HGVbase: a curated resource describing human DNA variation and phenotype relationships

The Human Genome Variation Database (HGVbase; http://hgvbase.cgb.ki.se) has provided a curated summary of human DNA variation for more than 5 years, thus facilitating research into DNA sequence variation and human phenotypes. The database has undergone many changes and improvements to accommodate increasing volumes and new types of data. The focus of HGVbase has recently shifted towards information on haplotypes and phenotypes, relationships between phenotypes and DNA variation, and collaborative efforts to provide a global resource for genome-phenome data. Open sharing and precise phenotype definitions are necessary to advance the current understanding of common diseases that are typified by complex aetiologies, small genetic effect sizes and multiple confounding factors that obscure positive study results. Association data will increasingly be collected as part of this new project thrust. This report describes the evolving features of HGVbase, and covers in detail the technological choices we have made to enable efficient storage and data mining of increasingly large and complex data sets.

HGVbase: a human sequence variation database emphasizing data quality and a broad spectrum of data sources

HGVbase (Human Genome Variation database; http://hgvbase.cgb.ki.se, formerly known as HGBASE) is an academic effort to provide a high quality and non-redundant database of available genomic variation data of all types, mostly comprising single nucleotide polymorphisms (SNPs). Records include neutral polymorphisms as well as disease-related mutations. Online search tools facilitate data interrogation by sequence similarity and keyword queries, and searching by genome coordinates is now being implemented. Downloads are freely available in XML, Fasta, SRS, SQL and tagged-text file formats. Each entry is presented in the context of its surrounding sequence and many records are related to neighboring human genes and affected features therein. Population allele frequencies are included wherever available. Thorough semi-automated data checking ensures internal consistency and addresses common errors in the source information. To keep pace with recent growth in the field, we have developed tools for fully automated annotation. All variants have been uniquely mapped to the draft genome sequence and are referenced to positions in EMBL/GenBank files. Data utility is enhanced by provision of genotyping assays and functional predictions. Recent data structure extensions allow the capture of haplotype and genotype information, and a new initiative (along with BiSC and HUGO-MDI) aims to create a central repository for the broad collection of clinical mutations and associated disease phenotypes of interest.

Posttraumatic stress disorder and the use of health services

OBJECTIVE

Prior research has demonstrated increased use of medical services among persons with anxiety and depression. This investigation examined the possible association of posttraumatic stress disorder (PTSD) with the use of nonmental health services.

METHOD

A case-comparison design enrolled 102 high users of health services and 54 low users who were assessed for PTSD diagnosis and severity of PTSD symptoms. Subjects were male veterans receiving services from the primary care clinics of the VA Boston Healthcare System during an 18-month period. Data were collected by interview by use of standardized instruments including the Clinician Administered PTSD Scale for DSM-IV, the Life Events Checklist, and the Beck Depression Inventory. Data analysis employed odds ratios, linear and logistic regression, and path analyses.

RESULTS

High users of health care were almost twice as likely as low users (27.5% vs. 14.8%) to meet diagnostic criteria for current PTSD. The two groups differed significantly on both symptom frequency and intensity. Path analyses showed an indirect positive association between PTSD and health services use, with physician-diagnosed health conditions as a mediating variable. Auxiliary analysis demonstrated that the combined mental health burden of PTSD and depression symptoms also is positively associated with number of health conditions.

CONCLUSIONS

The findings indicate that PTSD, alone and in combination with depression, has a direct negative relationship with physical health that, in turn, is associated with more frequent use of primary health care services. These results do not suggest that PTSD leads to inappropriate (eg, distress-motivated) use of services.

HGBASE: a database of SNPs and other variations in and around human genes

Human genome polymorphism is expected to play a key role in defining the etiologic basis of phenotypic differences between individuals in aspects such as drug responses and common disease predisposition. Relevant functional DNA changes will probably be located in or near to transcribed sequences, and include many single nucleotide polymorphisms. To aid the future analysis of such genome variation, HGBASE (Human Genic Bi-Allelic SEquences) was constructed as a means to gather human gene-linked polymorphisms from all possible public sources, and show these as a non-redundant set of records in a standardized and user-friendly database endowed with text and sequence based search facilities. After 1 year of presence on the WWW, the HGBASE project has compiled data for over 22 000 records, and this number continues to triple every 6-12 months with data harvested or submitted from all major public genome databases and published literature from the previous decade. Extensive annotation enhancement, internal consistency checking and manual review of every record is undertaken to address potential errors and deficiencies sometimes present in the original source data. The fully polished and comprehensive database is made freely available to all at http://hgbase.cgr.ki.se

Identification of 167 polymorphisms in 88 genes from candidate neurodegeneration pathways

Catalogs of intra-gene polymorphisms are needed to facilitate wide-ranging candidate gene-based association studies in common complex diseases. With this in mind, we have scanned multiple alignments of expressed sequence tags and of genomic DNA sequences (PCR products from four to eight unrelated individuals) to find polymorphisms in 195 genes putatively involved in neurodegenerative illness (including components of oxidative stress, excitotoxicity, inflammation, apoptosis and aging). This led to the discovery of 167 polymorphisms in 88 genes. These comprised 163 single nucleotide polymorphisms, one insertion/deletion, and three other variations involving more than one base pair. The polymorphisms were distributed in the exons (87), introns (70), and gene flanking regions (10). Of the exonic polymorphisms, 17 would give rise to non-synonymous amino acid substitutions. These findings now provide a valuable resource for association studies in neurodegenerative disorders such as Alzheimer's disease and Parkinson's disease.

Protective effects of the specific thromboxane receptor antagonist (+)-S145Na in splanchnic artery occlusion shock in rats

We studied the effects of a new potent thromboxane A2 receptor antagonist as a protective measure in circulatory shock induced by splanchnic artery occlusion and reperfusion. The celiac and superior mesenteric arteries of anesthetized rats were occluded for 40 min followed by reperfusion, resulting in a large decrease in mean arterial blood pressure usually leading to a fatal outcome within 60 to 90 min. Rats were treated with the specific thromboxane A2 receptor antagonist, (+)-S145Na, at one of three doses (50, 200 or 500 micrograms/kg) or with its vehicle (0.9% NaCl). In isolated rat aortic rings, (+)-S145Na was found to be a highly specific and potent thromboxane receptor antagonist having an IC50 of 1 ng/ml. The highest dose of the drug exhibited protection characterized by an attenuation in the increases in hematocrit (P less than .05), plasma cathepsin D activity (P less than .05), plasma aminonitrogen concentration (P less than .05), and plasma myocardial depressant factor activity (P less than .01) as well as increased survival rate and time (P less than .01), compared to the splanchnic artery occlusion shock group given the vehicle. The lowest dose of (+)-S145Na failed to provide protection, whereas the intermediate dose (i.e., 200 micrograms/kg) exerted less dramatic protective effects than the 500 micrograms/kg dose. These findings suggest an important role of thromboxane A2 in the pathogenesis of splanchnic artery occlusion shock, and that (+)-S145Na may be a useful agent in the treatment of bowel ischemia and its complications.

Acute effects of unsaturated fatty acids in splanchnic artery occlusion shock

Diets enriched with omega-3 unsaturated fatty acids are associated with decreased hypercholesterolemia and decreased risk of ischemic and atherosclerotic diseases. We studied the acute intravascular effects of some of these unsaturated fatty acids (i.e., eicosapentaenoic acid, EPA; docosahexaenoic acid, DHA) along with omega-6 unsaturated fatty acids, (i.e., linoleic and linolenic acid) in splanchnic artery occlusion (SAO) shock in rats. Anesthetized rats subjected to total occlusion of the celiac and superior mesenteric arteries for 40 minutes followed by reperfusion usually resulted in a fatal outcome 90-120 minutes after releasing the clamps. SAO shock rats treated with the omega-3 unsaturated fatty acid, EPA, exhibited an improved survival time and rate (p less than 0.05 from vehicle) compared to those receiving only vehicle (i.e., 50% ethanol). EPA and DHA treated SAO rats also exhibited lower plasma activities of the lysosomal protease, cathepsin D, free amino-nitrogen compounds, and the cardiotoxic peptide, myocardial depressant factor. These results indicate that omega-3 unsaturated fatty acids, especially EPA, have some acute beneficial effects in SAO shock in rats.

Anti-EDRF effect of tumor necrosis factor in isolated, perfused cat carotid arteries

Cat carotid arteries that have an intact endothelium were isolated and perfused with Krebs-Henseleit solution containing recombinant human tumor necrosis factor (rhTNF). Perfused arteries were preconstricted with KCl and then dilated with acetylcholine (ACh) or acidified NaNO2. After perfusion with TNF (4 micrograms/ml) for 120 min, the ACh-induced vasodilator response was markedly blunted, but the NaNO2 vasodilator response was not significantly affected. Arteries perfused with 2 micrograms/ml TNF for 60-120 min or with 4 micrograms/ml for 60 min did not develop a significantly impaired relaxation to ACh. Moreover, perfusion with 20-100 micrograms/ml cycloheximide, an inhibitor of protein synthesis, blocked the TNF-induced impairment of the relaxation to ACh. On the other hand, the vasodilator response to acidified NaNO2 did not change in any perfused carotid arteries. These results suggest that TNF promotes the synthesis of proteins that contribute to the damage of endothelial cells directly, probably by inhibiting endothelium-derived relaxing factor release.

Beneficial mechanisms of action of a prostacyclin enhancing agent in splanchnic artery occlusion shock

Defibrotide stimulates PGI2 production and exerts significant antithrombotic, fibrinolytic and plasminogen-activating activities. We studied its effects in splanchnic artery occlusion (SAO) shock in rats. Anesthetized rats subjected to total occlusion of the celiac and superior mesenteric arteries for 40 minutes developed a severe shock state following reperfusion usually resulting in death 90-120 minutes after releasing the clamps. Defibrotide 910 mg/kg +25 mg/kg/h) treated SAO shock rats maintained higher post-reperfusion mean arterial blood pressure compared to those receiving only the vehicle (0.9% NaCl). SAO shock rats treated with defibrotide exhibited lower plasma activities of the lysosomal protease cathepsin D (p less than 0.05 from vehicle) and myocardial depressant factor (p less than 0.02 from vehicle) as well as the plasma accumulation of free amino-nitrogen compounds (p less than 0.05 from vehicle). All SAO shock rats treated with defibrotide survived the entire 120 post-release period compared with only a 42% survival rate for rats receiving only the vehicle (p less than 0.02). These results suggest a remarkable protective effect of defibrotide in SAO shock.