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At least 271 records · Page 15Linked to original sources
PubMed2006

Risk of celiac disease in children with type 1 diabetes is modified by positivity for HLA-DQB1*02-DQA1*05 and TNF -308A.

OBJECTIVE: The overlap between genetic susceptibility to celiac disease (CD) and to type 1 diabetes is incomplete; therefore, some genetic polymorphisms may significantly modify the risk of CD in subjects with type 1 diabetes. This study aimed to investigate whether the susceptibility to CD in diabetic children is modified by positivity for HLA-DQB1*02-DQA1*05 and DQB1*0302-DQA1*03 and by alleles of single nucleotide polymorphisms within the genes encoding CTLA4, transforming growth factor (TGF)-beta, tumor necrosis factor (TNF)-alpha, interferon (IFN)-gamma, interleukin (IL)-1, IL-2, IL-6, and IL-10. RESEARCH DESIGN AND METHODS: Genotypic data were compared between 130 case subjects (children with type 1 diabetes and CD diagnosed using endomysium antibodies) and 245 control subjects (children with type 1 diabetes only, optimally two per case, matched for center, age at type 1 diabetes onset, and type 1 diabetes duration). The subjects were recruited from 10 major European pediatric diabetes centers performing regular screening for CD. The polymorphisms were determined using PCR with sequence-specific primers, and the risk was assessed by building a step-up conditional logistic regression model using variables that were significantly associated with CD in the univariate analysis. RESULTS: The best-fitted model showed that risk of CD is increased by presence of HLA-DQB1*02-DQA1*05 (odds ratio 4.5 [95% CI 1.8-11], for homozygosity, and 2.0 [1.1-3.7], for a single dose) and also independently by TNF -308A (1.9 [1.1-3.2], for phenotypic positivity), whereas IL1-alpha -889T showed a weak negative association (0.6 [0.4-0.9]). CONCLUSIONS: The results indicate that the risk of CD in children with type 1 diabetes is significantly modified both by the presence of HLA-DQB1*02-DQA1*05 and by a variant of another gene within the major histocompatibility complex, the TNF -308A.

Adolescent↗
PubMed2003

Preinvasive pancreatic neoplasia of ductal phenotype induced by acinar cell targeting of mutant Kras in transgenic mice.

Activating mutation of the Kras oncogene is the most frequent and perhaps the earliest genetic alteration associated with pancreatic cancer. To examine the link between mutant Kras and exocrine pancreatic cancer, we generated transgenic mice carrying an elastase-mutant Kras transgene, which targets expression to pancreatic acinar cells. Most elastase-Kras founder mice displayed perinatal pancreatic acinar cell hyperplasia and dysplasia. However, adult mice in two surviving lineages displayed preinvasive pancreatic neoplastic lesions with ductal morphology, thereby providing a unique mouse model in which lesion histotype and initiating genetic alteration overlap with the human disease. Our findings suggest that Kras mutation is associated with development of early stage duct-like lesions in pancreas, but that additional alterations must accompany progression to malignancy.

Animals↗
PubMed2004

[From circular insanity (in double form) to the bipolar spectrum: the chronic tendency for depressive recurrence].

From a cycling standpoint, "circular insanity" (Falret) and "dual-form insanity" (Baillarger), both described in hospital patients in 1854, are at the severe end of the spectrum of what we now call "bipolar disorders". Falret was prescient in suggesting that circular insanity was rare in the community, where depressive cycles are prevalent. These disorders are now respectively referred to as the "hard" (manic-depressive) and "soft" (bipolar spectrum) phenotypes of the disorder. This paper focuses on the latter, more prevalent depressive expressions of the spectrum, which share with the manic and circular forms a lifelong tendency to recur. Their cyclicity may involve putative "clock genes". The genetics of psychotic mania overlaps somewhat with the genetics of schizophrenia. As regards depressive recurrence, putative genetic factors have been identified, including a polymorphism of the serotonin transporter, which significantly increases the subject's vulnerability to stress; a mediating pathogenetic variable appears to be temperamental dysregulation (e.g. neuroticism and cyclothymic lability), which produces hyperemotional reactivity to such stressors. The growing recognition that many depressive recurrences belong to a broad spectrum, affecting 5-10% of the population, represents a new public health challenge. Although the new class of serotoninergic antidepressants offer a practical approach to the management of depressive episodes, further research is needed to determine the point of the spectrum at which mood-stabilizing therapy should be started--and in what combinations--in order to prevent recurrence and suicide.

Bipolar Disorder↗
PubMed2005

Quality control for microarray experiments.

OBJECTIVES: In this paper we give an overview of post-hybridization quality control methods for gene expression chips, including methods for the gene/spot level, the hybridization/chip level and the process level. We present quality control methods that can be applied after hybridization and image analysis, i.e. that use data from the chip experiment itself. Wet lab quality control steps, which should be applied before the probe is measured on a chip, are not discussed. This review is aimed towards statisticians and data analysts. METHODS: We give examples of some of the quality control measures available for spotted cDNA and Affymetrix GeneChips, the most common chip types. As quality control measures are technology and design-dependent, we will stress on methods that have the potential to be applied platform-independently. RESULTS: Quality control should identify poor quality chips or hybridizations, as well as faulty measurements for individual genes/spots. Additionally, high throughput laboratories processing several tens or hundreds of microarrays per week have the need for an appropriate process control to be able to identify changes in the production process as early as possible. CONCLUSION: Microarrays have become a standard research tool for biologists and medical researchers. As a consequence, there is a great need for standardized quality control, as false findings due to problem in data quality can lead to a substantial loss of resources.

DNA Probes↗
PubMed1989

Ig VH, DH, and JH germ-line gene segments linked by overlapping cosmid clones of rabbit DNA.

Overlapping cosmid clones of rabbit germ-line DNA containing VH, DH and JH gene segments were isolated. The map of this cluster of cosmid clones indicated that the rabbit VH and JH regions were separated by 63 kb. Hybridization of Southern blots of these cosmid clones with two different DH segment probes identified a total of six DH segments within the region between the VH and JH regions. The nucleotide sequences of the JH region and one of the DH segments have been determined. The DH segment has conserved heptamer and nonamer sequences separated by 12 and 11 bp at the 3' and 5' sides, respectively, of the coding region and hence, appears to be a functional gene. The nucleotide sequence of the JH region revealed four functional JH gene segments and one JH pseudogene. Inasmuch as the JH region had previously been linked by contiguous overlapping clones with C mu, C gamma, C epsilon, and one C alpha gene, this VH-DH-JH cluster and the clones containing the Ig H chain C region genes represent 190 kb of contiguous germ-line DNA of the Ig H chain locus.

Amino Acid Sequence↗
PubMed1988

Molecular organization of the DQ subregion (DO-DX-DV-DQ) of the human MHC and its evolutionary implications.

An overlapping set of cosmid clones from the homozygous DR7 B lymphoblastoid cell line MANN linking the HLA-DO through -DQ subregions is described. This region encompasses 280 kb of DNA, including DQ alpha, DQ beta, DX alpha, DX beta, DO beta, and recently indentified L chain sequences termed DV beta. The orientation and grouping of the alpha- and beta-chains is comparable with an analogous murine class II subregion and also with the HLA-DR alpha and -DR beta chains, suggesting that the arrangement of the constituent genes of class II subregions predates the mouse/human divergence.

Biological Evolution↗
PubMed1992

Human GLUT4/muscle-fat glucose-transporter gene. Characterization and genetic variation.

Four overlapping DNA fragments spanning 32 kb containing the human GLUT4 facilitative glucose-transporter gene were isolated and characterized. The sequence of the GLUT4 gene (approximately 6.3 kb) and 2.0 kb of the promoter region was determined. The sequence of the promoter revealed potential binding sites for transcription factors known to regulate gene expression in muscle cells and adipocytes. However, transfection of constructs including 2 kb of the GLUT4 promoter fused to the bacterial CAT gene into 3T3-L1 adipocytes displayed only weak promoter activity. Because insulin resistance plays a prominent role in the development of NIDDM, genetic variation in the sequence of GLUT4 also was evaluated. Oligonucleotide primer pairs were selected that allowed the protein-coding region of the human GLUT4 gene to be amplified by PCR. The sequence of the protein-coding region of the GLUT4 gene and all intron-exon junctions was determined for a single diabetic Pima Indian and was identical to that of the cloned gene and cDNA. SSCP analysis was used to screen patients with diabetes mellitus and normal, healthy nondiabetic individuals for mutations at the GLUT4 locus. In addition to the silent substitution in the codon for Asn130 (AAC or AAT) and a Val383 (GTC)-->Ile(ATC) replacement described previously, two new variants were identified. One was a T-->A substitution in intron 1 that was found in 1 of 36 NIDDM patients who were typed for this variant. The second was a Ile385(ATT)-->Thr(ACT) replacement that occurred in 1 normal individual and was not found in any of 676 other normal and diabetic subjects. A large and racially diverse group of normal and diabetic individuals also was screened for the Ile383 polymorphism. It occurred in both diabetic and nondiabetic subjects. There is no indication from our data that these polymorphisms are associated with NIDDM.

3T3 Cells↗
PubMed1999

Towards a complete North American Anabaptist genealogy: A systematic approach to merging partially overlapping genealogy resources.

Genetic studies on closed populations benefit from comprehensive, searchable genealogy resources. To support studies of Anabaptists, a computerized database has been developed that merges two large genealogy books, the "Fisher Family History" and the "Amish and Amish Mennonite Genealogies." The former is more current but the latter is more comprehensive for the 18th and 19th centuries. Therefore, the merger of the two books is significantly more useful than either book alone. We demonstrate the utility of the merged database with two results: an increase in inbreeding coefficients and the identification of parent-child relationships that do not exist in either book. Am. J. Med. Genet. 86:156-161, 1999. Published 1999 Wiley-Liss, Inc.

Consanguinity↗
PubMed2004

Genetic correlations among texture characteristics in the human iris.

PURPOSE: To estimate the magnitude of genetic correlations among five general textural characteristics of the human iris. METHODS: Color photographs of iris were available from 100 monozygotic and 99 dizygotic twin pairs. Comparative scales were constructed based on ratings of the subjects' left iris. To explore the genetic and environmental covariation among frequency of Fuchs' crypts, frequency of pigment dots, iris color, the extension, and distinction of Wolfflin nodules, and contraction furrows, a structural equation model with Cholesky decomposition was applied to variance-covariance matrices for monozygotic (MZ) and dizygotic (DZ) pairs. RESULTS: Significant genetic correlations fell between -0.22 and 0.44 and accounted almost entirely for the phenotypic correlations among the iris characteristics. No evidence for individual specific environmental effects in common to the characteristics was found. CONCLUSIONS: The modest genetic correlations indicate that there is little overlap in the genetic influence for these characteristics. Candidate genes with embryological and histological expression patterns in the eye could potentially influence the iris characteristics' variability.

Adolescent↗
PubMed2005

Shared genetic contributions to pathological gambling and major depression in men.

CONTEXT: Although pathological gambling (PG) and major depression (MD) frequently co-occur, little is known regarding the relative contributions of environmental and genetic factors to the codevelopment of the disorders. OBJECTIVES: To estimate environmental and genetic contributions to PG and MD as defined in DSM-III-R and the lifetime co-occurrence of PG and MD. DESIGN: Survey data from the Vietnam Era Twin Registry were examined in biometric models. SETTING: Telephone interview. PARTICIPANTS: Of 10, 253 eligible participants, 7869 were successfully interviewed. MAIN OUTCOME MEASURES: Estimated genetic, shared environmental, and unique environmental contributions to PG and MD and their lifetime co-occurrence in bivariate models. RESULTS: Elevated odds ratios for MD were associated with those of PG (4.06; 95% confidence interval, 2.68-6.13), and the association remained significant following adjustment for sociodemographic and other psychiatric variables (odds ratio = 1.98; 95% confidence interval, 1.14-3.45). The best-fitting bivariate model indicated that 66% of the variance in PG and 41% of the variance in MD were owing to genetic factors, and 34% of the variance in PG and 59% of the variance in MD were owing to unique environmental factors. There was a substantial correlation between the genetic components of PG and MD (r(A) = 0.58), with 34% of the genetic variance for each disorder also contributing to that of the other. The best-fitting model estimated that 100% of the total overlap between PG and MD was genetic. CONCLUSIONS: The correlation between PG and MD in middle-aged men appears to be largely influenced by overlapping genetic factors. Future research is needed to determine the extent to which these findings extend to other groups (eg, women), identify specific genes, and generate improved prevention and treatment strategies.

Adult↗
PubMed2004

Genetics of monoamine metabolites in baboons: overlapping sets of genes influence levels of 5-hydroxyindolacetic acid, 3-hydroxy-4-methoxyphenylglycol, and homovanillic acid.

BACKGROUND: Monoamine neurotransmitters (serotonin, dopamine, and norepinephrine) are associated with several psychiatric disorders. Limited evidence suggests that monoamine levels are heritable, but no information concerning genetic relationships among monoamines is available. Further genetic analysis can help explain phenotypic correlations among monoamine levels and might eventually help identify genes involved in response to therapy or risk of psychopathology. METHODS: Levels of the monoamine metabolites homovanillic acid (HVA), 5-hydroxyindolacetic acid (5-HIAA), and 3-hydroxy-4-methoxyphenylglycol (MHPG) were measured in cerebrospinal fluid from 271 baboons (Papio hamadryas). Variance components methods were used to estimate heritabilities, and multivariate analyses were used to estimate genetic correlations (pleiotropy) and environmental correlations between metabolites. RESULTS: Each metabolite exhibited significant heritability in baboons (5-HIAA: h(2) =.30 +/-.17; MHPG: h(2) =.36 +/-.16; HVA: h(2) =.50 +/-.19). Multivariate analyses revealed genetic correlations between 5-HIAA and HVA and between HVA and MHPG. Environmental correlations were found between 5-HIAA and HVA and between 5-HIAA and MHPG. CONCLUSIONS: Overlapping, nonidentical sets of genes influence individual variation in 5-HIAA, MHPG, and HVA levels among baboons. The phenotypic correlation between 5-HIAA and HVA observed in nonhuman primates and humans is likely due to both shared genetic and environmental factors. Genetic analyses of monoamine levels in primates can provide novel information concerning the genetics of variation among humans.

Analysis of Variance↗
PubMed1999

Prediction of genetic contributions and generation intervals in populations with overlapping generations under selection.

A method to predict long-term genetic contributions of ancestors to future generations is studied in detail for a population with overlapping generations under mass or sib index selection. An existing method provides insight into the mechanisms determining the flow of genes through selected populations, and takes account of selection by modeling the long-term genetic contribution as a linear regression on breeding value. Total genetic contributions of age classes are modeled using a modified gene flow approach and long-term predictions are obtained assuming equilibrium genetic parameters. Generation interval was defined as the time in which genetic contributions sum to unity, which is equal to the turnover time of genes. Accurate predictions of long-term genetic contributions of individual animals, as well as total contributions of age classes were obtained. Due to selection, offspring of young parents had an above-average breeding value. Long-term genetic contributions of youngest age classes were therefore higher than expected from the age class distribution of parents, and generation interval was shorter than the average age of parents at birth of their offspring. Due to an increased selective advantage of offspring of young parents, generation interval decreased with increasing heritability and selection intensity. The method was compared to conventional gene flow and showed more accurate predictions of long-term genetic contributions.

Animals↗
PubMed2005

Overlaps in the transcriptional profiles of Medicago truncatula roots inoculated with two different Glomus fungi provide insights into the genetic program activated during arbuscular mycorrhiza.

Arbuscular mycorrhiza (AM) is a widespread symbiotic association between plants and fungal microsymbionts that supports plant development under nutrient-limiting and various stress conditions. In this study, we focused on the overlapping genetic program activated by two commonly studied microsymbionts in addition to identifying AM-related genes. We thus applied 16,086 probe microarrays to profile the transcriptome of the model legume Medicago truncatula during interactions with Glomus mosseae and Glomus intraradices and specified a total of 201 plant genes as significantly coinduced at least 2-fold, with more than 160 being reported as AM induced for the first time. Several hundred genes were additionally up-regulated during a sole interaction, indicating that the plant genetic program activated in AM to some extent depends on the colonizing microsymbiont. Genes induced during both interactions specified AM-related nitrate, ion, and sugar transporters, enzymes involved in secondary metabolism, proteases, and Kunitz-type protease inhibitors. Furthermore, coinduced genes encoded receptor kinases and other components of signal transduction pathways as well as AM-induced transcriptional regulators, thus reflecting changes in signaling. By the use of reporter gene expression, we demonstrated that one member of the AM-induced gene family encoding blue copper binding proteins (MtBcp1) was both specifically and strongly up-regulated in arbuscule-containing regions of mycorrhizal roots. A comparison of the AM expression profiles to those of nitrogen-fixing root nodules suggested only a limited overlap between the genetic programs orchestrating root endosymbioses.

Carrier Proteins↗
PubMed2026

Common genetic mechanisms between obesity and COVID-19 severity: unravelling pleiotropic loci and biological pathways.

COVID-19 and obesity are complex conditions marked by immune and metabolic dysfunction, with the former still ranking among the leading causes of death from infectious diseases worldwide and the latter reaching pandemic proportions. Clinical evidence consistently shows that obesity increases the risk of severe COVID-19, yet the biological mechanisms underlying this association remain unclear. Given their physiological and clinical overlap, they may share genetic pathways. We investigated genetic variants jointly associated with body mass index (BMI) and COVID-19 using publicly available genome-wide data. A conjunctional false discovery rate (conjFDR) approach identified shared variants between BMI and three COVID-19 phenotypes: infection, hospitalization and very severe respiratory illness. Functional annotation and pathway enrichment analyses were performed to explore the biological context of these variants, followed by a phenome-wide association study (PheWAS) to characterize pleiotropy. Shared variants were enriched in immune, metabolic and hormonal signaling pathways, including metal ion transport and glycosylation. The overlap with BMI was strongest for hospitalized and severe cases, suggesting common mechanisms underlying disease progression rather than infection. These findings suggest a biologically meaningful genetic overlap between obesity and COVID-19 severity, highlighting pleiotropy as a key feature in complex disease interactions and potential shared therapeutic targets.

BMI↗
PubMed2026

Shared genetic architecture between major depression and intrinsic brain functional connectome organization.

BACKGROUND: Major depression (MD) is increasingly understood as a disorder characterized by widespread abnormalities in intrinsic brain functional network organization. Although both MD and brain functional connectome architecture are highly heritable, the genetic architecture underlying their relationship remains poorly characterized. METHODS: We integrated genome-wide association studies of MD with 191 ICA-based resting-state functional connectome traits to investigate their shared genetic architecture. These traits captured intrinsic connectome organization across amplitude, functional connectivity, and global connectivity domains. Cross-trait genetic analyses were used to assess pleiotropic overlap between traits. Locus-level and gene-based analyses integrating multi-omics evidence were performed to characterize the biological relevance of shared genetic signals. RESULTS: We identified significant genetic overlap between MD and 148 of 191 brain functional connectome traits. Cross-trait analyses revealed widespread shared genetic signals organized into 627 genomic loci across amplitude, functional connectivity, and global connectivity measures. Among these, 193 loci showed evidence consistent with shared causal variants based on colocalization analyses. Gene-level integration mapped these loci to 1459 protein-coding genes (390 unique genes). Multi-layer prioritization identified 17 high-confidence genes supported by convergent genomic, transcriptomic, and proteomic evidence, with enrichment in neurodevelopmental and lipid-related metabolism pathways. CONCLUSIONS: This study provides a multi-scale characterization of the shared genetic architecture between MD and intrinsic brain functional connectome organization, revealing that shared genetic signals between MD and brain functional systems are distributed across multiple functional levels and converge at the molecular level.

Connectome↗
PubMed2006

The regulation of pathogenicity and mutualism in Photorhabdus.

Photorhabdus is a genus of insect-pathogenic bacteria that also maintains a mutualistic interaction with Heterorhabditid nematodes. Bacteria in this genus are members of the family Enterobacteriaceae and are, therefore, closely related to many important mammalian pathogens. This bacteria-nematode complex has been exploited as a biocontrol agent that is active against several insect pests. However, this model system is also uniquely placed to address important fundamental questions about pathogenicity and mutualism. Indeed, recent genetic studies have suggested that there is a significant overlap in the genetic requirements of Photorhabdus for these contrasting interactions. In addition, the identification of key regulators of pathogenicity and symbiosis only serves to highlight the similarities between Photorhabdus, a genus of bacteria that infects invertebrate hosts, and closely related mammalian enteric pathogens.

Animals↗
PubMed2025

Dissecting the shared genetic architecture of schizophrenia with ventricular subregion volumes.

Schizophrenia is characterized by cerebral ventricular enlargement as an early and consistent structural anomaly. While genetic factors significantly influence both schizophrenia and cerebral ventricular enlargement, the shared genetic etiology between them requires further investigation. Using summary statistics from recent large genome-wide association studies on schizophrenia and 9 ventricular subregion volumes phenotypes. Gaussian causal mixture modeling was applied to characterize the genetic architecture and overlap between schizophrenia and ventricular subregion volumes phenotypes. Local genetic correlation was investigated with Local Analysis of Variant Association. The conjunctional false discovery rate framework was used to identify the specific shared genetic loci, annotated with FUMA. Gaussian causal mixture modeling estimated schizophrenia to be more polygenic more polygenic (9574 trait-influencing variants) than ventricular subregion volumes phenotypes (157-1267 trait-influencing variants). Conjunctional false discovery rate analysis identified 42 shared genetic loci, 17 loci were identified as novel for both schizophrenia and the ventricular subregion volumes phenotypes. Local Analysis of Variant Association revealed that 11 distinct loci demonstrated significant differences, among which 4 loci were situated in the Major Histocompatibility Complex region. Annotated genes in shared loci were enriched in molecular signaling pathways involved in inflammation and the brain structure. The shared loci between them were annotated and enriched in Major Histocompatibility Complex and inflammation-related pathways, highlighting new opportunities for future investigation.

Schizophrenia↗
PubMed1996

Patterns of genetic polymorphism maintained by fluctuating selection with overlapping generations.

We study the form of polymorphisms that can be maintained by the joint effects of generation overlap and randomly fluctuating selection, acting on a quantitative trait affecting offspring viability. The genetic system can be single locus or multilocus, haploid or diploid. Selection is assumed to be stabilizing with a randomly fluctuating optimum, and we assume additive allelic effects without epistasis. For fluctuations above a certain threshold, nonzero genetic variance is maintained in an evolutionarily stable population. Our model allows a continuum of alleles with arbitrary effects at each locus. Nonetheless, the genotype distribution in an evolutionarily stable population is discrete--a polymorphism of a few alleles with distinctly different effects--and often involves only a pair of alleles at each locus. The form of the genotype distribution depends on the number of loci affecting the trait, and on the kurtosis of the distribution of the phenotypic optimum theta. If the trait is affected by several loci, the number of polymorphic loci increases with increased variance of fluctuations in selection. For distributions of theta with negative kurtosis (i.e., lower kurtosis than a Gaussian) the number of polymorphic loci increases gradually (0-->1-->2--> ...M), and the genetic variability is in the form of a few diallelic or triallelic loci with alleles of large effect. For distributions with positive kurtosis, the increase is abrupt (0 -> many) and involves many diallelic loci. These results do not fit the conventional multivariate Gaussian or near-Gaussian models for quantitative traits, but may partially explain recent findings that heritable variation in natural populations is often due to genes of large effect.

Diploidy↗