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PubMed2004

TraitMap: an XML-based genetic-map database combining multigenic loci and biomolecular networks.

MOTIVATION: Most ordinary traits are well described by multiple measurable parameters. Thus, in the course of elucidating the genes responsible for a given trait, it is necessary to conduct and integrate the genetic mapping of each parameter. However, the integration of multiple mapping results from different publications is prevented by the fact that they are conventionally published and accumulated in printed forms or graphics which are difficult for computers to reuse for further analyses. RESULTS: We have defined an XML-based schema as a container of genetic mapping results, and created a database named TraitMap containing curator-checked data records based on published papers of mapping results in Homosapiens, Mus musculus, and Arabidopsis thaliana. TraitMap is the first database of mapping charts in genetics, and is integrated in a web-based retrieval framework: termed Genome <--> Phenome Superhighway (GPS) system, where it is possible to combine and visualize multiple mapping records in a two-dimensional display. Since most traits are regulated by multiple genes, the system associates every combination of genetic loci to biomolecular networks, and thus helps us to estimate molecular-level candidate networks responsible for a given trait. It is demonstrated that a combined analysis of two diabetes-related traits (susceptibility to insulin resistance and non-HDL cholesterol level) suggests that molecular-level relationships such as the interaction among leptin receptor (Lepr), peroxisome proliferators-activated receptor-gamma (Pparg) and insulin receptor substrate 1 (Irs1), are candidate causal networks affecting the traits in a multigenic manner. AVAILABILITY: TraitMap database and GPS are accessible at http://omicspace.riken.jp/gps/

Chromosome Mapping↗
PubMed2006

National and ethnic mutation databases: recording populations' genography.

Genetic databases are gradually assuming an increasing importance in all areas of health care. The national and ethnic mutation databases (NEMDBs) are continuously updated mutation depositories, recording extensive information over the described genetic heterogeneity of an ethnic group or population. Together with the central and locus-specific databases, those resources not only enhance awareness of the various genetic disorders but also facilitate the provision of genetic services and provide useful insights into the genographic history of human populations. Fifteen independent NEMDBs devoted to the documentation of the extant genetic heterogeneity in various population groups within 57 different countries were assessed; 13 of the NEMDBs were fully functional. The contents of the 13 fully functional NEMDBs were thoroughly analyzed for the presence or absence of 39 criteria, pertaining database general information, operating platform, data source and submission, and querying capacity. This study provides a strong case for uniformity of data to make the NEMDBs content maximally useful. In this direction, a hypothetical content for the ideal NEMDB is derived, which is currently being incorporated in an upgraded version of the ETHNOS NEMDB development and curation software, as well as a community structure that would enhance the chances of mutation frequency capture and documentation in human populations. The ultimate goal is that interested parties and granting bodies will assist in achieving the vision of a comprehensive resource that collects and displays all population-specific genetic information discovered.

Computational Biology↗
PubMed2003

Antenatal detection of skeletal dysplasias.

OBJECTIVE: To assess the accuracy of the prenatal diagnosis of skeletal dysplasias. METHODS: All antenatally detected anomalies are coded in our ultrasound database, which is linked with a genetics database that includes outcomes. A final diagnosis is sought on the basis of radiographic studies, molecular testing, or both. Our ultrasound and genetics databases were queried for "skeletal dysplasias." All cases were reviewed specifically for the degree of bone shortening and other distinguishing characteristics on antenatal sonography. RESULTS: Thirty-seven cases of skeletal dysplasia were antenatally diagnosed over an 8-year period. Complete follow-up was available in 31 cases. The mean gestational age at diagnosis was 22.7 weeks (range, 14-32.3 weeks). Twenty-one cases were diagnosed before 24 weeks. A final diagnosis was obtained in 80% of cases. The antenatal diagnosis was correct in 20 (65%) of 31 cases. There were 2 false-positive diagnoses. Specific final diagnoses included thanatophoric dysplasia (8), osteogenesis imperfecta (6), Roberts syndrome (2), achondroplasia (3), Ellis-van Creveld syndrome (1), metaphyseal dysplasia (1), spondyloepiphyseal dysplasia (1), distal arthrogryposis (1), caudal regression (1), and glycogen storage disorder (1). The condition was correctly thought to be lethal in 16 of the fetuses on the basis of early severe long bone shortening (13), femur length-abdominal circumference ratio of less than 0.16 (12), hypoplastic thorax (10), marked bowing or fractures (4), short ribs (4), caudal regression (1), and cloverleaf skull (1). The ability to predict lethality was 100%. There were no false-positive findings with respect to lethality. CONCLUSIONS: Accurate antenatal diagnosis of skeletal dysplasias is problematic; in this series, only 20 of 31 cases were correctly diagnosed. However, the antenatal prediction of lethality was highly accurate. The most common predictors of lethal skeletal dysplasias included early and severe shortening of the long bones, femur length-abdominal circumference ratio of less than 0.16, hypoplastic thorax, and certain distinguishing characteristics.

Abdomen↗
PubMed1997

Isolation and regional mapping of cDNAs expressed during early human development.

A cDNA sequencing project was initiated with the aim of isolating and mapping new genes expressed during early human development. A human embryo cDNA library was constructed, and a prescreening procedure was used to select cDNAs corresponding to poorly transcribed genes. Partial sequences were generated from one or both ends of 231 cDNA clones, and sequence comparison with genetic databases revealed that 28% were already annotated genes, 42% matched with partial sequences expressed sequence tags that had already been detected, 3% contained no insert, 5% were highly similar to sequences from other species, and 23% of the cDNAs appeared to be unknown in genetic databases. All new sequences were deposited in public genetic databases, and most of the corresponding cDNAs were regionally mapped on human chromosome bands using both fluorescence and radioactive in situ hybridization. Several cDNAs colocalized with critical regions of the genome regarding mapped disorders, thus providing candidate genes for human genetic diseases.

Chromosome Mapping↗
PubMed2006

Bio-Ontology and text: bridging the modeling gap.

MOTIVATION: Natural language processing (NLP) techniques are increasingly being used in biology to automate the capture of new biological discoveries in text, which are being reported at a rapid rate. Yet, information represented in NLP data structures is classically very different from information organized with ontologies as found in model organisms or genetic databases. To facilitate the computational reuse and integration of information buried in unstructured text with that of genetic databases, we propose and evaluate a translational schema that represents a comprehensive set of phenotypic and genetic entities, as well as their closely related biomedical entities and relations as expressed in natural language. In addition, the schema connects different scales of biological information, and provides mappings from the textual information to existing ontologies, which are essential in biology for integration, organization, dissemination and knowledge management of heterogeneous phenotypic information. A common comprehensive representation for otherwise heterogeneous phenotypic and genetic datasets, such as the one proposed, is critical for advancing systems biology because it enables acquisition and reuse of unprecedented volumes of diverse types of knowledge and information from text. RESULTS: A novel representational schema, PGschema, was developed that enables translation of phenotypic, genetic and their closely related information found in textual narratives to a well-defined data structure comprising phenotypic and genetic concepts from established ontologies along with modifiers and relationships. Evaluation for coverage of a selected set of entities showed that 90% of the information could be represented (95% confidence interval: 86-93%; n = 268). Moreover, PGschema can be expressed automatically in an XML format using natural language techniques to process the text. To our knowledge, we are providing the first evaluation of a translational schema for NLP that contains declarative knowledge about genes and their associated biomedical data (e.g. phenotypes). AVAILABILITY: http://zellig.cpmc.columbia.edu/PGschema

Abstracting and Indexing↗
PubMed2005

Securing our genetic health: engendering trust in UK Biobank.

The recent development of genetic databases, or 'biobanks', in a number of countries reflects scientists' and policy makers' beliefs in the future health benefits to be derived from genetics research. In Britain, however, a proposal for a genetic database, UK Biobank, has been the focus of a number of concerns. Establishing consent and legitimacy for any controversial biomedical research involving the participation of human subjects is difficult; it is however, acute for UK Biobank given the scale of the project and the criticisms levelled at it. Analysing recently published documents pertaining to UK Biobank, this article examines how consent for the project has been discursively framed and how this is reflected in its governance. It is argued that the problem of organising consent has been framed narrowly in terms of adherence to a well-established repertoire of institutional mechanisms which serves to limit debate on the substantive issues at stake. There is little evidence of reflection on the adequacy of such mechanisms for dealing with the unique challenges posed by UK Biobank, including achieving the confidence and participation of a population with diverse perspectives on genetic research. It is concluded that a restricted public discourse about UK Biobank may contribute to a decline in confidence in regulatory systems governing biotechnology and science more generally.

Aged↗
PubMed2001

dbSNP: the NCBI database of genetic variation.

In response to a need for a general catalog of genome variation to address the large-scale sampling designs required by association studies, gene mapping and evolutionary biology, the National Center for Biotechnology Information (NCBI) has established the dbSNP database [S.T.Sherry, M.Ward and K. Sirotkin (1999) Genome Res., 9, 677-679]. Submissions to dbSNP will be integrated with other sources of information at NCBI such as GenBank, PubMed, LocusLink and the Human Genome Project data. The complete contents of dbSNP are available to the public at website: http://www.ncbi.nlm.nih.gov/SNP. The complete contents of dbSNP can also be downloaded in multiple formats via anonymous FTP at ftp://ncbi.nlm.nih.gov/snp/.

Animals↗
PubMed2004

GSD: a genetic screen database.

The systematic assignment of gene function to a sequenced genome is one of the outstanding challenges in the post-genomic era. Large-scale systematic mutagenesis screens are important tools for reaching this goal. Here we describe GSD, a software package that allows storage and integration of data from genetic screens. GSD was initially developed for a large-scale F3 mutagenesis screen for developmental mutants of medaka (Oryzias latipes). The version presented here supports a wide range of different screens (mutagenesis, RNAi, morpholinos, transgenesis and others) using different organisms. Data are stored in a relational database and can be made accessible through web interfaces. Researchers can enter data describing their screened embryos: They can track statistics, submit images and describe the resulting phenotypes using a phenotype classification ontology. We developed a fish phenotype classification ontology of medaka and zebrafish for this software package and made it available to the public. In addition, a list of genetic lines resulting from each screen can be generated. These lines (mutant alleles, transgenic lines) can be described and categorized in the same ways as the screened individuals. Raw data from the screen can be integrated to describe these lines. A query module that searches this list can be used to publish the screen results on the Internet. A test version is available at and the software can be downloaded from this site.

Animals↗
PubMed1991

[Possibilities of creating a genetic information database and its processing based on the DBase3-plus system].

Special methods are required for computing information on biological objects under complex research. The DBASE3-PLUS system offers vast possibilities for working with large quantity of different sets of information in multi-aspect statistical analysis. Usefulness of this system for creation of and operation with the data on distribution of genetic and non-genetic traits in a population was shown by means of the special set of applied programs in the dBase language. An example presented is aimed at distinguishing those genetic markers which probably can influence common individual health of the members of population. Special regression procedure was suggested to divide the population sample into subgroups with different health levels. Significant differences in distribution of some genetic markers were demonstrated between healthy persons and those who were suffering from chronic diseases.

Databases, Bibliographic↗
PubMed2002

Ethical dimensions of genetics in pediatric neurology: a look into the future.

Health care providers and families with children who participate in genetic research or who need specialized genetic services, including genetic testing, will encounter not only medical but difficult social, ethical, and legal questions surrounding pediatric genetic neurology. Children are often at the center of much of the genetic revolution and their unique needs raise special concerns about the risks and benefits associated with genetic research, particularly the issues of consent, the use of genetic databases, and gene therapy. Moreover, genetic research and testing raise important psychosocial risks. In this article we discuss some of the benefits and consequences of genetic technologies for children in relation to national and international guidelines. In particular, physicians, policy-makers, and families should be knowledgeable about the guidelines and have a good understanding of the psychosocial and ethical issues associated with genetics in pediatric neurology.

Canada↗
PubMed2003

DNA databanks and consent: a suggested policy option involving an authorization model.

BACKGROUND: Genetic databases are becoming increasingly common as a means of determining the relationship between lifestyle, environmental exposures and genetic diseases. These databases rely on large numbers of research subjects contributing their genetic material to successfully explore the genetic basis of disease. However, as all possible research questions that can be posed of the data are unknown, an unresolved ethical issue is the status of informed consent for future research uses of genetic material. DISCUSSION: In this paper, we discuss the difficulties of an informed consent model for future ineffable uses of genetic data. We argue that variations on consent, such as presumed consent, blanket consent or constructed consent fail to meet the standards required by current informed consent doctrine and are distortions of the original concept. In this paper, we propose the concept of an authorization model whereby participants in genetic data banks are able to exercise a certain amount of control over future uses of genetic data. We argue this preserves the autonomy of individuals at the same time as allowing them to give permission and discretion to researchers for certain types of research. SUMMARY: The authorization model represents a step forward in the debate about informed consent in genetic databases. The move towards an authorization model would require changes in the regulatory and legislative environments. Additionally, empirical support of the utility and acceptability of authorization is required.

Advance Directives↗
PubMed2004

Microsatellite instability in gastric MALT lymphoma.

The role of microsatellite instability and defects in DNA mismatch repair mechanism in the pathogenesis of gastric lymphoma of mucosa-associated lymphoid tissue (MALT) type is still controversial, as both negative and positive findings have been reported. This may be explained mainly by arbitrary selection of the tested loci, the use of various techniques of microsatellite instability analysis and by different definitions of replication error positive phenotype. The aim of our study was to evaluate the instability at selected microsatellite markers using the GeneScan Analysis Software. DNA from paraffin-embedded tissue blocks of 13 previously untreated patients with localized gastric MALT lymphoma was extracted. Five microsatellite markers, which are located in hMSH2, hMLH1, P16, APC and MLL loci, were selected from the genetic database. We found genetic instability in tumors of 9/13 patients with gastric MALT lymphoma (69%). Seven of them had replication-error-positive phenotype (54%). Microsatellite instability was found in 39% of the samples in the MLL locus, 39% in the APC, 46% in the P16, 23% in the hMLH1 and none in the hMSH2. This study demonstrates that microsatellite instability has more prominent role in pathogenesis of gastric MALT lymphoma than reported to date. We suggest that microsatellite instability should be analyzed with markers adjacent to chromosomal loci that are involved in lymphomas. Our findings support the 'Real Common Target genes' theory of high rate of microsatellite instability in specific genes, which are associated with related tumors.

Adult↗
PubMed1999

Discovering diagnostic rules from a neurotologic database with genetic algorithms.

Data on patients with Meniere's disease, vestibular schwannoma, traumatic vertigo, sudden deafness, benign paroxysmal positional vertigo, or vestibular neuritis were retrieved from the database of otoneurologic expert system ONE for the development and testing of a genetic algorithm (GA). The accuracy of the diagnostic rules in solving the test cases was 81%, 91%, 92%, 95%, 96%, and 98% for the respective diseases. The best rules retrieved from the GA were described by a set of questions with the most likely answers. The most important questions concerned the duration of hearing loss and the occurrence of head injury. The validity and structure of the rules created with a GA can be analyzed in detail. For rare diseases, some other reasoning process can be used, for example, case-based reasoning.

Algorithms↗
PubMed2024

Reference Sequence Browser: An R application with a user-friendly GUI to rapidly query sequence databases.

Land managers, researchers, and regulators increasingly utilize environmental DNA (eDNA) techniques to monitor species richness, presence, and absence. In order to properly develop a biological assay for eDNA metabarcoding or quantitative PCR, scientists must be able to find not only reference sequences (previously identified sequences in a genomics database) that match their target taxa but also reference sequences that match non-target taxa. Determining which taxa have publicly available sequences in a time-efficient and accurate manner currently requires computational skills to search, manipulate, and parse multiple unconnected DNA sequence databases. Our team iteratively designed a Graphic User Interface (GUI) Shiny application called the Reference Sequence Browser (RSB) that provides users efficient and intuitive access to multiple genetic databases regardless of computer programming expertise. The application returns the number of publicly accessible barcode markers per organism in the NCBI Nucleotide, BOLD, or CALeDNA CRUX Metabarcoding Reference Databases. Depending on the database, we offer various search filters such as min and max sequence length or country of origin. Users can then download the FASTA/GenBank files from the RSB web tool, view statistics about the data, and explore results to determine details about the availability or absence of reference sequences.

User-Computer Interface↗
PubMed1999

Sequence Analysis of 47 Low-abundance ESTs Expressed in Early Human Embryo.

The availability of high quality cDNA libraries has proven essential to positional gene cloning efforts differential gene expression studies and EST sequencing/mapping projects.In order to isolate and identify new genes expressed during early human development a 3-week-old human embryo cDNA library was constructed and a pre-screening procedure was used to select cDNAs corresponding to low abundance mRNAs. 6 508 clones were hybridized with a mixture of cDNA probes. Approximately 1 677 clones (26%) did not hybridize with the cDNA probes and represent low abundance mRNAs as well as empty vectors.Partial sequences were generated from one or both end of 47 low abundance cDNA clones and the sequences comparisons with genetic databases revealed that 38.3% of them was annotated human genes 10.6% was highly similar to those from either human or other species 40.4% was partial sequence matched with ESTs that had already been detected and 8.5% of the cDNAs appeared to be unknown in the genetic databases.

Journal Article↗