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Results for “Candidate genes”

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PubMed1992

Adrenergic receptor genes as candidate genes for panic disorder: a linkage study.

OBJECTIVE: Several lines of investigation suggest that the noradrenergic neurotransmitter system may be involved in the pathogenesis of panic disorder. Since a mutation in a gene coding for one of the adrenergic receptors could account for both the familial nature and autonomic dysfunction of panic disorder, the authors performed analyses of the linkage between panic disorder and five adrenergic receptor loci. METHOD: The subjects were 14 multiplex pedigrees with DSM-III panic disorder or agoraphobia with panic attacks. The loci tested were the alpha 1/beta 2 pair on chromosome 5q32-q34, the alpha 2/beta 1 pair on chromosome 10q24-q26, and a second alpha 2 locus on chromosome 4. Flanking loci were included in the analysis on chromosomes 5 and 10 to increase the informativeness of the adrenergic receptor loci. RESULTS: Lod scores less than -2.0 were found at all five receptor loci. CONCLUSIONS: These findings provide strong evidence against the possibility that genetic mutation at any of these loci is responsible for panic disorder in these pedigrees.

Adolescent↗

PubMed1999

Probing the gene expression database for candidate genes.

We report on a strategy for the identification of candidate genes for multiple malformation syndromes using expression data available in public databases. The basis for this pilot study was the assumption that, for a multiple malformation syndrome, the expression pattern of the causative gene should at least cover the organs or tissues affected by the syndrome. Twenty malformation syndromes were selected from the OMIM and defined by three to five main symptoms. These key symptoms were translated into anatomical terms that were used to query the Gene eXpression Database (GXD). The searches covered 65% of the database and yielded an average of 16 candidate genes per syndrome. Of these, 23% were ubiquitously expressed or housekeeping genes. Further database evaluation of these potential candidate genes was based on positional information and on information from mouse knockouts. In a first experiment, the correct gene was identified as a candidate in four of seven syndromes for which the causative gene is already known. In addition, this strategy identified new candidate genes for disorders for which the genetic basis is unknown. We identified candidate genes for the Walker-Warburg, DOOR, C, scalp-ear-nipple and oculocerebral hypopigmentation syndromes. Our results suggest that it may ultimately be feasible to identify disease genes by probing gene expression databases with simple syndrome descriptions.

Abnormalities, Multiple↗

PubMed1999

Systematic mutation analysis of the catechol O-methyltransferase gene as a candidate gene for schizophrenia.

OBJECTIVE: Catechol O-methyltransferase (COMT) is involved in the degradation of catecholamine neurotransmitters. Recent linkage studies of schizophrenia and molecular studies of velocardiofacial syndrome suggest that the COMT gene might be a candidate gene for schizophrenia. METHOD: The authors systematically searched for mutations and microdeletion of the COMT gene in 177 Chinese schizophrenic patients from Taiwan; 99 comparison subjects were also studied. RESULTS: Five molecular variants were identified: c.186C > T at exon 3, c.408C > G at exon 4, c.472G > A at exon 4, c.597G > A at exon 5, and c.821-827insC at the 3' untranslated region. However, no differences in the genotype and haplotype frequencies of these molecular variants between the schizophrenic and comparison subjects were detected. Furthermore, no microdeletion was identified among the patients. CONCLUSIONS: These data suggest that the COMT gene does not play a major role in the pathogenesis of schizophrenia, and the genotypic overlap between schizophrenia and velocardiofacial syndrome was rare in this cohort.

Catechol O-Methyltransferase↗

PubMed1997

Exclusion of the p75 neurotrophin receptor gene as a candidate gene for Meckel syndrome.

Nerve growth factor receptor p75 (NGFR) gene was investigated as a potential candidate gene in Meckel syndrome (MKS) because of its important role in embryonic development, chromosomal localization adjacent to the MKS locus and Meckel syndrome-resembling findings in knock-out mice phenotype. The sequence analysis of the coding region of the gene revealed one polymorphism but no potential disease mutation. Physical mapping of the critical chromosomal region finally showed that the NGFR gene lies outside the MKS locus.

Abnormalities, Multiple↗

PubMed1994

Evaluation of the angiotensin II receptor AT1B gene as a candidate gene for blood pressure.

OBJECTIVE: To answer two specific questions concerning the possible role played by the angiotensin II receptor AT1B (AT1B) locus in genetic hypertension. First, do alleles at the AT1B locus cosegregate with blood pressure in F2 populations in the rat and, if so, is this due to AT1B or a closely linked quantitative trait locus (QTL)? Secondly, are there any significant nucleotide differences between the coding regions of the AT1B gene of the inbred Dahl salt-sensitive (SS/Jr) strain and various control strains, or between the Lyon hypertensive (LH) strain the Lyon normotensive (LN) strain? DESIGN: The first objective was achieved by studying several F2 rat populations and by analyzing DNA markers around the AT1B locus. The second objective was accomplished by amplifying the AT1B coding regions by polymerase chain reaction from the genomic DNA, and by sequencing the relevant coding regions of the AT1B genes. RESULTS: In two F2 populations involving the SS/Jr rat, AT1B cosegregated only weakly with systolic blood pressure. Also, nucleotide differences resulting in conservative changes in three amino acids were detected between the coding region of the SS/Jr AT1B allele and the AT1B alleles of the several control strains. No nucleotide differences were found in the coding regions of the AT1B alleles between the LH and LN strains. CONCLUSION: There appeared to be a QTL which had a minor effect on blood pressure, located near the AT1B locus on rat chromosome 2. However, the AT1B gene itself is not supported as the candidate gene for causing blood pressure differences, because no nucleotide changes in the coding region that were functionally meaningful or concordant with the cosegregation analysis were detected.

Angiotensin II↗

PubMedDate not supplied

The Wiskott-Aldrich syndrome gene as a candidate gene for atopic dermatitis.

Atopic dermatitis is a multifactorial disorder probably caused by environmental factors in combination with susceptibility genes. The clinical similarity between atopic dermatitis and the eczema manifestation in patients with Wiskott-Aldrich syndrome made the previously identified WAS gene in chromosome sub-band Xpl 1.23 an interesting candidate gene for atopic dermatitis. We studied linkage and association to the WAS gene region using four polymorphic microsatellite markers in 406 Swedish families with at least two siblings affected with atopic dermatitis (in total 1514 individuals). In the analyses, we studied two qualitative traits: atopic dermatitis and elevated allergen-specific serum IgE antibodies, and one quantitative trait, a severity score of atopic dermatitis. We found that the marker MAOB gave positive linkage with a maximum lod score of 1.68 (p<0.05) to the severity score of atopic dermatitis. Association could not be seen to atopic dermatitis nor to elevated allergen-specific serum IgE antibodies in this region using the transmission disequilibrium test. Our results indicate that either the WAS gene or another gene in the area contributes to the severity of atopic dermatitis.

Age of Onset↗

PubMed2003

The human cystatin M/E gene (CST6): exclusion candidate gene for harlequin ichthyosis.

Cystatin M/E is a recently discovered cysteine proteinase inhibitor whose expression is largely confined to cutaneous epithelia. In human skin it is expressed in sweat glands, hair follicles, and stratum granulosum of the epidermis where it presumably acts as a substrate for transglutaminase. Very recently we reported that a null mutation in the mouse cystatin M/E gene (Cst6) causes the murine ichq phenotype, which is characterized by abnormalities in cornification and desquamation, demonstrating an essential role for cystatin M/E in the final stages of epidermal differentiation. We here obtained the complete sequence of the human cystatin M/E gene (CST6), which provides a tool to investigate CST6 as a candidate gene in skin diseases characterized by abnormal cornification. The involvement of CST6 in harlequin ichthyosis in humans was evaluated by sequencing the entire coding region and intron-exon boundaries for mutations in 11 sporadic harlequin ichthyosis patients. No CST6 mutations were detected in this group, which comprised type 1 and type 2 harlequin ichthyosis patients. Disturbed transcription/translation due to mutations in regulatory and noncoding regions of cystatin M/E was unlikely because cystatin M/E protein expression was observed in all patients examined, as assessed by immunohistochemistry. Although our results indicate that CST6 is not a major gene contributing to type 1 and 2 harlequin ichthyosis, these data may facilitate further analysis of the role of cystatin M/E in normal human skin and other genetic disorders of cornification.

Animals↗

PubMed2003

Selective breeding, quantitative trait locus analysis, and gene arrays identify candidate genes for complex drug-related behaviors.

Acute functional tolerance to ethanol develops during a single exposure to ethanol; it has been suggested to be a predisposing factor for the development of ethanol dependence. Genetic determinants of acute functional tolerance, as well as of ethanol dependence, have been clearly demonstrated. We describe a novel approach that uses a combination of selective breeding (to segregate genes contributing to the phenotype of interest, i.e., acute functional tolerance to the incoordinating effect of ethanol), quantitative trait locus analysis (to define chromosomal regions associated with acute functional tolerance), and DNA microarray technology (to identify differentially expressed genes in the brains of the selected lines of mice) to identify candidate genes for the complex phenotype of ethanol tolerance. The results indicate the importance of a signal transduction cascade that involves the glutamate receptor delta2 protein, the Ephrin B3 ligand, and the NMDA receptor, as well as a transcriptional regulatory protein that may be induced by activation of the NMDA receptor (zinc finger protein 179) and a protein that can modulate downstream responses to NMDA receptor activation (peroxiredoxin), in mediating acute tolerance to the incoordinating effect of ethanol.

Alcohol-Induced Disorders↗

PubMed1995

Investigation of the phenylethanolamine N-methyltransferase gene as a candidate gene for hypertension.

Genetic mapping studies have located a gene, Bp1, that accounts for approximately 30% of the genetic variation in the stroke-prone spontaneously hypertensive rat (SHRSP) to a region on chromosome 10 containing the angiotensin-converting enzyme gene. In humans, the gene encoding phenylethanolamine N-methyltransferase (PNMT) was localized near the angiotensin-converting enzyme gene on human chromosome 17. Since most of human chromosome 17 is known to be homologous to rat chromosome 10 and PNMT is known to play a role in blood pressure homeostasis, we reasoned (1) that the rat gene encoding PNMT (Pnmt) may reside on chromosome 10 within the confidence interval containing Bp1 and (2) that Pnmt is a good candidate gene for Bp1. With the use of a somatic cell hybrid panel and genetic mapping techniques, Pnmt mapped within the confidence interval that contains Bp1. To examine further this possibility of Pnmt as a candidate for Bp1, we cloned and characterized Pnmts of the original parental strains, the Wistar-Kyoto rat and SHRSP from the Heidelberg colony. We did not identify any sequence differences between the Wistar-Kyoto rats and SHRSP in the primary structure, in 1077 bp of the 5'-flanking region, or in the 256-bp 3'-end region, making Pnmt an unlikely gene for the genetic basis of salt-loaded hypertension.

Amino Acid Sequence↗

PubMed2002

Cold sweetening in diploid potato: mapping quantitative trait loci and candidate genes.

A candidate gene approach has been used as a first step to identify the molecular basis of quantitative trait variation in potato. Sugar content of tubers upon cold storage was the model trait chosen because the metabolic pathways involved in starch and sugar metabolism are well known and many of the genes have been cloned. Tubers of two F(1) populations of diploid potato grown in six environments were evaluated for sugar content after cold storage. The populations were genotyped with RFLP, AFLP, and candidate gene markers. QTL analysis revealed that QTL for glucose, fructose, and sucrose content were located on all potato chromosomes. Most QTL for glucose content mapped to the same positions as QTL for fructose content. QTL explaining >10% of the variability for reducing sugars were located on linkage groups I, III, VII, VIII, IX, and XI. QTL consistent across populations and/or environments were identified. QTL were linked to genes encoding invertase, sucrose synthase 3, sucrose phosphate synthase, ADP-glucose pyrophosphorylase, sucrose transporter 1, and a putative sucrose sensor. The results suggest that allelic variants of enzymes operating in carbohydrate metabolic pathways contribute to the genetic variation in cold sweetening.

Carbohydrate Metabolism↗

PubMed1999

Human cochlear expressed sequence tags provide insight into cochlear gene expression and identify candidate genes for deafness.

To identify candidate genes for human hearing disorders and to understand better human hearing at the molecular level, we constructed a human cochlear cDNA library. An aliquot of the unsubtracted cochlear library was contributed to the IMAGE Consortium at Lawrence Livermore National Laboratory for the generation of expressed sequence tags (ESTs) by the Merck/WashU EST project. Over 4000 ESTs were developed from the cochlear cDNA library and deposited in the GenBank EST database. Sequence clustering shows that the majority of clones are in low copy numbers, demonstrating the high complexity of the library. The sequences of 1388 cochlear ESTs (33%) match 517 known human genes. Among these are genes previously shown to cause both syndromic and non-syndromic hearing loss. A number of the cochlear ESTs show high homology to non-human genes, suggesting new gene family members or human homologs of animal genes. We also report the chromosomal map positions of 437 cochlear ESTs. These provide positional candidate genes for 18 different non-syndromic hearing disorders. A Human Cochlear EST Database web site (http://www.bwh.partners. org/pathology ) has been created to provide access to the cochlear clone data for gene discovery investigations.

Animals↗

PubMed2005

No pathogenic mutations identified in the COL8A2 gene or four positional candidate genes in patients with posterior polymorphous corneal dystrophy.

PURPOSE: To identify the genetic basis of posterior polymorphous corneal dystrophy (PPCD) through screening of four positional candidate genes and the COL8A2 gene, in which a presumed pathogenic mutation has previously been identified in affected patients. METHODS: DNA extraction, PCR amplification, and direct sequencing of the COL8A2, BFSP1, CST3, MMP9, and SLPI genes were performed in 14 unrelated, affected patients and in unaffected family members. RESULTS: In the COL8A2 gene, the previously identified, presumed pathogenic mutation (Gln455Lys) was not discovered in any of the affected patients. A missense mutation, Thr502Met, was identified in 2 of the 14 affected probands, although it was not considered to be pathogenic, as it has been identified in unaffected individuals. Although several novel and previously identified single nucleotide polymorphisms producing synonymous and missense amino acid substitutions were identified in the COL8A2, BFSP1, CST3, MMP9, and SLPI genes, no presumed pathogenic sequence variants were found. CONCLUSIONS: No pathogenic mutations were identified in the COL8A2 gene or in several positional candidate genes in a series of patients with PPCD, indicating that other genetic factors are involved in the development of this autosomal dominant corneal dystrophy.

Collagen Type VIII↗

PubMed2025

Candidate genes at the Rmi1 locus for resistance to Meloidogyne incognita in soybean.

The RKN resistance locus Rmi1 was fine-mapped to two genes on chromosome 10, a glycosyl hydrolase family 9 β-1,4-endoglucanase gene and a type I pectin methylesterase gene. Root-knot nematodes (Meloidogyne spp.) are a serious threat to soybean production in the southeast USA, with yield losses of more than $165 million in 2023. Development and deployment of resistant soybean cultivars is the most effective strategy for managing these nematode pests; however, the identity of the resistance genes and underlying mechanism of resistance remains obscure. An additive resistance gene, Resistance to M. incognita-1 (Rmi1), to the predominant species, was first identified in soybean cultivar Forrest but never mapped to a genomic region. Multiple mapping studies have identified a major quantitative trait locus (QTL) with additive action on chromosome 10. In this study, a population consisting of 170 F2:3 families derived from a cross of Bossier (susceptible) × Forrest (resistant) was initially used to confirm that Rmi1 is in the chromosome 10 QTL. Subsequently, 884 F5:6 recombinant inbred lines (RILs) derived from the same cross were used to fine-map the Rmi1 causal gene(s) to two genes - a β-1,4-endoglucanase (Glyma.10G017000, EG) and a pectin methylesterase/methylesterase inhibitor (Glyma.10G017100, PME1). Both gene candidates have the potential to play a role in the resistance response to M. incognita. Both gene promoters harbor SNPs and indels and the encoded proteins exhibit amino acid polymorphisms, including a premature stop in PME1 of resistant soybeans. Additionally, both genes show a higher expression level in susceptible roots compared to resistant roots in the absence of infection. This suggests that Rmi1 may confer one or more pre-existing differences related to cell wall modification in soybean roots, ultimately leading to a decrease in susceptibility.

Tylenchoidea↗

PubMed1998

Genetic and physical mapping of the Lps locus: identification of the toll-4 receptor as a candidate gene in the critical region.

On the basis of 2093 meioses analyzed in two separate intraspecific backcrosses, the location of the mouse Lpsd mutation was circumscribed to a genetic interval 0.9 cM in size. A total of 19 genetic markers that lie in close proximity to the mutation were examined in mapping. Most of these were previously unpublished polymorphic microsatellites, identified by fragmentation of YAC and BAC clones spanning the region of interest. Lpsd was found to be inseparable from the microsatellite marker D4MIT178, and from three novel polymorphic microsatellites identified near D4MIT178. The mutation was confined between two novel microsatellite markers, herein designated "B" and "83.3." B lies centromeric to the mutation, and was separated by four crossovers in a panel of 1600 mice; 83.3 lies distal to the mutation and was separated by three crossovers in a panel of 493 mice. 66 BAC clones and one YAC clone were assembled to cover > 95% of the critical region. Estimates based on pulsed field gel electrophoresis and fluorescence in situ hybridization indicate that the The B-->83.3 interval is about 3.2 Mb in length. A minimal area of zero recombinational distance from Lpsd was also assigned, and found to occupy approximately 1.2 Mb of physical size. To identify gene candidates, nearly 40,000 sequencing runs were performed across the critical region. Selective hybridization and exon trapping were also employed to identify genes throughout the "zero" region. Only a single intact gene was identified within the entire critical region. This gene encodes the Toll-4 receptor, a member of the IL-1 receptor family.

Animals↗

PubMed2002

[Genes and kidney disease. Candidate genes].

Molecular biology techniques have provided important advances in the search for causal relationships in complex diseases supporting traditional epidemiologic studies. Genetic epidemiology allows us to detect genetic variants that could be related to the onset and progression of different diseases. In cardiovascular and renal diseases, this approach linking traditional risk factors to new described ones and those allelic variants, which contribute to the development of these manifestations permits a better understanding of individual disease susceptibility. This is usually afforded through case-control studies evaluating allelic variants of candidate genes previously associated with the disease. Even in this candidate gene search, association-based methods are more powerful than linkage studies in complex traits if we assume that some of the typed polymorphisms are causative although with subtle phenotypic effects. Some brief examples may illustrate the progress in the understanding of renal and cardiovascular diseases.

DNA↗

PubMed2006

Quantitative trait loci for carbohydrate and total energy intake on mouse chromosome 17: congenic strain confirmation and candidate gene analyses (Glo1, Glp1r).

Quantitative trait loci (QTL) for carbohydrate (Mnic1) and total energy (Kcal2) intake on proximal mouse chromosome 17 were identified previously from a C57BL/6J (B6) X CAST/Ei (CAST) intercross. Here we report that a new congenic strain developed in our laboratory has confirmed this complex locus by recapitulating the original linked phenotypes: B6.CAST-17 homozygous congenic mice consumed more carbohydrate (27%) and total energy (17%) compared with littermate wild-type mice. Positional gene candidates with relevance to carbohydrate metabolism, glyoxalase I (Glo1) and glucagon-like peptide-1 receptor (Glp1r), were evaluated. Glo1 expression was upregulated in liver and hypothalamus of congenic mice when compared with B6 mice. Analyses of Glp1r mRNA and protein expression revealed tissue-specific strain differences in pancreas (congenic>B6) and stomach (B6>congenic). These results suggest the possibility of separate mechanisms for enhanced insulin synthesis and gastric accommodation in the presence of high carbohydrate intake and larger food volume, respectively. Sequence analysis of Glp1r found a G insert at nt position 1349, which results in earlier termination of the open reading frame, thus revealing an error in the public sequence. Consequently, the predicted length of GLP-1R is 463 aa compared with 489 aa, as previously reported. Also, we found a polymorphism in Glp1r between parental strains that alters the amino acid sequence. Variation in Glp1r could influence nutrient intake in this model through changes in the regulatory or protein coding regions of the gene. These congenic mice offer a powerful tool for investigating gene interactions in the control of food intake.

Animals↗

PubMed1999

Depression and bipolar disorder: relationships to impaired fatty acid and phospholipid metabolism and to diabetes, cardiovascular disease, immunological abnormalities, cancer, ageing and osteoporosis. Possible candidate genes.

Depression and bipolar disorder are two of the commonest illnesses in the developed world. While some patients can be treated effectively with available drugs, many do not respond, especially in the depression related to bipolar disorder. Depression is associated with diabetes, cardiovascular disease, immunological abnormalities, multiple sclerosis, cancer, osteoporosis and ageing: in each case depressed individuals have a worse outcome than non-depressed individuals. In all of these conditions there is now evidence of impaired phospholipid metabolism and impaired fatty acid-related signal transduction processes. Impaired fatty acid and phospholipid metabolism may be a primary cause of depression in many patients and may explain the interactions with other diseases. Several novel gene candidates for involvement in depression and bipolar disorder are proposed.

Aging↗

PubMedDate not supplied

Association study of eight candidate genes with renin status in mild-to-moderate hypertension in patients of African ancestry.

AIM: We evaluated whether any one variant of genes that encode for substances that could modulate renin-angiotensin-aldosterone (RAA) system activity can account for a substantial proportion of the variability of plasma RAA system profiles in black South African hypertensives (HTs). METHODS: Plasma renin activity (PRA) and aldosterone concentrations (ALD) were determined in 59 black subjects with mild-to-moderate HT off therapy on an ad libitum diet. Patients were genotyped for the angiotensin-converting enzyme (ACE) gene insertion/deletion, angiotensinogen (AGT) gene M235T, A-20C and G-6A, aldosterone synthase (CYP11B2) gene C-344T, G protein beta3-subunit (GNB3) gene C825T, G(s) protein gene C131T, atrial natriuretic peptide (ANP) gene exon 3 stop condon and intron 2, alpha-adducin gene Gly460Trp, and epithelial Na(+) channel (eNa(+) (c)) gene T594M polymorphisms. RESULTS: Risk genotype frequencies for the G(s) (7%), ANP intron 2 (0%), and eNa(+)(c)(7%) variants were too low for each to account for a substantial portion of the variability of plasma RAA profiles in the group studied. Moreover, assuming either recessive or dominant inheritance models, neither ACE, AGT, GNB3, CYP11B2, ANP exon 3 nor alpha-adducin polymorphisms were significantly associated with the variance of PRA, ALD or ALD/PRA. CONCLUSIONS: These results do not support a substantial individual role for the gene candidates studied in contributing to plasma RAA system profiles in black South African HTs. However, a potential small role for some loci may exist, and epistasis or genotype-phenotype interactions as well as alternative inheritance models and variants still need to be evaluated.

Aldosterone↗