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At least 613 records · Page 34Linked to original sources

Genetic profiling of a central Venezuelan population using 15 STR markers that may be of forensic importance.

The AmpFlSTR Identifiler kit has recently been accepted for use in DNA databasing of forensic samples in the FBI's National DNA Index System. In the present study, we used this kit to analyze the allele distribution of 15 short tandem repeat markers (STR) in individuals living in Caracas city, Venezuela. The allele frequencies of two of these STR, D2S1338 and D19S433, have not previously been reported for this or any other Latin American population. The results indicate that for the population here studied, the 15 STR tested are useful markers for paternity testing and forensic casework.

Alleles↗

Frequency Finder: a multi-source web application for collection of public allele frequencies of SNP markers.

Publicly available single nucleotide polymorphism (SNP) allele frequencies are an important resource for the selection of genetic markers that may be most useful for gene mapping and association studies. Data mining these allele frequencies through disparate public databases and Websites is time consuming and can result in inconsistent findings. We have developed a web-based software tool, Frequency Finder, to acquire SNP allele frequencies from multiple public data sources and return a summarized result to the user. Our software optimizes and automates the search of candidate markers, decreasing the amount of time it would take to extract pertinent data manually. We have included several methods to output the data, including on-screen and as a compressed text file. We show that Frequency Finder accurately retrieves available frequency data from the available sources. Using this tool, we detect significant differences between Asian, African and Caucasian populations in the allele frequency spectra of 246 097 SNPs. While limited to public databases that provide web-based access to allele frequencies, Frequency Finder provides a single, user-friendly interface for retrieving allele frequencies for large batches of SNPs from multiple data sources.

Algorithms↗

Integrated genetic map of human chromosome 2.

A framework genetic map of human chromosome 2 is described, integrating data from the Centre d'Etude du Polymorphisme Humain (CEPH) version 6 database, the CEPH chromosome 2 consortium database, the National Institute of Health (NIH)/CEPH Collaborative Mapping group and other laboratories. A comprehensive map is also presented, showing regional locations of a large number of additional loci. The framework map is used to identify an informative set of meiotic breakpoints within the CEPH families, and the utility of this information for mapping new markers is discussed. The degree of typing error within the data set is estimated, as are the sex-specific interference parameters. A location database for these genetic and additional cytogenetic data is constructed using algorithms which map genetic distances on to a physical scale, and the potential for this approach to aid the integration of genetic and physical data is examined.

Chromosome Mapping↗

QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species.

BACKGROUND: Single nucleotide polymorphisms (SNPs) are important tools in studying complex genetic traits and genome evolution. Computational strategies for SNP discovery make use of the large number of sequences present in public databases (in most cases as expressed sequence tags (ESTs)) and are considered to be faster and more cost-effective than experimental procedures. A major challenge in computational SNP discovery is distinguishing allelic variation from sequence variation between paralogous sequences, in addition to recognizing sequencing errors. For the majority of the public EST sequences, trace or quality files are lacking which makes detection of reliable SNPs even more difficult because it has to rely on sequence comparisons only. RESULTS: We have developed a new algorithm to detect reliable SNPs and insertions/deletions (indels) in EST data, both with and without quality files. Implemented in a pipeline called QualitySNP, it uses three filters for the identification of reliable SNPs. Filter 1 screens for all potential SNPs and identifies variation between or within genotypes. Filter 2 is the core filter that uses a haplotype-based strategy to detect reliable SNPs. Clusters with potential paralogs as well as false SNPs caused by sequencing errors are identified. Filter 3 screens SNPs by calculating a confidence score, based upon sequence redundancy and quality. Non-synonymous SNPs are subsequently identified by detecting open reading frames of consensus sequences (contigs) with SNPs. The pipeline includes a data storage and retrieval system for haplotypes, SNPs and alignments. QualitySNP's versatility is demonstrated by the identification of SNPs in EST datasets from potato, chicken and humans. CONCLUSION: QualitySNP is an efficient tool for SNP detection, storage and retrieval in diploid as well as polyploid species. It is available for running on Linux or UNIX systems. The program, test data, and user manual are available at http://www.bioinformatics.nl/tools/snpweb/ and as Additional files.

Base Sequence↗

Rights and obligations of the persons concerning their genetic data.

The right to privacy is a right that is universally recognised and which encompasses the protection of the genetic codes. However, this is not an absolute right and is limited when certain interests come into play. This article highlights such limits, analysing the different uses that can be made with the genetic data, as well as the dangers that such uses can entail.

Databases, Genetic↗

Using interval logic for order assembly.

Temporal logic, in particular, interval logic has been used to represent genome maps and to assist genome map constructions. However, interval logic itself appears to be limited in its expressive power because genome mapping requires various information such as partial order, distance and local orientation. In this paper, we first propose an integrated formalism based on a spatial-temporal logic where the concepts of metric information, local orientation and uncertainty are merged. Then, we present and discuss a deductive and object-oriented data model based on this formalism for a genetic deductive database, and the inference rules required. The formalism supports the maintenance of coarser knowledge of unordered, partially ordered and completely ordered genetic data in a relational hierarchy. We believe that this integrated formalism also provides a formal basis for designing a declarative query language.

Animals↗

Mapping and expression analysis of the mouse ortholog of Xenopus Eomesodermin.

The T-box gene family has been conserved throughout metazoan evolution. The genes code for putative transcription factors which share a uniquely defining DNA binding domain, known as the T-box ([Bollag et al., 1994]). They are implicated in the control of diverse developmental processes by their highly specific expression patterns throughout gastrulation and organogenesis in mouse and other species ([Chapman et al., 1996]) ([Gibson-Brown et al., 1998]), and by mutations in T-box genes that have profound developmental effects ([Papaioannou, 1997]; [Chapman and Papaioannou, 1998]; [Papaioannou and Silver, 1998]). In this report, we describe the mapping and expression pattern of the mouse ortholog of a gene, Eomesodermin, first identified in Xenopus ([Ryan et al., 1996]). The mouse gene was previously reported ([Wattler et al., 1998]) under the name MmEomes. The gene maps to mouse chromosome 9 in a region syntenic with human chromosome 3p. Mouse eomesodermin is expressed in the trophoblast of the blastocyst and in its derivative, the chorionic ectoderm. At gastrulation, eomesodermin is expressed in the primitive streak and embryonic mesoderm as well, but this expression disappears prior to the end of gastrulation. Later, eomesodermin is expressed in the developing forebrain, in a pattern largely overlapping a closely related T-box gene, Tbr1 ([Bulfone et al., 1995]), and is also seen in a localized area of each limb.

Animals↗

Scaling up orphan crop research: genebank genetics highlight geographic structure in cultivated cowpea from 10 617 global accessions.

Vigna unguiculata (L.) Walp. is a dryland legume crop, providing essential food and nutritional security for millions of people across the semi-arid tropics, in Africa, Asia and Latin America. However, as a typical 'orphan crop', cowpea has long remained underrepresented in global genomic research to support crop improvement. Here, we conducted the largest genetic diversity analysis of cowpea to date, comprising 10 617 accessions sourced from seven international collections. Using genotyping-by-sequencing, we characterised the global patterns of genetic diversity, assessed redundancy within and across collections, and examined the geographic structure of the cowpea global allele pool. Our results revealed nine distinct genetic groups with clear geographic associations and fine-scale population differentiation, reflecting dispersal history, regional adaptation and the influence of modern breeding. Duplication across collections was detected, highlighting the need for improved curation and integration of germplasm resources. Landraces from sub-Saharan Africa do not fully capture the genetic diversity present in several other geographic regions, indicating the existence of abundant and untapped genetic resources worldwide. These findings not only provide insights into the genetic structure and evolutionary history of cowpea but also offer a valuable foundation for harnessing global germplasm diversity to enhance breeding potential and accelerate crop improvement.

Vigna↗

Comparative and functional analysis of cardiovascular-related genes.

The ability to detect putative cis-regulatory elements in cardiovascular-related genes has been accelerated by the availability of genomic sequence data from numerous vertebrate species and the recent development of comparative genomic tools. This improvement is anticipated to lead to a better understanding of the complex regulatory architecture of cardiovascular (CV) genes and how genetic variants in these non-coding regions can potentially play a role in cardiovascular disease. This manuscript reviews a recently established database dedicated to the comparative sequence analysis of 250 human CV genes of known importance, 37 of which currently contain sequence comparison data for organisms beyond those of human, mouse and rat. These data have provided a glimpse into the variety of possible insights from deep vertebrate sequence comparisons and the identification of putative gene regulatory elements.

Animals↗

[Analysis for spatial distribution of Oncomelania snail in mainland China by geographic information system(GIS) database].

OBJECTIVE: To analyze spatial distribution of Oncomelania snail populations in mainland China by geographic information system (GIS) database. METHODS: Genetic variation experiment data and experimental data of susceptibility of 34 snail populations were collected from nine provinces in China, to set up a database. A world digital map was linked with the database in a software ArcView Release 3.0 a to be used to divide zones with ArcView spatial analyze function and GIS overlaying function. AVHRR NDVI satellite images were collected to form a new one for prevalent season, which were overlaid with distribution maps of heterozygous indices of snail populations, polymorphic locus percentage and infection rates of snail population with schistosome for classifying the images. RESULTS: Spatial analysis showed that distribution maps of genetic heterozygous indices of snail, percentage of polymophic loci and infection rate of snail can be divided into two large zones, i.e., east zone and west zone, both with varied pictures. Analysis for overlaying three-stratum distribution map with AVHRR NDVI satellite image showed four distinctly different spatial zones, including west Sichuan zone, west Yunnan zone, middle zone of river, lake and marshland, and southeast coastal zone. CONCLUSION: It is the first time using GIS to analyze data of Oncomelania population genetics and confirmed the population structure of Oncomelania snails presented discrete sub-population model, which supports the theory of sub-species of Oncomelania spp. Exited in mainland China.

Animals↗

Genetical genomics in humans and model organisms.

Genetical genomics has been proposed to map loci controlling gene-expression differences (eQTLs) that might underlie functional trait variation. We briefly review the studies in model species and conclude that, although they successfully demonstrate the utility of genetical genomics, they are too limited to unlock the full potential of this approach and some results should be interpreted with caution. We subsequently elaborate on two recent studies that use this approach in humans. The many differences between these studies complicate meaningful comparisons between them. A joint analysis of the two experiments offers some scope for more powerful genetical genomics.

Animals↗

[Protection of genetic data in Spain. Analysis based on the general principles of personal data protection].

The genetic data is Spain is not regulated specifically, rather, we must look at the regulation on the protection of data of a personal nature. This is turn, establishes a series of general principles to apply to any type of data. Analysing this with other regulations that are dispersed both in the national and international regulations, we can deduce the rights and obligations in this field. This highlights the fact that one can't dispose of the genetic data in the same manner as the personal data.

Computer Security↗

A prototype object database for mitochondrial DNA variation.

Surveys of biochemical and molecular genetic variation in natural populations have generated a wealth of data, but this valuable resource has not been adequately preserved. We hope to prevent further loss by establishing a community database for population genetic surveys. We explored the feasibility of a population genetics database by developing a prototype for animal mitochondrial DNA (mtDNA) surveys. This prototype includes the specification of a format for data files that are to be submitted to the database, an open-source object database that encapsulates data with methods to display and analyze data, and a website where data can be retrieved in either its original form or extensible markup language (XML). Data from more than 50 published surveys of mtDNA variation were retrieved from the literature and entered into the database. We hope that the population genetics community will support this project by contributing both data and expertise.

Animals↗

Analysis of genetic abnormalities provides insights into genetic evolution of hyperdiploid myeloma.

Aneuploidy is ubiquitous in human cancer and is seen as whole chromosome gains and losses, unbalanced translocations and inversions, duplications, deletions and loss of heterozygosity. Within this complexity, some subgroups of aneuploid tumors emerge as distinct biological and clinical entities. Hyperdiploid myeloma (H-MM), characterized by hyperdiploid chromosome numbers because of nonrandom trisomies, is one such example. We undertook a comprehensive survey of the karyotypes of a large number of H-MM (n = 469) to describe fully genomic instability in these tumors, to dissect pathways of genetic evolution, and identify distinct subgroups based on their genetic changes. While selective pressure apparently favors the emergence of clones with gains of chromosomes 3, 5, 7, 9, 11, 15, 19, and 21, a background of ongoing genomic instability results in gains of other chromosomes, albeit at a much lower prevalence. A deduced temporal analysis of these karyotypes indicates that selected gains are early events. Other events occurring later in the course of the disease include secondary chromosome translocations and monosomies. The development of these genetic aberrations is thus highly ordered and undoubtedly of biological relevance. Within this framework, we propose a model of genetic evolution in H-MM.

Chromosome Aberrations↗