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Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project.

Immunogenetics | Jan 18, 2008

The human major histocompatibility complex (MHC) is contained within about 4 Mb on the short arm of chromosome 6 and is recognised as the most variable region in the human genome. The primary aim of the MHC Haplotype Project was to provide a comprehensively annotated reference sequence of a single, human leukocyte antigen-homozygous MHC haplotype and to use it as a basis against which variations could be assessed from seven other similarly homozygous cell lines, representative of the most common MHC haplotypes in the European population. Comparison of the haplotype sequences, including four haplotypes not previously analysed, resulted in the identification of >44,000 variations, both substitutions and indels (insertions and deletions), which have been submitted to the dbSNP database. The gene annotation uncovered haplotype-specific differences and confirmed the presence of more than 300 loci, including over 160 protein-coding genes. Combined analysis of the variation and annotation datasets revealed 122 gene loci with coding substitutions of which 97 were non-synonymous. The haplotype (A3-B7-DR15; PGF cell line) designated as the new MHC reference sequence, has been incorporated into the human genome assembly (NCBI35 and subsequent builds), and constitutes the largest single-haplotype sequence of the human genome to date. The extensive variation and annotation data derived from the analysis of seven further haplotypes have been made publicly available and provide a framework and resource for future association studies of all MHC-associated diseases and transplant medicine.

Pubmed ID: 18193213 RIS Download

Mesh terms: Computational Biology | Databases, Genetic | Genetic Variation | Genome, Human | HLA Antigens | Haplotypes | Humans | Terminology as Topic

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BacPac Resources Center: BAC Clones Distribution Center

It is the distribution arm of their academic laboratory. They operate on a cost-recovery mechanism in order to make the resources generated in their laboratory available to the academic scientific community. While clones and screening services are widely available, library arrays are primarily available to researchers with a scientific need to analyze most clones in the library. This site contains information on currently available BAC and PAC genomic DNA libraries, BAC Clones, PAC Clones, Fosmid Clones, cDNA collections, high-density colony hybridization filters, and BAC and PAC cloning vectors. Protocols used in our laboratory for the hybridization-based screening of colony filters, purification of BAC and PAC DNA, and end-sequencing methodologies, are also provided. BPRC does not list clones, for two reasons: 1)most clones have not been characterized and lack specific data. 2)all clones are part of libraries and all clones from a particular library share common characteristics. Hence, to find out if BPRC has a particular clone, one needs either use Automatic Clone Validation or else find out if the clone is compatible with the range of clone names for a corresponding clone library. Typically (although not always), clone names are derived from the library name. BPRC uses the NCBI-recommended clone nomenclature & library nomenclature. Most arrayed libraries are available in frozen microtiter dish format to academic and non-academic users provided that there is a scientific need for complete-library access. (for instance to annotate, modify or analyze all BAC clones as part of a genome project).

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dbSNP

Database serving as a central repository for both single base nucleotide substitutions and short deletion and insertion polymorphisms. Once discovered, these polymorphisms could be used by additional laboratories, using the sequence information around the polymorphism and the specific experimental conditions. (Note that dbSNP takes the looser "variation" definition for SNPs, so there is no requirement or assumption about minimum allele frequency.) The database accepts data submissions. dbSNP distinguishes a report of how to assay a SNP from the use of that SNP with individuals and populations. This separation simplifies some issues of data representation. However, these initial reports describing how to assay a SNP will often be accompanied by SNP experiments measuring allele occurrence in individuals and populations.

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IMGT/HLA

Database for sequences of the human major histocompatibility complex (HLA) and includes the official sequences for the WHO Nomenclature Committee For Factors of the HLA System. It currently contains 9,310 allele sequences (2013) along with detailed information concerning the material from which the sequence was derived and data on the validation of the sequences. It is established procedure for authors to submit the sequences directly to the IMGT/HLA Database for checking and assignment of an official name prior to publication, this avoids the problems associated with renaming published sequences and the confusion of multiple names for the same sequence. The need for reasonably rapid publication of new HLA allele sequences has necessitated an annual meeting of the WHO Nomenclature Committee for Factors of the HLA System. Additionally they now publish monthly HLA nomenclature updates both in journals and online to provide quick and easy access to new sequence information. The IMGT/HLA Database is part of the international ImMunoGeneTics project. In collaboration with the Imperial Cancer Research Fund (ICRF) and European Bioinformatics Institute (EBI) they have developed an Oracle database to house the HLA sequences in such a way as to allow users to present complex queries about the sequence, sequence features, references, contacts and allele designations to the database via a graphical user interface over the web. The IMGT/HLA Database Submission Tool allows direct submission of sequences to the WHO HLA Nomenclature Committee for Factors of the HLA System. The IMGT/HLA Database provides an FTP site for the retrieval of sequences in a number of pre-formatted files.

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Pompep

FTP site to access Schizosaccharomyces pombe protein data.

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RepeatMasker

A software tool that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Currently over 56% of human genomic sequence is identified and masked by the program. Sequence comparisons in RepeatMasker are performed by one of several popular search engines including nhmmer, cross_match, ABBlast/WUBlast, RMBlast and Decypher. RepeatMasker makes use of curated libraries of repeats and currently supports Dfam ( profile HMM library ) and RepBase ( consensus sequence library ).

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European Molecular Biology Laboratory; Heidelberg; Germany

An international research organization that is one of the world''s top research institutions dedicated to basic research in the molecular life sciences. Outstanding training is available at multiple levels: predoctoral students, postdocs and visiting scientists are provided with exceptional training opportunities. The cornerstones of EMBL''s mission are: to perform basic research in molecular biology, to train scientists, students and visitors at all levels, to offer vital services to scientists in the member states, and to develop new instruments and methods in the life sciences, and technology transfer. Research at EMBL is conducted by approximately 85 independent groups covering the spectrum of molecular biology. The Laboratory has five units: the main Laboratory in Heidelberg, and outstations in Hinxton near Cambridge (the European Bioinformatics Institute), Grenoble, Hamburg, and Monterotondo near Rome. EMBL is international, innovative and interdisciplinary. Its 1,400 employees from 60 nations represent scientific disciplines including biology, physics, chemistry and computer science.

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