[A rare diagnosis: a case report of an isolated pulmonary valve endocarditis].
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Adult↗
Biomedical subjects
J Ott
Publications and source records attributed to J Ott.
Genetic and phenotypic heterogeneity in pattern dystrophy.
BACKGROUND: The pattern dystrophies (PD) represent a clinically heterogeneous family of inherited macular diseases frequently caused by mutations in the peripherin/RDS gene. Most previous studies have detailed the clinical findings in single families, making it difficult to derive data from which progression and visual outcome can be generalised. METHODS: Families were ascertained and clinically evaluated including angiography and electrophysiology where appropriate. RESULTS: In each of the six families with autosomal dominant PD, a mutation in the peripherin/RDS gene was identified, including a novel Cys250Phe variant. These data suggest that the condition is characterised by the accumulation of yellow to grey subretinal flecks, followed by pigmentary change accompanied by patches of chorioretinal atrophy. Subsequently, 50% (16/32) of individuals with PD developed poor central vision because of chorioretinal geographic atrophy or subretinal neovascularisation. The risk of these complications appears to increase with age. CONCLUSION: PD should not necessarily be considered a benign condition. Instead, patients should be counselled that there is a significant chance of losing central vision in their later years. Some elderly patients with probands showing PD may be misdiagnosed with age related macular degeneration owing to the phenotypic similarities between these conditions in the advanced state.
Adult↗
Substantial attributable risk related to a functional mu-opioid receptor gene polymorphism in association with heroin addiction in central Sweden.
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Amino Acid Substitution↗
Tradeoff between no-call reduction in genotyping error rate and loss of sample size for genetic case/control association studies.
Single nucleotide polymorphisms (SNP) may be genotyped for use in case-control designs to test for association between a SNP marker and a disease using a 2 x 3 chi-squared test of independence. Genotyping is often based on underlying continuous measurements, which are classified into genotypes. A "no-call" procedure is sometimes used in which borderline observations are not classified. This procedure has the simultaneous effect of reducing the genotype error rate and the expected number of genotypes observed. Both quantities affect the power of the statistic. We develop methods for calculating the genotype error rate, the expected number of genotypes observed, and the expected power of the resulting test as a function of the no-call procedure. We examine the statistical properties of the chi-squared test using a no-call procedure when the underlying continuous measure of genotype classification is a three-component mixture of univariate normal distributions under a range of parameter specifications. The genotype error rate decreases as the no-call region is increased. The expected number of observations genotyped also decreases. Our key finding is that the expected power of the chi-squared test is not sensitive to the no-call procedure. That is, the benefits of reduced genotype error rate are almost exactly balanced by the losses due to reduced genotype observations. For an underlying univariate normal mixture of genotype classification to be analyzed with a 2 x 3 chi-squared test, there is little, if any, increase in power using a no-call procedure.
Case-Control Studies↗
Evidence for a putative bipolar disorder locus on 2p13-16 and other potential loci on 4q31, 7q34, 8q13, 9q31, 10q21-24, 13q32, 14q21 and 17q11-12.
Bipolar disorder (BP) is a severe and common psychiatric disorder characterized by extreme mood swings. Family, twin and adoption studies strongly support a genetic component. The mode of inheritance is complex and likely involves multiple, as yet unidentified genes. To identify susceptibility loci, we conducted a genome-wide scan with 343 microsatellite markers in one of the largest, well-characterized pedigree samples assembled to date (373 individuals in 40 pedigrees). To increase power to detect linkage, scan statistics were used to examine the logarithm of odds (lod) scores based on evidence at adjacent chromosomal loci. This analysis yielded significant evidence of linkage (genome-wide P&<0.05) for markers on 2p13-16. Standard linkage analysis was also supportive of linkage to 2p13-16 (lod=3.20), and identified several other interesting regions: 4q31 (lod=3.16), 7q34 (lod=2.78), 8q13 (lod=2.06), 9q31 (lod=2.07), 10q24 (lod=2.79), 13q32 (lod=2.2), 14q21 (lod=2.36) and 17q11-12 (lod=2.75). In this systematic, large-scale study, we identified novel putative loci for BP (on 2p13-16, 8q13 and 14q21) and found support for previously proposed loci (on 4q31, 7q34, 9q31, 10q21-24, 13q32 and 17q11-12). Two of the regions implicated in our study, 2p13-14 and 13q32, have also been linked to schizophrenia, suggesting that the two disorders may have susceptibility genes in common.
Adolescent↗
Sequence variations in the collagen IX and XI genes are associated with degenerative lumbar spinal stenosis.
BACKGROUND: Degenerative lumbar spinal stenosis (LSS) is usually caused by disc herniation or degeneration. Several genetic factors have been implicated in disc disease. Tryptophan alleles in COL9A2 and COL9A3 have been shown to be associated with lumbar disc disease in the Finnish population, and polymorphisms in the vitamin D receptor gene (VDR) (FokI and TaqI), the matrix metalloproteinase-3 gene (MMP-3) and an aggrecan gene (AGC1) VNTR have been reported to be associated with disc degeneration. In addition, an IVS6-4 a>t polymorphism in COL11A2 has been found in connection with stenosis caused by ossification of the posterior longitudinal ligament in the Japanese population. OBJECTIVE: To study the role of genetic factors in LSS. METHODS: 29 Finnish probands were analysed for mutations in the genes coding for intervertebral disc matrix proteins, COL1A1, COL1A2, COL2A1, COL9A1, COL9A2, COL9A3, COL11A1, COL11A2, and AGC1. VDR and MMP-3 polymorphisms were also analysed. Sequence variations were tested in 56 Finnish controls. RESULTS: Several disease associated alleles were identified. A splice site mutation in COL9A2 leading to a premature translation termination codon and the generation of a truncated protein was identified in one proband, another had the Trp2 allele, and four others the Trp3 allele. The frequency of the COL11A2 IVS6(-4) t allele was 93.1% in the probands and 72.3% in controls (p = 0.0016). The differences in genotype frequencies for this site were less significant (p = 0.0043). CONCLUSIONS: Genetic factors have an important role in the pathogenesis of LSS.
Adult↗
Association study of PHOX2B as a candidate gene for Hirschsprung's disease.
BACKGROUND: Hirschsprung's disease (HSCR) is a congenital disorder characterised by an absence of ganglion cells in the nerve plexuses of the lower digestive tract. Manifestation of the disease has been linked to mutations in genes that encode the crucial signals for the development of the enteric nervous system-the RET and EDNRB signalling pathways. The Phox2b gene is involved in neurogenesis and regulates Ret expression in mice, in which disruption of the Phox2b results in a HSCR-like phenotype. AIMS: To investigate the contribution of PHOX2B to the HSCR phenotype. METHODS: Using polymerase chain reaction amplification and direct sequencing, we screened PHOX2B coding regions and intron/exon boundaries for mutations and polymorphisms in 91 patients with HSCR and 71 ethnically matched controls. Seventy five HSCR patients with no RET mutations were independently considered. Haplotype and genotype frequencies were compared using the standard case control statistic. RESULTS: Sequence analysis revealed three new polymorphisms: two novel single nucleotide polymorphisms (A-->G(1364); A-->C(2607)) and a 15 base pair deletion (DEL(2609)). Statistically significant differences were found for A-->G(1364). Genotypes comprising allele G were underrepresented in patients (19% v 36%; chi(2)=9.30; p=0.0095 and 22% v 36%; chi(2)=7.38; p=0.024 for patients with no RET mutations). Pairwise linkage disequilibrium (LD) analysis revealed no LD between physically close polymorphisms indicating a hot spot for recombination in exon 3. CONCLUSION: The PHOX2B A-->G(1364) polymorphism is associated with HSCR. Whether it directly contributes to disease susceptibility or represents a marker for a locus in LD with PHOX2B needs further investigation. Our findings are in accordance with the involvement of PHOX2B in the signalling pathways governing the development of enteric neurones.
Base Sequence↗
Errors and linkage disequilibrium interact multiplicatively when computing sample sizes for genetic case-control association studies.
Single nucleotide polymorphisms (SNP) may be used in case-control designs to test for association between a SNP marker and a disease. Such designs may assume that the genotype data are reported without error. Our goal is quantifying the effects that errors have on sample size for case-control studies with haplotypes formed by a disease locus and a SNP marker locus in the presence of linkage disequilibrium (LD). We consider the effects of a recently published error model on 2x3 chi-square analysis. We study the joint relation of LD and errors with sample size for three specific genetic disease models and two settings each of marker allele frequencies (total of 6 studies). Minimal sample size necessary for fixed asymptotic power is estimated as a 4th degree polynomial in the variables S (error) and D' (LD measure) via a backward step-wise regression. We find that increased error rates lower power. In all studies, we observe that LD and errors interact in a non-linear fashion. In particular, regression analyses shows that several higher order interaction terms have coefficients significantly different from 0 in each study, with fraction of variance explained greater than 0.9999. Finally, the increase in sample size necessary to maintain constant asymptotic power and level of significance as a function of S is smallest when D' = 1 (perfect LD). The increase grows monotonically as D' decreases to 0.5 for all studies.
Case-Control Studies↗
The p53MH algorithm and its application in detecting p53-responsive genes.
A computer algorithm, p53MH, was developed, which identifies putative p53 transcription factor DNA-binding sites on a genomewide scale with high power and versatility. With the sequences from the human and mouse genomes, putative p53 DNA-binding elements were identified in a scan of 2,583 human genes and 1,713 mouse orthologs based on the experimental data of el-Deiry et al. [el-Deiry, W. S., Kern, S. E., Pietenpol, J. A., Kinzler, K. W. & Vogelstein, B. (1992) Nat. Genet. 1, 45-49] and Funk et al. [Funk, W. D., Pak, D. T., Karas, R. H., Wright, W. E. & Shay, J. W. (1992) Mol. Cell. Biol. 12, 2866-2871] (http://linkage.rockefeller.edu/p53). The p53 DNA-binding motif consists of a 10-bp palindrome and most commonly a second related palindrome linked by a spacer region. By scanning from the 5' to 3' end of each gene with an additional 10-kb nucleotide sequence appended at each end (most regulatory DNA elements characterized in the literature are in these regions), p53MH computes the binding likelihood for each site under a discrete discriminant model and then outputs ordered scores, corresponding site positions, sequences, and related information. About 300 genes receiving scores greater than a theoretical cut-off value were identified as potential p53 targets. Semiquantitative reverse transcription-PCR experiments were performed in 2 cell lines on 16 genes that were previously unknown regarding their functional relationship to p53 and were found to have high scores in either proximal promoter or possible distal enhancer regions. Ten (approximately 63%) of these genes responded to the presence of p53.
Algorithms↗
[Specific countertransference experience and interpersonal problem description in psychodynamic psychotherapy].
In psychodynamic psychotherapy, countertransference and its professional use is seen as an important means to identify central difficulties of patients. The present study examines the correspondence of countertransference and interpersonal difficulties in 30 therapist-patient couples in day hospital psychodynamic psychotherapy. Interpersonal problems were recorded using the inventory of interpersonal problems (IIP) and countertransference was measured using the impact message inventory (IMI). Correspondence was measured as the correlation of IIP data from the patients and IMI data from the therapists. Data were collected at the start of therapy, after 4 weeks of treatment, and at the end of treatment. Over the course of the therapy, an increase in the correspondence of interpersonal problems as reported by patients and countertransference could be observed, starting with r = 0.22 at the beginning of therapy and continuing through r = 0.47 after 4 weeks to r = 0.58 at the end of therapy. The mean correlation was slightly above that of a control group of 20 nonclinical couples associated for at least 6 months.
Adult↗
Multi-locus interactions predict risk for post-PTCA restenosis: an approach to the genetic analysis of common complex disease.
The complexity of recognizing the potential contribution of a number of possible predictors of complex disorders is increasingly challenging with the application of large-scale single nucleotide polymorphism (SNP) typing. In the search for putative genetic factors predisposing to coronary artery restenosis following balloon angioplasty, we determined genotypes for 94 SNPs representing 62 candidate genes, in a prospectively assembled cohort of 342 cases and 437 controls. Using a customized coupled-logistic regression procedure accounting for both additive and interactive effects, we identified seven SNPs in seven genes that, together, showed a statistically significant association with restenosis incidence (P <0.0001), accounting for 11.6% of overall variance observed. Among them are candidate genes for cardiovascular pathophysiology (apolipoprotein-species and NOS), inflammatory response (TNF receptor and CD14), and cell-cycle control (p53 and p53-associated protein). Our results emphasize the need to account for complex multi-gene influences and interactions when assessing the molecular pathology of multifactorial medical entities.
Angioplasty, Balloon, Coronary↗
ILAE genetics commission conference report: molecular analysis of complex genetic epilepsies.
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Epilepsy↗
The Ising model in physics and statistical genetics.
Interdisciplinary communication is becoming a crucial component of the present scientific environment. Theoretical models developed in diverse disciplines often may be successfully employed in solving seemingly unrelated problems that can be reduced to similar mathematical formulation. The Ising model has been proposed in statistical physics as a simplified model for analysis of magnetic interactions and structures of ferromagnetic substances. Here, we present an application of the one-dimensional, linear Ising model to affected-sib-pair (ASP) analysis in genetics. By analyzing simulated genetics data, we show that the simplified Ising model with only nearest-neighbor interactions between genetic markers has statistical properties comparable to much more complex algorithms from genetics analysis, such as those implemented in the Allegro and Mapmaker-Sibs programs. We also adapt the model to include epistatic interactions and to demonstrate its usefulness in detecting modifier loci with weak individual genetic contributions. A reanalysis of data on type 1 diabetes detects several susceptibility loci not previously found by other methods of analysis.
Algorithms↗
A genomewide screen for autism susceptibility loci.
We report the analysis of 335 microsatellite markers genotyped in 110 multiplex families with autism. All families include at least two "affected" siblings, at least one of whom has autism; the remaining affected sibs carry diagnoses of either Asperger syndrome or pervasive developmental disorder. Affected sib-pair analysis yielded multipoint maximum LOD scores (MLS) that reach the accepted threshold for suggestive linkage on chromosomes 5, X, and 19. Nominal evidence for linkage (point-wise P<.05) was obtained on chromosomes 2, 3, 4, 8, 10, 11, 12, 15, 16, 18, and 20, and secondary loci were found on chromosomes 5 and 19. Analysis of families sharing alleles at the putative X chromosomal linked locus and one or more other putative linked loci produced an MLS of 3.56 for the DXS470-D19S174 marker combination. In an effort to increase power to detect linkage, scan statistics were used to evaluate the significance of peak LOD scores based on statistical evidence at adjacent marker loci. This analysis yielded impressive evidence for linkage to autism and autism-spectrum disorders with significant genomewide P values <.05 for markers on chromosomes 5 and 8 and with suggestive linkage evidence for a marker on chromosome 19.
Asperger Syndrome↗
A transmission/disequilibrium test that allows for genotyping errors in the analysis of single-nucleotide polymorphism data.
The present study assesses the effects of genotyping errors on the type I error rate of a particular transmission/disequilibrium test (TDT(std)), which assumes that data are errorless, and introduces a new transmission/disequilibrium test (TDT(ae)) that allows for random genotyping errors. We evaluate the type I error rate and power of the TDT(ae) under a variety of simulations and perform a power comparison between the TDT(std) and the TDT(ae), for errorless data. Both the TDT(std) and the TDT(ae) statistics are computed as two times a log-likelihood difference, and both are asymptotically distributed as chi(2) with 1 df. Genotype data for trios are simulated under a null hypothesis and under an alternative (power) hypothesis. For each simulation, errors are introduced randomly via a computer algorithm with different probabilities (called "allelic error rates"). The TDT(std) statistic is computed on all trios that show Mendelian consistency, whereas the TDT(ae) statistic is computed on all trios. The results indicate that TDT(std) shows a significant increase in type I error when applied to data in which inconsistent trios are removed. This type I error increases both with an increase in sample size and with an increase in the allelic error rates. TDT(ae) always maintains correct type I error rates for the simulations considered. Factors affecting the power of the TDT(ae) are discussed. Finally, the power of TDT(std) is at least that of TDT(ae) for simulations with errorless data. Because data are rarely error free, we recommend that researchers use methods, such as the TDT(ae), that allow for errors in genotype data.
Alleles↗
Identification of a novel common genetic risk factor for lumbar disk disease.
CONTEXT: Lumbar disk disease (LDD) is one of the most common musculoskeletal diseases, with a prevalence of about 5%. A tryptophan (Trp) allele (Trp2) was recently discovered in the COL9A2 gene that is associated with dominantly inherited LDD but is only present in about 4% of Finnish patients with LDD. OBJECTIVE: To determine if other collagen IX gene sequence variations play a role in the pathogenesis of LDD. DESIGN AND SETTING: Case-control study conducted from February 1997 to May 1998 at university hospitals in Finland. PARTICIPANTS: A total of 171 individuals with LDD (evaluated clinically and by magnetic resonance imaging or computed tomography) and 321 controls without LDD (186 healthy individuals, 83 patients with primary osteoarthritis, 31 with rheumatoid arthritis, and 21 with chondrodysplasias). MAIN OUTCOME MEASURES: Frequencies of sequence variations covering the entire coding sequences and exon boundaries of the collagen IX genes, COL9A1, COL9A2, and COL9A3, which code for the alpha1, alpha2, and alpha3 chains of the protein, detected by conformation-sensitive gel electrophoresis and confirmed by sequencing, compared between individuals with and without LDD. RESULTS: Mutation analysis of all 3 collagen IX genes resulted in identification of an Arg103-->Trp (arginine-->tryptophan) substitution in the alpha3 chain (Trp3 allele). The frequency of the Trp3 allele was 12.2% in LDD cases, excluding 7 individuals who were carriers of the previously identified Gln326-->Trp (glutamine-->tryptophan) substitution in the alpha2 chain (Trp2 allele), and was 4.7% among controls. The difference in the frequency was statistically significant (P =.000013). Presence of at least 1 Trp3 allele increases risk of LDD about 3-fold. CONCLUSION: This study led to the identification of a novel common genetic risk factor for LDD, confirming that genetic risk factors likely play a significant role in LDD.
Adult↗
Further evidence for linkage of Gilles de la Tourette syndrome (GTS) susceptibility loci on chromosomes 2p11, 8q22 and 11q23-24 in South African Afrikaners.
Utilizing DNA samples from 91 Afrikaner nuclear families with one or more affected children, five genomic regions on chromosomes 2p, 8q, 11q, 20q, and 21q that gave evidence for association with GTS in previous case-control association studies were investigated for linkage and association with GTS. Highly polymorphic markers with mean heterozygosity of 0.77 were typed and resulting genotypes evaluated using single marker transmission disequilibrium (TDT), single marker haplotype relative risk (HRR), and multi-marker "extended" TDT and HRR methods. Single marker TDT analysis showed evidence for linkage or association, with p-values near 0.05, for markers D2S139, GATA28F12, and D11S1377 on chromosomes 2p11, 8q22 and 11q23-24, respectively. Extended, two-locus TDT and HRR analysis provided further evidence for linkage or association on chromosome 2 with p-values of 0.007 and 0.025, and chromosome 8 with p-values of 0.059 and 0.013, respectively. These results provide important additional evidence for the location of GTS susceptibility loci.
Case-Control Studies↗
Neural networks and disease association studies.
After a brief introduction to neural networks, specific applications are proposed for the analysis of association between single nucleotide polymorphisms and putative disease genes in case-control studies.
Alleles↗