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PubMed2005

Mega2: data-handling for facilitating genetic linkage and association analyses.

UNLABELLED: Mega2, the manipulation environment for genetic analysis, transparently allows users to process genetic data for family-based or case/control studies accurately and efficiently. In addition to data validation checks, Mega2 provides analysis setup capabilities for a broad choice of commonly used genetic analysis programs, including SimWalk2, ASPEX, GeneHunter, SLINK, SIMULATE, S.A.G.E., SOLAR, Vitesse, Allegro, PREST, PAP, Loki, Merlin and MENDEL. AVAILABILITY: http://watson.hgen.pitt.edu/register/

Chromosome Mapping↗
PubMed2005

Effects of natural selection on interpopulation divergence at polymorphic sites in human protein-coding Loci.

To develop new strategies for searching for genetic associations with complex human diseases, we analyzed 2784 single-nucleotide polymorphisms (SNPs) in 396 protein-coding genes involved in biological processes relevant to cancer and other complex diseases, with respect to gene diversity within samples of individuals representing the three major historic human populations (African, European, and Asian) and with respect to interpopulation genetic distance. Reduced levels of both intrapopulation gene diversity and interpopulation genetic distance were seen in the case of SNPs located within the 5'-UTR and at nonsynonymous SNPs, causing radical changes to protein structure. Reduction of gene diversity at SNP loci in these categories was evidence of purifying selection acting at these sites, which in turn causes a reduction in interpopulation divergence. By contrast, a small number of SNP sites in these categories revealed unusually high genetic distances between the two most diverged populations (African and Asian); these loci may have historically been subject to divergent selection pressures.

Databases, Genetic↗
PubMed2003

The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tags.

Whereas genome sequencing defines the genetic potential of an organism, transcript sequencing defines the utilization of this potential and links the genome with most areas of biology. To exploit the information within the human genome in the fight against cancer, we have deposited some two million expressed sequence tags (ESTs) from human tumors and their corresponding normal tissues in the public databases. The data currently define approximately 23,500 genes, of which only approximately 1,250 are still represented only by ESTs. Examination of the EST coverage of known cancer-related (CR) genes reveals that <1% do not have corresponding ESTs, indicating that the representation of genes associated with commonly studied tumors is high. The careful recording of the origin of all ESTs we have produced has enabled detailed definition of where the genes they represent are expressed in the human body. More than 100,000 ESTs are available for seven tissues, indicating a surprising variability of gene usage that has led to the discovery of a significant number of genes with restricted expression, and that may thus be therapeutically useful. The ESTs also reveal novel nonsynonymous germline variants (although the one-pass nature of the data necessitates careful validation) and many alternatively spliced transcripts. Although widely exploited by the scientific community, vindicating our totally open source policy, the EST data generated still provide extensive information that remains to be systematically explored, and that may further facilitate progress toward both the understanding and treatment of human cancers.

Chromosome Mapping↗
PubMed2006

[Genetic typing of classical swine fever viruses--a review].

Classical swine fever (CSF) is a notifiable disease of domestic pigs and wild boar. It is caused by the highly contagious CSF virus and in its acute form the disease generally results in high morbidity and mortality. Due to the great economical impact an outbreak can cause to the pig industry it is one of the most important swine diseases worldwide. To limit the damage in the case of a new outbreak it is necessary to identify the virus as fast as possible. This information helps epidemiologists to trace the origin of the virus and to follow the virus spread. Genetic typing revealed that CSF virus genotypes, subgroups and types show a regional distribution making it an important tool for epidemiologists. Meanwhile, besides epidemiological data and nucleotide sequences from European isolates, information from isolates from South- and Central America, the Caribbean, Asia and recently from South Africa have become available. The data are stored in a database in the EU Reference Laboratory for CSF, accessible by the WWW (http://viro08.tiho-hanno ver.de). A new module was implemented that allows efficient automated genotyping.

Animals↗
PubMed2003

PubMatrix: a tool for multiplex literature mining.

BACKGROUND: Molecular experiments using multiplex strategies such as cDNA microarrays or proteomic approaches generate large datasets requiring biological interpretation. Text based data mining tools have recently been developed to query large biological datasets of this type of data. PubMatrix is a web-based tool that allows simple text based mining of the NCBI literature search service PubMed using any two lists of keywords terms, resulting in a frequency matrix of term co-occurrence. RESULTS: For example, a simple term selection procedure allows automatic pair-wise comparisons of approximately 1-100 search terms versus approximately 1-10 modifier terms, resulting in up to 1,000 pair wise comparisons. The matrix table of pair-wise comparisons can then be surveyed, queried individually, and archived. Lists of keywords can include any terms currently capable of being searched in PubMed. In the context of cDNA microarray studies, this may be used for the annotation of gene lists from clusters of genes that are expressed coordinately. An associated PubMatrix public archive provides previous searches using common useful lists of keyword terms. CONCLUSIONS: In this way, lists of terms, such as gene names, or functional assignments can be assigned genetic, biological, or clinical relevance in a rapid flexible systematic fashion. http://pubmatrix.grc.nia.nih.gov/

Cell Line, Tumor↗
PubMed2004

Frequent occurrence of recognition site-like sequences in the restriction endonucleases.

BACKGROUND: There are two different theories about the development of the genetic code. Woese suggested that it was developed in connection with the amino acid repertoire, while Crick argued that any connection between codons and amino acids is only the result of an "accident". This question is fundamental to understand the nature of specific protein-nucleic acid interactions. RESULTS: The nature of specific protein-nucleic acid interaction between restriction endonucleases (RE) and their recognition sequences (RS) was studied by bioinformatics methods. It was found that the frequency of 5-6 residue long RS-like oligonucleotides is unexpectedly high in the nucleic acid sequence of the corresponding RE (p < 0.05 and p < 0.001 respectively, n = 7). There is an extensive conservation of these RS-like sequences in RE isoschizomers. A review of the seven available crystallographic studies showed that the amino acids coded by codons that are subsets of recognition sequences were often closely located to the RS itself and they were in many cases directly adjacent to the codon-like triplets in the RS.Fifty-five examples of this codon-amino acid co-localization are found and analyzed, which represents 41.5% of total 132 amino acids which are localized within 8 A distance to the C1' atoms in the DNA. The average distance between the closest atoms in the codons and amino acids is 5.5 +/- 0.2 A (mean +/- S.E.M, n = 55), while the distance between the nitrogen and oxygen atoms of the co-localized molecules is significantly shorter, (3.4 +/- 0.2 A, p < 0.001, n = 15), when positively charged amino acids are involved. This is indicating that an interaction between the nucleic- and amino acids might occur. CONCLUSION: We interpret these results in favor of Woese and suggest that the genetic code is "rational" and there is a stereospecific relationship between the codes and the amino acids.

Amino Acids↗
PubMed2006

Determining the effective dimensionality of the genetic variance-covariance matrix.

Determining the dimensionality of G provides an important perspective on the genetic basis of a multivariate suite of traits. Since the introduction of Fisher's geometric model, the number of genetically independent traits underlying a set of functionally related phenotypic traits has been recognized as an important factor influencing the response to selection. Here, we show how the effective dimensionality of G can be established, using a method for the determination of the dimensionality of the effect space from a multivariate general linear model introduced by Amemiya (1985). We compare this approach with two other available methods, factor-analytic modeling and bootstrapping, using a half-sib experiment that estimated G for eight cuticular hydrocarbons of Drosophila serrata. In our example, eight pheromone traits were shown to be adequately represented by only two underlying genetic dimensions by Amemiya's approach and factor-analytic modeling of the covariance structure at the sire level. In contrast, bootstrapping identified four dimensions with significant genetic variance. A simulation study indicated that while the performance of Amemiya's method was more sensitive to power constraints, it performed as well or better than factor-analytic modeling in correctly identifying the original genetic dimensions at moderate to high levels of heritability. The bootstrap approach consistently overestimated the number of dimensions in all cases and performed less well than Amemiya's method at subspace recovery.

Animals↗
PubMed2006

Combinations of single nucleotide polymorphisms in neuroendocrine effector and receptor genes predict chronic fatigue syndrome.

OBJECTIVE: This paper asks whether the presence of chronic fatigue syndrome (CFS) can be more accurately predicted from single nucleotide polymorphism (SNP) profiles than would occur by chance. METHODS: Specifically, given SNP profiles for 43 CFS patients, together with 58 controls, we used an enumerative search to identify an ensemble of conjunctive rules that predict whether a patient has CFS. RESULTS: The accuracy of the rules reached 76.3%, with the highest accuracy rules yielding 49 true negatives, 15 false negatives, 28 true positives and nine false positives (odds ratio [OR] 8.94, p < 0.0001). Analysis of the SNPs used most frequently in the overall ensemble of rules gave rise to a list of 'most important SNPs', which was not identical to the list of 'most differentiating SNPs' that one would calculate via studying each SNP independently. The top three genes containing the SNPs accounting for the highest accumulated importances were neuronal tryptophan hydroxylase (TPH2), catechol-O-methyltransferase (COMT) and nuclear receptor subfamily 3, group C, member 1 glucocorticoid receptor (NR3C1). CONCLUSION: The fact that only 28 out of several million possible SNPs predict whether a person has CFS with 76% accuracy indicates that CFS has a genetic component that may help to explain some aspects of the illness.

Algorithms↗
PubMed2003

Inferring population history from genealogical trees.

Inference about population history from DNA sequence data has become increasingly popular. For human populations, questions about whether a population has been expanding and when expansion began are often the focus of attention. For viral populations, questions about the epidemiological history of a virus, e.g., HIV-1 and Hepatitis C, are often of interest. In this paper I address the following question: Can population history be accurately inferred from single locus DNA data? An idealised world is considered in which the tree relating a sample of n non-recombining and selectively neutral DNA sequences is observed, rather than just the sequences themselves. This approach provides an upper limit to the information that possibly can be extracted from a sample. It is shown, based on Kingman's (1982a) coalescent process, that consistent estimation of parameters describing population history (e.g., a growth rate) cannot be achieved for increasing sample size, n. This is worse than often found for estimators of genetic parameters, e.g., the mutation rate typically converges at rate under the assumption that all historical mutations can be observed in the sample. In addition, various results for the distribution of maximum likelihood estimators are presented.

DNA↗
PubMed2006

EPConDB: a web resource for gene expression related to pancreatic development, beta-cell function and diabetes.

EPConDB (http://www.cbil.upenn.edu/EPConDB) is a public web site that supports research in diabetes, pancreatic development and beta-cell function by providing information about genes expressed in cells of the pancreas. EPConDB displays expression profiles for individual genes and information about transcripts, promoter elements and transcription factor binding sites. Gene expression results are obtained from studies examining tissue expression, pancreatic development and growth, differentiation of insulin-producing cells, islet or beta-cell injury, and genetic models of impaired beta-cell function. The expression datasets are derived using different microarray platforms, including the BCBC PancChips and Affymetrix gene expression arrays. Other datasets include semi-quantitative RT-PCR and MPSS expression studies. For selected microarray studies, lists of differentially expressed genes, derived from PaGE analysis, are displayed on the site. EPConDB provides database queries and tools to examine the relationship between a gene, its transcriptional regulation, protein function and expression in pancreatic tissues.

Animals↗
PubMed2006

In silico criterion for prediction of effects of p53 gene missense mutations on p53-Mdm2 feedback loop.

The Informational Spectrum Method (ISM) is the tool for the in silico analysis of proteins which interprets protein sequence linear information using signal analyses methods. In this paper the ISM was employed to characterize the products of genetic variants of tumor suppressor gene p53 and its natural binding regulator protein Mdm2. Based on this we propose the criterion for identification of missense mutations that have impact on the p53-Mdm2 feedback loop. The efficiency of the proposed criterion was confirmed by the ISM analyses of p53 mutants reported in: (i) healthy individuals, (ii) germline mutations database and (iii) somatic mutations database.

Amino Acid Sequence↗
PubMed2005

IMGT-Choreography for immunogenetics and immunoinformatics.

IMGT, the international ImMunoGeneTics information system (http://imgt.cines.fr), was created in 1989 at Montpellier, France. IMGT is a high quality integrated knowledge resource specialized in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrates, and related proteins of the immune system (RPI) which belong to the immunoglobulin superfamily (IgSF) and MHC superfamily (MhcSF). IMGT provides a common access to standardized data from genome, proteome, genetics and three-dimensional structures. The accuracy and the consistency of IMGT data are based on IMGT-ONTOLOGY, a semantic specification of terms to be used in immunogenetics and immunoinformatics. IMGT-ONTOLOGY has been formalized using XML Schema (IMGT-ML) for interoperability with other information systems. We are developing Web services to automatically query IMGT databases and tools. This is the first step towards IMGT-Choreography which will trigger and coordinate dynamic interactions between IMGT Web services to process complex significant biological and clinical requests. IMGT-Choreography will further increase the IMGT leadership in immunogenetics and immunoinformatics for medical research (repertoire analysis of the IG antibody sites and of the TR recognition sites in autoimmune and infectious diseases, AIDS, leukemias, lymphomas, myelomas), veterinary research (IG and TR repertoires in farm and wild life species), genome diversity and genome evolution studies of the adaptive immune responses, biotechnology related to antibody engineering (single chain Fragment variable (scFv), phage displays, combinatorial libraries, chimeric, humanized and human antibodies), diagnostics (detection and follow up of residual diseases) and therapeutical approaches (grafts, immunotherapy, vaccinology). IMGT is freely available at http://imgt.cines.fr.

Alleles↗
PubMed2005

High-throughput discovery of germ-cell-specific genes.

As a specialized cell population that plays the unique role of transmitting genetic information to subsequent generations, germ cells have been intensively studied to unravel their unique physiology from the specification of primordial germ cells to the fateful reunion of gametes during fertilization. For their differential expression, germ-cell-specific genes are the keys to understanding these unique features. In the last decade, the emerging methodologies designed for large-scale and high-throughput analysis have created an ever-increasing amount of data. Among these methodologies, expressed sequence tag libraries, serial analysis of gene expression, and microarrays provide valuable expression data that can be further analyzed. Using the mouse as a model system, we describe a strategy starting from the quick identification of germ-cell-specific genes using public domain expression data to the functional characterization of the identified genes using targeted gene disruption. This strategy should accelerate the process to fill in the missing pieces of the germ cell physiology puzzle and the construction of genetic networks to help us to understand the etiology of infertility. Furthermore, these identified germ-cell-specific genes may lead to the development of new contraceptives targeted specifically to germ cells.

Animals↗
PubMed2001

GRR: graphical representation of relationship errors.

SUMMARY: A graphical tool for verifying assumed relationships between individuals in genetic studies is described. GRR can detect many common errors using genotypes from many markers. AVAILABILITY: GRR is available at http://bioinformatics.well.ox.ac.uk/GRR.

Alleles↗
PubMed2005

Methodology and recruitment of probands and their families for the Genes in Myopia (GEM) Study.

PURPOSE: Myopia is considered to be a complex disease involving both environmental and genetic factors. The Genes in Myopia (GEM) Study aims to recruit probands with myopia and their family members to allow genetic analysis of myopia to be undertaken. The purpose of this paper is to describe the methodology and recruitment of probands and families for the GEM Study. METHODS: In a sample-based prospective study, 2,095 probands with myopia of -0.50 DS or worse and a positive family history of myopia were contacted via the Melbourne Excimer Laser Group (MELG) database. Probands and family members recruited into the study undertook a detailed assessment including questionnaire, best-corrected visual acuity, objective and subjective refraction, axial length, anterior chamber depth, keratometry readings, slit-lamp examination, height, weight and head circumference measurements, and blood sample collection for DNA analysis. RESULTS: 280 probands with myopia have been recruited into the GEM Study. Probands had a mean age of 49.33 yrs. (SD +/- 11.64) with the average age of myopia onset being 12.58 years (SD +/- 6.71). The average spherical-component refractive error was: right eye -5.13 DS (SD +/- 3.06) and left eye -5.14 DS (SD +/- 3.16). Probands with extreme myopia (-10 DS or worse) showed the highest study participation rate of 56%, when compared to high (-5 DS < -10 DS) (20%), moderate (-3 DS < - 5 DS) (18%) and low myopia (-0.5 DS < -3 DS) (10%). A total of 279 out of 505 (55%) additional family members recruited were also found to be myopic. CONCLUSIONS: The GEM study has used a targeted approach to identify an Australian cohort with a diverse spread of myopia, ranging from low to extreme. Recruitment of probands via the use of an excimer laser practice has proved to be an efficient and economic means of identifying probands with a family history of myopia. In addition, the participation rate in the study appears to vary reflecting a proband's perception of disease severity.

Adolescent↗
PubMed2001

[Host genetic epidemiology by single nucleotide polymorphism(SNP) analysis].

The completion of the whole human genome sequences is now a reality. Emphasis on the analysis of genetic variations on both an individual level and a population level is more important than ever. The identification and characterization of single nucleotide polymorphisms (SNPs) in target genes or candidate genes plays a crucial role in identification of disease genes and in expediting drug discovery/development. Identification of known SNPs can be easily accomplished by searching the ever-expanding public domain databases. However, discovery of new SNPs is best accomplished by sequencing a reasonable subset of the applicable population groups. Particular SNPs of interest will be the ones that affect coding changes and regulatory functions of genes. Once SNPs have been identified, the next step is to examine their frequency in disease models by accurate, cost-effective and high-throughput SNP genotyping methods. This presentation will cover the overview of principal techniques of SNP genotyping which have been developed so far. And also will be discussed the importance of well-defined disease model and error-free high-throughput SNP genotyping in candidate genes and genome-wide SNP screening in the near future.

Alleles↗
PubMed2006

Sequencing the whole genome of infected human cells obtained from diseased patients--a proposed strategy for understanding and overcoming AIDS or other deadest virus-infected diseases.

As the worry and pandemic about deadest virus such as AIDS and bird flu are intensified, eradical treatments for these virus-infected diseases are in high demand. However we currently know little about the virus involvement in human cells, which results poor therapeutic outcome. We propose that these viruses may penetrate into human genome in diseased cells that may finally result resistance to present applicable therapeutic options. Here proposes a strategy--sequence the whole genome (chromosomal as well as other genetic systems) of infected human cells obtained from diseased patients. This might help us to know greatly more about the consequences of virus infection and achieve biotherapy of specifically targeted in future.

Acquired Immunodeficiency Syndrome↗
PubMedDate not supplied

Epileptic seizures and syndromes in twins: the importance of genetic factors.

The role of genetic factors in the occurrence of epilepsy syndromes was studied in twins recruited from the population-based Danish Twin Registry. A total of 34,076 twins were screened for epilepsy. Cases were confirmed and classified by two neurologists according to the classification systems of the International League Against Epilepsy (ILAE). A total of 214 twin pairs with epileptic seizures and 190 pairs with epilepsy were ascertained. Significantly higher concordance rates were found for monozygotic (MZ) compared to dizygotic (DZ) twins for both epileptic seizures (0.56 for MZ and 0.21 for DZ pairs, P<0.001) and for epilepsy (0.49 for MZ and 0.16 for DZ pairs, P<0.001). Concordance rates were also higher for MZ twins compared to DZ twins for both generalized epilepsy (0.65 for MZ and 0.12 for DZ) and for localization-related epilepsy (0.30 for MZ and 0.10 for DZ). In twin pairs where both members had seizures, 83% of MZ and 65% of DZ pairs had the same major epilepsy syndrome. Genetic factors were found to account for 80% of the liability to both epileptic seizures and epilepsy. In conclusion, analysis of this neurologist-verified epilepsy twin data set has confirmed that genetic factors have a substantial impact on the etiology of epileptic seizures as well as on the occurrence of both generalized and partial epilepsies.

Adolescent↗