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J Hampe

Publications and source records attributed to J Hampe.

At least 37 records · Page 2Linked to original sources
PubMed2001

An integrated system for high throughput TaqMan based SNP genotyping.

UNLABELLED: We have developed an integrated laboratory information system that allows the flexible handling of pedigree, phenotype and genotype information. Specifically, it includes client applications for an integrated data import from TaqMan typing files, Mendel checking, data export, handling of pedigree and phenotype information and analysis features. AVAILABILITY: The SQL source code, sources and binaries of the client applications (NT and Windows95/98 platforms) and additional documentation are available at http://www.mucosa.de/.

Clinical Laboratory Information Systems↗
PubMed2001

Fine mapping of the chromosome 3p susceptibility locus in inflammatory bowel disease.

BACKGROUND AND AIMS: Genetic predisposition for inflammatory bowel disease (IBD) has been demonstrated by epidemiological and genetic linkage studies. Genetic linkage of IBD to chromosome 3 has been observed previously. A high density analysis of chromosome 3p was performed to confirm prior linkages and elucidate potential genetic associations. METHODS: Forty three microsatellite markers on chromosome 3 were genotyped in 353 affected sibling pairs of North European Caucasian extraction (average marker density 2 cM in the linkage interval). Marker order was defined by genetic and radiation hybrid techniques. RESULTS: The maximum single point logarithm of odds (LOD) score was observed for Crohn's disease at D3S3591. Peak multipoint LOD scores of 1.65 and 1.40 for the IBD phenotype were observed near D3S1304 (distal 3p) and near D3S1283 in the linkage region previously reported. Crohn's disease contributed predominantly to the linkage. The transmission disequilibrium test showed significant evidence of association (p=0.009) between allele 4 of D3S1076 and the IBD phenotype (51 transmitted v 28 non-transmitted). Two known polymorphisms in the CCR2 and CCR5 genes were analysed, neither of which showed significant association with IBD. Additional haplotype associations were observed in the vicinity of D3S1076. CONCLUSIONS: This study provides confirmatory linkage evidence for an IBD susceptibility locus on chromosome 3p and suggests that CCR2 and CCR5 are unlikely to be major susceptibility loci for IBD. The association findings in this region warrant further investigation.

Alleles↗
PubMed2000

The conserved phosphoinositide 3-kinase pathway determines heart size in mice.

Phosphoinositide 3-kinase (PI3K) has been shown to regulate cell and organ size in Drosophila, but the role of PI3K in vertebrates in vivo is not well understood. To examine the role of PI3K in intact mammalian tissue, we have created and characterized transgenic mice expressing constitutively active or dominant-negative mutants of PI3K in the heart. Cardiac- specific expression of constitutively active PI3K resulted in mice with larger hearts, while dominant-negative PI3K resulted in mice with smaller hearts. The increase or decrease in heart size was associated with comparable increase or decrease in myocyte size. Cardiomyopathic changes, such as myocyte necrosis, apoptosis, interstitial fibrosis or contractile dysfunction, were not observed in either of the transgenic mice. Thus, the PI3K pathway is necessary and sufficient to promote organ growth in mammals.

Animals↗
PubMed2000

Anticipation in inflammatory bowel disease: a phenomenon caused by an accumulation of confounders.

Inflammatory bowel disease (IBD) has a definite genetic component as documented by epidemiological and linkage evidence. It shows an earlier onset of disease in children of affected patients than in their parents. This has lead to speculations about genetic anticipation in this disorder. 2,007 IBD patients with sporadic disease and 472 multiplex familial cases (including 103 affected parents and 99 children of affected patients) were evaluated with a multi-item questionnaire as part of a study of inflammatory bowel disease genetics. The Mann-Whitney U-test and the general linear model were used for analysis. Clinical characteristics such as presence of fistulae, stenoses, extraintestinal manifestations, and other parameters, which are related to the severity of the disease, were found to be similar between familial and sporadic cases of IBD (corrected P > or = 0.31 for all tests). The mean-age-of onset in children of affected patients was 19.4 years earlier than in their parents. However, the age of the parental cohort was significantly higher (27 years) and the diagnostic interval also longer (1.7 years). If these confounders are corrected in a general linear model, no significant difference is evident for the age-of-onset between the groups (P > or = 0.52). There is no evidence for genetic anticipation in inflammatory bowel disease. The absence of genetic anticipation is consistent with the clinical similarity of familial and sporadic inflammatory bowel disease. This finding justifies the primary genetic analysis of familial disease under the assumption that their genetic background will be representative for all presentations of IBD.

Adult↗
PubMed2000

Analysis of single-nucleotide polymorphisms in the interleukin-4 receptor gene for association with inflammatory bowel disease.

Genetic linkage analysis in families with multiple cases of inflammatory bowel disease (IBD) has mapped a gene which confers susceptibility to IBD to the pericentromeric region of chromosome 16 (IBD1). The linked region includes the interleukin(IL)-4 receptor gene (IL4R). Since IL-4 regulation and expression are abnormal in IBD, the IL4R gene is thus both a positional and functional candidate for IBD1. We screened the gene for single-nucleotide polymorphisms (SNPs) by fluorescent chemical cleavage analysis, and tested a subset of known and novel SNPs for allelic association with IBD in 355 families, which included 435 cases of Crohn's disease and 329 cases of ulcerative colitis. No association was observed between a haplotype of four SNPs (val50ile, gln576arg, A3044G, G3289A) and either the Crohn's disease or ulcerative colitis phenotypes using the transmission disequilibrium test. There was also no evidence for association when the four markers were analyzed individually. The results indicate that these variants are not significant genetic determinants of IBD, and that the IL4R gene is unlikely to be IBD1. Linkage disequilibrium analyses showed that the val50ile and gln576arg variants are in complete equilibrium with each other, although they are separated by only about 21 kilobases of genomic DNA. This suggests that a very dense SNP map may be required to exclude or detect disease associations with some candidate genes.

Alleles↗
PubMed2000

Genomics and inflammatory bowel disease.

Genomic technologies offer new approaches to the investigation of etiology and pathophysiology of inflammatory bowel disease (IBD). Several areas of application for these new technologies are possible. One such application is the search for gene variations predisposing to the development of the disorder in multiply-affected families. Genome-wide linkage studies have defined replicated susceptibility regions for IBD on chromosomes 6, 12, and 16. These susceptibility regions are still very large and each contain several hundred positional candidate genes. Efforts are under way at several centers to define the underlying molecular variants using systematic linkage disequilibrium and candidate gene methods. The pharmacogenetic investigation of gene variations may predict response to certain medications to target these therapeutic interventions more precisely. The use of global gene expression technologies may allow the identification of new pathways or molecules in the inflammatory process. This seems to be especially relevant because currently only approximately 8,000 of the estimated 100,000 human genes are characterized. In summary, genomic methodologies will profoundly influence the progress of IBD research and may lead to novel insights into both etiology and pathophysiology of chronic intestinal inflammation.

Journal Article↗
PubMed2000

Role of the angiotensin AT(1) receptor in rat aortic and cardiac PAI-1 gene expression.

Although the renin-angiotensin system has been implicated in increasing plasminogen activator inhibitor-1 (PAI-1) expression, the role of the angiotensin type 1 (AT(1)) receptor is controversial. This report examines the effects of angiotensin peptides, angiotensin-converting enzyme inhibition, and AT(1) antagonism on rat aortic and cardiac PAI-1 gene expression. In vitro, angiotensin (Ang) I, Ang II, and angiotensin Arg(2)-Phe(8) (Ang III) were potent agonists of PAI-1 mRNA expression in rat aortic smooth muscle cells (RASMCs), and stimulation of PAI-1 by these peptides was blocked by the AT(1) antagonist candesartan. Angiotensin Val(3)-Phe(8) (Ang IV) and angiotensin Asp(1)-Pro(7) (Ang [1-7]) did not affect PAI-1 expression in RASMCs. In neonatal rat cardiomyocytes, Ang II increased PAI-1 mRNA expression by 4-fold (P<0.01), and this response was completely blocked by AT(1) receptor antagonism. Continuous intrajugular infusion of Ang II into Sprague-Dawley rats for 3 hours increased aortic and cardiac PAI-1 mRNA expression by 17- and 9 fold, respectively, and these Ang II responses were completely blocked by coinfusion with candesartan. Aortic and cardiac PAI-1 expressions were compared in spontaneously hypertensive rats and Wistar-Kyoto rats. PAI-1 expression in the aorta and heart from spontaneously hypertensive rats was 5.8-fold and 2-fold higher, respectively, than in control Wistar-Kyoto rats (P<0.05). Candesartan treatment for 1 week reduced aortic and cardiac PAI-1 expression in spontaneously hypertensive rats by 94% and 72%, respectively (P<0.05), but did not affect vascular PAI-1 levels in Wistar-Kyoto rats. These results demonstrate a role for the AT(1) receptor in mediating the effects of Ang II on aortic and cardiac PAI-1 gene expression.

Angiotensin II↗
PubMed1999

Tumour necrosis factor alpha and interleukin 1beta in relapse of Crohn's disease.

BACKGROUND: Concentrations of proinflammatory cytokines are increased in the intestinal mucosa of patients with active Crohn's disease. Experimental immunotherapeutic interventions with anticytokine agents in refractory Crohn's disease show that tumour necrosis factor alpha (TNF alpha) may be an important mediator of inflammation. We investigated the relation between production of TNF alpha and interleukin 1beta by mononuclear cells of the colonic lamina propria in patients with remitting Crohn's disease and the risk of relapse. METHODS: We followed up 137 patients with Crohn's disease in steroid-induced remission for 1 year. Secretion of proinflammatory cytokines (tumour necrosis factor alpha [TNF alpha] and interleukin 1beta) was assessed after short-term culture of human lamina propria mononuclear cells. FINDINGS: Increased secretion of TNF alpha and interleukin 1beta were predictive for acute relapses within the next year. Site and extent of disease, baseline demographics, and serum acute-phase proteins had little predictive value. INTERPRETATION: TNF alpha is important as a target molecule for immune interventions in Crohn's disease. The capacity to produce TNF alpha or interleukin 1beta may identify patients who would benefit from anti-inflammatory remission maintenance.

Biomarkers↗
PubMed1999

Changes in methylation patterns identified by two-dimensional DNA fingerprinting.

Two-dimensional DNA fingerprinting (2-D fingerprinting) is a sensitive tool for genomic difference analysis between tumor DNA and constitutive DNA of glioma patients. Numerous differences were found even in low-grade gliomas. They can be interpreted as deletions, amplifications, rearrangements, HaeIII restriction site mutations, tandem repeat instabilities, or methylation differences. The influence of methyl groups on the melting behavior of double-stranded DNA fragments in a denaturing gradient gel was demonstrated by analyzing the migration of lambda-phage DNA fragments in 2-D fingerprint gels. A characteristic intensity shift between two neighboring spots in several glioma samples was identified and verified by rehybridization of 2-D filters with a cloned DNA fragment corresponding to the lower spot in 10 out of 11 pilocytic astrocytomas. We hypothesized that this shift may be related to an alteration in the methylation pattern of the tumor DNA. This was specifically tested by analyzing the underlying 750 bp genomic fragment (including 21 CpG dinucleotides) with bisulfite treatment of agarose-embedded DNA. A methylation grade of 88% in tumor DNA as compared to 96% in blood DNA was found. Although only one CpG is located in the melting domain of the cloned fragment, this particular CpG is methylated in all blood samples, but mostly demethylated in the tumor samples. In conclusion, we demonstrate that 2-D fingerprinting may be a powerful tool for the detection of DNA methylation changes in genomic difference analysis.

Astrocytoma↗
PubMed1999

A genomewide analysis provides evidence for novel linkages in inflammatory bowel disease in a large European cohort.

Inflammatory bowel disease (IBD) is characterized by a chronic relapsing intestinal inflammation, typically starting in early adulthood. IBD is subdivided into two subtypes, on the basis of clinical and histologic features: Crohn disease and ulcerative colitis (UC). Previous genomewide searches identified regions harboring susceptibility loci on chromosomes 1, 3, 4, 7, 12, and 16. To expand our understanding of the genetic risk profile, we performed a 9-cM genomewide search for susceptibility loci in 268 families containing 353 affected sibling pairs. Previous linkages on chromosomes 12 and 16 were replicated, and the chromosome 4 linkage was extended in this sample. New suggestive evidence for autosomal linkages was observed on chromosomes 1, 6, 10, and 22, with LOD scores of 2.08, 2.07, 2.30, and 1.52, respectively. A maximum LOD score of 1.76 was observed on the X chromosome, for UC, which is consistent with the clinical association of IBD with Ullrich-Turner syndrome. The linkage finding on chromosome 6p is of interest, given the possible contribution of human leukocyte antigen and tumor necrosis-factor genes in IBD. This genomewide linkage scan, done with a large family cohort, has confirmed three previous IBD linkages and has provided evidence for five additional regions that may harbor IBD predisposition genes.

Cohort Studies↗
PubMed1999

Linkage of inflammatory bowel disease to human chromosome 6p.

Inflammatory bowel disease (IBD) is characterized by a chronic relapsing intestinal inflammation. IBD is subdivided into Crohn disease and ulcerative colitis phenotypes. Given the immunologic dysregulation in IBD, the human-leukocyte-antigen region on chromosome 6p is of significant interest. Previous association and linkage analysis has provided conflicting evidence as to the existence of an IBD-susceptibility locus in this region. Here we report on a two-stage linkage and association analysis of both a basic population of 353 affected sibling pairs (ASPs) and an extension of this population to 428 white ASPs of northern European extraction. Twenty-eight microsatellite markers on chromosome 6 were genotyped. A peak multipoint LOD score of 4.2 was observed, at D6S461, for the IBD phenotype. A transmission/disequilibrium test (TDT) result of P=.006 was detected for D6S426 in the basic population and was confirmed in the extended cohort (P=.004; 97 vs. 56 transmissions). The subphenotypes of Crohn disease, ulcerative colitis, and mixed IBD contributed equally to this linkage, suggesting a general role for the chromosome 6 locus in IBD. Analysis of five single-nucleotide polymorphisms in the TNFA and LTA genes did not reveal evidence for association of these important candidate genes with IBD. In summary, we provide firm linkage evidence for an IBD-susceptibility locus on chromosome 6p and demonstrate that TNFA and LTA are unlikely to be susceptibility loci for IBD.

Alleles↗
PubMed1999

Genetics and inflammatory bowel disease.

Genetic factors have a definite role in the etiology of inflammatory bowel disease (IBD). The mode of inheritance suggests a polygenic disease with the penetrance of the genetic factors being strongly influenced by the lifestyle of an industrialized society. Molecular techniques, which have become available through the progress of the human genome project, allowed a first series of linkage studies in pairs of affected siblings with IBD, which suggested multiple genomic susceptibility regions. These regions are still large, but considerable progress is being made toward the identification of actual disease genes. It is hoped that an understanding of the genetic etiology of IBD will lead to enhanced diagnostic procedures, more effective therapeutic interventions, and preventive strategies in the future.

Journal Article↗
PubMed1998

Genomic difference analysis by two-dimensional DNA fingerprinting reveals typical changes in human low-grade gliomas.

Cytogenetic and molecular analyses such as allelotyping studies have revealed several genetic changes typical for human glial neoplasms. However, most studies to date have involved malignant gliomas and thus are likely to reflect late events of tumor progression. To elucidate the initial events of glial tumor growth, we performed a genome-wide search for genetic alterations in the DNA of 43 low-grade gliomas as compared to the constitutional DNA of the patients' peripheral blood leucocytes using the two-dimensional (2D) DNA fingerprint approach. Reliable results were obtained for 28 blood/tumor sample pairs (13 astrocytomas, 9 pilocytic astrocytomas, 1 oligodendroglioma, 3 oligoastrocytomas, and 2 ependymomas). DNA was digested with the restriction enzyme HaeIII and the resulting fragments were separated on 2D gels according to size and sequence in the first and second dimensions, respectively. Patterns of hundreds of spots were generated by hybridization with four different mini- and microsatellite core probes. A total of 655 to 1,122 spots could be visualized per sample. Comparison of blood and tumor spot patterns revealed two to 11 reproducible changes per patient. Most of the differences were spot losses (77.1%), while the others appeared to be gains or amplifications. Exactly the same changes were found in tumor recurrences which lacked histological signs of progression. When comparing different patients, many of the affected spots tended to cluster in particular areas of the gel as revealed by computer-aided comparison of all spot patterns. Eleven different spot clusters were identified which may correspond to several major deletion targets. This study provides the basis for the future molecular cloning of the candidate tumor suppressor genes affected by the common spot losses and will allow new insights into the genetic mechanisms of glial tumorigenesis.

Adolescent↗
PubMed1998

The interferon-gamma gene as a positional and functional candidate gene for inflammatory bowel disease.

Epidemiological and genome-wide linkage analyses have provided firm evidence for a genetic component in the pathogenesis of inflammatory bowel disease. The linkage regions on chromosomes 12 and 16 have been replicated in several independent samples. These represent the best positional evidence in the search for inflammatory bowel disease susceptibility genes. While systematic association and physical mapping studies in these regions are under way, the direct analysis of immunologically relevant genes as positional and functional candidates may provide a shortcut in this process. The interferon-gamma gene resides in the chromosome 12 linkage region near the marker D12S83. Interferon-gamma is an important proinflammatory cytokine in the interleukin-12 cascade and has been implicated in the pathogenesis of mucosal inflammation. We tested this gene for evidence of linkage and association in 133 German multiplex families and 506 single patients with their parents. An intragenic, highly informative CA-repeat marker in intron 1 of the gene was typed using fluorescence-labeled polymerase chain reaction and analysis on an automated sequencer. In the nonparametric linkage analysis using GENEHUNTER, a nonsignificant maximum LOD score of 0.67 was obtained. The transmission disequilibrium test for association was negative (P > or = 0.22) for Crohn's disease, ulcerative colitis, and the combined inflammatory bowel disease phenotype. In summary, the findings make interferon-gamma a very unlikely candidate for the major susceptibility gene in the chromosome 12 linkage interval. Future efforts can concentrate on other transcripts in the region.

Base Sequence↗
PubMed1998

Genetic analysis of inflammatory bowel disease in a large European cohort supports linkage to chromosomes 12 and 16.

BACKGROUND & AIMS: Inflammatory bowel disease (IBD) is a complex disorder of unknown etiology. Epidemiological investigations suggest a genetic basis for IBD. Recent genetic studies have identified several IBD linkages. The significance of these linkages will be determined by studies in large patient collections. The aim of this study was to replicate IBD linkages on chromosomes 12 and 16 in a large European cohort. METHODS: Three hundred fifty-nine affected sibling pairs from 274 kindreds were genotyped using microsatellite markers spanning chromosomes 12 and 16. Affection status of the sibling pairs was defined as Crohn's disease (CD) or ulcerative colitis (UC). RESULTS: Nonparametric statistical analyses showed linkage for both chromosomes. Two-point results for chromosome 12 peaked at D12S303 (logarithm of odds [LOD], 2.15; P = 0.003) for CD and at D12S75 (LOD, 0.92; P = 0.03) for UC. Multipoint analyses produced a peak LOD of 1.8 for CD. Chromosome 16 showed linkage for CD at marker D16S415 (LOD, 1.52; P = 0.007). Multipoint support peaked above markers D16S409 and D16S411 (LOD, 1.7). CONCLUSIONS: These data are consistent with linkage of IBD to chromosomes 12 and 16. The replication of genetic risk loci in a large independent family collection indicates important and common susceptibility genes in these regions and will facilitate identification of genes involved in IBD.

Chromosomes, Human, Pair 12↗
PubMed1998

POPSIM: a general population simulation program.

MOTIVATION: The investigation of common disorders of polygenic inheritance using both population-based association designs and non-parametric linkage analysis within families is gaining increasing importance. We have created a program that allows for the flexible simulation of populations as a tool to investigate the properties of population-based mapping approaches. RESULTS: We have created a population simulation program, POPSIM, that (i) creates a virtual representation of every individual, (ii) makes no prior assumptions but the Mendelian rules and (iii) allows populations of several million individuals in size to be generated and to be followed over hundreds of generations. The parameters of the disease model, population structure and population expansion rate can be specified. Flexible sampling options exist that allow samples of families and individuals to be drawn at any given point during the population history. The program may be a useful tool in the study of the influence of genetic drift, recombination and admixture on the generation and maintenance of linkage disequilibrium in populations, as well as the evaluation of stochastic sampling characteristics of families and individuals conditional on a complex genetic phenotype from homogeneous and heterogeneous populations. AVAILABILITY: The source code as well as Sun and Windows NT4.0 console executables of the program are available under http://www.ukrv. de/ch/medgen/html/benutzer/j.hampe/popsim. html. CONTACT: J. Hampe@mucosa.de

Computational Biology↗