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Results for “Heterogeneity Mapping”

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PubMed1981

Heterogeneity of DNA deletion in gamma delta beta-thalassemia.

By restriction endonuclease mapping, gene cloning, and DNA sequencing we have determined the region of DNA that is deleted in a family with gamma delta beta-thalassemia. The deletion removes the linked epsilon, gamma-, and delta-globin structural genes and terminates within the coding portion of the beta-globin gene. Since the extent of DNA deletion in this family differs from that reported in another family, we conclude that gamma delta beta-thalassemia is heterogeneous at the molecular level.

Base Sequence↗

PubMed2006

Dissecting the locus heterogeneity of autism: significant linkage to chromosome 12q14.

Autism is a common neurodevelopmental disorder with a significant genetic component and locus heterogeneity. To date, 12 microsatellite genome screens have been performed using various data sets of sib-pair families (parents and affected children) resulting in numerous regions of potential linkage across the genome. However, no universal region or consistent candidate gene from these regions has emerged. The use of large, extended pedigrees is a recognized powerful approach to identify significant linkage results, as these families potentially contain more potential linkage information than sib-pair families. A genome-wide linkage analysis was performed on 26 extended autism families (65 affected, 184 total individuals). Each family had two to four affected individuals comprised of either avuncular or cousin pairs. For analysis, we used a high-density single-nucleotide polymorphism genotyping assay, the Affymetrix GeneChip Human Mapping 10K array. Two-point analysis gave peak heterogeneity limit of detection (HLOD) of 2.82 at rs2877739 on chromosome 14q. Suggestive linkage evidence (HLOD>2) from a two-point analysis was also found on chromosomes 1q, 2q, 5q, 6p,11q and 12q. Chromosome 12q was the only region showing significant linkage evidence by multipoint analysis with a peak HLOD=3.02 at rs1445442. In addition, this linkage evidence was enhanced significantly in the families with only male affected (multipoint HLOD=4.51), suggesting a significant gender-specific effect in the etiology of autism. Chromosome-wide haplotype analyses on chromosome 12 localized the potential autism gene to a 4 cM region shared among the affected individuals across linked families. This novel linkage peak on chromosome 12q further supports the hypothesis of substantial locus heterogeneity in autism.

Autistic Disorder↗

PubMed2004

Clinical and electrophysiological characteristics of autosomal recessive axonal Charcot-Marie-Tooth disease (ARCMT2B) that maps to chromosome 19q13.3.

Charcot-Marie-Tooth disease (CMT) comprises a heterogeneous group of hereditary motor and sensory peripheral neuropathies. The autosomal recessive axonal form of CMT (ARCMT2) is rare. Eight patients of a large consanguineous family of Spanish ancestry in Costa Rica were diagnosed with ARCMT2B; previous genetic studies of this family revealed linkage to chromosome 19q13.3. The clinical and electrophysiological features of these patients are reported. All patients presented with a symmetric motor and sensory neuropathy, which was more pronounced in the lower limbs. Further, distal muscle wasting and impaired deep tendon reflexes were found. Age at onset was between 26 and 42 years, and the disease duration ranged from 2 to 19 years. Electrophysiological studies revealed a primary axonal degenerative process. The clinical characteristics of this family differed in several aspects from previously reported families with ARCMT2.

Action Potentials↗

PubMed2002

Homologous recombination between the inverted terminal repeats of defective transposon TCp3.2 causes an inversion in the genome of Cydia pomonella granulovirus.

In this study, a new mutant of the Cydia pomonella granulovirus (CpGV), which shows spontaneous inversion of a transposable element during in vivo replication, is described. CpGV-MCp4 is a natural mutant of CpGV-M, containing the transposable element TCp3.2, which originated from the genome of the host C. pomonella. During in vivo cloning studies of CpGV-MCp4, a mutant called CpGV-MCp4inv was isolated. CpGV-MCp4inv shows heterogeneity in the genome area of transposon insertion. Restriction mapping, PCR analysis and subsequent sequence analysis gave strong evidence that an inversion of TCp3.2 is caused by homologous recombination between the long inverted terminal repeats (ITRs) of the transposon. This finding demonstrated that extensive homologous repeat regions such as the ITRs of transposons cause inversions by homologous recombination during in vivo replication. The observed in vivo inversion between the ITRs can be considered as a model for the contribution of repeated sequences in the genome rearrangement of baculoviruses and a source for genetic heterogeneity among different baculoviruses and baculovirus genotypes.

Animals↗

PubMed2001

Power to detect linkage based on multiple sets of data in the presence of locus heterogeneity: comparative evaluation of model-based linkage methods for affected sib pair data.

The development of rigorous methods for evaluating the overall strength of evidence for genetic linkage based on multiple sets of data is becoming increasingly important in connection with genomic screens for complex disorders. We consider here what happens when we attempt to increase power to detect linkage by pooling multiple independently collected sets of families under conditions of variable levels of locus heterogeneity across samples. We show that power can be substantially reduced in pooled samples when compared to the most informative constituent subsamples considered alone, in spite of the increased sample size afforded by pooling. We demonstrate that for affected sib pair data, a simple adaptation of the lod score (which we call the compound lod), which allows for intersample admixture differences can afford appreciably higher power than the ordinary heterogeneity lod; and also, that a statistic we have proposed elsewhere, the posterior probability of linkage, performs at least as well as the compound lod while having considerable computational advantages. The companion paper (this issue, pp 217-225) shows further that in application to multiple data sets, familiar model-free methods are in some sense equivalent to ordinary lod scores based on data pooling, and that they therefore will also suffer dramatic losses in power for pooled data in the presence of locus heterogeneity and other complicating factors.

Chromosome Mapping↗

PubMed2003

A gene for nonsyndromic X-linked mental retardation (MRX77) maps to Xq12-Xq21.33.

Nonsyndromic X-linked mental retardation (MRX) is a highly heterogeneous condition in which mental retardation appears to be the only consistent manifestation. According to the most recent data, 77 MRX families with a lod score of >2 have been mapped and eight genes have been cloned. We hereby report on a linkage analysis performed on a Greek family with apparently nonsyndromic MRX. The affected males have moderate to severe mental retardation, severe speech problems, and aggressive behavior. Two-point linkage analysis with 26 polymorphic markers spanning the entire X chromosome was carried out. We could assign the causative gene to a 27 Mb interval in Xq12-Xq21.33. The maximum LOD score was found for markers DXS1225, DXS8114, and DXS990 at 2.36, 2.06, 2.06, respectively at theta = 0.00. Recombination was observed for DXS983 at the proximal side and DXS6799 at the distal side. Nineteen other MRX families have been described with a partial overlapping disease gene interval in proximal Xq. No mutations were found in the MRX77 family for three known or candidate MRX genes, from this region OPHN1, RSK4, and ATR-X. These data indicate that the Xq12-Xq21.33 interval contains at least one additional MRX gene.

Chromosome Mapping↗

PubMed2005

A novel autosomal recessive non-syndromic deafness locus, DFNB66, maps to chromosome 6p21.2-22.3 in a large Tunisian consanguineous family.

Hereditary non-syndromic deafness is extremely heterogeneous. Autosomal recessive forms account for approximately 80% of genetic cases. Autosomal recessive non-syndromic sensorineural deafness segregating in a large consanguineous Tunisian family was mapped to chromosome 6p21.2-22.3. A maximum lod score of 5.36 at theta=0 was obtained for the polymorphic microsatellite marker IR2/IR4. Haplotype analysis defined a 16.5-Mb critical region between microsatellite markers D6S1602 and D6S1665. The screening of 3 candidate genes, COL11A2, BAK1 and TMHS, did not reveal any disease causing mutation, suggesting that this is a novel deafness locus, which has been named DFNB66. A search in the Human Cochlear EST Library for ESTs located in this critical interval allowed us to identify several candidates. Further investigations on these candidates are needed in order to identify the deafness-causing gene in this Tunisian family.

Chromosome Mapping↗

PubMed1990

[The distribution of neurons in the caudate nucleus of the cat that respond to sensory stimulation and the organization of the topical projections].

It has been shown in chronic experiments that cells responding to somatic and visual stimuli are unevenly distributed in the caudate nucleus of a cat and areas of high and low activity alternate. Representational maps of somatic and visual space in the caudate nucleus are not single. These data as well as those on the morphological heterogeneity of the caudate nucleus suggest the presence of multiple somato- and retinotopic maps projecting independently on striosome surfaces.

Animals↗

PubMed1993

Characterization of human T-lymphotropic virus type I- and II-infected T-cell lines: antigenic, phenotypic, and genotypic analysis.

Eighteen long-term T-cell lines were established from peripheral blood mononuclear cells of individuals infected with human T-lymphotropic virus type I (HTLV-I) or II (HTLV-II). These cell lines (10 HTLV-I and 8 HTLV-II), representing diverse pathologic profiles and geographic regions, have been in culture for over 6 months and have constitutively produced p24gag antigen. Antigenic characterization of the cell lines by Western blot analysis demonstrated that all but one produced gag (p24) and env (gp46 or gp52) structural proteins; one HTLV-I-infected cell line exhibited an aberrant protein profile. Phenotypic analysis of the HTLV-infected cell lines demonstrated phenotypes consistent with activated T-cells (CD5+, CD25+, HLA-DR+). The HTLV-I-infected cell lines were predominantly CD4+ (IR, FS, A212, SP, 1657, 1742, 3669, 1996, and 3614), whereas EG was CD8+. The HTLV-II-infected cell lines were either CD4+ (H2A, Y17, G12.1), CD8+ (H1H, H2E, Y03, Y06), or both (H1B). Restriction map analysis and subtyping of the viral genomes demonstrated heterogeneity among these isolates. Of the HTLV-I-infected cell lines, six were subtype II, one was subtype III and, on the basis of additional restriction sites, another subtype, tentatively classified as subtype IV, could be identified for three of the HTLV-I-infected cell lines. Of the HTLV-II-infected cell lines, six were subtype HTLV-IIa and two were subtype HTLV-IIb. While the majority of the cell lines resemble the prototypic HTLV-I-infected (MT-2) and HTLV-II-infected (MoT) cell lines, the antigenic, phenotypic, and genotypic data collectively demonstrate heterogeneity among viral isolates representing diverse geographic regions.

Adult↗

PubMed1980

Baboon endogenous virus genome. I. Restriction enzyme map of the unintegrated DNA genome of a primate retrovirus.

A detailed restriction map was deduced for the genome of an endogenous retrovirus of a higher primate, that of baboon. The cleavage sites for 12 restriction enzymes were mapped. The unintegrated linear viral DNA intermediate that is produced by infection of permissive cells with baboon endogenous virus was isolated. Hybridization with a strong-stop complementary DNA probe demonstrated presence of a terminal repetition in the linear viral DNA. The positions of restriction sites for two particular enzymes, SmaI and XhoI, near each end were consistent with this result and indicated that the length of the repetition is 0.55 +/- 0.01 kilobase. The linear viral DNA had a unique restriction map indicating that it is not a set of random circular permutations of the RNA genome. From hybridization with a 3'-specific probe, the DNA restriction map was aligned relative to the 5'-to-3' orientation of the viral RNA. We observed a minor heterogeneity in a BamHI recognition site 1.95 kilobases from the right end of the linear map.

Animals↗

PubMed2004

Replication in genetic studies of complex traits.

Disappointments in replicating initial findings in gene mapping for complex traits are often attributed to small sample sizes and inadequate techniques to determine the threshold value. This is clearly not the whole truth. More fundamental reasons lie in the inherent heterogeneity related to disease, including genetic heterogeneity, differences in allele frequencies, and context-dependency in genetic architecture. There are also other reasons related to the data collection and analysis. Replication may remain a source of frustration unless more emphasis is put on controlling these sources of heterogeneity between studies.

Bayes Theorem↗

PubMed2004

Spatial heterogeneity of endocardial voltage amplitude in viable, chronically dysfunctional myocardium.

BACKGROUND: Although electromechanical mapping has been used to assess cardiac physiology, interpretation is dependent upon the spatial variability of endocardial voltage and local shortening in normal and viable dysfunctional myocardium, which is currently unknown. METHODS: NOGA mapping was performed in 13 pigs with an established model of viable dysfunctional myocardium produced by a chronic LAD stenosis, and five uninstrumented controls. Voltage maps (122 +/- 7 points each) were obtained in the closed-chest anesthetized state, and (18)F-2-deoxyglucose uptake and TTC staining confirmed viability. RESULTS: There were systematic regional variations in voltage amplitude in both chronically-instrumented and control animals. Unipolar voltage was ~15% higher in LAD-supplied versus remote myocardium (10.8 +/- 0.3 vs. 8.9 +/- 0.4 mV, p < 0.001), with a similar relative difference in controls (14.0 +/- 0.5 vs. 12.0 +/- 0.4 mV, p < 0.02). In contrast, bipolar voltage was ~35% lower in the LAD territory of both groups (2.2 +/- 0.2 vs. 3.5 +/- 0.2 mV, p < 0.01 and 3.1 +/- 0.3 vs. 5.1 +/- 0.3 mV in controls, p < 0.01). The relative dispersion (SD/mean) of voltage was large, but significantly lower for unipolar versus bipolar measurements (39 +/- 1% vs. 70 +/- 2%, p < 0.001). Variability between hearts was partially related to end-systolic volume (r = 0.58, p < 0.05). Linear local shortening measurements were insensitive to detect anterior hypokinesis. CONCLUSIONS: Our data demonstrates significant regional and spatial heterogeneity of endocardial voltage and NOGA-derived linear shortening in normal and viable dysfunctional myocardium, with large confidence intervals for individual measurements. Even though the absence of necrosis in this model precludes assessment of the sensitivity and specificity of NOGA mapping to identify infarction, our findings highlight important methodological limitations in using electromechanical mapping to determine viability.

Animals↗

PubMed1997

Mapping of the antigenic determinants of the Leishmania infantum gp63 protein recognized by antibodies elicited during canine visceral leishmaniasis.

The gp63 gene encoding the major surface antigen of Leishmania infantum has been cloned and sequenced. In spite of the overall sequence homology with the gp63 genes from other Leishmania species, particularly with the constitutively expressed Leishmania chagasi Gp63 gene, the carboxy-terminal ends of these genes are clearly divergent (62% homology). To study the prevalence of anti-gp63 antibodies in the sera from dogs with visceral leishmaniasis, a recombinant L. infantum gp63 protein was expressed in Escherichia coli. It was found that 100% of the sera from these dogs recognized the recombinant gp63 protein, suggesting that it must function as a potent B cell immunogen during natural canine visceral leishmaniasis. However, heterogeneity in the level of response was observed. Fine mapping of the antigenic determinants was performed by means of 6 overlapping subfragments of the gp63 protein and by the use of a library of synthetic peptides. The data showed that there is some degree of immunological restriction in the recognition of the protein since reactivity was observed preferentially against the most divergent region. The epitope mapping of this region showed 2 immunodominant peptides the response to which seems to be preferentially of the IgG2 type.

Amino Acid Sequence↗

PubMed2002

A genomewide linkage screen for relative hand skill in sibling pairs.

Genomewide quantitative-trait locus (QTL) linkage analysis was performed using a continuous measure of relative hand skill (PegQ) in a sample of 195 reading-disabled sibling pairs from the United Kingdom. This was the first genomewide screen for any measure related to handedness. The mean PegQ in the sample was equivalent to that of normative data, and PegQ was not correlated with tests of reading ability (correlations between minus sign0.13 and 0.05). Relative hand skill could therefore be considered normal within the sample. A QTL on chromosome 2p11.2-12 yielded strong evidence for linkage to PegQ (empirical P=.00007), and another suggestive QTL on 17p11-q23 was also identified (empirical P=.002). The 2p11.2-12 locus was further analyzed in an independent sample of 143 reading-disabled sibling pairs, and this analysis yielded an empirical P=.13. Relative hand skill therefore is probably a complex multifactorial phenotype with a heterogeneous background, but nevertheless is amenable to QTL-based gene-mapping approaches.

Chromosome Mapping↗

PubMedDate not supplied

[Cerebral glucose metabolism in autistic children. Study and positron emission tomography].

Brain glucose metabolism was measured in 18 autistic children, using high resolution positron emission tomography (PET Scan), with fluorodeoxyglucose (FDG) as tracer. Measurements were performed on an ECAT III tomograph (CTI). Global brain glucose utilization in the autistic population was slightly more elevated than in young adult volunteers, particularly in frontal cortical regions, an observation previously reported for adult autists (Rumsey et al., 1985). However, mean brain glucose metabolism did not differ significantly from that of control children. Regional metabolic maps were also normal, although there was evidence for heterogeneities, particularly at the level of prefrontal and parieto-occipital association areas: 6 children showed a relative hyperfrontality whilst hypofrontality was found in 2 cases. These data suggest that PET might be useful for a better definition of subsets of autistic syndrome in children.

Adolescent↗

PubMed2003

Self-organizing map for cluster analysis of a breast cancer database.

The purpose of this study was to identify and characterize clusters in a heterogeneous breast cancer computer-aided diagnosis database. Identification of subgroups within the database could help elucidate clinical trends and facilitate future model building. A self-organizing map (SOM) was used to identify clusters in a large (2258 cases), heterogeneous computer-aided diagnosis database based on mammographic findings (BI-RADS) and patient age. The resulting clusters were then characterized by their prototypes determined using a constraint satisfaction neural network (CSNN). The clusters showed logical separation of clinical subtypes such as architectural distortions, masses, and calcifications. Moreover, the broad categories of masses and calcifications were stratified into several clusters (seven for masses and three for calcifications). The percent of the cases that were malignant was notably different among the clusters (ranging from 6 to 83%). A feed-forward back-propagation artificial neural network (BP-ANN) was used to identify likely benign lesions that may be candidates for follow up rather than biopsy. The performance of the BP-ANN varied considerably across the clusters identified by the SOM. In particular, a cluster (#6) of mass cases (6% malignant) was identified that accounted for 79% of the recommendations for follow up that would have been made by the BP-ANN. A classification rule based on the profile of cluster #6 performed comparably to the BP-ANN, providing approximately 25% specificity at 98% sensitivity. This performance was demonstrated to generalize to a large (2177) set of cases held-out for model validation.

Adult↗

PubMed2001

Megacystis-microcolon-intestinal hypoperistalsis syndrome and aganglionosis in trisomy 18.

Ultrasonography at 23 weeks of gestation documented the presence of megacystis with horseshoe kidney, microcolon, intestinal malrotation, and decreased amniotic fluid volume. After pregnancy termination, an autopsy was performed. The external phenotype was diagnostic of the trisomy 18 syndrome confirmed by chromosome examination. The fetus also had a massively distended bladder with parchment-thin wall, microcolon, intestinal malrotation but no urethral obstruction or hydronephrosis. No ganglion cells were present in the colon or bladder. This has not been mentioned in other reported cases and, therefore, suggests pathogenic heterogeneity. The megacystis-microcolon-intestinal hypoperistalsis syndrome (MMIHS) is a rare autosomal recessive condition of unknown pathogenesis whose genes map to 15q24. Thus, its previously undescribed presence in trisomy 18 further suggests etiologic heterogeneity.

Abnormalities, Multiple↗

PubMed2025

Mapping Species Birth Across the Recombination Landscapes of Marine Snails.

Understanding the drivers of heterogeneous genomic divergence is essential for uncovering the mechanisms that generate and constrain biodiversity. The extent to which adaptation and speciation are facilitated by reorganisation of the recombination landscape remains untested in many systems. Marine ecosystems, with their dynamic and fluid habitats, offer a compelling context to investigate genomic divergence. In this study, we mapped genomic divergence and selection across recombination landscapes of parapatric marine snail sister species that we show have recently undergone secondary contact. Regions of reduced recombination were enriched for genes exhibiting signatures of negative selection, whereas regions of high recombination were associated with genes under putative positive selection. Notably, the recombination landscape of the population in parapatry of one species (Scurria viridula) differs markedly from that of the other population within this same species, highlighting the role of introgression in reshaping recombination landscapes. In the other species (Scurria zebrina), conservation of the recombination landscape and divergent selection among populations suggest trapping of beneficial allele combinations in regions of low recombination maintains the identity of this species. Among species, signals of divergence with gene flow consistently cluster within specific genomic regions characterised by high recombination rate variation among the populations of S. viridula. These results challenge traditional theoretical expectations of recombination evolution by showing that the causes of genomic divergence can be population-specific. This study demonstrates that recombination landscapes are key modulators of genomic divergence, with contemporary evolutionary shifts that could enable populations to adapt to distinct environments. Our findings provide new insights into the interplay between recombination, selection, and gene flow during speciation, underscoring the complexity of evolutionary trajectories in marine systems.

Genetic Introgression↗