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PubMed1997

A newly identified locus for Usher syndrome type I, USH1E, maps to chromosome 21q21.

Usher syndrome (USH) is a clinically and genetically heterogeneous disorder characterized by congenital hearing loss combined with retinitis pigmentosa. This dual sensorineural deficiency is transmitted in an autosomal recessive mode. Usher syndrome type I (USH1) is the most severe form. Four loci responsible for USH1 (USH1A, 1B, 1C and 1D) have previously been mapped, among which only the USH1B gene has been cloned. Using homozygosity mapping in a consanguineous family from Morocco, we identified a novel locus for USH1, USH1E, mapping to chromosome band 21q21. The delimited 15 cM interval is flanked by the loci D21S1905 and D21S1913. Subsequent segregation analysis of two families affected by USH1, in which the A, B, C and D loci had been excluded, also excluded the involvement of the USH1E locus, therefore indicating the existence of at least one more locus for USH1.

Child↗
PubMed2004

[Preliminary linkage analysis of a Chinese family with benign familial infantile convulsion].

OBJECTIVE: Benign familial infantile convulsions (BFIC) is a recently recognized autosomal dominant inherited disorder. This epileptic syndrome typically begins between 3 and 12 months of age with clusters of partial seizures in most cases and carries a good prognosis. So far, three loci have been linked to chromosome 19q12.1-13.1, chromosome 2q24 and chromosome 16p12-q12. The authors performed linkage analysis on this pedigree. METHODS: A four-generation Chinese family was investigated. The total number of members was 32 in this family and two neurologists in Xiangya Hospital gave systemic physical examinations and interictal neurological examinations to nineteen members of this family. Venous blood samples were taken for genetic analysis. DNA was extracted from peripheral blood leukocytes using phenol-chloroform method. Seventeen microsatellite markers spanning the critical regions on chromosomes 19q12-13.1, 2q24, and 16p12-q12 were genotyped. These markers included D19S49, D19S250, D19S414, D19S416 and D19S245 for the 19q region, D2S2380, D2S399, D2S111, D2S2195, D2S2330 and D2S2345 for the 2q region, D16S401, D16S3131, D16S3093, D16S517, D16S3120 and D16S415 for the 16p-q region. The DNA from each sample was amplified for the 17 markers. After polymerase chain reactions (PCR), PCR products of chromosome 19 with markers D19S49, D19S250, D19S414, D19S416 and D19S245 were subjected to electrophoresis on 8% denatured polyacrylamide gel for at least 2 hours and 20 minutes. Then the length of the PCR products was judged in the Strategene Eagle Eye II automated gel image analyzer. For the markers from chromosome 2 and 16, PCR products were scanned at ABI 377 autosequencer. The data of PCR products were analyzed using the software Genescan v3.1, Genetyper v2.1 (Applied Biosystem, CA. USA) and GenoDB v1.0. After Mendelian checking, the eligible genotyping data were used for linkage analysis. LOD scores were calculated by using MLINK program of LINKAGE v5.1, under an assumption of autosomal dominant inheritance and the estimated penetrance was 0.9. The allele frequencies of each marker were assumed to be equal and the disease-allele frequencies were designated to be 1/10,000. The LOD scores were calculated at combination rate (theta) 0.0, 0.1, 0.2, 0.3, and 0.4. RESULTS: Among the 17 selected microsatellite markers, which cover the previously reported regions, seven markers' data (D16S3131, D16S517, D16S3120, D16S3093, D2S2380, D19S250 and D19S414) were omitted due to failed genotyping, low genetic heterogeneity, or failure to pass Mendelian checking. Omission of these markers was to ensure the reliability of our raw data. The two-point LOD scores were below zero for all the markers and the maximum LOD scores at theta = 0.0 were less than -2 for markers D19S49, D19S416, D19S245, D16S401, D16S415, D2S399, D2S111, D2S2195, D2S2330 and D2S2345. Thus, the linkage result showed no evidence that the disease locus is linked to any of these selected markers, which excludes the previously reported candidate regions found in other ethnic families. CONCLUSION: There is no evidence that this Chinese family was linked to one of the following loci: 19q12.1-13.1, 16p12-q12 and 2q24. The results indicated that BFIC showed genetic heterogeneity and the Chinese BFIC families might be mapped on another new locus.

China↗
PubMed2002

Mining Bacillus subtilis chromosome heterogeneities using hidden Markov models.

We present here the use of a new statistical segmentation method on the Bacillus subtilis chromosome sequence. Maximum likelihood parameter estimation of a hidden Markov model, based on the expectation-maximization algorithm, enables one to segment the DNA sequence according to its local composition. This approach is not based on sliding windows; it enables different compositional classes to be separated without prior knowledge of their content, size and localization. We compared these compositional classes, obtained from the sequence, with the annotated DNA physical map, sequence homologies and repeat regions. The first heterogeneity revealed discriminates between the two coding strands and the non-coding regions. Other main heterogeneities arise; some are related to horizontal gene transfer, some to t-enriched composition of hydrophobic protein coding strands, and others to the codon usage fitness of highly expressed genes. Concerning potential and established gene transfers, we found 9 of the 10 known prophages, plus 14 new regions of atypical composition. Some of them are surrounded by repeats, most of their genes have unknown function or possess homology to genes involved in secondary catabolism, metal and antibiotic resistance. Surprisingly, we notice that all of these detected regions are a + t-richer than the host genome, raising the question of their remote sources.

Bacillus subtilis↗
PubMed2002

[Familial prostate carcinoma in Germany].

Epidemiologic studies have shown that hereditary forms account for approximately 10% of all prostate cancers. The identification of several susceptibility loci harboring predisposing genes indicates the genetic heterogeneity of prostate cancer. The conflicting results of different linkage analyses may be explained by a varying contribution of each locus within different family collections and reflect differences of allele frequencies across different populations. In the present study we recorded the incidence of familial prostate cancer in Germany and performed descriptive analysis of the epidemiological data. In spite of a significant ascertainment bias, only 19% of all prostate cancers were familial. In 94% of families there were three affected relatives at most. Large prostate cancer families with at least five affected persons were rare (2%). Descriptive analysis revealed that only 42% of all pedigrees followed an autosomal-dominant pattern of transmission; the other pedigrees showed an X-chromosomal or recessive mode of inheritance. These data confirm the genetic heterogeneity of hereditary prostate cancer and imply that previously published epidemiological data cannot be transferred to the German population.

Adult↗
PubMed2002

A major susceptibility gene for asthma maps to chromosome 14q24.

Asthma is a complex genetic disorder with a heterogeneous phenotype, largely attributed to the interactions among many genes and between these genes and the environment. Numerous loci and candidate genes have been reported to show linkage and association to asthma and atopy. Although some studies reporting these observations are compelling, no gene has been mapped that confers a sufficiently high risk of asthma to meet the stringent criteria for genomewide significance. Using 175 extended Icelandic families that included 596 patients with asthma, we performed a genomewide scan with 976 microsatellite markers. The families were identified by cross-matching a list of patients with asthma from the Department of Allergy/Pulmonary Medicine of the National University Hospital of Iceland with a genealogy database of the entire Icelandic nation. We detected linkage of asthma to chromosome 14q24, with an allele-sharing LOD score of 2.66. After we increased the marker density within the locus to an average of one microsatellite every 0.2 cM, the LOD score rose to 4.00. We designate this locus "asthma locus one" (AS1). Taken together, these results provide evidence of a novel susceptibility gene for asthma on chromosome 14q24.

Alleles↗
PubMed1997

Limb girdle muscular dystrophy in Manitoba Hutterites does not map to any of the known LGMD loci.

Limb girdle muscular dystrophy (LGMD) is a heterogeneous group of disorders affecting primarily the shoulder and pelvic girdles. Autosomal dominant and recessive forms have been identified; 8 have been mapped and 1 more has been postulated on the basis of exclusion of linkage. An autosomal recessive muscular dystrophy was first described in 1976 in the Hutterite Brethren, a North American genetic and religious isolate [Shokeir and Kobrinsky, 1976; Clin Genet 9:197-202]. In this report, we discuss the results of linkage analysis in 4 related Manitoba Hutterite sibships with 21 patients affected with a mild autosomal recessive form of LGMD. Because of the difficulties in assigning a phenotype in some asymptomatic individuals, stringent criteria for the affected phenotype were employed. As a result, 7 asymptomatic relatives with only mildly elevated CK levels were assigned an unknown phenotype to prevent their possible misclassification. Two-point linkage analysis of the disease locus against markers linked to 7 of the known LGMD loci and 3 other candidate genes yielded lod scores of < or = -2 at theta = 0.01 in all cases and in most cases at theta = 0.05. This suggests that there is at least 1 additional locus for LGMD.

Adolescent↗
PubMed1992

Heterogeneity of messenger RNA that encodes the rat insulin receptor is limited to the domain of exon 11. Analysis by RNA heteroduplex mapping, amplification of cDNA, and in vitro translation.

Structural isoforms of the insulin receptor that occur in various tissues have been postulated to be involved in certain actions of insulin in target cells. To determine whether these insulin-receptor subtypes are caused by alterations in the receptor primary structure, we used RNA heteroduplex mapping and amplification of cDNA to detect variation in the coding region of insulin-receptor mRNA from 5 rat tissues. A complete series of overlapping antisense [32P]RNA probes was prepared from plasmids containing segments of a full-length rat insulin-receptor cDNA, and probes were hybridized individually in solution with polyadenylated RNA from rat brain, kidney, liver, skeletal muscle, and spleen. After ribonuclease digestion, probe fragments were analyzed by denaturing gel electrophoresis. Tissue-specific cleavage of the mRNA:RNA probe heteroduplex, attributable to sequence mismatch, was detected only for a single probe covering the distal alpha-subunit, as expected for the known alternative splicing of rat insulin-receptor mRNA in this region. No evidence for additional heterogeneity of the receptor mRNA coding region was observed in the 5 tissues studied either by RNA heteroduplex mapping or, in some areas, by regional amplification of insulin-receptor cDNA. Cell-free translation of size-fractionated polyadenylated RNA was used to further demonstrate that each of the major insulin-receptor mRNA size classes in rat liver contained both forms of the alternatively spliced mRNA transcripts and produced two insulin-proreceptor polypeptides. These results suggest that heterogeneity of the insulin-receptor mRNA coding region affecting the receptor primary structure is limited to the distal alpha-subunit near the subunit cleavage site.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1977

Origin of replication, oriC, of the Escherichia coli chromosome: mapping of genes relative to R.EcoRI cleavage sites in the oriC region.

A precise genetic-physical map of the tna-ilv region at 82 min on the genetic map of E. coli is obtained through deletion mapping and analysis by restriction endonuclease EcoRI of plasmids, derived from an F' carrying the genes between aroE and ilv. A locus, designated het, which in its diploid state results in slow growth and heterogeneity of cell size due to distorted cell division, maps between bglB and asn, 30-45 kb counterclockwise of ilv. The pattern of R.EcoRI cleavage sites in the het region is identical with the pattern obtained by Marsh and Worcel (1977) who analyzed DNA labeled preferentially in the region of the DNA replication origin (oriC). We suggest that oriC is identical with the het site and that it can be allocated to a position 32 kb counterclockwise of the ilv operon.

Chromosome Mapping↗
PubMed1985

Variation in foot-and-mouth disease virus isolates in Kenya: an examination of field isolates by T1 oligonucleotide fingerprinting.

Ribonuclease T1 oligonucleotide maps of strains of 4 of the endemic serotypes of foot-and-mouth disease virus isolated in Kenya between 1964 and 1982 have been compared with data obtained in complement-fixation and neutralization tests. There was a continual change in the oligonucleotide maps obtained for all the serotypes examined. This genetic heterogeneity was generally associated with antigenic variation. Viruses isolated during the 12-month course of an epidemic of the SAT 1 serotype showed few changes in their oligonucleotide fingerprints, and were serologically related. These maps form a data base that will be useful in future epidemiological studies on the maintenance and spread of foot-and-mouth disease virus in this region.

Animals↗
PubMed2000

A new locus for autosomal recessive spastic paraplegia associated with mental retardation and distal motor neuropathy, SPG14, maps to chromosome 3q27-q28.

Hereditary spastic paraplegias (HSPs), a group of neurodegenerative disorders that cause progressive spasticity of the lower limbs, are characterized by clinical and genetic heterogeneity. To date, three loci for autosomal recessive HSP have been mapped on chromosomes 8p, 16q, and 15q. After exclusion of linkage at these loci, we performed a genomewide search in a consanguineous Italian family with autosomal recessive HSP complicated by mild mental retardation and distal motor neuropathy. Using homozygosity mapping, we obtained positive LOD scores for markers on chromosome region 3q27-q28, with a maximum multipoint LOD score of 3.9 for marker D3S1601. Haplotype analysis allowed us to identify a homozygous region (4.5 cM), flanked by markers D3S1580 and D3S3669, that cosegregates with the disease. These data strongly support the presence, on chromosome 3q27-28, of a new locus for complicated recessive spastic paraplegia, which we have named "SPG14."

Adult↗
PubMed1994

The t(X;18)(p11.2;q11.2) translocation found in human synovial sarcomas involves two distinct loci on the X chromosome.

A high proportion of synovial sarcomas contain the reciprocal translocation t(X;18)(p11.2;q11.2). We have previously localized the breakpoint on the X chromosome between the X chromosome marker DXS255 and an ornithine aminotransferase (OAT) pseudogene region designated OATL2. Subsequently by fluorescence in situ hybridization (FISH) we provided evidence that YACs corresponding to the OATL2 locus spanned the break-point. In order to confirm the position of this breakpoint cosmids corresponding to the OATL2 region were isolated. Most of these cosmids mapped to four cosmid contigs designated C1-C4. Analysis of two contigs, C1- and C4, using FISH established that in four of six synovial sarcomas examined the breakpoint occurs between these two contigs: C1 lies distal to the break-point while C4 is proximal. In contrast we provide evidence that the breakpoint in the remaining two tumours mapped to a second pseudogene region called OATL1 that is telomeric to the OATL2 locus. This heterogeneity of the breakpoint position on the X chromosome explains why in previous mapping studies there have been discrepancies between the results obtained by different laboratories.

Chromosome Mapping↗
PubMed2004

Heterogeneity of action potential durations in isolated mouse left and right atria recorded using voltage-sensitive dye mapping.

An imaging system for di-4-ANEPPS (4-[beta-[2-(di-n-butylamino)-6-naphthylvinyl]pyridinium]) voltage-sensitive dye recordings has been adapted for recording from an in vitro mouse heart preparation that consists of both atria in isolation. This approach has been used to study inter- and intra-atrial activation and conduction and to monitor action potential durations (APDs) in the left and right atrium. The findings from this study confirm some of our previous findings in isolated mouse atrial myocytes and demonstrate that many electrophysiological properties of mouse atria closely resemble those of larger mammals. Specifically, we made the following observations: 1) Activation in mouse atria originates in the sinoatrial node and spreads into the right atrium and, after a delay, into the left atrium. 2) APD in the left atrium is shorter than in the right atrium. 3) Sites in the posterior walls have longer APDs than sites in the atrial appendages. 4) Superfusion of this preparation with 4-aminopyridine and tetraethylammonium resulted in increases in APD, consistent with their inhibitory effects on the K+ currents known to be expressed in mouse atria. 5) The muscarinic agonist carbachol shortened APD in all areas of the preparation, except the left atrial appendage, in which carbachol had no statistically significant effect on APD. These results validate a new approach for monitoring activation, conduction, and repolarization in mouse atria and demonstrate that the physiological and pharmacological properties of mouse atria are sufficiently similar to those of larger animals to warrant further studies using this preparation.

Action Potentials↗
PubMed2000

The tprK gene is heterogeneous among Treponema pallidum strains and has multiple alleles.

We have previously shown that the TprK antigen of T. pallidum, Nichols strain, is predominantly expressed in treponemes obtained 10 days after infection and that the hydrophilic domain of TprK is a target of opsonic antibodies and confers significant protection against homologous challenge. The T. pallidum genome sequence reported the presence of a single copy of the tprK gene in the Nichols strain. In the present study we demonstrate size heterogeneity in the central portions of the TprK hydrophilic domains of 14 treponemal isolates. Sequence analysis of the central domains and the complete open reading frames (ORFs) of the tprK genes confirms this heterogeneity. Further, multiple tprK sequences were found in the Nichols-defined tprK locus in three isolates (Sea 81-4, Bal 7, and Bal 73-1). In contrast, only a single tprK sequence could be identified in this locus in the Nichols strain. Alignment of the DNA and deduced amino acid sequences of the whole tprK ORFs shows the presence of seven discrete variable domains flanked by highly conserved regions. We hypothesize that these heterogeneous regions may be involved in antigenic heterogeneity and, in particular, evasion of the immune response. The presence of different tprK alleles in the tprK locus strongly suggests the existence of genetically different subpopulations within treponemal isolates.

Alleles↗
PubMed2003

Intracellular calcium handling heterogeneities in intact guinea pig hearts.

Regional heterogeneities of ventricular repolarizing currents and their role in arrhythmogenesis have received much attention; however, relatively little is known regarding heterogeneities of intracellular calcium handling. Because repolarization properties and contractile function are heterogeneous from base to apex of the intact heart, we hypothesize that calcium handling is also heterogeneous from base to apex. To test this hypothesis, we developed a novel ratiometric optical mapping system capable of measuring calcium fluorescence of indo-1 at two separate wavelengths from 256 sites simultaneously. With the use of intact Langendorff-perfused guinea pig hearts, ratiometric calcium transients were recorded under normal conditions and during administration of known inotropic agents. Ratiometric calcium transients were insensitive to changes in excitation light intensity and fluorescence over time. Under control conditions, calcium transient amplitude near the apex was significantly larger (60%, P < 0.01) compared with the base. In contrast, calcium transient duration was significantly longer (7.5%, P < 0.03) near the base compared with the apex. During isoproterenol (0.05 microM) and verapamil (2.5 microM) administration, ratiometric calcium transients accurately reflected changes in contractile function, and, the direction of base-to-apex heterogeneities remained unchanged compared with control. Ratiometric optical mapping techniques can be used to accurately quantify heterogeneities of calcium handling in the intact heart. Significant heterogeneities of calcium release and sequestration exist from base to apex of the intact heart. These heterogeneities are consistent with base-to-apex heterogeneities of contraction observed in the intact heart and may play a role in arrhythmogenesis under abnormal conditions.

Animals↗
PubMedDate not supplied

Heterogeneity analysis of Gd-DTPA uptake: improvement in breast lesion differentiation.

PURPOSE: The aim of this study was to assess whether lesion heterogeneity through pixel-by-pixel analysis of contrast-enhanced MR parameter maps would improve breast lesion differentiation. METHOD: Forty-nine female patients with primary tumors of the breast were imaged using contrast-enhanced MRI. The rate of transfer of contrast medium between the lesion and plasma was calculated via compartmental modeling over semiautomatically delineated regions of interest. The distributions of transfer rate values were subdivided into 10 segments for each lesion. The rate of change of the statistical moments of the transfer rate measured over the 10 segments allowed a quantitative measure of heterogeneity. RESULTS: In this patient group of 25 malignant and 25 benign lesions, improved differentiation was achieved by using a measure of lesion heterogeneity. The sensitivity and specificity obtained were 88 and 88%, respectively, compared with 84 and 76% when using the mean value of the transfer rate coefficient. CONCLUSION: Pixel-by-pixel analysis of contrast medium transfer rate maps allows the examination of lesion heterogeneity and offers improved lesion differentiation. The new method used to quantify lesion heterogeneity relies on the manner in which the exchange rate parameter varies when calculated over different segments of the distribution.

Adult↗
PubMed1999

Evidence for linkage of adolescent-onset idiopathic generalized epilepsies to chromosome 8-and genetic heterogeneity.

Several loci and candidate genes for epilepsies or epileptic syndromes map or have been suggested to map to chromosome 8. We investigated families with adolescent-onset idiopathic generalized epilepsy (IGE), for linkage to markers spanning chromosome 8. The IGEs that we studied included juvenile myoclonic epilepsy (JME), epilepsy with only generalized tonic-clonic seizures occurring either randomly during the day (random grand mal) or on awakening (awakening grand mal), and juvenile absence epilepsy (JAE). We looked for a gene common to all these IGEs, but we also investigated linkage to specific subforms of IGE. We found evidence for linkage to chromosome 8 in adolescent-onset IGE families in which JME was not present. The maximum multipoint LOD score was 3.24 when family members with IGE or generalized spike-and-waves (SW) were considered affected. The LOD score remained very similar (3.18) when clinically normal family members with SW were not considered to be affected. Families with either pure grand mal epilepsy or absence epilepsy contributed equally to the positive LOD score. The area where the LOD score reaches the maximum encompasses the location of the gene for the beta3-subunit of the nicotinic acetylcholine receptor (CHRNB3), thus making this gene a possible candidate for these specific forms of adolescent-onset IGE. The data excluded linkage of JME to this region. These results indicate genetic heterogeneity within IGE and provide no evidence, on chromosome 8, for a gene common to all IGEs.

Adolescent↗
PubMed2004

A novel locus for pure recessive hereditary spastic paraplegia maps to 10q22.1-10q24.1.

The hereditary spastic paraplegias (HSPs) are a group of clinically and genetically heterogeneous disorders characterized by progressive lower-limb spasticity. In this study, we performed linkage analysis on an autosomal recessive pure HSP family and mapped the disease to chromosome 10q22.1-10q24.1, a locus partially overlapping the existing SPG9 locus. We have either identified a novel locus for pure recessive HSP (SPG27), or we have found the first case of allelic disorders with different mode of inheritance in HSP. If the disorders are indeed allelic, our results have reduced the SPG9 interval by 3Mb with D10S536 and D10S1758 as flanking markers.

Chromosome Mapping↗