towards the null hypothesis for both GRRs and AR. If one GRR was not increased, as e.g. in a recessive genetic model, biases away from the null could be observed. If both GRRs were in identical directions and if both were substantially larger than 1, the bias always was towards the null. When applying point estimates and confidence intervals for GRRs and AR in candidate gene studies, great care is needed. Effect estimates are substantially biased towards the null if either the allele frequencies at the marker SNP and the true disease locus are different or if the LD between the marker SNP and the disease locus is not at its maximum. A bias away from the null occurs only in uncommon study situations; it is small and can therefore be ignored for applications.

Confidence Intervals↗
PubMed2007

Association of GABRB3 polymorphisms with autism spectrum disorders in Korean trios.

BACKGROUND/AIMS: Autism spectrum disorders (ASD) are complex neuropsychiatric disorders having a genetic risk factor. The association and linkage study for the gamma-aminobutyric acid type A receptor beta3 subunit gene (GABRB3), located within the chromosome 15q11-q13 autism candidate region, and ASD have been evaluated. The aim of this study was to investigate the association between GABRB3 and ASD in the Korean population. METHODS: The present study was conducted with the detection of four single-nucleotide polymorphisms (rs1426217, rs2081648, rs890317, rs981778) in GABRB3 and association analysis in 104 Korean ASD trios using the transmission disequilibrium test. RESULTS: The transmission disequilibrium test demonstrated that an allele at rs2081648 showed preferential transmission (p = 0.027). One haplotype, including all examined markers in GABRB3, demonstrated significant association (p = 0.043), but the global chi2 test for haplotype transmission did not reveal an association between GABRB3 and ASD (chi2 = 15.516, d.f. = 15). CONCLUSION: Our finding suggested that single-nucleotide polymorphisms in GABRB3 may play a significant role in the genetic predisposition to ASD in the Korean population.

Adolescent↗
PubMed2026

Trio-based whole-exome sequencing identifies convergent epithelial junction-related pathways in syndromic hidradenitis suppurativa.

INTRODUCTION: Hidradenitis suppurativa (HS)-related autoinflammatory syndromes, simply termed as syndromic HS (sHS), represent a group of rare immune-mediated inflammatory disorders in which HS coexists with systemic or cutaneous autoinflammatory features like PASH (pyoderma gangrenosum-PG-, acne and HS), PAPASH (PASH, pyogenic arthritis), PASS (PG, acne, HS, and ankylosing spondylitis), and SAPHO syndrome (synovitis, acne, pustulosis, hyperostosis, and osteitis). In recent years, genetic studies identified several novel pathogenic variants underlying sHS; however, most investigations rely exclusively on affected individuals sequencing and the absence of parental genomic information limits the possibility to determine inheritance patterns. METHODS: To address these gaps, we performed trio-based whole-exome sequencing (WES) on five individuals diagnosed with sHS and their unaffected parents. RESULTS: The pathway related to epidermal adhesion and desmosome organization was the most represented across our cohort, encompassing seven genes: DSC3, DSG1, FAT1, LAMA3, MICALL2, PLEC and TJP2. Integrin-extracellular matrix (ECM) adhesion signaling pathway, represented by ten genes (CSPG4, FERMT3, ITGA3, LAMA3, LAMA5, LIMS2, LTBP3, PLEC, TGM2, TNC) was also retrieved. Also, variants affecting innate immune pathways, including cytokine signalling and antigen presentation, have been observed. CONCLUSION: Our exploratory findings suggest that genetically heterogeneous variants in syndromic HS converge on biological processes involving epithelial junction organisation, extracellular matrix interactions and innate immune regulation. Although not establishing a unique pathogenic mechanism, these observations identify epithelial barrier biology as a candidate pathway warranting validation in larger cohorts and functional studies.

Journal Article↗
PubMed2006

Analysis of case-parent trios at a locus with a deletion allele: association of GSTM1 with autism.

BACKGROUND: Certain loci on the human genome, such as glutathione S-transferase M1 (GSTM1), do not permit heterozygotes to be reliably determined by commonly used methods. Association of such a locus with a disease is therefore generally tested with a case-control design. When subjects have already been ascertained in a case-parent design however, the question arises as to whether the data can still be used to test disease association at such a locus. RESULTS: A likelihood ratio test was constructed that can be used with a case-parents design but has somewhat less power than a Pearson's chi-squared test that uses a case-control design. The test is illustrated on a novel dataset showing a genotype relative risk near 2 for the homozygous GSTM1 deletion genotype and autism. CONCLUSION: Although the case-control design will remain the mainstay for a locus with a deletion, the likelihood ratio test will be useful for such a locus analyzed as part of a larger case-parent study design. The likelihood ratio test has the advantage that it can incorporate complete and incomplete case-parent trios as well as independent cases and controls. Both analyses support (p = 0.046 for the proposed test, p = 0.028 for the case-control analysis) an association of the homozygous GSTM1 deletion genotype with autism.

Adult↗
PubMed2002

[Use of case-parents trio for epidemiological studies of association between genetic polymorphisms and complex diseases].

In case-control studies, spurious associations between allelic variants in candidate genes and disease may arise as a result of population stratification by ethnicity. In epidemiological terms, the ethnic group would act as a confounding factor if both the genotype frequency and the incidence/prevalence of a given chronic disease vary across ethnic groups. Population stratification is a key element in the study of population dynamics and the knowledge of the disparity in health-related conditions among strata has important social and public health implications. However, it would not be scientifically correct to conclude a causal gene-disease association in situations in which the association arises as a consequence of a particular population structure. Although the relevance and magnitude of the bias derived from this confounding, effect would be different depending on the population considered, there has been an increased use of study designs such as the case-parent study, that avoids the effect of population stratification by ethnicity. In this article, we review the analysis of case-parent trios using unrelated affected cases as an epidemiological study design for testing association between genetic polymorphisms and disease.

Alleles↗
PubMed2003

[Transmission disequilibrium test of polymorphisms of serotonin transporter gene and schizophrenia based on family trios].

OBJECTIVE: To investigate the relationship between two polymorphisms (Intronic VNTR and 5-HTTLPR) of the serotonin transporter gene and schizophrenia. METHODS: A set of 314 schizophrenic trio samples collected from Shanghai, Xi'an and Jilin regions of China independently was subjected to analysis of the polymorphisms by transmission/disequilibrium test(TDT). RESULTS: No significantly preferential transmission of any allele was detected from both polymorphisms investigated. CONCLUSION: The results suggest that the serotonin transporter gene is unlikely to have a major contribution to susceptibility to schizophrenia in Han Chinese population.

Adult↗
PubMed2003

[Evaluation of the association between microsatellite markers located on 6p22-25 and no syndromic cleft lip palate using the case-parents trio design in Chilean population ].

BACKGROUND: Genetic studies indicate that nonsyndromic cleft lip/palate (NSCLP) has the characteristics of a complex genetic trait. Reports from different authors have suggested several candidate genes mapping in different chromosome regions. Association studies have suggested that a clefting locus is located on chromosome 6p. On these grounds we have investigated the possible association between five microsatellite markers located on 6p22-25 and NSCLP. AIM: To test the hypothesis on the possible association of a clefting locus with microsatellite markers located in 6p22-25. PATIENTS AND METHODS: The sample consisted of 54 unrelated case-parent trios that comprise 54 NSCLP probands and 108 parents. Five microsatellite markers spanning the region 6p22-25 were analyzed for each individual by means of polymerase chain reaction with fluorescent labeled microsatellite markers. Electrophoresis of the PCR products was performed on a laser-fluorescent DNA sequencer. Nonparametric ETDT and MCETDT programs, were used to analyze the genotype data. RESULTS: The family based association study showed that for the genotype wise analysis, only D6S259 presented a significant p-value (0.03). Nevertheless no individual allele of this marker showed an evident preferential transmission from heterozygous parents to affected offspring. CONCLUSIONS: The results of the present study do not show a clear evidence that a candidate gene for NSCLP may be located within or near the analyzed chromosome region in our sample. Nevertheless, it must be emphasized that the genotype wise analysis shows a significant p-value for D6S259 marker.

Alleles↗
PubMed2005

Family-based association study of the serotonin transporter gene polymorphisms in Korean ADHD trios.

The dopamine (DA) system has been implicated in attention deficit hyperactivity disorder (ADHD) based on pharmacologic evidence. Because of an interaction between the serotonin (5-HT) and DA systems, the serotonin transporter gene (SLC6A4) has been considered as a candidate ADHD susceptibility gene. Two common polymorphisms, 5-HTTLPR and the intron 2 VNTR, have been studied for association in ADHD, with both positive (increased frequency of long allele of 5-HTTLPR and decreased frequency of 12 repeats of the intron 2 VNTR) and negative findings. However, there has not been an association study in an East Asian ADHD population. In this study, we examined the genotypes of these two polymorphisms in 126 Korean ADHD families and investigated linkage disequilibrium (LD) between SLC6A4 and ADHD, using the transmission disequilibrium test (TDT) and haplotype analysis. Additionally, association with quantitative measures of inattention, hyperactivity-impulsivity, and overall severity was tested using logistic regression and QTDT analysis. TDT of both polymorphisms and haplotype analysis failed to detect LD. However, after excluding ADHD NOS subtype, TDT revealed nominally significant LD between 5-HTTLPR and ADHD (chi2 = 4.9, P = 0.036). QTDT revealed positive association between 12 repeats of the intron 2 VNTR and attention (P = 0.031), but case-control and TDT logistic regression analyses were negative. These markers have low heterozygosity in the Korean population, which would be expected to reduce the power of association. This result suggests that future studies should include more polymorphic markers and subjects to thoroughly investigate a potential association between SLC6A4 and ADHD in the Korean population.

Attention Deficit Disorder with Hyperactivity↗
PubMed2004

Neurotrophins and their receptors: signaling trios in complex biological systems.

The neurotrophins, a class of four related growth factors, utilize a dual receptor system consisting of Trk receptor tyrosine kinases and the structurally unrelated p75(NTR) to modulate diverse and sometimes opposing biological actions. The identification of novel ligands for p75(NTR), unconventional mechanisms for Trk activation and unique signaling intermediates further underscores the complex nature of neurotrophin: receptor interactions, as well as their functions within and outside of the nervous systems. This review summarizes recent surprises of how ligand-receptor pairing may affect diverse developmental events, regulate response to injury and extend their influence on memory and learning.

Animals↗