The Human Variome Project (HVP) 2009 Forum "Towards Establishing Standards".

The May 2009 Human Variome Project (HVP) Forum "Towards Establishing Standards" was a round table discussion attended by delegates from groups representing international efforts aimed at standardizing several aspects of the HVP: mutation nomenclature, description and annotation, clinical ontology, means to better characterize unclassified variants (UVs), and methods to capture mutations from diagnostic laboratories for broader distribution to the medical genetics research community. Methods for researchers to receive credit for their effort at mutation detection were also discussed.

Human mutation databases.

The first part of this unit compares general and locus-specific mutation databases. The second section deals with submitting data. The third part provides guidance for accessing mutation data.

Human mutation databases.

The first part of this unit compares general and locus-specific mutation databases. The second section deals with submitting data. The third part provides guidance for accessing mutation data.

General mutation databases: analysis and review.

Databases of mutations causing Mendelian disease play a crucial role in research, diagnostic and genetic health care and can play a role in life and death decisions. These databases are thus heavily used, but only gene or locus specific databases have been previously reviewed for completeness, accuracy, currency and utility. We have performed a review of the various general mutation databases that derive their data from the published literature and locus specific databases.

A survey of locus-specific database curation. Human Genome Variation Society.

It is widely accepted that curation of variation in genes is best performed by experts in those genes and their variation. However, obtaining funding for such variation is difficult even though up-to-date lists of variations in genes are essential for optimum delivery of genetic healthcare and for medical research. This study was undertaken to gather information on gene-specific databases (locus-specific databases) in an effort to understand their functioning, funding and needs.

The challenge of documenting mutation across the genome: the human genome variation society approach.

New methods for the detection of mutations and the completion of the human genome sequencing project have contributed to an exponential rise in variation information that must be collected, quality controlled, documented, and stored safely to ensure future availability to health care professionals, researchers, and others. There may be anywhere from one to more than 1,000 mutations in any given gene. To date, this information has been collected by general databases such as Online Mendelian Inheritance in Man (OMIM) or the Human Gene Mutation Database (HGMD), which collect only published mutations and, in the case of OMIM, selected published mutations.

Novel TP53 gene mutations in tumors of Russian patients with breast cancer detected using a new solid phase chemical cleavage of mismatch method and identified by sequencing.

Mutations in the tumor-suppressor p53 gene TP53 are frequent in most human cancers including breast cancer. A new solid phase chemical cleavage of mismatch method (CCM) allowed rapid and efficient screening and analysis of the TP53 gene in DNA samples extracted from tumors of 89 breast cancer patients. The novel CCM technique utilized silica beads and the potassium permanganate/tetraethylammonium chloride (KMnO(4)/TEAC) and hydroxylamine (NH(2)OH) reactions were performed sequentially in a single tube.

Time for a unified system of mutation description and reporting: a review of locus-specific mutation databases.

Mutation databases of human genes are assuming an increasing importance in all areas of health care. In addition, more and more experts in the mutations and diseases of particular genes are curating published and unpublished mutations in locus-specific databases (LSDB). These databases contain such extensive information that they have become known as knowledge bases.

7th International HUGO Mutation Database Meeting, October 19, 1999, San Francisco, USA.

The 7th International HUGO Mutation Database Meeting was held on October 19, 1999 in conjunction with the annual meeting of the American Society of Genetics in San Fransisco, California, U.S.A.

Quality control in the discovery, reporting, and recording of genomic variation.

The usefulness of any database is dependent on the quality of its content. This is so for mutation databases and has been a continuing concern for those interested in such databases. This article discusses the critical points that determine the quality of the data, such as PCR errors, incomplete scanning, examination of the effect of the variation, and reporting and deposition of the mutations in a database.

6th International HUGO Mutation Database Meeting, March 27, 1999, Brisbane, Australia.

The 6th International HUGO Mutation Database Meeting was held on March 27, 1999, in conjunction with the Human Genome Meeting HGM 1999, at the Brisbane Conference and Exhibition Centre, Brisbane, Australia. Meeting highlights are described.

Complete DNA sequence of yeast chromosome XI.

The complete DNA sequence of the yeast Saccharomyces cerevisiae chromosome XI has been determined. In addition to a compact arrangement of potential protein coding sequences, the 666,448-base-pair sequence has revealed general chromosome patterns; in particular, alternating regional variations in average base composition correlate with variations in local gene density along the chromosome. Significant discrepancies with the previously published genetic map demonstrate the need for using independent physical mapping criteria.

The complete sequencing of a 24.6 kb segment of yeast chromosome XI identified the known loci URA1, SAC1 and TRP3, and revealed 6 new open reading frames including homologues to the threonine dehydratases, membrane transporters, hydantoinases and the phospholipase A2-activating protein.

We report the entire sequence of a 26.4 kb segment of chromosome XI of Saccharomyces cerevisiae. Identification of the known loci URA1, TRP3 and SAC1 revealed a translocation compared to the genetic map.

Improved shuttle vectors for cloning and high-level Cu(2+)-mediated expression of foreign genes in yeast.

New yeast episomal vectors having a high degree of utility for cloning and expression in Saccharomyces cerevisiae are described. One vector, pYEULlacZ, is based on pUC19 and employs the pUC19 multiple cloning site for the selection of recombinants in Escherichia coli by lacZ inactivation. In addition, the vector contains two genes, URA3 and leu2-d, for selection of the plasmid in ura3 or leu2 yeast strains.

Constitutive expression of the Saccharomyces cerevisiae CUP1 gene in Kluyveromyces lactis.

Shuttle plasmids, pE1.CUP1B and pE1.CUP1E of 10.