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Results for “Heterogeneity Mapping”

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PubMed1999

The Fanconi anemia group E gene, FANCE, maps to chromosome 6p.

Fanconi anemia (FA) is a genetically heterogeneous autosomal recessive disease with bone marrow failure and predisposition to cancer as major features, often accompanied by developmental anomalies. The cells of patients with FA are hypersensitive to DNA cross-linking agents in terms of cell survival and chromosomal breakage. Of the eight complementation groups (FA-A to FA-H) distinguished thus far by cell fusion studies, the genes for three-FANCA, FANCC, and FANCG-have been identified, and the FANCD gene has been localized to chromosome 3p22-26. We report here the use of homozygosity mapping and genetic linkage analysis to map a fifth distinct genetic locus for FA. DNA from three families was assigned to group FA-E by cell fusion and complementation analysis and was then used to localize the FANCE gene to chromosome 6p21-22 in an 18.2-cM region flanked by markers D6S422 and D6S1610. This study shows that data from even a small number of families can be successfully used to map a gene for a genetically heterogeneous disorder.

Cell Fusion↗

PubMed1998

Periodically-modulated inhibition of living pacemaker neurons--III. The heterogeneity of the postsynaptic spike trains, and how control parameters affect it.

Codings involving spike trains at synapses with inhibitory postsynaptic potentials on pacemakers were examined in crayfish stretch receptor organs by modulating presynaptic instantaneous rates periodically (triangles or sines; frequencies, slopes and depths under, respectively, 5.0 Hz, 40.0/s/s and 25.0/s). Timings were described by interspike and cross-intervals ("phases"); patterns (dispersions, sequences) and forms (timing classes) were identified using pooled graphs (instant along the cycle when a spike occurs vs preceding interval) and return maps (plots of successive intervals). A remarkable heterogeneity of postsynaptic intervals and phases characterizes each modulation. All cycles separate into the same portions: each contains a particular form and switches abruptly to the next. Forms differ in irregularity and predictability: they are (see text) "p:q alternations", "intermittent", "phase walk-throughs", "messy erratic" and "messy stammering". Postsynaptic cycles are asymmetric (hysteresis). This contrasts with the presynaptic homogeneity, smoothness and symmetry. All control parameters are, individually and jointly, strongly influential. Presynaptic slopes, say, act through a postsynaptic sensitivity to their magnitude and sign; when increasing, hysteresis augments and forms change or disappear. Appropriate noise attenuates between-train contrasts, providing modulations are under 0.5 Hz. Postsynaptic natural intervals impose critical time bases, separating presynaptic intervals (around, above or below them) with dissimilar consequences. Coding rules are numerous and have restricted domains; generalizations are misleading. Modulation-driven forms are trendy pacemaker-driven forms. However, dissimilarities, slight when patterns are almost pacemaker, increase as inhibition departs from pacemaker and incorporate unpredictable features. Physiological significance-(1) Pacemaker-driven forms, simple and ubiquitous, appear to be elementary building blocks of synaptic codings, present always but in each case distorted typically. (2) Synapses are prototype: similar behaviours should be widespread, and networks simulations benefit by nonlinear units generating all forms. (3) Relevant to periodic functions are that few variables need be involved in form selection, that distortions are susceptible to noise levels and, if periods are heterogeneous, that simple input cycles impose heterogeneous outputs. (4) Slow Na inactivations are necessary for obtaining complex forms and hysteresis. Formal significance--(1) Pacemaker-driven forms and presumably their modulation-driven counterparts, pertain to universal periodic, intermittent, quasiperiodic and chaotic categories whose formal properties carry physiological connotations. (2) Only relatively elaborate, nonlinear geometric models show all forms; simpler ones, show only alternations and walk-throughs. (3) Bifurcations resemble those of simple maps that can provide useful guidelines. (4) Heterogeneity poses the unanswered question of whether or not the entire cycle and all portions have the same behaviours: therefore, whether trajectories are continuous or have discontinuities and/or singular points.

Action Potentials↗

PubMed1994

Localization of merosin-negative congenital muscular dystrophy to chromosome 6q2 by homozygosity mapping.

Congenital muscular dystrophies (CMD) are autosomal recessive, heterogeneous disorders. The commonest forms are the Fukuyama CMD (FCMD), associated with mental retardation and structural brain anomalies, and classical (occidental) CMD, with pure muscle expression. FCMD has been localized to chromosome 9q31-q33. Following the discovery of merosin deficiency in some CMD cases, we have localized, by homozygosity mapping and linkage analysis (Zmax = 5.6; theta = 0.0 for marker AFM127xb2) in four merosin-negative families a CMD gene in a 16 cM region of chromosome 6q2 in the region of the laminin M chain gene. In three consanguineous, merosin-positive, CMD families there was no linkage to either chromosome 6q2 or 9q31-q33.

Chromosome Mapping↗

PubMed1984

Promoter recognition and transcription initiation in E. coli.

Analysis of stability maps of sequences harbouring E. coli RNA polymerase promoters shows a characteristic splitting in homostable domains, despite the heterogeneity of the sequences. Correlation of stability maps with results from static approaches giving the contact points of the enzyme on promoters and functional studies employing abortive initiation assay allow us to propose a general mechanism for recognition of promoters and transcription start.

Base Composition↗

PubMed2000

Mapping of a syndrome of X-linked thrombocytopenia with Thalassemia to band Xp11-12: further evidence of genetic heterogeneity of X-linked thrombocytopenia.

X-linked thrombocytopenia with thalassemia (XLTT; Online Mendelian Inheritance in Man [OMIM] accession number 314050) is a rare disorder characterized by thrombocytopenia, platelet dysfunction, splenomegaly, reticulocytosis, and unbalanced hemoglobin chain synthesis. In a 4-generation family, the gene responsible for XLTT was mapped to the X chromosome, short arm, bands 11-12 (band Xp11-12). The maximum lod score possible in this family, 2.39, was obtained for markers DXS8054 and DXS1003, at a recombination fraction of 0. Recombination events observed for XLTT and markers DXS8080 and DXS8023 or DXS991 define a critical region that is less than or equal to 7.65 KcM and contains the gene responsible for the Wiskott-Aldrich syndrome (WAS; OMIM accession number 301000) and its allelic variant X-linked thrombocytopenia (XLT; OMIM accession number 313900). Manifestations of WAS include thrombocytopenia, eczema, and immunodeficiency. In WAS/XLT the platelets are usually small, and bleeding is proportional to the degree of thrombocytopenia. In contrast, in XLTT the platelet morphology is normal, and the bleeding time is disproportionately prolonged. In this study no alteration in the WAS gene was detected by Northern blot or Western blot analysis, flow cytometry, or complimentary DNA dideoxynucleotide fingerprinting or sequencing. As has been reported for WAS and some cases of XLT, almost total inactivation of the XLTT gene-bearing X chromosome was observed in granulocytes and peripheral blood mononuclear cells from 1 asymptomatic obligate carrier. The XLTT carrier previously found to have an elevated alpha:beta hemoglobin chain ratio had a skewed, but not clonal, X-inactivation pattern favoring activity of the abnormal allele. Clinical differences and results of the mutation analyses make it very unlikely that XLTT is another allelic variant of WAS/XLT and strongly suggest that X-linked thrombocytopenia mapping to band Xp11-12 is a genetically heterogeneous disorder.

Blotting, Northern↗

PubMed1978

Heterogeneity of Epstein-Barr virus. III. Comparison of a transforming and a nontransforming virus by partial denaturation mapping of their DNAs.

The DNAs of a transforming and a nontransforming Epstein-Barr virus strain, B95-8 AND P3HR-1, were compared by partial denturation mapping. B95-8 viral DNA showed a homogeneous denaturation pattern. In contrast, P3HR-1 viral DNA was heterogeneous, containing at least two classes of molecules, classified into groups A and B and present in a ratio of about 2:1 to 3:1. No evidence could be obtained that molecules from both groups A and B contain identical sequences present in different orientations as described for herpes simplex viral DNA. The majority of sequences present in B95-8 and in P3HR-1 viral DNA group A could be correlated by assuming that different sequences, about 12,000 base pairs long, were inserted or deleted, respectively, at different position of both viral genomes.

Adenine↗

PubMed2003

Ultra-early study of edema formation in cerebral contusion using diffusion MRI and ADC mapping.

OBJECTIVE: Our previous studies have reported that heterogeneous mechanisms exist in early edema formation in cerebral contusion, and cytotoxic edema plays an important role within 48 hours post-trauma. It is remains unclear, when edema begins to develop following injury. In order to determine the time course of edema development, diffusion imaging and ADC (apparent diffusion co-efficient) mapping was performed in 10 patients within 24 hours post-trauma with cerebral contusion. METHODS: Diffusion imaging and ADC mapping were performed employing 1.0 T echo planar MRI. ADC values were indicated as a ration relative to the values of intact brain areas. RESULTS: Within 3 hours post-trauma, diffusion MRI showed no remarkable changes, and the ADC values were within normal limit (ADC ratio (=contused/normal brain) = 1.00 +/- 0.21, (mean +/- SD)). At 6 hours post-trauma, diffusion images demonstrated a low intensity core in the contusion proper and a high intensity rim in the peripheral area of contusion. The ADC value increased in the contusion proper (ADC ratio = 1.26 +/- 0.13) and decreased in the peripheral area (ADC ratio = 0.58 +/- 0.19). CONCLUSIONS: These findings indicated that early cellular swelling in the peripheral area of contusion begins within 6 hours following injury. This delayed occurrence of contusion-induced cellular swelling suggests that the CBF does not decrease to ischemic level immediately following injury.

Brain Edema↗

PubMed1977

Human papillomavirus DNA: physical mapping of the cleavage sites of Bacillus amyloliquefaciens (BamI) and Haemophilus parainfluenzae (HpaII) endonucleases and evidence for partial heterogeneity.

The DNA of human papillomavirus (HPV) obtained from a pool of plantar warts is cleaved by bacillus amyloliquefaciens (BamI) and Haemophilus parainfluenzae (HpaII) restriction endonucleases at one and four specific sites, respectively. These sites were localized on the previously established cleavage map of HPV DNA, using the Hind, HindIII, HpaI, and EcoRI endonuclease restriction sites as reference. The four HpaII sites were mapped, clockwise, at 1.4, 41.1, 44.3, and 52.8% of the genome length from the unique BamI cleavage site taken as point zero. The HpaII site mapped at 1.4% of the genome length was absent in 40 to 50% of the molecules, thus showing a genetic heterogeneity of HPV DNA.

Bacillus↗

PubMed1999

Linkage analysis in heterogeneous and complex traits.

Linkage analysis is generally carried out under single-gene models, while complex traits are thought to be under the control of multiple interacting genes. Current issues related to linkage analysis for complex traits are discussed. It is argued that linkage analyses should be carried out for sub-phenotypes, in addition to classical "affected-unaffected" phenotypes. Correlations for phenotypes among family members are often computed on the basis of extreme phenotypes of a proband, which results in biased estimates. Methods for ascertainment corrections are recommended. A generalized version of heterogeneity analysis is introduced and are shown to provide an effective single-locus analysis for complex traits.

Adult↗

PubMed2002

Audiologic evidence for further genetic heterogeneity at DFNA2.

A large American family has been mapped to the DFNA2 locus. However, mutation screening of CX31 and KCNQ4, the two genes associated with deafness at this locus, did not identify any mutations. The purpose of this report was to characterize the otologic and audiometric phenotype of this large American family with non-syndromic, autosomal-dominant sensorineural hereditary hearing impairment (HHI). Anamnestic data were obtained, pure-tone audiometry was performed and transient-evoked otoacoustic emissions were recorded. The findings in affected family members were compared to those in unaffected family members and to the respective p50 thresholds of the normal age-matched population. Mutational analysis of the CX26 gene was also performed. The affected members of this family demonstrated progressive symmetric sensorineural hearing impairment. The hearing loss was downward sloping, with mild-to-moderate loss in the low and mid frequencies and severe-to-profound loss in frequencies > 4,000 Hz. The onset of disease was predominantly in the first or early in the second decade. Hearing impairment progressed at approximately 1 dB per year across all frequencies. Transient-evoked otoacoustic emissions revealed a minimal response over all frequencies in affected members but robust responses in all unaffected members. Mutation in the CX26 gene was not present. The affected frequencies observed in this family were similar to those in the original family mapped to DFNA2; however, the age of onset of disease was different and the hearing loss progressed at a slower rate. Therefore, this family provides clinical evidence of genetic heterogeneity at the DFNA2 locus and can serve as a model for age-related hearing loss.

Adolescent↗

PubMed1991

Respiratory syncytial virus heterogeneity during an epidemic: analysis by limited nucleotide sequencing (SH gene) and restriction mapping (N gene).

The genes encoding the small hydrophobic (SH) proteins of a series of respiratory syncytial (RS) virus strains were amplified using the polymerase chain reaction, cloned and sequenced. Analysis of the SH gene sequences from 12 RS virus strains isolated between 1956 and 1989 confirmed the homogeneity of the two subgroups. A and B, previously defined serologically. Although there is only 76% deduced amino acid sequence identity of SH proteins between subgroups, there was little variation in deduced amino acid sequences within the subgroups; nucleotide homologies within the subgroups ranged between 93% and 99%. Forty-two isolates of RS virus from a single epidemic season (autumn/winter 1989) were also examined to determine their relatedness. For these isolates regions of both the SH and nucleocapsid protein genes of each isolate were amplified and these regions were further analysed by direct nucleotide sequencing or restriction mapping. It was possible to discriminate at least six different lineages (or substrains) of RS virus circulating at the same time and in the same locality.

Amino Acid Sequence↗

PubMed2006

Pulmonary nodule characterization: a comparison of conventional with quantitative and visual semi-quantitative analyses using contrast enhancement maps.

PURPOSE: To determine whether conventional nodule densitometry or analysis based on contrast enhancement maps of indeterminate lung nodules imaged with contrast-enhanced CT can distinguish benign from malignant lung nodules. MATERIALS AND METHOD: Thin section, contrast-enhanced CT (baseline, and post-contrast series acquired at 45, 90,180, and 360 s) was performed on 29 patients with indeterminate lung nodules (14 benign, 15 malignant). A thoracic radiologist identified the boundary of each nodule using semi-automated contouring to form a 3D region-of-interest (ROI) on each image series. The post-contrast series having the maximum mean enhancement was then volumetrically registered to the baseline series. The two series were subtracted volumetrically and the subtracted voxels were quantized into seven color-coded bins, forming a contrast enhancement map (CEM). Conventional nodule densitometry was performed to obtain the maximum difference in mean enhancement values for each nodule from a circular ROI. Three thoracic radiologists performed visual semi-quantitative analysis of each nodule, scoring each map for: (a) magnitude and (b) heterogeneity of enhancement throughout the entire volume of the nodule on a five-point scale. Receiver operator characteristic (ROC) analysis was conducted on these features to evaluate their diagnostic efficacy. Finally, 14 quantitative texture features were calculated for each map. A statistical analysis was performed to combine the 14 texture features to a single factor. ROC analysis of the derived aggregate factor was done as an indicator of malignancy. All features were analyzed for differences between benign and malignant nodules. RESULTS: Using 15 HU as a threshold, 93% (14/15) of malignant and 79% (11/14) of benign nodules demonstrated enhancement. The ROC curve when higher values of enhancement indicate malignancy was generated and area under the curve (AUC) was 0.76. The visually scored magnitude of enhancement was found to be less effective in distinguishing malignant from benign lesions, with an average AUC of 0.62. The visually scored pattern of enhancement was found to be more effective with an average AUC of 0.79. From the statistical analysis performed to combine the texture features to a single factor, the area under the ROC curve was 0.84. CONCLUSION: The present study suggests that visual semi-quantitative and quantitative characterization of contrast enhancement patterns may potentially enhance the discrimination between benign and malignant nodules. Further studies and correlation with pathologic material will be important to better understand the potential interplay between CT enhancement features, host stromal elements, and neovascularity that may contribute to these patterns.

Adult↗

PubMed1996

Recognition of subsets of the mammalian A/B-type core heterogeneous nuclear ribonucleoprotein polypeptides by novel autoantibodies.

The structurally related A/B-type core heterogeneous nuclear ribonucleoprotein (hnRNP) polypeptides of 34-39 kDa (A1, A2, B1 and B2) belong to a family of RNA-binding proteins that are major components of 40 S hnRNP complexes. By two-dimensional gel electrophoresis and peptide mapping analysis we compared each member of the A/B-type core proteins in the human and rat liver cells. This comparison revealed the unique presence in rat cells of major protein species, referred to as mBx polypeptides, that appeared as three charge isoforms at a position corresponding to the minor HeLa B1b protein spot. In addition, clear differences in the ratios of the A1 polypeptide to the A1b isoform were observed. The detection, in sera of patients with rheumatic autoimmune diseases, of two novel autoantibody specificities, one recognizing solely B2 protein and the second both the B2 and mBx polypeptides, helped to identify mBx proteins as new A/B-type hnRNP components, immunologically related to B2 protein. A common immunoreactive V8 protease peptide of approx. 17 kDa has been identified in B2 and mBx hnRNP polypeptides. mBx protein species are identified in cells of murine origin, and have a ubiquitous tissue distribution and developmental appearance.

Animals↗

PubMed2005

Linkage analysis of the GAW14 simulated dataset with microsatellite and single-nucleotide polymorphism markers in large pedigrees.

Recent studies have suggested that a high-density single nucleotide polymorphism (SNP) marker set could provide equivalent or even superior information compared with currently used microsatellite (STR) marker sets for gene mapping by linkage. The focus of this study was to compare results obtained from linkage analyses involving extended pedigrees with STR and single-nucleotide polymorphism (SNP) marker sets. We also wanted to compare the performance of current linkage programs in the presence of high marker density and extended pedigree structures. One replicate of the Genetic Analysis Workshop 14 (GAW14) simulated extended pedigrees (n = 50) from New York City was analyzed to identify the major gene D2. Four marker sets with varying information content and density on chromosome 3 (STR [7.5 cM]; SNP [3 cM, 1 cM, 0.3 cM]) were analyzed to detect two traits, the original affection status, and a redefined trait more closely correlated with D2. Multipoint parametric and nonparametric linkage analyses (NPL) were performed using programs GENEHUNTER, MERLIN, SIMWALK2, and S.A.G.E. SIBPAL. Our results suggested that the densest SNP map (0.3 cM) had the greatest power to detect linkage for the original trait (genetic heterogeneity), with the highest LOD score/NPL score and mapping precision. However, no significant improvement in linkage signals was observed with the densest SNP map compared with STR or SNP-1 cM maps for the redefined affection status (genetic homogeneity), possibly due to the extremely high information contents for all maps. Finally, our results suggested that each linkage program had limitations in handling the large, complex pedigrees as well as a high-density SNP marker set.

Chromosome Mapping↗

PubMed2000

Linkage and LOH studies in 19 cylindromatosis families show no evidence of genetic heterogeneity and refine the CYLD locus on chromosome 16q12-q13.

Familial cylindromatosis is an autosomal dominant predisposition to multiple neoplasms of the skin appendages. The susceptibility gene has previously been mapped to chromosome 16q12-q13 and has features of a recessive oncogene/tumour suppressor gene. We have now evaluated 19 families with this disease by a combination of genetic linkage analysis and loss of heterozygosity in cylindromas from affected individuals. All 15 informative families show linkage to this locus, providing no evidence for genetic heterogeneity. Recombinant mapping has placed the gene in an interval of approximately 1 Mb. There is no evidence, between families, of haplotype sharing that might be indicative of common founder mutations.

Carcinoma, Adenoid Cystic↗

PubMed1999

Mapping the major susceptibility loci for familial Graves' and Hashimoto's diseases: evidence for genetic heterogeneity and gene interactions.

The autoimmune thyroid diseases (AITDs), comprising Graves' disease (GD) and Hashimoto's thyroiditis (HT), appear to develop as a result of a complex interaction between predisposing genes and environmental triggers. The goals of the present study were to identify the susceptibility loci for GD and HT and to study the relationships between them. We performed a whole genome linkage study on a dataset of 56 multiplex, multigenerational AITD families (354 individuals), using 387 microsatellite markers. We identified 6 loci that showed evidence for linkage to AITD. Only one locus, on chromosome 6 [AITD-1; 80 centimorgans (cM)], was linked with both GD and HT [maximum LOD score (MLS), 2.9]. This locus was close to, but distinct from, the human leukocyte antigen region. One locus on chromosome 13 (HT-1; 96 cM) was linked to HT (MLS, 2.1), and another locus on chromosome 12 (HT-2; 97 cM) was linked to HT in a subgroup of the families (MLS, 3.8). Three loci showed evidence for linkage with GD: GD-1 on chromosome 14 (99 cM; MLS, 2.5), GD-2 on chromosome 20 (56 cM; MLS, 3.5), and GD-3 on chromosome X (114 cM; MLS, 2.5). Since GD-2 showed the strongest evidence for linkage to GD we fine-mapped this locus to a 1-cM interval between markers at 55 and 56 cM on chromosome 20. These results demonstrated that 1) Graves' and Hashimoto's diseases are genetically heterogeneous, with only one locus in common to both diseases on chromosome 6; 2) only one HT locus was identified in all families, probably due to heterogeneity of the HT phenotype; and 3) three loci were shown to induce genetic susceptibility to GD by interacting with each other. One of them (GD-2) was fine-mapped to a 1-cM interval.

Chromosome Mapping↗

PubMed1995

Mapping of a gene for long QT syndrome to chromosome 4q25-27.

Long QT syndrome (LQTS) is a heterogeneous inherited disorder causing syncope and sudden death from ventricular arrhythmias. A first locus for this disorder was mapped to chromosome 11p15.5. However, locus heterogeneity has been demonstrated in several families, and two other loci have recently been located on chromosomes 7q35-36 and 3p21-24. We used linkage analysis to map the locus in a 65-member family in which LQTS was associated with more marked sinus bradycardia than usual, leading to sinus node dysfunction. Linkage to chromosome 11p15.5, 7q35-36, or 3p21-24 was excluded. Positive linkage was obtained for markers located on chromosome 4q25-27. A maximal LOD score of 7.05 was found for marker D4S402. The identification of a fourth locus for LQTS confirms its genetic heterogeneity. Locus 4q25-27 is associated with a peculiar phenotype within the LQTS entity.

Chromosome Mapping↗

PubMed1994

Optical mapping of repolarization and refractoriness from intact hearts.

BACKGROUND: Heterogeneities of repolarization (R) across the myocardium have been invoked to explain most reentrant arrhythmias. The measurement of refractory periods (RPs) has been widely used to assess R, but conventional electrode and extrastimulus mapping techniques have not provided reliable maps of RPs. METHODS AND RESULTS: Guinea pig hearts were stained with a voltage-sensitive dye to measure fluorescence (F) action potentials (APs) from 124 sites with a photodiode array. AP duration (APD) was defined as the time between depolarization (dF/dt)max and R time points (ie, the time when AP returns to baseline or some percent thereof). However, R time points are difficult to determine because AP downstrokes are often encumbered by drifting baselines and motion artifacts, which make this definition ambiguous. In optical and microelectrode recordings, the second derivative of AP downstrokes is shown to contain an easily detected, unique local maximum. The correlation between the position of this maximum (d2F/dt2)max and R has been tested during altered AP characteristics induced by changes in cycle length, ischemia, and hypoxia. Under these various modifications of the AP, the time points of (d2F/dt2)max fell at 97.0 +/- 2.1% of recovery to baseline. Extrastimulus techniques applied to (1) isolated myocytes, (2) intact hearts, and (3) mathematical simulations indicated that (d2V/dt2)max coincided with the effective RPs of APs. The coincidence of RPs and (d2V/dt2)max was valid within 5 milliseconds, for resting potentials of -75 to -90 mV and extrastimuli three times threshold voltage. CONCLUSIONS: Thus, optical APs and (d2F/dt2)max can be used to map activation, R, and RPs with AP recordings from a single heartbeat.

Animals↗