We describe a map of 1.42 million single nucleotide polymorphisms (SNPs) distributed throughout the human genome, providing an average density on available sequence of one SNP every 1.9 kilobases. These SNPs were primarily discovered by two projects: The SNP Consortium and the analysis of clone overlaps by the International Human Genome Sequencing Consortium. The map integrates all publicly available SNPs with described genes and other genomic features. We estimate that 60,000 SNPs fall within exon (coding and untranslated regions), and 85% of exons are within 5 kb of the nearest SNP. Nucleotide diversity varies greatly across the genome, in a manner broadly consistent with a standard population genetic model of human history. This high-density SNP map provides a public resource for defining haplotype variation across the genome, and should help to identify biomedically important genes for diagnosis and therapy.

Background: Previous studies have indicated that the thread carpal tunnel release (TCTR) is a safe and effective technique. Through a study on 11 cadaveric wrists, the TCTR procedure was modified and the needle control accuracy was improved to 0.15 to 0.2 mm, which is precise enough to preserve superficial palmar aponeurosis (SupPA), Berrettini branch, and common digital nerves. The aim of the present study was to verify the modified TCTR clinically. Methods: The modified TCTR was performed on 159 hands of 116 patients. The Boston Carpal Tunnel Syndrome Questionnaire was used for assessing the outcomes. Statistical analyses were used to compare the outcomes with the available data from the literature for the open and endoscopic techniques. Results: TCTR led to significant improvement in the short-term results, and the outcomes were better in long-term results compared with the open or endoscopic release. The SupPA, Berrettini branch, and common digital nerves were protected. There was no neurovascular complication for any case. Significant relief of symptoms was observed 3 to 5 hours post procedure. Most patients used their hands on the day of the procedure for simple daily activity. Patients reported their sleep quality was improved on the surgical day. Most patients with office jobs were able to return to work on postoperative day 1, and those with repetitive jobs returned to work in about 2 weeks. The statistical evidence proves that the modified TCTR procedure results in improved clinical outcomes as compared with open carpal tunnel release (CTR) and endoscopic CTR. Conclusions: The TCTR procedure has been shown to be a safe and effective technique for CTR. The modified TCTR procedure minimizes postoperative complications, such as pillar pain, scar tenderness, or functional weakness, by avoiding unnecessary injuries to the surrounding structures around the transverse carpal ligament during the procedure.

Gramene (http://www.gramene.org) is a comparative genome mapping database for grasses and a community resource for rice (Oryza sativa). It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, and publications, with a curated database of rice mutants (genes and alleles), molecular markers, and proteins. Gramene curators read and extract detailed information from published sources, summarize that information in a structured format, and establish links to related objects both inside and outside the database, providing seamless connections between independent sources of information. Genetic, physical, and sequence-based maps of rice serve as the fundamental organizing units and provide a common denominator for moving across species and genera within the grass family. Comparative maps of rice, maize (Zea mays), sorghum (Sorghum bicolor), barley (Hordeum vulgare), wheat (Triticum aestivum), and oat (Avena sativa) are anchored by a set of curated correspondences. In addition to sequence-based mappings found in comparative maps and rice genome displays, Gramene makes extensive use of controlled vocabularies to describe specific biological attributes in ways that permit users to query those domains and make comparisons across taxonomic groups. Proteins are annotated for functional significance using gene ontology terms that have been adopted by numerous model species databases. Genetic variants including phenotypes are annotated using plant ontology terms common to all plants and trait ontology terms that are specific to rice. In this paper, we present a brief overview of the search tools available to the plant research community in Gramene.

Gramene (http://www.gramene.org/) is a comparative genome database for cereal crops and a community resource for rice. We are populating and curating Gramene with annotated rice (Oryza sativa) genomic sequence data and associated biological information including molecular markers, mutants, phenotypes, polymorphisms and Quantitative Trait Loci (QTL). In order to support queries across various data sets as well as across external databases, Gramene will employ three related controlled vocabularies. The specific goal of Gramene is, first to provide a Trait Ontology (TO) that can be used across the cereal crops to facilitate phenotypic comparisons both within and between the genera. Second, a vocabulary for plant anatomy terms, the Plant Ontology (PO) will facilitate the curation of morphological and anatomical feature information with respect to expression, localization of genes and gene products and the affected plant parts in a phenotype. The TO and PO are both in the early stages of development in collaboration with the International Rice Research Institute, TAIR and MaizeDB as part of the Plant Ontology Consortium. Finally, as part of another consortium comprising macromolecular databases from other model organisms, the Gene Ontology Consortium, we are annotating the confirmed and predicted protein entries from rice using both electronic and manual curation.

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