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PubMed2005

Variability of the tryptophan hydroxylase gene: study in victims of violent suicide.

Tryptophan hydroxylase (TPH), the enzyme controlling serotonin synthesis, is considered to be a potential contributor to the biological substrate of suicide. The association of the promoter (-7065CT) and intron 7 (218AC) polymorphisms, and the related haplotype, of the Tph1 gene with suicidal behavior was investigated in a sample of 160 victims of violent suicide and 284 healthy controls. All individuals were males of Croatian (Slavic) origin. Allele frequencies of both polymorphisms in Croatian controls were similar to control values reported for other European populations. Alleles at the two loci demonstrated highly significant linkage disequilibrium. No differences between controls and victims for the Tph1 genetic variation, either at single loci, or at a haplotypic level, were demonstrated, albeit there was a tendency, not reaching statistical significance, towards an increase of the intron 7CC genotype in the suicide group. Negative association results on the individual Tph1 loci, in accordance with the majority of previous reports, confirmed the lack of their major effect also in the Slavic ethnicity. Haplotypic results, on the other hand, opposing the previous positive finding, point to the possible influence of ethnicity (or gender) on the association between the Tph1 gene polymorphism and suicide.

Adult↗

PubMed1996

Group-I intron family in the nuclear ribosomal RNA small subunit genes of Cenococcum geophilum isolates.

A family of optional group-I introns was found near the 3' end of the nuclear small subunit rRNA genes in 61 out of 70 isolates of the deuteromycete mycorrhizal fungus Cenococcum geophilum. DNA sequence polymorphisms among the introns (termed CgSSU introns) from ten of the isolates were studied. The sequences, ranging in size from 488 to 514 nucleotides, were from 93.2% to 99.6% similar to each other. Mutations were less common in predicted base-paired regions (33% of all mutations) than in free-standing regions (67%). The introns were self-spliced in vitro and were closest to subgroup IC1 according to sequence and predicted secondary structure. Group-I intron pairing regions P1 through P10, including core regions P, Q, R and S, were present in all ten CgSSU introns studied. No lengthy open reading frames were found in any of the introns, indicating that the introns do not encode a protein, and therefore may not be mobile. It is likely that a single intron entered a progenote of C. geophilum and changed as the species evolved.

Base Sequence↗

PubMed1999

Population studies of polymorphisms of the serotonin transporter protein gene.

The range of allele frequency variation in humans for any locus that may have functionally important genetic variation needs to be documented. Therefore, we tested two polymorphisms at the serotonin transporter protein locus (SLC6A4) in samples from seven specific populations from five continental regions. We studied the promoter polymorphism which is reported to have functional significance and to be associated with anxiety- and depression-related phenotypes [Lesch et al., 1996: Science 274:1527-1531], and the intron 2 VNTR polymorphism [Lesch et al., 1994: J Neural Transm 95:157-162]. Allele frequencies for both systems show significant global variation, and consequently so do haplotype frequencies. Linkage disequilibrium varied among the populations, being absent in some and highly significant in others. These differences further document a large potential for population stratification in association studies of either of these SLC6A4 polymorphisms.

Carrier Proteins↗

PubMed1993

Molecular analysis of factor VII deficiency in Italy: a frequent mutation (FVII Lazio) in a repeated intronic region.

Molecular defects and polymorphic haplotypes of coagulation factor VII gene were studied in eight unrelated Italian subjects with factor VII deficiency, seven having the factor VII- variant, one the factor VIIR variant. An intron 7 mutation, which alters the consensus donor splice site sequence, was found in six subjects. The presence of the founder effect is suggested by their common geographical origin (a mountain area in the Lazio region) and by the identical polymorphic haplotype underlying the mutation. A different mutation, also located in the 5' monomer of the repeated intron 7 sequence, was found in the heterozygous condition in a subject from Northern Italy. New polymorphic alleles were detected in the repeated intron 7 region in subjects from Eastern Africa. Two missense mutations in codon 97 (Gly-->Cys, Gly-->Ser), the first found in the compound heterozygous condition with the frequent intron 7 mutation, suggest the presence of a hot spot mutation site in the second epidermal growth factor domain. Two neutral dimorphisms at codon 333Ser and 115His were detected, the last in linkage disequilibrium with the 353Arg/Gln polymorphism, and showing differences in frequency in the FVII deficient and control subjects.

Base Sequence↗

PubMed2005

Association of IL-1Ra gene polymorphism, but no association of IL-1beta and IL-4 gene polymorphisms, with Kawasaki disease.

The purpose of this study was to evaluate whether IL-1 beta (IL-1beta promoter and IL-1beta exon 5), IL-1 receptor antagonist (IL-1 Ra), and IL-4 (IL-4 promoter and IL-4 intron 3) gene polymorphisms act as markers of susceptibility to Kawasaki disease (KD), or of the severity of the disease. The study included 107 KD patients and 103 normal controls. Polymorphisms for cytokine genes were detected by polymerase chain reaction (PCR). Genotypes and allelic frequencies for cytokine gene polymorphisms in both groups were compared. No significant difference was observed in the genotypes and allelic frequencies of cytokines between patients with coronary aneurysm and without. In addition, there was no significant association in the genotype and allelic frequencies of IL-1 beta, IL-4, and IL-6 in patients with KD. The genotype I/II for IL1-Ra and the frequency of allele II for IL1-Ra are associated with a higher susceptibility to KD, and thus may be useful markers for predicting the development of KD.

Asian People↗

PubMed2003

Polymorphisms in an interferon-gamma receptor-1 gene marker and susceptibility to periodontitis.

Chronic marginal periodontitis is an inflammatory condition in which the supporting tissues of the teeth are destroyed. Interferon (IFN)-gamma is a cytokine that plays a pivotal role in the defense against infection, and mutations in the gene coding for the ligand binding chain (alpha, R1) of the IFN-gamma receptor (IFNGR1) confer suseptibility on infections caused by poorly virulent mycobacteria. Using an intronic (CA)n polymorphic microsatellite marker within the IFNGR1 gene we investigated whether genetic polymorphisms are associated with periodontitis. In 62 periodontitis patients and 56 healthy controls we found a total of 13 polymorphisms, 11 of which were found in the periodontitis patients and 9 in the controls. Although we observed a trend towards an association with disease for allele 192, there were no significant differences in allele frequency between patients and controls. We therefore cannot find any evidence to suggest that IFNGR1, as a single dominant gene, contributes to susceptibility to periodontitis. However, in combination with the environmental risk factor, smoking, the same allelic marker was significantly associated [OR = 5.56 (1.16<OR<36.31), P=0.014, Pcorr=0.027] with periodontitis. Our results support the multigene-environment interaction model of disease susceptibility to periodontitis.

Adult↗

PubMed1995

Characterization of the human gene for microfibril-associated glycoprotein (MFAP2), assignment to chromosome 1p36.1-p35, and linkage to D1S170.

Microfibril-associated glycoprotein, MAGP (gene symbol MFAP2), is a component of connective tissue microfibrils and a candidate for involvement in the etiology of inherited connective tissue diseases. We have cloned a human MAGP cDNA that is highly homologous to the previously characterized bovine and murine genes. Like the bovine and murine loci, the human gene has eight coding exons, but it contains two alternatively used 5' untranslated exons, whereas only one untranslated exon was described in the bovine and murine Magp genes. By using rodent x human somatic cell hybrid panels and fluorescence chromosomal in situ hybridization, we have assigned the locus to human chromosome 1p36.1-p35. An insertion/deletion polymorphism has been identified within intron 7. Linkage analysis between this polymorphism and markers on distal chromosome 1 revealed that MAGP is tightly linked to the anonymous marker D1S170. Physical mapping revealed a distance of < 100 kb between the two markers. This information can be used to screen for linkage in families with microfibrillar abnormalities that are not linked to the fibrillin genes on chromosomes 15 or 5.

Adult↗

PubMed2000

ACE-gene polymorphism is associated with the development of allograft vascular disease in heart transplant recipients.

BACKGROUND: Cardiac allograft vascular disease is (CAVD) the most important cause of death following heart transplantation (HTX). Although in the past, researchers focused predominantly on mechanisms of endothelial injury, the possible role of recipient-related and genetically determined factors has not been studied in detail. METHODS: Stimulated by recent observations in native coronary artery disease, we analyzed the potential impact of angiotensin-converting enzyme (ACE) polymorphism (insertion/deletion [I/D], intron 16) on development and progression of CAVD. We characterized genotype in 146 patients 1 to 12 years after HTX (121 men; mean age, 46.2+/-11.3 years; observation period, 6.1+/-3.8 years) and correlated genotype to the onset and progression of CAVD, defined as luminal obstruction > 50%. RESULTS: We found allelic frequencies to be 28.8% (n = 42) for ACE-DD, 49.3% (n = 72) for ACE-DI, and 21.9% (n = 32) for ACE-II. Differences in actuarial freedom from vasculopathy were significant 6 years after transplantation, with 84.6% for ACE-II compared with 54.4% for ACE-DD. We observed intermediate results for ACE-DI genotype (77.3%, p = 0.015). CONCLUSIONS: In this large cohort study, we demonstrated a close relationship between the recipient-related ACE-D genotype and development of advanced CAVD. These observations suggest that gene-environment interactions might be clinically important in coronary vasculopathy after HTX.

Actuarial Analysis↗

PubMed2006

Adiponectin, type 2 diabetes and the metabolic syndrome: lessons from human genetic studies.

Adiponectin, a protein exclusively secreted by adipose tissue but present at low levels in obesity, is now widely recognised as a key determinant of insulin sensitivity and of protection against obesity-associated metabolic syndrome. In this review we explain how genetic findings have contributed to a better understanding of the physiological role of adiponectin in humans. The adiponectin-encoding gene, ADIPOQ (ACDC), is very polymorphic: many frequent exonic synonymous, intronic and promoter single-nucleotide polymorphisms (SNPs) have been identified, as well as a few rare exonic amino acid substitutions. Several of these variations additively contribute to the modulation of adiponectin level and function, and associate with insulin sensitivity, type 2 diabetes and vascular complications of obesity.

Adiponectin↗

PubMed2002

The glucocorticoid receptor gene and its association to metabolic syndrome.

In recent decades, there has been an increasing interest in the role of endogenous glucocorticoids such as cortisol in the pathogenesis of metabolic syndrome. Studies in humans have suggested a positive association between obesity, hypertension, and insulin resistance, with alleles at the glucocorticoid receptor (GR) gene. For instance, the BclI polymorphism within the intron upstream of GR exon 2 has been associated with cardiovascular risk factors such as visceral obesity, hypertension, insulin resistance, and elevated cortisol concentrations. However, the location of the BclI polymorphism is not known, and the variant has so far not been compared with the wild-type receptor for its ability to be activated by glucocorticoids. Although several other mutations in the GR gene have been postulated as being relevant to the progression to type 2 diabetes and cardiovascular diseases, conflicting results makes it difficult to determine exactly what effect these GR variations have on metabolic syndrome incidence and progression. Further studies focusing on the most compelling GR mutations might offer a better understanding of metabolic syndrome pathogenesis and progression, aiding in the development of more effective treatments for this condition.

Alleles↗

PubMed1990

The utility of a HindIII polymorphism of factor VIII examined by rapid DNA analysis.

A previously described HindIII restriction fragment length polymorphism (RFLP) of factor VIII (FVIII) has its polymorphic site in the unsequenced nineteenth intron. We have located the polymorphic site, as well as an invariant site, by amplifying and sequencing IVS 19 using the polymerase chain reaction (PCR). The oligonucleotide primers were synthesized from known FVIII sequence on either side of the 19-20 splice junction. The amplified product was cloned into a plasmid and sequenced by the dideoxy chain termination method. The polymorphic HindIII site was 103 bp and the invariant site 184 bp from the 3' end of the nineteenth exon. The frequency of the polymorphism was determined in 457 subjects (643 chromosomes) of seven ethnic groups on whom frequency of the BclI RFLP of IVS 18 was also assessed. The HindIII site is highly polymorphic in all groups, approximately 0.25:0.75, the expected heterozygosity averaging 37.6%, and the observed number of heterozygotes did not differ significantly from expectation. The (+):(-) allelic ratio is similar in all groups, except African-Americans in whom it is reversed. Strong allelic association (linkage disequilibrium) is present between the HindIII polymorphism of IVS 19 and the BclI polymorphism of IVS 18.

Alleles↗

PubMed2005

Interleukin 4, interleukin 6 and interleukin 10 polymorphisms in children with acute and chronic immune thrombocytopenic purpura.

Immune thrombocytopenic purpura (ITP) is an immune-mediated disorder. We investigated the polymorphisms of interleukin (IL)-4 intron 3, IL-6 (-572 G/C), and IL-10 (-627 C/A) in 50 children with acute ITP, 30 children with chronic TIP, and 100 healthy individuals. There were significant differences in the RP1/RP2 genotype proportion (P = 0.04) and the RP2 allelic frequency (P = 0.03) of IL-4 intron 3 and the A/C genotype proportion (P = 0.01) of IL-10 (-627) between children with chronic ITP and controls. This finding suggests that the IL-4 intron 3 and IL-10 (-627) polymorphisms contribute to the susceptibility of developing childhood chronic ITP.

Acute Disease↗

PubMed2005

Evaluation of the relationship between interleukin-1 gene cluster polymorphisms and early implant failure in non-smoking patients.

OBJECTIVE: The aim of the present study was to investigate the relationship between specific polymorphisms of the interleukin-1 gene cluster and the early failure of osseointegrated implants. MATERIAL AND METHODS: The subject population was composed by a test group comprising 28 non-smoking patients (mean age 52.7) that had suffered one or more early implant failures and by a control group consisting of 34 individuals (mean age 43.3) with one or more healthy implants. Genomic DNA from buccal mucosa was amplified by the polymerase chain reaction (PCR), followed by restriction fragment length polymorphism (RFLP) and submitted to polyacrylamide gel electrophoresis to distinguish the alleles of the interleukin-1A (-889), interleukin-1B (+3953), interleukin-1B (-511) and interleukin-RN (intron 2) gene polymorphisms. Differences in the allele and genotype frequencies between control and test groups were assessed by chi(2) test or by Monte Carlo simulations (P<0.05). Haplotype frequencies, linkage disequilibrium and Hardy-Weinberg equilibrium were also estimated. RESULTS: No statistically significant differences were found in the genotype distribution or allelic frequencies of the polymorphisms. No differences were observed between control and test groups when different interleukin-1 gene cluster haplotypes were compared. Nevertheless, the interleukin-1A (-889) and interleukin-1B (+3953) polymorphic sites were in strong linkage disequilibrium (P=0.00014 for control group and P=0.0238 for the test group). CONCLUSION: This study suggests that polymorphisms in the interleukin-1 gene cluster are not associated with early implant failure in a non-smoking Brazilian population.

Adult↗

PubMed1996

Evolutionary relationship of HLA-DRB genes inferred from intron sequences.

The major histocompatibility complex (Mhc) consists of class I and class II genes. In the human Mhc (HLA) class II genes, nine DRB loci have been identified. To elucidate the origin of these duplicated loci and allelic divergences at the most polymorphic DRB1 locus, introns 4 and 5 as well as the 3' untranslated region (altogether approximately 1,000 base pairs) of seven HLA-DRB loci, three HLA-DRB1 alleles, and nine nonhuman primate DRB genes were examined. It is shown that there were two major diversification events in HLA-DRB genes, each involving gene duplications and allelic divergences. Approximately 50 million years (my) ago, DRB1*04 and an ancestor of the DRB1*03 cluster (DRB1*03, DRB1*15, and DRB3) diverged from each other and DRB5, DRB7, DRB8, and an ancestor of the DRB2 cluster (DRB2, DRB4, and DRB6) arose by gene duplication. Later, about 25 my ago, DRB1*15 diverged from DRB1*03, and DRB3 was duplicated from DRB1*03. Then, some 20 my ago, the lineage leading to the DRB2 cluster produced two new loci, DRB4 and DRB6. The DRB1*03 and DRB1*04 allelic lineages are extraordinarily old and have persisted longer than some duplicated genes. The orthologous relationships of DRB genes between human and Old World monkeys are apparent, but those between Catarrhini and New World monkeys are equivocal because of a rather rapid expansion and contraction of primate DRB genes by duplication and deletion.

Alleles↗

PubMed1995

Association of the prohormone convertase 2 gene (PCSK2) on chromosome 20 with NIDDM in Japanese subjects.

Proinsulin is converted to insulin by the concerted action of two sequence-specific subtilisin-like proteases termed prohormone convertase 2 (PC2) and prohormone convertase 3. PC2 is a type II proinsulin-processing enzyme, and it cleaves the proinsulin molecule on the COOH-terminal side of dibasic peptide, Lys64-Arg65, which joins the C-peptide and the A-chain domains. We have previously cloned and characterized the exon-intron organization of the human PC2 gene (gene symbol PCSK2), localized this gene to human chromosome 20 band p11.2 by fluorescence in situ hybridization, and identified a simple tandem-repeat DNA polymorphism (STRP) in intron 2 of the form (CA)n, suitable for genetic studies. Since non-insulin-dependent diabetes mellitus (NIDDM) is associated with increased secretion of proinsulin and proinsulin-like molecules, we conducted a case-control study to determine whether a genetic variation in PCSK2 might contribute to the development of NIDDM. The study population consisted of 152 Japanese NIDDM subjects and 102 normal healthy nondiabetic control subjects matched for age and body mass index. The subjects were genotyped at the STRP in intron 2, and the results indicated a significant difference (P = 0.004) in the overall allele frequency distribution between the two groups. The A1 allele was found more frequently in NIDDM than in nondiabetic subjects (11 vs. 4%, P = 0.0068). The NIDDM patients were divided into two subgroups according to the presence or absence of the A1 allele.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Sequence↗

PubMed2006

A novel PITX2 mutation and a polymorphism in a 5-generation family with Axenfeld-Rieger anomaly and coexisting Fuchs' endothelial dystrophy.

PURPOSE: To investigate the clinical and genetic appearance of Axenfeld-Rieger anomaly or syndrome (ARAS) and Fuchs' endothelial dystrophy (FED) in a 5-generation pedigree coexpressing both pathologic features in a large number of family members. DESIGN: Observational case-control and DNA linkage and screening study. PARTICIPANTS: Of 114 family members, 50 underwent clinical investigation and DNA analysis between July 2001 and March 2004. METHODS: Linkage at the PITX2 locus was demonstrated using a number of microsatellites mapping to the critical region 4q25 to 4q26. The PITX2 gene was subsequently screened for mutations in all investigated family members. MAIN OUTCOME MEASURE: Linkage of the ARAS and FED phenotype and mutation detection in the PITX2 gene. RESULTS: Twenty-seven patients were identified as being affected by ARAS. Fuchs' endothelial dystrophy was found in 19 patients. Fifteen patients presented both kinds of anomaly. Deoxyribonucleic acid sequencing revealed 2 heteroallelic DNA variants that segregated together (on the same allele) and were present in all severely affected ARAS individuals. The first variant, g.20913G>T, assumed to be the causative mutation for ARAS, causes amino acid substitution at codon 137 (G137V). A statistically significant 2-point logarithm of the odds score of 4.06 was obtained with marker D4S406. The second variant is likely a polymorphism in the intron between exons 2 and 3 (IVS2+8delCinsGTT) and was detected in heterozygous form in 20% of control individuals. CONCLUSION: This gene analysis revealed a novel PITX2 mutation and a polymorphism in a family with ARAS. Whether FED, also manifested in the severely affected individuals, is due to a different but cosegregating gene is to be determined.

Adolescent↗

PubMed2004

Isolation, characterization, and development of WRKY genes as useful genetic markers in Theobroma cacao.

There is currently an international effort in improving disease resistance and crop yield in Theobroma cacao L., an economically important crop of the tropics, using marker-assisted selection for breeding. We are developing molecular genetic markers focusing upon gene families involved with disease resistance. One such family is the WRKY proteins, which are plant-specific transcriptional factors associated with regulating defense responses to both abiotic and biotic stresses. Degenerate PCR primers were designed to the highly conserved DNA-binding domain and other conserved motifs of group I and group II, subgroups a-c, WRKY genes. Sixteen individual WRKY fragments were isolated from a mixture of T. cacao DNA using one pair of primers. Of the 16 WRKY loci investigated, seven contained single nucleotide polymorphisms within the intron as detected by sequence comparison of the PCR products. Four of these were successfully converted into molecular markers and mapped in an F2 population by capillary electrophoresis-single strand conformation polymorphism analysis. This is the first report of a pair of degenerate primers amplifying WRKY loci directly from genomic DNA and demonstrates a simple method for developing useful genetic markers from members of a large gene family.

Base Sequence↗

PubMed2002

The hormone-sensitive lipase gene and body composition: the HERITAGE Family Study.

OBJECTIVE: To investigate whether the C-60G polymorphism and other markers in the hormone-sensitive lipase (LIPE) gene are associated with baseline body composition and free-fatty acid (FFA) concentrations measured at rest and during low-intensity exercise in white and black subjects participating in the HERITAGE Family Study. SUBJECTS: Adult sedentary white (245 men and 258 women) and black (91 men and 185 women) subjects. MEASUREMENTS: body mass index (BMI); fat mass (FAT); percentage body fat (%FAT); fat-free mass (FATFR); sum of eight skinfolds (SF8); subcutaneous (ASF), visceral (AVF) and total (ATF) abdominal fat areas assessed by CT scan; plasma FFA concentrations measured at rest (FFAR), at a power output of 50 W (FFA50) and at a relative power output of 60% of VO(2max) (FFA60%); and fasting insulin (INS). STATISTICAL ANALYSIS: Association between the C-60G polymorphism of the LIPE gene and each phenotype was tested separately in men and women using ANCOVA with the effects of age and race as covariates and with further adjustment for FAT for ASF, AVF, ATF, FFAR, FFA50 and FFA60%. Secondly, owing to significant gene-by-race interaction, associations were investigated separately in each of the two race groups. Linkage was tested with the C-60G polymorphism, a dinucleotide repeat polymorphism in the intron 7 of the LIPE gene and two microsatellites markers (D19S178 and D19S903) flanking the LIPE gene. RESULTS: There were no race differences in the allele frequencies of the C-60G polymorphism of the LIPE gene. No association or gene-by-race interaction was observed in men. However, in women, strong gene-by-race interactions were observed for BMI (P=0.0005), FAT (P=0.0007), %FAT (P=0.0003), SF8 (P=0.0001), ASF (P=0.03) and ATF (P=0.01). When the analysis was performed separately in each race, white women carriers of the -60G allele exhibited lower %FAT (P=0.005) and SF8 (P=0.01) than non-carriers, while in black women, the -60G allele was associated with higher BMI (P=0.004), FAT (P=0.009), %FAT (P=0.01) and SF8 (P=0.0009). These associations were no longer significant after adjusting for INS. Evidence of linkage was observed in whites with ATF, FFAR, FFA50 and FFA60%. CONCLUSION: These results suggest that the C-60G polymorphism in the LIPE gene plays a role in determining body composition and that its effect is sex-, race- and insulin-dependent.

Abdomen↗