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PubMedDate not supplied

Genomic relatedness of five equine rotavirus strains with different G serotype and P type specificities.

Overall genomic relatedness among five equine rotavirus strains and their relatedness to representative human and animal rotavirus strains were investigated by RNA-RNA hybridization tests. The genomes of strains FI-14, FI-23 and H2 were highly related to one another. Strain L338 had only a low degree of genomic relatedness to the other four equine rotavirus strains. Strain H1 also showed little genetic relatedness to the other equine strains. The genome of the strain H1, however, was highly related to those of porcine rotavirus strains OSU, Gottfried and YM. Genomic relatedness of four equine rotavirus strains (FI-14, FI-23, H2 and L338) to human and other animal rotavirus strains was low, whereas several RNA segments of strain H1 showed a relatedness to those of human strain Wa.

Animals↗
PubMed2004

From genomic advances to public health benefits: the unbearable lightness of being stuck.

Genetic determinants of common human diseases are still poorly understood. Due to large investments, many small successes have been made and the research field is rapidly expanding. However, genetic susceptibility variants showing repeatable associations with common diseases are usually of small effect. They are therefore unlikely to individually explain substantial share of disease burden in any community or provide new insights into disease pathogenesis that could lead to development of new drugs effective in considerable portion of the disease cases in a population. Genetic architecture of common diseases is beginning to reveal an incredible diversity of potential genetic causes that act through somewhat limited number of mechanisms with important contribution of environmental interactions. In light of these findings, we present current understanding of genetic architecture of a spectrum of human diseases. We address the encountered problems in susceptibility gene identification, review the success of leading gene identification strategies and discuss current prospects for translating genomic advances into measurable public health benefits.

Genetic Predisposition to Disease↗
PubMed2005

Chemical genetics and genomics and drug discovery. Highlights from the Society for Medicines Research symposium held Thursday March 10, 2005, in London, United Kingdom.

The SMR Symposium Chemical Genetics and Genomics: What Are They and Are They Helping Drug Discovery was held on March 10, 2005 at the National Heart and Lung Institute, Imperial College London. The conference program brought together an international line up of speakers representing academia, biotechnology and large pharmaceutical companies to discuss a variety of drug discovery strategies, falling under the umbrella terminology Chemical Genomics and Genetics. Highlights of the meeting are discussed.

Drug Design↗
PubMed1987

The polymorphic locus for glycogen storage disease VI (liver glycogen phosphorylase) maps to chromosome 14.

Human liver glycogen phosphorylase deficiency, also known as glycogen storage disease type VI (GSD VI) or Hers disease, is characterized by hepatomegaly and reduced or absent glycogenolytic response to the injection of glucagon. The recently isolated cDNA encoding the liver isozyme of glycogen phosphorylase was used to map the gene and identify restriction-fragment polymorphisms in normal Caucasians as a prerequisite for detecting linked GSD VI abnormalities. Results of restriction-enzyme analysis using a downstream fragment of the liver glycogen phosphorylase cDNA indicated the existence of a single gene copy per haploid genome. Hybridization of this downstream liver phosphorylase probe to dual laser-excited, sorted human chromosomes localized the gene to human chromosome 14. When the downstream probe was tested on genomic DNA cut with seven different restriction enzymes, a single MspI restriction-fragment-length polymorphism (RFLP) was observed in a single individual. In contrast, similar Southern blots performed with an upstream portion of the cDNA encoding liver phosphorylase revealed common RFLPs for four of eight enzymes tested, with minor polymorphic allele frequencies ranging from 33% to 44%. One of the four enzymes (TaqI) revealed two independent polymorphisms. If random distribution of these haplotypes among normal and disease loci, is assumed, approximately 92% of fetuses at risk for Hers disease will be informative when tested with the upstream liver phosphorylase probe.

Chromosome Mapping↗
PubMed2003

Two genome-wide linkage disequilibrium screens in Scandinavian multiple sclerosis patients.

We report the first two genome-wide screens for linkage disequilibrium between putative multiple sclerosis (MS) susceptibility genes and genetic markers performed in the genetically homogenous Scandinavian population, using 6000 microsatellite markers and DNA pools of approximately 200 MS cases and 200 controls in each screen. Usable data were achieved from the same 3331 markers in both screens. Nine markers from eight genomic regions (1p33, 3q13, 6p21, 6q14, 7p22, 9p21, 9q21 and Xq22) were identified as potentially associated with MS in both screens.

Alleles↗
PubMed1996

Survey of mycoplasmal bacteremia detected in children by polymerase chain reaction.

To determine whether mycoplasmal bacteremia occurs during ordinary or complicated diseases due to M. pneumoniae (and if so, how frequently), we used polymerase chain reaction (PCR) to detect M. pneumoniae in serum samples. The PCR primers used were modified for nested amplification. The genome of this organism was detected in 1 of the 25 patients with pneumonia and 10 of the 17 patients without pneumonia (P < .001, chi test). The genome was detected more frequently in patients who had encephalitis of which the neurological onset was within 7 days of the onset of fever rather than later. We hypothesize that mycoplasmal bacteremia occurs more frequently than previously appreciated, specifically in the absence of pneumonia, and that certain types of complications (e.g., encephalitis of early onset) are associated with its occurrence.

Adolescent↗
PubMed2025

KpSC-ID: a multiplex real-time PCR assay for the simultaneous detection of the Klebsiella pneumoniae species complex and specific identification of Klebsiella pneumoniae, Klebsiella quasipneumoniae and Klebsiella variicola.

The Klebsiella pneumoniae species complex (KpSC) comprises five closely related bacterial species, namely Klebsiella pneumoniae, Klebsiella quasipneumoniae, Klebsiella variicola, Klebsiella quasivariicola and Klebsiella africana. The KpSC is ubiquitous in the environment and is also an important human pathogen, particularly associated with healthcare-associated infections. The accurate detection and differentiation of the KpSC is challenging owing to the close phenotypic and genotypic identity (93-95%&#x2009;average nucleotide identity) shared between these members. Current diagnostic assays either fail to detect and identify all KpSC members or misidentify some KpSC members as K. pneumoniae sensu stricto. It is currently estimated that ~20% of human infections are caused by members of the KpSC other than K. pneumoniae. This leads to underreporting of some KpSC members in both clinical and environmental settings, which impacts our understanding of the importance of each species. Furthermore, it limits our understanding of the global and local epidemiological impact of some members of the KpSC. In this study, a rapid multiplex real-time PCR assay (KpSC-ID) was designed and developed to detect all KpSC members while simultaneously identifying the predominant human pathogens K. pneumoniae, K. quasipneumoniae and K. variicola. Assay performance was verified in silico using a panel of over 1,000 publicly available genome sequences and experimentally validated using a panel of genomic DNA extracted from 54 Enterobacteriaceae. The assay displayed excellent specificity against over 1,000 genome sequences tested in silico. During in vitro validation, the pan-KpSC assay detected each (29/29) KpSC species and strains tested. For the species-specific assays, 100% specificity was demonstrated in the K. pneumoniae, K. quasipneumoniae and K. variicola assays, respectively. Sensitivity of 10 genomic equivalents was demonstrated for each assay. Ultimately, the diagnostic assay developed in this study can improve our understanding of the significance of KpSC members, which is important when investigating their routes of transmission and epidemiology.

Klebsiella↗
PubMed2005

Primers for clinical detection of Paracoccidioides brasiliensis.

From a 0.72-kb fragment universally generated in Paracoccidioides brasiliensis strains, primers were designed and tested on genomic DNA of this and other pathogenic fungi. They were specific and highly sensitive for P. brasiliensis DNA. Positive results were obtained when these were tested in clinical samples.

Adult↗
PubMed2005

The influenza A virus M2 cytoplasmic tail is required for infectious virus production and efficient genome packaging.

The M2 integral membrane protein encoded by influenza A virus possesses an ion channel activity that is required for efficient virus entry into host cells. The role of the M2 protein cytoplasmic tail in virus replication was examined by generating influenza A viruses encoding M2 proteins with truncated C termini. Deletion of 28 amino acids (M2Stop70) resulted in a virus that produced fourfold-fewer particles but >1,000-fold-fewer infectious particles than wild-type virus. Expression of the full-length M2 protein in trans restored the replication of the M2 truncated virus. Although the M2Stop70 virus particles were similar to wild-type virus in morphology, the M2Stop70 virions contained reduced amounts of viral nucleoprotein and genomic RNA, indicating a defect in vRNP packaging. The data presented indicate the M2 cytoplasmic tail plays a role in infectious virus production by coordinating the efficient packaging of genome segments into influenza virus particles.

Animals↗
PubMed2006

Nonlinear tests for genomewide association studies.

As millions of single-nucleotide polymorphisms (SNPs) have been identified and high-throughput genotyping technologies have been rapidly developed, large-scale genomewide association studies are soon within reach. However, since a genomewide association study involves a large number of SNPs it is therefore nearly impossible to ensure a genomewide significance level of 0.05 using the available statistics, although the multiple-test problems can be alleviated, but not sufficiently, by the use of tagging SNPs. One strategy to circumvent the multiple-test problem associated with genome-wide association tests is to develop novel test statistics with high power. In this report, we introduce several nonlinear tests, which are based on nonlinear transformation of allele or haplotype frequencies. We investigate the power of the nonlinear test statistics and demonstrate that under certain conditions, some nonlinear test statistics have much higher power than the standard chi2-test statistic. Type I error rates of the nonlinear tests are validated using simulation studies. We also show that a class of similarity measure-based test statistics is based on the quadratic function of allele or haplotype frequencies, and thus they belong to nonlinear tests. To evaluate their performance, the nonlinear test statistics are also applied to three real data sets. Our study shows that nonlinear test statistics have great potential in association studies of complex diseases.

Acyltransferases↗
PubMed1997

Improvement of the power to detect complex disease genes by regional inference procedures.

Theoretical studies and simulations suggest that "true" linkage peaks are longer than "false" peaks of the same significance level. Our goal for this study was to improve the power of linkage detection by using a regional criterion for linkage; that is, requiring more than one p-value in a given region to pass a threshold. We tested this method by determining the power and type I error for finding the underlying loci on chromosomes 5 and 8 that contribute to the variability of Q1 (after adjusting Q1 for covariates). We used the Haseman-Elston sib-pair statistic to test for linkage of all 367 markers to the adjusted Q1 trait in 100 replicates. We compared the regional inference procedure to that of the Lander and Kruglyak (LK) criteria for significant and suggestive linkage. For example, the power to detect the chromosome 5 locus was 48% for the LK criterion for significant linkage (p < or = 0.0001) and 63% when we required two p-values out of five consecutive ones to be < or = 0.001. The type I error was not more than 5% for either method (2% for the LK and 5% for our criterion). This suggests that using a criterion based on length may improve the power of linkage detection for complex traits.

Chromosome Mapping↗
PubMed2026

The costs of genomic newborn screening in England: A micro-costing analysis from the Generation Study.

PURPOSE: This study estimates the total cost per newborn of delivering genomic newborn screening (gNBS) within the Genomics England-led Generation Study. METHODS: A time-driven activity-based costing approach was used to estimate gNBS costs from recruitment to confirmatory testing. Resource use data were obtained through document review, semi-structured interviews with study staff, and direct observation across six English National Health Service Trusts. Inputs were categorized as labor, consumables, or equipment, with unit costs sourced from published pay scales, catalogs, or literature. Equipment costs were annualized at a discount rate of 3.5%. All costs were estimated in 2025 Great British Pounds (&#xa3;) from the healthcare providers perspective, including overheads and data storage. A one-way deterministic sensitivity analysis was conducted, varying key cost parameters (&#xb1;20%) and testing alternative delivery scenarios. RESULTS: gNBS costs &#xa3;1208 per newborn, with sequencing comprising 58% of the total costs, mainly consumables. The cost was reduced by 20% to &#xa3;963 when excluding research-specific recruitment and consent activities to reflect the delivery of gNBS as part of routine clinical care. CONCLUSION: This study provides an estimate of gNBS costs, highlighting sequencing as the main cost driver. Combined with evidence on outcomes and health care utilization, these findings will inform future cost-effectiveness analyses, supporting policy decisions regarding national implementation in England.

Neonatal Screening↗
PubMed2003

Updated results of the United Kingdom linkage-based genome screen in multiple sclerosis.

In 1996, we reported the results of a linkage genome screen based on 129 UK multiple sclerosis multiplex families, together with follow-up typing of interesting regions in a second set of families. We have now completed screening the remainder of the genome in this second set of United Kingdom families by typing 242 microsatellite markers. These data have been analysed together with those previously published, resulting in the largest currently available whole genome linkage dataset from a single population in multiple sclerosis. Four new regions of potential linkage (chromosomes 10p, 11p, 19p, 20p) not previously described were identified. In the combined analysis of all 226 families, a total of five regions of suggestive linkage are seen (chromosomes 1p, 6p, 14q, 17q, Xq), where only one would have been expected to occur by chance alone.

Alleles↗