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Results for “Heterogeneity Mapping”

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PubMed1997

Segregation of Allgrove (triple-A) syndrome in Puerto Rican kindreds with chromosome 12 (12q13) polymorphic markers.

Allgrove syndrome (AS), also known as triple-A syndrome, is a rare cause of congenital adrenal insufficiency due to adrenocorticotropic hormone resistance. It is inherited in an autosomal recessive manner and is associated with achalasia, alacrima, and other neurological abnormalities, including autonomic, sensory, and upper- and lower-motor neuropathy, deafness, and mental retardation. Although the etiology of AS remains unknown, recently the disease was linked to a chromosome 12 locus (corresponding cytogenetic band 12q13) in consanguineous families of European ancestry. In the present study, we investigated four nonconsanguineous families with documented inheritance of AS for linkage with the reported 12q13 locus. Eighteen subjects were studied, of whom five were affected by AS. DNA was extracted from peripheral blood lymphocytes and amplified by standard methods with primers from polymorphic sequence tagged sites (STSs) located in the chromosome 12q13 region. Two-point logarithm-of-odds (LOD) score analysis revealed a maximum LOD score of 1.7 for STSs D12S361 and D12S368 without any recombinants [recombination distance (theta) = 0]. Multipoint linkage analysis defined an area of estimated genetic distance less than 0.5 cM (approximately 500,000 bp) between STSs D12S361 and D12S359 that is most likely to contain the AS gene(s). We conclude that, in Puerto Rican families, AS segregates with polymorphic markers that have been mapped to the chromosome 12q13 locus, revealing the absence of heterogeneity for this syndrome in a genetically distinct population. Candidate genes in the region include those that code for several of the keratin proteins, transcription factors, and others.

Abnormalities, Multiple↗

PubMed1998

The senegalese cholera epidemic of 1995 to 1996, an example of the geographic approach to health studies

There have been many cholera outbreaks in Senegal since 1971. The last outbreak began in the Dakar region in August 1995. It spread to the Diourbel, Fatick, Saint-Louis and Thies regions. In January 1996, the outbreak hit the Niakhar study area in the Fatick region. A team from ORSTOM (the French Institute of Scientific Research for Development in Cooperation) has been recording demographic events in this area for almost 15 years. The geographic approach is based on the automated mapping of cholera in hamlets and villages. Such studies investigate the factors determining the spread of diseases, within the context of land use. Three sets of data were used: demographic data that had been routinely collected and were available from a database, digitized maps and epidemiological data from a surveillance system set up to monitor the outbreak. A series of incidence maps, over time and on various scales, were generated using specialized software. The maps were analyzed and the outbreak was found to be heterogeneous over time. There were two waves of the outbreak and differences according to age and gender. The degree of heterogeneity depended on the place of residence. Heterogeneity was probably determined by village size, roads and the concentration of inhabitants within hamlets, which is roughly equivalent to the number of people per bore hole. These preliminary results suggest that further research is necessary, looking at different geographical scales (e.g. households, districts and regions). Qualitative studies of water use and the organization of the water supply are also required.

Journal Article↗

PubMed1994

Genetic heterogeneity of severe childhood autosomal recessive muscular dystrophy with adhalin (50 kDa dystrophin-associated glycoprotein) deficiency.

Severe autosomal recessive muscular dystrophy (SCARMD), McKusick n. 253700, has been originally described in North-African populations, in which significant linkage has been established with DNA markers mapping to the proximal region of the long arm of chromosome 13, without evidence for heterogeneity of the SCARMD locus in these populations. A striking feature of this disease is the isolated deficiency of adhalin, a sarcolemmal 50 kDa dystrophin-associated glycoprotein. We report a non-inbred French family with a milder progressive form of muscular dystrophy affecting subjects of both sexes. The parents are not affected suggesting an autosomal recessive transmission. In 4 siblings displaying mild to overt clinical signs of muscular dystrophy, serum creatine kinase was high, and muscle specimens showed variable degree of necrosis-regeneration with little fibrosis. In the 4 cases adhalin was completely absent in muscle sections, whereas dystrophin and the other members of the dystrophin-associated protein complex were normal, except for the 35 kDa dystrophin-associated glycoprotein which was decreased as usually observed in SCARMD. Linkage and homogeneity analysis using 4 microsatellite markers of chromosome 13q that are linked to the North-African SCARMD locus were performed in this family. Results show that the morbid locus involved in this family does not map to the same region as the SCARMD locus. This second locus may be involved in sporadic cases of muscular dystrophy with adhalin deficiency that have been reported in Europe.

Adolescent↗

PubMedDate not supplied

Phosphotyrosyl proteins in childhood rhabdomyosarcomas: phosphorylation of catenins and components of the insulin-like growth factor type I receptor signaling cascade.

PURPOSE: Rhabdomyosarcomas (RMS) are heterogeneous in their clinical presentation, histology, and cytogenetics. The growth of some RMS cells has been found to be regulated by the tyrosine kinase insulin-like growth factor (IGF) type I receptor. However, RMS cells exhibit variable sensitivity to inhibitors of tyrosine kinases and IGF receptors. Collectively, these heterogeneous features suggest that differences exist in the growth regulatory pathways of RMS. The objective of this study is to identify active tyrosine kinase signal transduction pathways in embryonal and alveolar RMS cells. METHODS: RMS tumor samples and cell lines representing both embryonal and alveolar histologic subtypes have been analyzed by immunoprecipitation and immunoblotting techniques to characterize phosphotyrosyl protein patterns and to identify tyrosine phosphorylated proteins. RESULTS: RMS cells can be characterized based on the patterns of phosphotyrosyl proteins, including the phosphorylation status of the catenin-like protein Cas1 and the signal adapter protein SHC, and the activation of IGF type I receptor signaling cascades including the formation of SHC-GRB2 signal protein complexes and MAP kinase activation. CONCLUSIONS: Rhabdomyosarcomas, especially the embryonal histologic subtype, are heterogeneous at the level of tyrosine kinase signal transduction. It will be important to characterize the growth regulatory pathways active in individual RMS tumors before targeting molecular therapies to this malignancy.

Adaptor Proteins, Signal Transducing↗

PubMed2005

Familial hyperaldosteronism type II is linked to the chromosome 7p22 region but also shows predicted heterogeneity.

BACKGROUND: Familial hyperaldosteronism type II (FH-II) is characterized by the familial occurrence of primary aldosteronism; unlike FH-I, it is not glucocorticoid-remediable and not associated with the hybrid CYP11B1/CYP11B2 gene mutation. Linkage to a 5-Mbp region of chromosome 7p22 was previously reported in an Australian family with eight affected members. Mutations in the exons or intron-exon boundaries of PRKAR1B (7p22, closely related to PRKAR1A, which is mutated in Carney complex) have been excluded in this family. OBJECTIVE: To refine the region of linkage, and to seek evidence of linkage in a South American family and in three other Australian families with FH-II, using seven closely spaced markers at 7p22. METHODS: To establish phenotypes (affected, uncertain or unaffected), blood pressure, plasma aldosterone and plasma renin (activity or concentration) were measured and the aldosterone: renin ratio (ARR) calculated. Individuals with consistently increased ARR underwent fludrocortisone suppression testing. The genotypes of the five pedigrees were analysed using seven closely spaced microsatellite markers at 7p22, and two-point and multipoint logarithm of odds (LOD) scores were calculated to assess linkage with FH-II. RESULTS: The combined multipoint LOD score for three families (the original Australian, the South American and a new Australian family) showing linkage at 7p22 was highly significant at 4.61 (theta = 0) for markers D7S462 and D7S517. A newly found recombination event in the first Australian family narrowed the area of linkage by 1.8 Mbp, permitting exclusion of approximately half the candidate genes in the originally reported locus. It was not possible to demonstrate linkage at the 7p22 region in the remaining two Australian families. CONCLUSION: This study provides further evidence for linkage of FH-II to 7p22, refines the locus, and supports the notion that FH-II may be genetically heterogeneous.

Aldosterone↗

PubMed1998

Autosomal recessive juvenile parkinsonism maps to 6q25.2-q27 in four ethnic groups: detailed genetic mapping of the linked region.

Parkinson disease (PD) is a common neurodegenerative condition associated with degeneration of dopaminergic neurons in the zona compacta of the substantia nigra. There is increasing evidence that genetic factors play a role in the etiology of PD, although genetic heterogeneity is likely. An autosomal dominant syndrome with many similarities to sporadic PD has been mapped to 4q21-22 in a large Italian pedigree and has been found to be due to mutation of the alpha-synuclein gene. However, this gene appears to account for only a minority of PD, and a susceptibility locus for autosomal dominant parkinsonism has recently been mapped, on 2p13. Autosomal recessive juvenile parkinsonism (JP), which shows marked clinical similarity to PD, maps to 6q25.2-q27. We found linkage to this region in a group of 15 families from four distinct ethnic backgrounds. A full genomic screen excluded other candidate regions. We have constructed a detailed genetic map of the linked region and have mapped the position of the manganese superoxide dismutase gene (SOD2). Recombination events restricted the JP locus to a 6.9-cM region and excluded SOD2. The apparent homozygosity for null alleles at D6S955 in one family suggested a deletion and finer localization of the JP locus.

Age of Onset↗

PubMed2000

Evidence for a new locus for X-linked retinitis pigmentosa (RP23).

PURPOSE: X-linked retinitis pigmentosa (XLRP) is a degenerative disease of the retina characterized in the early stages of disease by night blindness as a result of rod photoreceptor loss, progressing to severe disease with loss of central vision by the third decade in affected males. XLRP displays exceptional genetic heterogeneity, with five reported loci on the human X-chromosome. To investigate the level of heterogeneity for XLRP in the patient pool in the current study, extensive haplotype analysis, linkage analysis, and mutation screening were performed. METHODS: Haplotype analysis of a family with diagnosed XLRP was scored with more than 34 polymorphic markers spanning the entire X-chromosome, including regions already identified as harboring XLRP genes and retina-specific genes. Two-point and multipoint lod scores were calculated. Affected male DNA was amplified with primers specific for the retinoschisis gene (XLRS1), and the products were screened for nucleic acid alterations by direct automated sequencing. RESULTS: In this article haplotype and linkage data are presented identifying a new locus for XLRP on the short arm of the X-chromosome, distinct from previously reported gene localizations for XLRP. The phenotype is atypical, in that the onset of vision loss in the male members of this family is unusually early, and female obligate carriers have normal fundi and waveforms. Informative recombination events in this family define a locus for XLRP (RP23) on Xp22 between the markers DXS1223 and DXS7161, spanning approximately 15 cM. A maximum lod score of 2.1 was calculated for the locus order DXS7103-8 cM-(RP23/DXS1224)-4 cM-DXS999. This new locus (RP23) encompasses the retinoschisis disease gene; therefore, XLRS1 was screened for a mutation. No sequence alteration was identified indicating that mutations in the coding region of the gene responsible for retinoschisis do not cause RP23. CONCLUSIONS: The results describe evidence for a new locus for XLRP (RP23), adding to the established genetic heterogeneity for this disease and the number of genes expressed in ocular tissue residing on the X-chromosome.

Adult↗

PubMed1994

A third locus for autosomal dominant cerebellar ataxia type I maps to chromosome 14q24.3-qter: evidence for the existence of a fourth locus.

The autosomal dominant cerebellar ataxias (ADCA) type I are a group of neurological disorders that are clinically and genetically heterogeneous. Two genes implicated in the disease, SCA1 (spinal cerebellar ataxia 1) and SCA2, are already localized. We have mapped a third locus to chromosome 14q24.3-qter, by linkage analysis in a non-SCA1/non-SCA2 family and have confirmed its existence in a second such family. We suggest designating this new locus "SCA3". Combined analysis of the two families restricted the SCA3 locus to a 15-cM interval between markers D14S67 and D14S81. The gene for Machado-Joseph disease (MJD), a clinically different form of ADCA type I, has been recently assigned to chromosome 14q24.3-q32. Although the SCA3 locus is within the MJD region, linkage analyses cannot yet demonstrate whether they result from mutations of the same gene. Linkage to all three loci (SCA1, SCA2, and SCA3) was excluded in another family, which indicates the existence of a fourth ADCA type I locus.

Adult↗

PubMed2006

Evaluation of bioreactor-cultivated bone by magnetic resonance microscopy and FTIR microspectroscopy.

We present a three-dimensional mineralizing model based on a hollow fiber bioreactor (HFBR) inoculated with primary osteoblasts isolated from embryonic chick calvaria. Using non-invasive magnetic resonance microscopy (MRM), the growth and development of the mineralized tissue around the individual fibers were monitored over a period of 9 weeks. Spatial maps of the water proton MRM properties of the intact tissue, with 78 microm resolution, were used to determine changes in tissue composition with development. Unique changes in the mineral and collagen content of the tissue were detected with high specificity by proton density (PD) and magnetization transfer ratio (MTR) maps, respectively. At the end of the growth period, the presence of a bone-like tissue was verified by histology and the formation of poorly crystalline apatite was verified by selected area electron diffraction and electron probe X-ray microanalysis. FTIR microspectroscopy confirmed the heterogeneous nature of the bone-like tissue formed. FTIR-derived phosphate maps confirmed that those locations with the lowest PD values contained the most mineral, and FTIR-derived collagen maps confirmed that bright pixels on MTR maps corresponded to regions of high collagen content. In conclusion, the spatial mapping of tissue constituents by FTIR microspectroscopy corroborated the findings of non-invasive MRM measurements and supported the role of MRM in monitoring the bone formation process in vitro.

Animals↗

PubMed2000

Cellular basis for dispersion of repolarization underlying reentrant arrhythmias.

Substantial heterogeneity in ion channel density and expression exists in cells isolated from various regions of the heart. Cell-to-cell coupling in the intact heart, however, is expected to attenuate the functional expression of the ion channel heterogeneities. Due to limitations of conventional electrophysiological recording techniques, the extent to which cellular electrical heterogeneities are functionally present in intact myocardium remains unknown. High-resolution optical mapping with voltage-sensitive dyes was used to measure transepicardial and transmural repolarization gradients in the Langendorff perfused guinea pig ventricle and the canine wedge preperation, respectively. Diversity of repolarization kinetics in the transepicardial direction modulated dispersion of repolarization in a biphasic fashion as premature coupling interval was shortened. Moreover, modulation of repolarization paralleled arrhythmia vulnerability in a predictable fashion. Transmural optical mapping revealed significant gradients of repolarization across the ventricular wall that were markedly increased in a surrogate model of LQTS. Transmural gradients of repolarization in LQTS were associated with an enhanced susceptibility to TdP. Therefore, despite strong cell-to-cell coupling in the normal heart, heterogeneities in the ionic make-up of cells across the epicardial and transmural surfaces result in functional heterogeneities of repolarization leading to arrhythmias.

Action Potentials↗

PubMed2002

Gene coding variant in Cas1 between the C57BL/6J and DBA/2J inbred mouse strains: linkage to a QTL for ethanol-induced locomotor activation.

BACKGROUND: Among some (e.g., DBA/2J or D2) but not all (C57BL/6J or B6) inbred strains of mice, ethanol has a marked psychostimulant effect. Intercrosses formed from the D2 and B6 strains have been used to detect quantitative trait loci (QTLs) for this phenotype. The major QTL is found at the mid-region of chromosome 2 (Demarest et al., 1999). This QTL has also been detected in heterogeneous stock mice (Demarest et al., 2001). A potential candidate gene in this region is Cas1, which codes for catalase. The current studies were conducted to determine (a) if there was difference in the open reading frame (ORF) of Cas1 between the D2 and B6 strains; (b) if a difference was found, was it likely that the difference had functional effects; and (c) if it could be established that Cas1 meets the criteria for QTL to gene. METHODS: The open reading frame (ORF) of Cas1 was sequenced in both the D2 and B6 mouse strains. A single polymorphism was found between the strains (see below); the strain distribution pattern for this polymorphism was determined in the 36 strains of the B6XD2 (BXD) recombinant inbred (RI) series. These data were used to map the position of Cas1 as described by Cudmore et al. (1999). RESULTS: The only difference between the D2 and B6 strains in the coding region was found at #349, G->A. This will result in a difference in the amino acid sequence between the strains at amino acid #117-alanine is found in the D2 strain while threonine is found in the B6 strain. The RI strain distribution pattern for this polymorphism was used to determine the relative placement of Cas1. The estimate suggests that Cas1 is flanked by D2Mit12 and D2Mit43 and relative to D2Mit94 (which was set at 47 cM), Cas1 is located at approximately 57 cM, confirming previous estimates (see www.jax.org). CONCLUSIONS: Pharmacological data (Correa et al., 2001) strongly support the idea that Cas1 meets the criteria for QTL to gene. However, based on the mapping data, Cas1 is clearly not included in the QTL for heterogeneous stock mice. Finally, other genetic data suggest that the polymorphism is not sufficient to generate the QTL.

Animals↗

PubMed2006

A method of focused classification, based on the bootstrap 3D variance analysis, and its application to EF-G-dependent translocation.

The bootstrap-based method for calculation of the 3D variance in cryo-EM maps reconstructed from sets of their projections was applied to a dataset of functional ribosomal complexes containing the Escherichia coli 70S ribosome, tRNAs, and elongation factor G (EF-G). The variance map revealed regions of high variability in the intersubunit space of the ribosome: in the locations of tRNAs, in the putative location of EF-G, and in the vicinity of the L1 protein. This result indicated heterogeneity of the dataset. A method of focused classification was put forward in order to sort out the projection data into approximately homogenous subsets. The method is based on the identification and localization of a region of high variance that a subsequent classification step can be focused on by the use of a 3D spherical mask. After initial classification, template volumes are created and are subsequently refined using a multireference 3D projection alignment procedure. In the application to the ribosome dataset, the two resulting structures were interpreted as resulting from ribosomal complexes with bound EF-G and an empty A site, or, alternatively, from complexes that had no EF-G bound but had both A and P sites occupied by tRNA. The proposed method of focused classification proved to be a successful tool in the analysis of the heterogeneous cryo-EM dataset. The associated calculation of the correlations within the density map confirmed the conformational variability of the complex, which could be interpreted in terms of the ribosomal elongation cycle.

Cryoelectron Microscopy↗

PubMed1998

Genatlas database, genes and development defects.

This article aims to illustrate the potentialities of the Genatlas database, taking, as an example, the developmental genes and their associated diseases in man. These genes belong to several categories intervening from the first stages of embryonic life. They operate at all steps of developmental cascades from extracellular signaling to activation of target genes. Quite a number of those genes have been identified in man, which are the orthologs of genes previously described in lower species. These genes are mapped and an increasing number are associated with developmental anomalies. These studies shed light on the mechanisms of congenital malformations. They disclose a large array of genetic and phenotypic heterogeneity and a high degree of complexity.

Body Patterning↗

PubMed2006

Subunit architecture of multimeric complexes isolated directly from cells.

Recent developments in purification strategies, together with mass spectrometry (MS)-based proteomics, have identified numerous in vivo protein complexes and suggest the existence of many others. Standard proteomics techniques are, however, unable to describe the overall stoichiometry, subunit interactions and organization of these assemblies, because many are heterogeneous, are present at relatively low cellular abundance and are frequently difficult to isolate. We combine two existing methodologies to tackle these challenges: tandem affinity purification to isolate sufficient quantities of highly pure native complexes, and MS of the intact assemblies and subcomplexes to determine their structural organization. We optimized our protocol with two protein assemblies from Saccharomyces cerevisiae (scavenger decapping and nuclear cap-binding complexes), establishing subunit stoichiometry and identifying substoichiometric binding. We then targeted the yeast exosome, a nuclease with ten different subunits, and found that by generating subcomplexes, a three-dimensional interaction map could be derived, demonstrating the utility of our approach for large, heterogeneous cellular complexes.

Chromatography, Affinity↗

PubMed1993

Genetics of epilepsy: an overview.

Studies of the genetics of epilepsy have, until recently, involved epidemiologic or segregation analyses of phenotypic characteristics of a number of seizure disorders. Technical advances in molecular biology involving gene mapping and gene identification have made it possible to examine the heritability of various epilepsy syndromes. Using "reverse genetics" or positional cloning, it is possible to identify an abnormal protein through gene isolation and cloning. Genes are localized through analysis of linkage to phenotypic markers (proteins) or DNA markers such as restriction fragment length polymorphisms, variable number of tandem repeats, and dinucleotides. Methods used to obtain DNA of interest involve digestion of genomic DNA with specific restriction endonucleases or amplification of DNA by polymerase chain reaction technology. Gel electrophoresis is the basis for the separation of different sized DNA. Inherited disorders for which a gene has been cloned or localized have highly penetrant, well-defined clinical phenotypes with no remissions and abundant clinical material. Genetic epilepsies, however, are variably penetrant age-dependent disorders with heterogeneous clinical phenotypes. Despite these difficulties, three genetic epilepsies have been mapped to specific chromosomes: benign familial neonatal convulsions to 20q, juvenile myoclonic epilepsy to 6p, and Baltic progressive myoclonus epilepsy to 21q. Further progress in understanding genetic epilepsies will depend on better definition of syndrome phenotypes, isolation of the epilepsy gene(s), and identification of the abnormal protein(s).

Animals↗

PubMed1992

Three DNA markers for hypophosphataemic rickets.

This paper presents three markers, 16D/E, pHMAI (DXS208), and CRI-L1391 (DXS274), that show close linkage for X-linked hypophosphataemic rickets (HYP). DXS274 is closely linked to HYP (theta max = 0.00, Zmax = 4.20), and DXS41 (99.6), (theta max = 0.00, Zmax = 5.20). Marker 16D/E maps distal to the disease locus (theta max = 0.05, Zmax = 3.11). The pHMAI probe recognises the same restriction fragment length polymorphism (RFLP) as 99.6. Multipoint analysis suggests that the most probable order of loci is Xpter-(DXS43, 16D/E)-HYP-DXS274-(DXS208, DXS41)-Xcen. The location of DXS274 distal to HYP cannot be excluded, as no recombinants were observed between DXS274 and HYP, or between DXS274 and DXS41/DXS208. One of the families contains a large number of recombinants, four of which are double recombinants. This most probably means that the disease in this family maps elsewhere on the X chromosome or on an autosome, indicating locus heterogeneity.

Blotting, Southern↗

PubMed1999

Autosomal recessive retinitis pigmentosa locus RP28 maps between D2S1337 and D2S286 on chromosome 2p11-p15 in an Indian family.

Retinitis pigmentosa (RP) is a group of clinically and genetically heterogeneous disorders characterised by night blindness, constriction of visual field, and dystrophic changes of the retina. Previous genetic studies have shown extensive allelic and non-allelic genetic heterogeneity of RP. Here we describe an Indian family with multiple consanguineous marriages and a total of four patients with autosomal recessive (AR) RP. The homozygosity mapping strategy was successfully used and indicated close linkage between the disease locus and D2S380, D2S441, D2S291, and D2S1394 with maximum lod scores between 1.51-3.07 at theta=0.00. The analysis of multiply informative meioses maps the locus (RP28) for ARRP in this family between D1S1337 and D2S286 on 2p11-p15. The involvement of visinin (VSNL1), a promising candidate gene assigned to chromosome 2p by previous studies, has been excluded by the absence of linkage.

Chromosome Mapping↗

PubMed2002

A locus for autosomal dominant keratoconus: linkage to 16q22.3-q23.1 in Finnish families.

PURPOSE: The estimated world-wide prevalence of keratoconus is 50 to 230 per 100,000 in the general population. Sporadic keratoconus is the leading cause of corneal transplantation surgery in Western countries. Positive family history has been reported in 6% to 8% of patients. The purpose of this study was to map the disease locus in 20 Finnish families with autosomal dominant keratoconus, each family having two or more affected members and with no other associated genetic disease. METHODS: DNA was extracted from blood samples, collected from 42 affected and 34 unaffected family members. Genomic DNA from patients and their parents, was typed for alleles of 292 polymorphic markers. A genome-wide screening was performed to localize the disease gene. Fluorescent markers were amplified by polymerase chain reaction and separated on an automated sequencer. Allele sizes were assigned to each family member, after which LOD scores were calculated. RESULTS: The disease locus was mapped to chromosome 16q, between the markers D16S2624 and D16S3090, with a maximum parametric multipoint LOD score of 4.10 and corresponding nonparametric score of 3.27 (NPL, P = 0.00006). Evidence from 20 families provided support for the linkage, consistent with a single locus for familial autosomal dominant keratoconus without heterogeneity. CONCLUSIONS: This study is the first genome-wide linkage study to map the keratoconus gene. The results suggest that the causative gene in keratoconus is located within the 16q22.3-q23.1 chromosomal region.

Adolescent↗