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Results for “Heterogeneity Mapping”
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The genetics of adult-onset neuropsychiatric disease: complexities and conundra?
Genetic factors play a major role in the etiology of adult-onset neurodegenerative and neuropsychiatric disorders. Several highly penetrant genes have been cloned for rare, autosomal-dominant, early-onset forms of neurodegenerative diseases. These genes have provided important insights into the mechanisms of these diseases (often altering neuronal protein processing). However, the genes associated with inherited susceptibility to late-onset neurodegenerative diseases, schizophrenia, and bipolar disorder appear to have smaller effects and are likely to interact with each other (and with nongenetic factors) to modulate susceptibility and/or disease phenotype. Several strategies have recently been applied to address this complexity, leading to the identification of a number of candidate susceptibility loci/genes.
Regulation of expression and nucleotide sequence of a late vaccinia virus gene.
A subset of vaccinia virus genes are expressed only after DNA replication. To investigate the regulation of such transcriptional units, a representative gene encoding a major late polypeptide (Mr, 28,000) was mapped and sequenced. Translatable mRNAs were heterogeneous in length and overlapped several early genes downstream. The 5' end of the message was located, and the DNA segment upstream was excised and ligated to the coding sequence of the easily assayable procaryotic chloramphenicol acetyltransferase gene. The resulting chimeric gene was recombined into the thymidine kinase locus of the vaccinia virus genome, and infectious recombinant virus was isolated. Both the time of chloramphenicol acetyltransferase synthesis in infected cells and the requirement for DNA replication indicate that the sequence upstream of the late gene contains cis-acting transcriptional regulatory signals.
Analysis of the genomic termini of tupaia herpesvirus DNA by restriction mapping and nucleotide sequencing.
A recombinant plasmid harboring both genomic termini of tupaia herpesvirus (THV) DNA was characterized by restriction enzyme analysis and by determination of the nucleotide sequence. A unique NotI cleavage site was found that is located approximately 19 base pairs upstream of the THV terminal junction. THV DNA fragments from virion DNA were analyzed by using the same restriction enzymes as for the recombinant plasmid. The comparative fine mapping of virion THV DNA revealed heterogeneous molecules of variable lengths with the NotI cleavage site conserved. A number of short direct and inverted repeats and palindromes were found surrounding the THV terminal joint. The THV repetitive sequences were compared with the repeats reported for the DNA termini of herpes simplex virus, varicella-zoster virus, and Epstein-Barr virus and are discussed in respect to signals for a site-specific endonuclease required for packaging.
Informatics in Radiology (infoRAD): Magnetic Resonance Imaging Workbench: analysis and visualization of dynamic contrast-enhanced MR imaging data.
Magnetic Resonance Imaging Workbench (MRIW) allows analysis of T1- and T2*-weighted dynamic contrast-enhanced magnetic resonance imaging data sets to extract tissue permeability and perfusion characteristics by using standard pharmacokinetic models. Parametric maps are calculated from individual pixel enhancement curves in regions of interest (ROIs) and displayed as color overlays on the anatomic images. User-defined ROIs can be saved to ensure consistency of later reanalysis. Individual parametric maps are visualized together with user-selected parameter time-series plots. The following selections are available: overall ROI enhancement curve and fit, histogram, and individual pixel enhancement curve and fit. Summary data (transfer constant, leakage space, rate constant, integrated area under the gadolinium curve after 60 seconds, relative blood volume, relative blood flow, and mean transit time) may be exported to permanent storage along with per-pixel results for statistical analysis. Numerical values for parameters are displayed below the plot for easy reference. The dynamic range of plots and parametric map overlays is interactively adjustable. Viewing individual enhancement curves and parametric maps allows radiologists to investigate the heterogeneity of contrast agent kinetics for lesion characterization and to scrutinize serial changes in response to therapy. MRIW is written in IDL, enabling it to be used on a variety of computer systems.
Genetic epidemiology of Parkinson's disease.
The cause of Parkinson's disease (PD) is unknown. The major risk factors identified to date are family history, age, and elements of rural living. Nearly one-third of all PD cases are familial, a small subset of which appears autosomal dominant; however, the majority exhibit no clear inheritance pattern. Autosomal dominant PD is genetically heterogeneous: two PD genes have been mapped to chromosomes 2 and 4 and there may be additional as yet unidentified genes. The common forms of PD-both familial and sporadic cases-appear to involve a complex interplay of genetic susceptibility and environmental exposure. The observations that rural residence and pesticide exposure increase the risk of developing PD, and that a synthetic drug, 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine, can cause parkinsonism, suggest that at least a subset of PD may be caused by a toxin. Furthermore, modest but significant associations have been reported between PD susceptibility and genes that regulate metabolism of drugs and neurotoxins. There is also evidence for mitochondrial dysfunction in PD, a finding that was recently traced to anomalies in mitochondrial DNA. At the present time, the genetics of PD appear to be complex, involving multiple nuclear genes and possibly mitochondrial genes as well.
Spinal muscular atrophy is not the result of mutations at the beta-hexosaminidase or GM2-activator locus.
The disease locus for the clinically heterogeneous childhood spinal muscular atrophies (SMA) maps to the chromosome 5 subregion, 5q11.2-13.3. The beta-subunit of beta-D-N-acetylhexosaminidase (hexosaminidase) (EC 3.2.1.52) (Hex B) maps to the same region, and the protein required for substrate recognition by this enzyme, GM2-activator protein, likewise maps to chromosome 5. We have investigated the possibility of allelic variation among some forms of SMA and hexosaminidase deficiency. Recombination between the Hex B and SMA loci eliminates this enzyme as a candidate site for defects causing the illness. Furthermore, we show that, despite previous evidence to the contrary, the GM2-activator locus does not map to chromosome 5, thereby eliminating it as a candidate gene for SMA.
Familial vesicoureteral reflux: testing replication of linkage in seven new multigenerational kindreds.
Vesicoureteral reflux (VUR) (OMIM %193000), a common cause of childhood renal failure, is strongly influenced by hereditary factors. Familial VUR most closely conforms to autosomal-dominant inheritance, but because of variable penetrance and expressivity, large multigenerational pedigrees tractable to linkage analysis have been difficult to ascertain. A single genome-wide study of familial VUR has demonstrated linkage to chromosome 1p13, with 78% locus heterogeneity. Previous studies in humans have also suggested loci on chromosomes 6p21, 10q26, and 19q13, whereas mutations in ROBO2 were recently reported in some patients with VUR. Replication of these studies was attempted in seven previously undescribed families from Italy and the United States. Simulation studies, assuming 50% locus heterogeneity, showed that these kindreds had 85% power to replicate linkage and 53% power to achieve genome-wide significance at candidate intervals. Thirty-five markers on chromosomes 1p13, 3p12, 6p21, 10q26, and 19q13 were genotyped and analysis of linkage under a variety of models was performed. Parametric analysis excluded linkage to all candidate loci under genetic homogeneity; moreover, the data did not support statistically significant linkage under models of locus heterogeneity. Similarly, nonparametric, allele-sharing analysis did not reveal any evidence of linkage at any of the loci tested. Thus, despite sufficient power, linkage of familial VUR to previously reported candidate intervals could not be replicated. These data demonstrate substantial genetic heterogeneity of VUR and suggest that mapping strategies relying on a large number of kindreds or single "loaded" pedigrees will be most effective to achieve replication or detection of linkage.
Evaluation of the monophyly of Fomitopsis using parsimony and MCMC methods.
To evaluate the monophyly of Fomitopsis and elucidate phylogenetic relationships of its members, partial nuclear large subunit (partial 28S) ribosomal RNA genes were sequenced from 10 species of Fomitopsis and 15 related species. Phylogenetic analyses indicated that Fomitopsis was phylogenetically heterogeneous and its members were divided into three subgroups. The constrained tree excluding F. palustris (the type species of Pilatoporus) from Fomitopsis core group was rejected, thus rejecting the taxonomic concept to segregate Pilatoporus from Fomitopsis. The monophyly of taxa belonging to F. rosea complex was rejected, thus rejecting the complex definition based on morphological similarities. The exclusion of Piptoporus betulinus (the type species of Piptoporus) from Fomitopsis core group was rejected and Piptoporus proved to be heterogeneous in both best MP and MAP trees. The monophyly of F. officinalis with Fomitopsis core group also was rejected. Fomitopsis officinalis was closely related to Antrodia xantha and formed an independent lineage from Fomitopsis core group at the basal position of brown rotting fungi comprising Antrodia, Daedalea, Fomitopsis, Piptoporus and Postia. The MAP tree topologyobtained from MCMC computation of Bayesian inference was similar to the one of the best MP tree based on the parsimony analysis but showed a higher likelihood score in the Kishino-Hasegawa test and reflected better evolutionary patterns for the phylogeny of Fomitopsis.
[A brief history of medical genetics].
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Clinical characteristics of prostate cancer in an analysis of linkage to four putative susceptibility loci.
PURPOSE: Hereditary prostate cancer is an etiologically heterogeneous disease with six susceptibility loci mapped to date. We aimed to describe a collection of high-risk prostate cancer families and assess linkage to multiple markers at four loci: HPC1 (1q24-25), PCaP (1q42.2-43), HPCX (Xq27-28), and CAPB (1p36). EXPERIMENTAL DESIGN: Medical record data on 505 affected men in 149 multiply-affected prostate cancer families were reviewed, and correlations of clinical traits within each family were calculated. Logarithm of odds (LOD) score and nonparametric (NPL) linkage analyses were performed; white families were stratified by age of diagnosis, grade and stage of disease, and evidence of linkage to the other loci to increase genetic homogeneity. RESULTS: Age at diagnosis was the most correlated clinical trait within families. A maximum NPL score of 2.61 (P = 0.007) appeared to confirm HPC1 linkage for families that had a prevalence of high-grade or advanced-stage prostate cancer and which were not likely to be linked to PCaP, HPCX, or CAPB. Because the NPL scores improved when families more likely to be linked to the other loci were excluded, HPC1 may act independently of the other loci. The relationship of HPC1 and aggressive disease was strongest in families with median age at diagnosis > or =65 years (NPL, 3.48; P = 0.0008). CONCLUSIONS: The current results suggest that HPC1 linkage may be most common among families with more severe prostate cancer. Stratification by clinical characteristics may be a useful tool in prostate cancer linkage analyses and may increase our understanding of hereditary prostate cancer.
[Molecular genetic analysis of essential tremor].
Essential tremor (ET) is the most common extrapyramidal disorder of the central nervous system with autosomal dominant transmission in the majority of cases and age-dependent penetrance of the mutant gene. In a number of cases, it shares some phenotypic features with autosomal dominant idiopathic torsion dystonia (locus DYT1 on chromosome 9q32-34) and is genetically heterogeneous: distinct variants of ET were mapped to chromosomes 3q13 (ETM1) and 2p22-25 (ETM2). We performed studies of candidate loci in a group of Slavonic (11 patients) and Tajik (19 patients) families with ET. Mutational analysis of the DYT gene in probands did not reveal the major deletion 946-948delGAG characteristic of idiopathic torsion dystonia, which allows one to genetically distinguish the studied hereditary forms of ET and torsion dystonia. Based on analysis of genetic linkage in informative Tajik pedigrees with ET, linkage to locus ETM1 on chromosome 3q13 was established in four families. Maximum pairwise Lod score was 2.46 at recombination fraction of theta = 0.00; maximum combined multipoint Lod score was 3.35 for marker D3S3720 and a common "mutant" haplotype for markers D3S3620, D3S3576, and D3S3720 allowed us to locate a mutant gene in a relatively narrow chromosome region spanning 2 cM. In one informative pedigree with ET, both candidate loci ETM1 and ETM2 were definitely excluded on the basis of negative Lod scores obtained by linkage estimations, which testifies to the existence of another distinct gene for autosomal dominant ET.
Immunoglobulins of colostrum. V. Localization of structural differences between serum and colostral ovine and bovine IgG1 and IgG2 immunoglobulins.
Studies on localization of structural differences between ovine and bovine serum and colostral IgG immunoglobulins are described. Comparison of heterogeneity, susceptibility to proteolytic enzymes, peptide maps, amino acid compositions, and antigenic properties of immunoglobulins and their Fab and Fc fragments and H and L chains showed that structural differences are localized in the Fc region. The strongest differences were found in case of IgG2. It was also shown that no Fc fragments could be obtained from bovine serm IgG2 and ovine serum and colostral IgG2 due to their susceptibility to papain and trypsin. The results obtained confirmed our suggestion that colostral IgG2 are locally synthesized in mammary glands, whereas colostral IgG1 might be a mixed population of molecules locally synthesized and transferred from the serum.
In vivo and in vitro characterization of several isolates of spodoptera exigua nuclear polyhedrosis virus.
Spodoptera exigua nuclear polyhedrosis viruses (SeNPVs), isolated form five geographically distinct regions of Japan and Thailand, were characterized by their DNA restriction endonuclease pattern, level of virus production in a continuous cell line of S. exigua and biological activity to S. exigua larvae. The EcoRI and PstI fragments exhibited similar overall patterns with minor differences. Digestion of virus DNA from a plaque-purified isolate, SeNPV-I1, with PstI yielded 14 fragments and the estimated genome size was approximately 123 kbp. The SeNPV wild isolate from Kagoshima, SeNPV-KW, showed the highest yield of extracellular virus (ECV) in the Se301 cell line of S. exigua among five wild isolates, but there was no significant difference in the level of polyhedral inclusion body (PIB) formation. In comparative studies of biological activity using 2nd-instar S. exigua larvae, SeNPV-KW had the highest virulence with an LD50 value of 3.0 PIBs per larva. When 16 clones, plaque-purified from the Isahaya isolate, SeNPV-IW, were examined for genetic relatedness, seven distinct EcoRI patterns were observed, indicating that SeNPV-IW wild isolate consisted of a mixture of different genotypes.
Phenotypic and genetic heterogeneity in Niemann-Pick disease type C: current knowledge and practical implications.
The eponym "Niemann-Pick disease" includes two metabolically distinct entities. Niemann-Pick type C (NPC) is characterized by unique abnormalities of intracellular transport of exogenous cholesterol with sequestration of unesterified cholesterol in lysosomes, while Niemann-Pick types A and B are acid sphingomyelinase deficiencies resulting from mutations in the gene coding for lysosomal sphingomyelinase. Current knowledge regarding abnormalities of cholesterol processing in cultured cells from NPC patients is reviewed. The wide spectrum of expression of the disease is outlined. Based on experience with more than 350 patients, the problems encountered in the author's laboratory in the diagnosis of patients are discussed, as well as the relatively poor correlation between clinical and biochemical phenotypes. Recent major developments are, furthermore, reviewed. Cell hybridization studies have established an intergenic heterogeneity within NPC, consisting of one major (90% of patients) and one minor complementation group. Both groups show a wide phenotypic heterogeneity. The major gene has been mapped to 18q11-12, while the minor gene has been excluded from this region of chromosome 18. The function of both genes is yet unknown.
Genetic heterogeneity of Phthorimaea operculella granulovirus: restriction analysis of wild-type isolates and clones obtained in vitro.
Genetic heterogeneity of a wild-type granulovirus (Tunisia isolate) of the potato tuber moth Phthorimaea operculella (Phthorimaea operculella granulovirus, Phop GV) has been studied. The heterogeneity was indicated by the presence of several submolar fragments in the profiles obtained by use of several restriction endonucleases. It was also demonstrated by variations in the restriction profile of the wild-type Tunisia isolate that had underwent since 1991 in our laboratory numerous passages in vivo. A comparison of the Tunisia isolate used in Egypt in the biological control programme with other PhopGV isolates indicated that it could not be related to any of the 3 genotypes previously defined. Five clones obtained from the Tunisia isolate in vitro were further grown both in vitro and in vivo. The restriction analysis of these clones demonstrated that none of them was identical to the parental wild type virus and to any other PhopGV geographic isolates. Genotypic differences between the clones were also shown. A 19 kbp BamHI fragment absent in the original Tunisia isolate but present in its passages since 1995 at a submolar concentration, was always present at a molar concentration in its clones. The presence of this fragment reflects probably a selection of one or more variants present in the original isolate and its possible adaptation to the growth in our laboratory conditions.
Homozygosity mapping of Portuguese and Japanese forms of ataxia-oculomotor apraxia to 9p13, and evidence for genetic heterogeneity.
Ataxia with oculomotor apraxia (AOA) is characterized by early-onset cerebellar ataxia, ocular apraxia, early areflexia, late peripheral neuropathy, slow progression, severe motor handicap, and absence of both telangiectasias and immunodeficiency. We studied 13 Portuguese families with AOA and found that the two largest families show linkage to 9p, with LOD scores of 4.13 and 3.82, respectively, at a recombination fraction of 0. These and three smaller families, all from northern Portugal, showed homozygosity and haplotype sharing over a 2-cM region on 9p13, demonstrating the existence of both a founding event and linkage to this locus, AOA1, in the five families. Three other families were excluded from this locus, demonstrating nonallelic heterogeneity in AOA. Early-onset cerebellar ataxia with hypoalbuminemia (EOCA-HA), so far described only in Japan, is characterized by marked cerebellar atrophy, peripheral neuropathy, mental retardation, and, occasionally, oculomotor apraxia. Two unrelated Japanese families with EOCA-HA were analyzed and appeared to show linkage to the AOA1 locus. Subsequently, hypoalbuminemia was found in all five Portuguese patients with AOA1 with a long disease duration, suggesting that AOA1 and EOCA-HA correspond to the same entity that accounts for a significant proportion of all recessive ataxias. The narrow localization of AOA1 should prompt the identification of the defective gene.
Genetic locus heterogeneity in Lafora's progressive myoclonus epilepsy.
In 1995, we mapped a gene for Lafora's progressive myoclonus epilepsy in chromosome 6q23-25. In 1997 and 1998, we reduced the size of the locus to 300 kb, and an international collaboration identified mutations in the protein tyrosine phosphatase gene. Here, we examine for heterogeneity through the admixture test in 22 families and estimate the proportion of linked families to be 75 to 85%. Extremely low posterior probabilities of linkage (Wi), exclusionary LOD scores, and haplotypes identify 4 families unlikely to be linked to chromosome 6q24.