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PubMed2004

Genetic analysis of 2299delG and C759F mutations (USH2A) in patients with visual and/or auditory impairments.

The most common mutation in the USH2A gene (Usherin), 2299delG, causes both typical Usher (USH) syndrome type II and atypical USH syndrome, two autosomal recessive disorders, characterised by moderate to severe sensorineural hearing loss and retinitis pigmentosa (RP). Furthermore, the C759F mutation in the USH2A gene has been described in 4.5% of patients with nonsyndromic recessive RP. We have investigated the presence of the 2299delG and/or the C759F mutations in 191 unrelated Spanish patients with different syndromic and nonsyndromic retinal diseases, or with nonsyndromic hearing impairment. The 2299delG mutation was observed in patients with clinical signs of USHII or of atypical USH syndrome, whereas the C759F mutation, regardless of being associated with the 2299delG mutation or not, was identified in cases with nonsyndromic RP, as well as in patients with RP associated with a variability of hearing impairment. The comparative analysis of both phenotypic and genotypic data supports the hypothesis that sensorineural hearing loss in patients with RP may depend on the nature and on the association of the USH2A allele variants present.

Alleles↗

PubMed1999

Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov.

The genus Shewanella has been studied since 1931 with regard to a variety of topics of relevance to both applied and environmental microbiology. Recent years have seen the introduction of a large number of new Shewanella-like isolates, necessitating a coordinated review of the genus. In this work, the phylogenetic relationships among known shewanellae were examined using a battery of morphological, physiological, molecular and chemotaxonomic characterizations. This polyphasic taxonomy takes into account all available phenotypic and genotypic data and integrates them into a consensus classification. Based on information generated from this study and obtained from the literature, a scheme for the identification of Shewanella species has been compiled. Key phenotypic characteristics were sulfur reduction and halophilicity. Fatty acid and quinone profiling were used to impart an additional layer of information. Molecular characterizations employing small-subunit 16S rDNA sequences were at the limits of resolution for the differentiation of species in some cases. As a result, DNA-DNA hybridization and sequence analyses of a more rapidly evolving molecule (gyrB gene) were performed. Species-specific PCR probes were designed for the gyrB gene and used for the rapid screening of closely related strains. With this polyphasic approach, in addition to the ten described Shewanella species, two new species, Shewanella oneidensis and 'Shewanella pealeana', were recognized; Shewanella oneidensis sp. nov. is described here for the first time.

Animals↗

PubMed2002

HLA and cytokine gene polymorphisms in biliary atresia.

BACKGROUND/AIMS: Extrahepatic biliary atresia remains one of the major hepatic causes of death in early childhood. Though a number of hypotheses have been developed to account for this disease, its aetiopathogenesis is poorly understood. One possibility is that this is an immune mediated disease which occurs following either toxic or infectious insult in a genetically susceptible host. Earlier studies suggested weak HLA associations but these remain unconfirmed. More recently studies of viral and autoimmune liver disease have begun to investigate non-MHC immunoregulatory gene polymorphisms. METHODS: In the present study we used molecular genotyping to investigate selected HLA A, B, DRB1, DQA1, DQB1 and DPB1 alleles as well as polymorphisms in the interleukin-1 gene family, interleukin-10 promoter sequence and tumour necrosis factor alpha promoter genes in 101 children referred for surgical assessment with extra hepatic biliary atresia. Genotyping data were compared with those of 134 racially and geographically matched healthy adult health care workers. RESULTS AND CONCLUSIONS: Overall there were no statistically significant differences in the distribution of any of the genes tested comparing patients and controls. These data suggest that biliary atresia is not an HLA-associated disease and that polymorphisms in both the interleukin-1 and interleukin-10 genes are not risk factors for this disease.

Adult↗

PubMed2000

SNP genotyping by combination of 192-well MADGE, ARMS and computerized gel image analysis.

A new modification of the microplate array diagonal gel electrophoresis (MADGE) system accommodates the dual amplification refractory mutation system (ARMS) products of 96 samples on one 192-well gel. Simultaneous electrophoresis of a number of horizontal ARMS-MADGE gels achieves high throughput. Gels are imaged digitally, here using the FluorImager 595 fluorescent scanning system. Customized software by Phoretix enables rapid computerized calling of band patterns in ARMS-MADGE arrays, in which the two wells receiving a pair of allele-specific assays for a single template are juxtaposed to form one virtual track, with genotype data exported directly into Microsoft Excel for statistical analysis. An ARMS assay of the A/T base change at the -23/HphI RFLP in the insulin gene promoter, which initiates from 2.5 ng template DNA, was used here to demonstrate this improved general approach for population SNP analyses.

Electrophoresis↗

PubMed2006

Genetic variation and relationships among eight Indian riverine buffalo breeds.

Twenty-seven microsatellite loci were used to define genetic variation and relationships among eight Indian riverine buffalo breeds. The total number of alleles ranged from 166 in the Toda breed to 194 each in the Mehsana and the Murrah. Significant departures from the Hardy-Weinberg equilibrium were observed for 26 locus-breed combinations due to heterozygote deficiency. Breed differentiation was analysed by estimation of F(ST) index (values ranging from 0.75% to 6.00%) for various breed combinations. The neighbour-joining tree constructed from chord distances, multidimensional scaling (MDS) display of F(ST) values and Bayesian clustering approach consistently identified the Toda, Jaffarabadi, and Pandharpuri breeds as one lineage each, and the Bhadawari, Nagpuri, Surati, Mehsana and Murrah breeds as admixture. Analysis of molecular variance refuted the earlier classification of these breeds proposed on the basis of morphological and geographical parameters. The Toda buffaloes, reared by a tribe of the same name, represent an endangered breed from the Nilgiri hills in South India. Divergence time of the Toda buffaloes from the other main breeds, calculated from Nei's standard genetic distances based on genotyping data on seven breeds and 20 microsatellite loci, suggested separation of this breed approximately 1800-2700 years ago. The results of the present study will be useful for development of rational breeding and conservation strategies for Indian buffaloes.

Animals↗

PubMed2006

Smoking and the platelet fibrinogen receptor glycoprotein IIb/IIIA PlA1/A2 polymorphism interact in the risk of lacunar stroke and midterm survival.

BACKGROUND AND PURPOSE: Smoking, increased fibrinogen levels, and platelet activation are related to the risk of ischemic stroke. The platelet fibrinogen receptor glycoprotein (Gp) IIb/IIIa Pl(A1/A2) polymorphism affects the binding of platelets to fibrinogen and is suggested to interact with smoking. METHODS: We explored the association of smoking and the Pl(A1/A2) polymorphism with ischemic stroke and survival in the Stroke Aging Memory cohort, comprising 486 consecutive patients (55 to 85 years old) who were analyzed 3 months after an ischemic stroke and followed up for 15 months. Stroke subtype determined by magnetic resonance imaging and GpIIb/IIIa Pl(A1/A2) genotype data were available for 272 patients. RESULTS: In multivariate analysis, smoking was the only factor related to the risk of lacunar infarcts (odds ratio [OR]=1.87, 95% CI=1.05 to 3.31; P=0.033), and it was also a predictor of death (n=24, 8.8%) at 15 months (OR=5.13, 95% CI=1.61 to 16.36; P=0.006), along with age (OR=1.10, 95% CI=1.01 to 1.19; P=0.008). The GpIIb/IIIa Pl(A1/A2) polymorphism alone showed no association with stroke subtype or survival. However, there was a smoking-by-genotype association with the risk of lacunar infarcts (OR=2.10, 95% CI=0.90 to 4.89; P=0.087) and with survival (OR=2.78, 95% CI=0.89 to 8.61; P=0.077). Among younger (55 to 69 years) stroke patients, smokers carrying the Pl(A2) allele were at a higher (OR=5.81, 95% CI=1.26 to 26.80; P=0.024) risk of lacunar infarcts than noncarrier smokers (OR=3.12, 95% CI=1.06 to 9.24; P=0.039). The effect of Pl(A2) and smoking combined on survival was also stronger (OR=8.86, 95% CI=1.68 to 46.55; P=0.010) than the effect of smoking alone (OR=5.06, 95% CI=1.20 to 21.35; P=0.027). CONCLUSIONS: Our results indicate that prothrombotic genetic factors may interact with smoking by modifying the stroke phenotype and affecting midterm survival.

Age Distribution↗

PubMed2000

Multiple interacting gene products may influence susceptibility to malignant hyperthermia.

Malignant hyperthermia (MH) is a potentially lethal disorder triggered in susceptible individuals on exposure to common anaesthetic agents. Crises reflect the consequences of disturbed skeletal muscle calcium homeostasis. MH is an autosomal dominant, genetically heterogeneous trait. Defects in a single major gene have been assumed to determine susceptibility status in individual families. However, in some pedigrees phenotypic and genotypic data are discordant. One explanation, in contrast to the current genetic model, is that susceptibility is dependent upon the effects of more than one gene. Using the transmission disequilibrium test we assessed the involvement of 8 MH candidate loci (RYR1, CACNA1S, CACNA2D1, MHS4 at 3q13.1, MHS6 at 5p, LIPE, DM1, dystrophin) by analysis of data from 130 MH nuclear families. Results suggested that variations in more than one gene may influence MH susceptibility in single families.

Anesthetics, Inhalation↗

PubMed2006

Mouse Phenome Database (MPD).

The Mouse Phenome Database (MPD; http://www.jax.org/phenome) is a repository of phenotypic and genotypic data on commonly used and genetically diverse inbred strains of mice. Strain characteristics data are contributed by members of the scientific community. Electronic access to centralized strain data enables biomedical researchers to choose appropriate strains for many systems-based research applications, including physiological studies, drug and toxicology testing and modeling disease processes. MPD provides a community data repository and a platform for data analysis and in silico hypothesis testing. The laboratory mouse is a premier genetic model for understanding human biology and pathology; MPD facilitates research that uses the mouse to identify and determine the function of genes participating in normal and disease pathways.

Animals↗

PubMed2001

PCR fingerprinting of Candida albicans associated with chronic hyperplastic candidosis and other oral conditions.

The purpose of this study was to genotype strains of Candida albicans to determine whether specific types were associated with chronic hyperplastic candidosis (CHC). A total of 67 candidal isolates from CHC patients (n = 17) and from patients with other oral conditions (n = 21) were genotyped by PCR fingerprinting employing two interrepeat primer combinations (1245 and 1246 primers or 1251 primer) and a single minisatellite-specific M13 primer. The most suitable primer for fingerprint analysis was found to be primer 1251, yielding well-resolved banding patterns. For the 67 isolates tested, PCR fingerprinting delineated 25 (1245 and 1246 primers), 27 (1251 primer), and 25 (M13 primer) profiles. The majority of C. albicans isolates from multiple sites within the mouth produced identical profiles (six out of nine subjects examined). For patients for whom a series of longitudinal isolates was available, strain persistence for up to 7 years was evident for five out of eight individuals, despite episodes of antifungal therapy. Computer-assisted comparison of the interrepeat PCR fingerprints identified seven distinct profiles that were shared among isolates from different individuals. However, no association was evident among isolates of C. albicans from specific clinical conditions. Eight isolates that were initially identified as C. albicans but having atypical PCR profiles were later confirmed as Candida dubliniensis. In conclusion, the genotypic data do not indicate clonal restriction of C. albicans with respect to CHC. Furthermore, these results have demonstrated that in the majority of individuals, colonizing populations of C. albicans are clonal in nature and exhibit strain persistence.

Candida albicans↗

PubMed2004

Health sequelae of human cryptosporidiosis in immunocompetent patients.

BACKGROUND: There have been no systematic studies following up the longer term health effects of cases of cryptosporidiosis for which genotype data exist. METHODS: We report a follow-up study of cases of laboratory-confirmed cryptosporidiosis. Case patients were sent a postal questionnaire asking about a wide range of symptoms occurring within 2 months after their initial diagnosis, and control subjects were sent the questionnaire 2 months after they had been recruited to the original study. RESULTS: Completed questionnaires were received from 235 case patients and 232 control subjects. For 111 of the case patients, the species of the infecting strain was known; 61 of these strains were Cryptosporidium hominis (human genotype), and 50 were Cryptosporidium parvum (bovine genotype). Forty percent of the case patients reported recurrence of intestinal symptoms after resolution of the acute stage of illness, irrespective of whether infection was with C. hominis or C. parvum. Reports of joint pain (odds ratio [OR], 2.8), eye pains (OR, 2.44), recurrent headache (OR, 2.10), dizzy spells (OR, 1.69), and fatigue (OR, 3.0) were significantly more common in case patients than in control subjects, but only in people who had experienced C. hominis infection. Joint symptoms experienced by case patients were of longer duration than those experienced by control subjects. CONCLUSIONS: Our results confirm previous reports of a high rate of relapse of gastrointestinal symptoms following recovery from an acute episode of cryptosporidiosis and show that C. hominis but not C. parvum is associated with an increased risk of nonintestinal sequelae. This study demonstrates that the impact of cryptosporidiosis on public health extends beyond that of the acute diarrheal illness and can lead to significant health sequelae.

Adolescent↗

PubMed2001

Burkholderia cepacia genomovar VI, a new member of the Burkholderia cepacia complex isolated from cystic fibrosis patients.

A polyphasic taxonomic study was performed on 23 strains isolated from cystic fibrosis (CF) patients in the USA. These strains were tentatively identified as Burkholderia cepacia, Burkholderia vietnamiensis and Burkholderia or Ralstonia sp. using biochemical tests and 16S rDNA-based PCR assays. Visual comparison of protein profiles indicated that they belonged to a single new group ('group 13'). The polyphasic taxonomic data showed that 18 of these strains represent a new member of the B. cepacia complex, referred to in this report as B. cepacia genomovar VI, whereas the other five strains belonged to Burkholderia multivorans. By means of biochemical tests, B. cepacia genomovar VI strains can be separated from B. cepacia genomovars I and III, Burkholderia stabilis, B. vietnamiensis and Burkholderia gladioli, but not from B. multivorans. Separation of B. cepacia genomovar VI and B. multivorans is possible using AFLP (amplified fragment length polymorphism) fingerprinting and DNA-DNA hybridizations. Retrospective analysis of epidemiological and genotypic data suggests that strains of B. cepacia genomovar VI have been involved in chronic colonization of CF patients and have been spread from person to person.

Bacterial Proteins↗

PubMed1992

Clinical and biological analysis of peripheral T-cell lymphomas: a single institution study.

Peripheral T-cell lymphoma (PTCL) accounts for 15-20% of non-Hodgkin's lymphoma in the Western World. Clinical, histopathologic, phenotypic and genotypic data were received from 33 cases of PTCL referred to our institution. The median age order was 50 years, 78% were males, and 18% had a history of a preceding disorder of the lymphoid system. 60% had stage 4 at diagnosis and B symptoms were also present in 60%. The most frequent sites of extranodal involvement were bone marrow (54%), liver (45%) and skin (33%). Twenty-eight of 33 cases were histologically classified according to the Working Formulation (most in the diffuse mixed and large-cell subgroups) and the Kiel updated system. Phenotypic and genotypic studies of malignant cells showed a considerable heterogeneity with respect to the expression of either T-cell receptor (TCR) alpha beta and gamma delta and pan-T differentiation molecules. Of the studied cases 63% expressed TCR-alpha beta. All five patients with PTCL of the TCR-gamma delta subtype had a peculiar extra-nodal presentation. The vast majority of cases expressed an abnormal T-cell phenotype with respect to the expression of pan-T antigens, including the lack of expression of the TCR-associated CD3 molecule in 2 cases. Rearrangements of the TCR beta and/or delta-chain genes showed clonality in 21 of the 23 studied cases. Twenty-five patients were treated with a multiagent chemotherapy regimen with curative intent and the remainder received a less intensive palliative regimen. Only 9 patients achieved CR (8 of whom had received an anthracycline-containing regimen) and the 4-year survival rate was 25%.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗

PubMed2001

Pendred syndrome, DFNB4, and PDS/SLC26A4 identification of eight novel mutations and possible genotype-phenotype correlations.

Mutations in PDS (SLC26A4) cause both Pendred syndrome and DFNB4, two autosomal recessive disorders that share hearing loss as a common feature. The hearing loss is associated with temporal bone abnormalities, ranging from isolated enlargement of the vestibular aqueduct (dilated vestibular aqueduct, DVA) to Mondini dysplasia, a complex malformation in which the normal cochlear spiral of 2(1/2) turns is replaced by a hypoplastic coil of 1(1/2) turns. In Pendred syndrome, thyromegaly also develops, although affected persons usually remain euthyroid. We identified PDS mutations in the proband of 14 of 47 simplex families (30%) and nine of 11 multiplex families (82%) (P=0.0023). In all cases, mutations segregated with the disease state in multiplex families. Included in the 15 different PDS allele variants we found were eight novel mutations. The two most common mutations, T416P and IVS8+1G>A, were present in 22% and 30% of families, respectively. The finding of PDS mutations in five of six multiplex families with DVA (83%) and four of five multiplex families with Mondini dysplasia (80%) implies that mutations in this gene are the major genetic cause of these temporal anomalies. Comparative analysis of phenotypic and genotypic data supports the hypothesis that the type of temporal bone anomaly may depend on the specific PDS allele variant present.

Abnormalities, Multiple↗

PubMed2006

The controversial association of ABCB1 polymorphisms in refractory epilepsy: an analysis of multiple SNPs in an Irish population.

Controversy has surrounded the reported association of the single nucleotide polymorphism (SNP) C3435T of the ATP-binding cassette subfamily B member 1 (ABCB1, MDR1) gene, with refractory epilepsy. Here we examine this question by: (1) attempting to replicate the original association, (2) assessing the association of other variants in high linkage disequilibrium (LD) with C3435T, and (3) evaluating and comparing our findings with other published studies. We defined drug-responsiveness as seizure freedom or a 50% or more reduction in seizure frequency in the preceding year. Drug resistance was defined as a less than 50% reduction in seizure frequency in the preceding year. We used a combination of map-based (tagging SNPs) and direct sequence-based methods allowing a comprehensive assessment of variation across the associated interval. Genotypic data on 8 SNPs was collected on 440 patients, of whom 242 were drug-responsive and 198 were drug-resistant. We were unable to observe the original association of drug-resistant epilepsy with C3435T, nor any association with other functional variants at SNP or haplotype level in the ABCB1 gene. Evaluation of other attempted replication studies suggest that if the original C3435T association is indeed real, it would appear highly sensitive to the phenotype used. Alternatively, the discrepant results of this and other association attempts may be indicative of the original report of the CC genotype at C3435T in ABCB1 being a false positive finding. Variability in phenotypic descriptions in genetic association studies may partly explain the inconsistency of attempted replications.

ATP Binding Cassette Transporter, Subfamily B↗

PubMed2004

Involvement of fumarate hydratase in nonsyndromic uterine leiomyomas: genetic linkage analysis and FISH studies.

Recently, germline mutations of the fumarate hydratase (FH) gene, in 1q42.1, have been found to be involved in syndromes associated with uterine leiomyomas (ULs). Compelling evidence also supports a genetic liability to develop nonsyndromic UL, although susceptibility genes have not been reported to date. Loss of heterozygosity (LOH) studies have found no or rare evidence of LOH of FH in nonsyndromic UL. However, the karyotypes of these tumors were not reported, and cytogenetic aberrations of 1q42-44 have been observed infrequently in UL. To determine whether FH mutations also may predispose women to developing nonsyndromic UL, we performed a genetic linkage study with DNA from 123 families containing at least one affected sister pair. In addition, to assess the frequency of FH loss specifically in UL with 1q rearrangements, we performed a fluorescence in situ hybridization (FISH) analysis of UL with 1q rearrangements. Analysis of the genotyping data revealed evidence suggestive of linkage to the FH region among study participants who were less than 40 years of age at diagnosis (Zlr 1.7 at D1S547, P = 0.04). FISH results showed that one copy of FH was absent in 9 of 11 ULs. These data indicate that loss of FH might be a significant event in the pathogenesis of a subset of nonsyndromic ULs.

Adult↗

PubMed2005

Agromyces subbeticus sp. nov., isolated from a cave in southern Spain.

An actinomycete, strain Z33(T), was isolated from a cyanobacterial biofilm in the Cave of Bats, near Zuheros (Cordoba, southern Spain). 16S rRNA gene sequence analysis showed that strain Z33(T) formed a distinct phyletic line within the genus Agromyces. This isolate could be readily distinguished from representatives of all recognized Agromyces species on the basis of a broad range of phenotypic characteristics and DNA-DNA relatedness data. Genotypic and phenotypic properties indicate that strain Z33(T) represents a novel species, for which the name Agromyces subbeticus sp. nov. is proposed. The type strain is Z33(T) (=HKI 0340(T)=DSM 16689(T)=NCIMB 14025(T)).

Actinomycetales↗

PubMed2002

A genome-wide linkage analysis of orchard grass-sensitive childhood seasonal allergic rhinitis in Japanese families.

Seasonal allergic rhinitis (SAR) is an inflammatory disease of the nose and eyes that follows sensitization to air-born pollens. We conducted a genome-wide linkage screening of 48 Japanese families (188 members) with orchard grass (OG)-sensitive SAR children (67 affected sib-pairs) in a farming community in central Japan where OG was planted for apple farming and OG pollen is a major cause of SAR. We used the GENEHUNTER program to performed nonparametric multipoint linkage analysis for OG-sensitive SAR as a qualitative trait and for log total serum IgE levels and OG-RAST IgE levels as quantitative traits. Genotyping data of 400 microsatellite markers suggested linkage of SAR to chromosomes 1p36.2, 4q13.3, and 9q34.3 (P < 0.001), linkage of serum total IgE levels to 3p24.1, 5q33.1, 12p13.1, and 12q24.2 (P < 0.001), and linkage of OG-RAST IgE levels to 4p16.1, 11q14.3, and 16p12.3 (P < 0.001). Weak evidence for linkage of SAR to 5q33.1 was also observed (P = 0.01). All these regions, with the exception of 9q34.3, have been previously reported to be linked to asthma and/or atopy. These data suggest that, although loci linked to SAR are likely to be common to asthma, a strong contribution by specific gene(s) to OG-sensitive SAR is unlikely.

Adolescent↗

PubMed2005

Illumina, Inc.

Illumina, Inc., based in San Diego (CA, USA), is a genomics tool company that develops and markets integrated array-based systems and assays for a broad range of applications including genotyping, gene expression and epigenetics. Product offerings range from focused assay sets (up to 1,536 multiplexed assays) to whole-genome analysis (>100,000 assays/sample). Illumina's two microarray platforms, the Sentrix Array Matrix and the Sentrix BeadChip, are characterized by small (3 microm) feature size, dense feature packing (over 10 million features can be deployed on a single microarray) and the ability to analyze, in parallel, multiple samples on the same device. Illumina has developed a spectrum of proprietary assays (GoldenGate, Infinium, and DASL) for application on our microarray platform. These assays have been successfully employed for a number of applications, including collection of the majority of the Phase I genotyping data for the International HapMap Project. Illumina are focusing our activities on extending the applications of the above assays and developing new assays for future products. Illumina's goal is to deliver high-performance, high-throughput solutions that enable researchers to expand experimental scale while reducing the cost of large-scale research.

Gene Expression↗