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PubMed2006

SNPs3D: candidate gene and SNP selection for association studies.

BACKGROUND: The relationship between disease susceptibility and genetic variation is complex, and many different types of data are relevant. We describe a web resource and database that provides and integrates as much information as possible on disease/gene relationships at the molecular level. DESCRIPTION: The resource http://www.SNPs3D.org has three primary modules. One module identifies which genes are candidates for involvement in a specified disease. A second module provides information about the relationships between sets of candidate genes. The third module analyzes the likely impact of non-synonymous SNPs on protein function. Disease/candidate gene relationships and gene-gene relationships are derived from the literature using simple but effective text profiling. SNP/protein function relationships are derived by two methods, one using principles of protein structure and stability, the other based on sequence conservation. Entries for each gene include a number of links to other data, such as expression profiles, pathway context, mouse knockout information and papers. Gene-gene interactions are presented in an interactive graphical interface, providing rapid access to the underlying information, as well as convenient navigation through the network. Use of the resource is illustrated with aspects of the inflammatory response and hypertension. CONCLUSION: The combination of SNP impact analysis, a knowledge based network of gene relationships and candidate genes, and access to a wide range of data and literature allow a user to quickly assimilate available information, and so develop models of gene-pathway-disease interaction.

Databases, Genetic↗
PubMed2004

The Zuker collection: a resource for the analysis of autosomal gene function in Drosophila melanogaster.

The majority of genes of multicellular organisms encode proteins with functions that are not required for viability but contribute to important physiological functions such as behavior and reproduction. It is estimated that 75% of the genes of Drosophila melanogaster are nonessential. Here we report on a strategy used to establish a large collection of stocks that is suitable for the recovery of mutations in such genes. From approximately 72,000 F(3) cultures segregating for autosomes heavily treated with ethyl methanesulfonate (EMS), approximately 12,000 lines in which the treated second or third chromosome survived in homozygous condition were selected. The dose of EMS induced an estimated rate of 1.2-1.5 x 10(-3) mutations/gene and predicts five to six nonessential gene mutations per chromosome and seven to nine alleles per locus in the samples of 6000 second chromosomes and 6000 third chromosomes. Due to mosaic mutations induced in the initial exposure to the mutagen, many of the lines are segregating or are now fixed for lethal mutations on the mutagenized chromosome. The features of this collection, known as the Zuker collection, make it a valuable resource for forward and reverse genetic screens for mutations affecting a wide array of biological functions.

Alleles↗
PubMed2006

Privacy and confidentiality--old concept, new challenges.

This paper concerns a privacy and confidentiality problem in cases of exceptional situations. It is primarily aimed at using DNA samples, and at a breach of genetic data protection. European legal provisions are especially mentioned.

Confidentiality↗
PubMed2001

The map problem: a comparison of genetic and sequence-based physical maps.

The genetic order of autosomal genome-scan markers from Marshfield panels 9 and 10 were compared with their physical order, on the basis of the assembled nonredundant human genome sequence from the Human Genome Project-Santa Cruz (HGP-sc; October 2000 and April 2001 releases) and Celera (CEL; February 2001 release) databases. The genetic order of 96% of the markers on the Marshfield map for panel 10 is supported by a likelihood ratio of > or = 3 (odds ratio of 1,000:1). Inconsistencies with the genetic panel 10 map were found for 5% and 2% of the markers in the CEL and HGP-sc sequences, respectively. These inconsistencies consisted of both positional and chromosomal-assignment disagreements. For the majority of these inconsistent markers, the genetic order was supported by a likelihood ratio of > or = 3, and the physical order in the other assembly matched the genetic order. The majority of the inconsistencies between the physical- and genetic-map order point to errors in the physical-map order. A Web site is made available that displays inconsistencies for genetic markers from Marshfield panels 9 and 10 between their genetic-map positions and sequence-based physical-map positions, as well as inconsistencies between their sequence-based physical position. This Web site also contains genetic-map distances, physical-map positions from the Celera and Human Genome Project sequence, and likelihood-ratio support for the genetic maps.

Chromosome Mapping↗
PubMed2006

Cellular transcriptomics -- the next phase of endocrine expression profiling.

Transcriptome analysis, or global gene expression profiling, has become a commonly used and valuable tool in both basic and clinical endocrine research. Novel endocrine regulators have 'surfaced' and greater consideration is now given to understanding function at the level of gene networks. Recent developments have shown that the transcriptome is considerably larger and more divergently expressed than was previously thought. Endocrine cells express a great variety of coding and noncoding RNAs in a highly cell-specific manner. If further value is to be taken from this research area, then steps towards defined cellular transcriptomics must be taken. New sampling techniques that utilize novel genetic models are a key first step.

Animals↗
PubMed2006

A wing expressed sequence tag resource for Bicyclus anynana butterflies, an evo-devo model.

BACKGROUND: Butterfly wing color patterns are a key model for integrating evolutionary developmental biology and the study of adaptive morphological evolution. Yet, despite the biological, economical and educational value of butterflies they are still relatively under-represented in terms of available genomic resources. Here, we describe an Expression Sequence Tag (EST) project for Bicyclus anynana that has identified the largest available collection to date of expressed genes for any butterfly. RESULTS: By targeting cDNAs from developing wings at the stages when pattern is specified, we biased gene discovery towards genes potentially involved in pattern formation. Assembly of 9,903 ESTs from a subtracted library allowed us to identify 4,251 genes of which 2,461 were annotated based on BLAST analyses against relevant gene collections. Gene prediction software identified 2,202 peptides, of which 215 longer than 100 amino acids had no homology to any known proteins and, thus, potentially represent novel or highly diverged butterfly genes. We combined gene and Single Nucleotide Polymorphism (SNP) identification by constructing cDNA libraries from pools of outbred individuals, and by sequencing clones from the 3' end to maximize alignment depth. Alignments of multi-member contigs allowed us to identify over 14,000 putative SNPs, with 316 genes having at least one high confidence double-hit SNP. We furthermore identified 320 microsatellites in transcribed genes that can potentially be used as genetic markers. CONCLUSION: Our project was designed to combine gene and sequence polymorphism discovery and has generated the largest gene collection available for any butterfly and many potential markers in expressed genes. These resources will be invaluable for exploring the potential of B. anynana in particular, and butterflies in general, as models in ecological, evolutionary, and developmental genetics.

Animals↗
PubMed2006

Positional cloning: single-gene cardiovascular disorders.

Positional cloning is a comprehensive genetic strategy used to identify a disease-causing gene without any prior knowledge of the pathogenesis or protein defects involved in the disease process. The basic process involves collection of accurately diagnosed patients and their family members, genotyping DNAs with polymorphic DNA markers mapped to specific regions on chromosomes, genetic linkage analysis to determine markers that are in close proximity to the chromosome location of the disease gene and to define the critical region by haplotype analysis, identification and selection of candidate genes residing in the critical region, and, eventually, identification of the disease-causing DNA sequence variants by various methods. Many molecular techniques are utilized in positional cloning. Bioinformatics and computation analysis are significant and indispensable components of such a study, and are detailed elsewhere in this volume. This chapter presents a few basic laboratory protocols for conducting positional cloning: genomic DNA preparation, genotyping polymorphic markers, DNA sequencing, and related procedures that serve on fluorescent-labeled and capillary electrophoresis-based semi-automated genetic analysis systems.

Cardiovascular Diseases↗
PubMed2003

Commercial biobanks and genetic research: ethical and legal issues.

Human biological material is recognized as an important tool in research, and the demand for collections that combine samples and data is increasing. For-profit companies have assumed a leading role in assembling and managing these collections. The emergence of commercial biobanks has raised significant ethical and legal issues. The growing awareness of the importance of human biological material in research has been accompanied by a growing awareness of the deficiencies of existing archives of tissue. Commercial biobanks are attempting to position themselves as a, if not the, solution to problems that include a lack of public trust in researchers and lack of financial resources to support the prospective creation of collections that meet the highest scientific and ethical standards in the non-profit sector. Broad social and policy questions surrounding the operation of commercial biobanks have been raised however. International documents, in particular, suggest discomfort with the idea of gain from the mere transfer or exchange of human genetic material and information. Commercial involvement in the development of useful products from tissue is generally not condemned, so long as there is attention to scientific and social norms. Views on the acceptability of commercial biobanks vary. Specific issues that arise when commercial biobanks are permitted--in the areas of consent, recruitment, confidentiality, and accountability--are also relevant to the operation of public and private, non-profit biobanks. Although many uncertainties remain, consensus seems to be forming on a number of issues. For example, there appears to be agreement that blanket consent to future unspecified research uses, with no conditions, is unacceptable. Indeed, many of the leading commercial biobanks have been attentive to concerns about consent, recruitment, and confidentiality. Unfortunately, the binding nature of assurances in these areas is unclear, especially given the risk of insolvency. Hence, accountability may be the most important area of concern in relation to commercial biobanks. A few countries have enacted general legislation providing for comprehensive regulation of biobanks, for example, through licensure. Efforts to achieve harmonization of standards at the international level, and cautions against an approach that focuses on biobanking for genetic research alone, are to be applauded.

Biological Specimen Banks↗
PubMed2004

Functional conservation and divergence of intersex, a gene required for female differentiation in Drosophila melanogaster.

In Drosophila melanogaster, somatic sexual differentiation is regulated by a well characterized genetic hierarchy, by which the ratio of X chromosomes to autosomes (X:A) ultimately directs the deployment of sex-specific transcription factors encoded by doublesex (dsx) and fruitless (fru). In other dipterans, the X:A ratio is not the primary sex-determination signal. Correspondingly, the Drosophila hierarchy is not fully conserved. In all non-drosophilid fly species examined, Sex-lethal (Sxl), the master switch at the top of the Drosophila hierarchy, does not control somatic sex. This rapid divergence contrasts with the apparently deep conservation of dsx, which in Drosophila controls virtually all aspects of somatic sex except for male courtship behavior (which is controlled by fru). Sex-specific dsx mRNAs have been reported in Diptera, Lepidoptera and Hymenoptera, and dsx homologs in nematodes and mammals are required for aspects of male differentiation. Thus, it seems that the bottom of the hierarchy is rather ancient, especially compared with the top. To test this, we cloned insect and vertebrate homologs of the Drosophila gene intersex (ix), which functions together with dsx at the bottom of the hierarchy in females. When expressed in D. melanogaster females mutant at the endogenous ix gene, dipteran and lepidopteran ix homologs restore proper sexual differentiation, substantiating the hypothesis that ix, like dsx, is broadly conserved. When the mouse homolog is expressed it produces a dominant-negative phenotype suggesting partial functional divergence. Our results raise the possibility that a functional association between ix- and dsx-related gene products existed before the origin of the bifunctional dsx gene used in insect sex determination.

Amino Acid Sequence↗
PubMed2001

Systematic genetic analysis with ordered arrays of yeast deletion mutants.

In Saccharomyces cerevisiae, more than 80% of the approximately 6200 predicted genes are nonessential, implying that the genome is buffered from the phenotypic consequences of genetic perturbation. To evaluate function, we developed a method for systematic construction of double mutants, termed synthetic genetic array (SGA) analysis, in which a query mutation is crossed to an array of approximately 4700 deletion mutants. Inviable double-mutant meiotic progeny identify functional relationships between genes. SGA analysis of genes with roles in cytoskeletal organization (BNI1, ARP2, ARC40, BIM1), DNA synthesis and repair (SGS1, RAD27), or uncharacterized functions (BBC1, NBP2) generated a network of 291 interactions among 204 genes. Systematic application of this approach should produce a global map of gene function.

Carrier Proteins↗