人类遗传突变数据库及其应用

随着人类基因组序列草图的完成,基因组突变的研究显得日益重要,而越来越多的突变信息的积累,使得各种突变数据库相继诞生。本文根据各种数据库的功能,对目前的人类突变相关数据库资源进行了分类总结,分类为突变数据库、单核苷酸多态信息数据库、与疾病相关的突变数据库、突变对蛋白质的影响、突变图谱以及特定基因的突变信息,分析该如何合理使用这些遗传突变数据资源,以及目前的突变数据库所存在的问题。Abstract：Researches on genome mutation are becoming more and more important with the finish of human genome DNA draft. This review is to classify the existing human mutation databases, including mutation database, SNP(single nucleotide polymorphisms) databases, mutation databases about disease, mutation databases about proteins, mutation databases about map and mutation information about specific gene. We also give advice on how to utilize these mutation databases, and discuss problems of existing databases.     

Identification of RNA editing sites in the SNP database

The relationship between human inherited genomic variations and phenotypic differences has been the focus of much research effort in recent years. These studies benefit from millions of single-nucleotide polymorphism (SNP) records available in public databases, such as dbSNP. The importance of identifying false dbSNP records increases with the growing role played by SNPs in linkage analysis for disease traits. In particular, the emerging understanding of the abundance of DNA and RNA editing calls for a careful distinction between inherited SNPs and somatic DNA and RNA modifications. In order to demonstrate that some of the SNP database records are actually somatic modification, we focus on one type of these modifications, namely A-to-I RNA editing, and present evidence for hundreds of dbSNP records that are actually editing sites. We provide a list of 102 RNA editing sites previously annotated in dbSNP database as SNPs, and experimentally validate seven of these. Interestingly, we show how dbSNP can serve as a starting point to look for new editing sites. Our results, for this particular type of RNA editing, demonstrate the need for a careful analysis of SNP databases in light of the increasing recognition of the significance of somatic sequence modifications.     

High-Resolution Multipoint Linkage-Disequilibrium Mapping in the Context of a Human Genome Sequence

A new method is presented for fine-scale linkage disequilibrium (LD) mapping of a disease mutation; it uses multiple linked single-nucleotide polymorphisms, restriction-fragment-length polymorphisms, or microsatellite markers and incorporates information from an annotated human genome sequence (HGS) and from a human mutation database. The method takes account of population demographic effects, using Markov chain Monte Carlo methods to integrate over the unknown gene genealogy and gene coalescence times. Information about the relative frequency of disease mutations in exons, introns, and other regions, from mutational databases, as well as assumptions about the completeness of the gene annotation, are used with an annotated HGS, to generate a prior probability that a mutation lies at any particular position in a specified region of the genome. This information is updated with information about mutation location, from LD at a set of linked markers in the region, to generate the posterior probability density of the mutation location. The performance of the method is evaluated by simulation and by analysis of a data set for diastrophic dysplasia (DTD) in Finland. The DTD disease gene has been positionally cloned, so the actual location of the mutation is known and can be compared with the position predicted by our method. For the DTD data, the addition of information from an HGS results in disease-gene localization at a resolution that is much higher than that which would be possible by LD mapping alone. In this case, the gene would be found by sequencing a region < or =7 kb in size.     

The use of single-nucleotide polymorphism maps in pharmacogenomics

Single-nucleotide polymorphisms (SNPs), common variations among the DNA of individuals, are being uncovered and assembled into large SNP databases that promise to enable the dissection of the genetic basis of disease and drug response (i.e., pharmacogenomics). Although great strides have been made in understanding the diversity of the human genome, such as the frequency, distribution, and type of genetic variation that exists, the feasibility of applying this information to uncover useful pharmacogenomic markers is uncertain. The health care industry is clamoring for access to SNP databases for use in research in the hope of revolutionizing the drug development process. As the reality of using SNPs to uncover drug response markers is rarely addressed, this review discusses practical issues, such as patient sample size, SNP density and genome coverage, and data interpretation, that will be important for determining the applicability of pharmacogenomic information to medical practice.     

MitoP2: An Integrative Tool for the Analysis of the Mitochondrial Proteome

Mitochondria are crucial for normal cell metabolism and maintenance. Mitochondrial dysfunction has been implicated in a spectrum of human diseases, ranging from rare monogenic to common multifactorial disorders. Important for the understanding of organelle function is the assignment of its constituents, and although over 1,500 proteins are predicted to be involved in mammalian mitochondrial function, so far only about 900 are assigned to mitochondria with reasonable certainty. Continuing efforts are being taken to obtain a complete inventory of the mitochondrial proteome by single protein studies and high-throughput approaches. To be of best value for the scientific community this data needs to be structured, explored, and customized. For this purpose, the MitoP2 database () was established and is maintained in order to incorporate such data. The central database contains manually evaluated yeast, mouse, and human reference proteins, which show convincing evidence of a mitochondrial location. In addition, entries from genome-wide approaches that suggest protein localization are integrated and serve to compile a combined score for each candidate, which provides a best estimate of mitochondrial localization. Furthermore, it integrates information on the orthology between species, including Saccharomyces cerevisiae, mouse, human, Arabidopsis thaliana, and Neurospora crassa, thus mutually enhancing evidence across species. In contrast to other known databases, MitoP2 takes into account the reliability by which the protein is estimated as being mitochondrially located, as described herein. Multiple search functions, as well as information on disease causing genes and available mouse models, makes MitoP2 a valuable tool for the genetic investigation of human mitochondrial pathology.     

The human gene mutation database.

The Human Gene Mutation Database (HGMD) represents a comprehensive core collection of data on published germline mutations in nuclear genes underlying human inherited disease. By September 1997, the database contained nearly 12 000 different lesions in a total of 636 different genes, with new entries currently accumulating at a rate of over 2000 per annum. Although originally established for the scientific study of mutational mechanisms in human genes, HGMD has acquired a much broader utility to researchers, physicians and genetic counsellors so that it was made publicly available at http://uwcm.ac.uk/uwcm/mg/hgmd0.html in April 1996. Mutation data in HGMD are accessible on the basis of every gene being allocated one web page per mutation type, if data of that type are present. Meaningful integration with phenotypic, structural and mapping information has been accomplished through bi-directional links between HGMD and both the Genome Database (GDB) and Online Mendelian Inheritance in Man (OMIM), Baltimore, USA. Hypertext links have also been established to Medline abstracts through Entrez , and to a collection of 458 reference cDNA sequences also used for data checking. Being both comprehensive and fully integrated into the existing bioinformatics structures relevant to human genetics, HGMD has established itself as the central core database of inherited human gene mutations.     

An inquiry into protein structure and genetic disease: introducing undergraduates to bioinformatics in a large introductory course

This inquiry-based lab is designed around genetic diseases with a focus on protein structure and function. To allow students to work on their own investigatory projects, 10 projects on 10 different proteins were developed. Students are grouped in sections of 20 and work in pairs on each of the projects. To begin their investigation, students are given a cDNA sequence that translates into a human protein with a single mutation. Each case results in a genetic disease that has been studied and recorded in the Online Mendelian Inheritance in Man (OMIM) database. Students use bioinformatics tools to investigate their proteins and form a hypothesis for the effect of the mutation on protein function. They are also asked to predict the impact of the mutation on human physiology and present their findings in the form of an oral report. Over five laboratory sessions, students use tools on the National Center for Biotechnology Information (NCBI) Web site (BLAST, LocusLink, OMIM, GenBank, and PubMed) as well as ExPasy, Protein Data Bank, ClustalW, the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, and the structure-viewing program DeepView. Assessment results showed that students gained an understanding of the Web-based databases and tools and enjoyed the investigatory nature of the lab.     

SNPCEQer II: the integrated detection and analysis of SNPs in DNA sequences

SNPCEQer II is a graphical user interface (GUI)-based application that integrates single nucleotide polymorphism (SNP) detection, SNP analysis and SNP editing in the Microsoft Windows (R) environment. SNPCEQer II detects SNPs in DNA sequences generated by the Beckman CEQ TM 2000 XL DNA analysis system. It provides tools to analyse SNPs by inspecting and comparing trace data (chromatograms) around putative SNPs with that of other related DNA sequences, and it can search for those SNPs in the National Center for Biotechnology Information (NCBI) databases. SNPCEQer II can determine the mutation type of a coding SNP and generate data for submission to the dbSNP database. The SNP report can be edited and printed, as can the chromatograms. SNPCEQer II is implemented in Visual C++.     

大规模单核苷酸多态性分析与肿瘤易感性

单核苷酸多态性(SNPs)是人类基因组中最常见的变异形式。作为第三代遗传标记,SNP在基因定位、克隆、遗传多态性方面具有广泛应用,特别是作为基因诊断标记在预防医学中具有十分重要的作用。近年来,随着人类基因组计划的发展,数以百万计的SNP被陆续发现,并可在公共数据库中免费获得。SNP数量的快速增加和SNP检测方法的发展,为其在肿瘤易感性领城的应用提供了可能。在本综述中,我们介绍了几种高通量检测SNP的分析方法,总结了大规模SNP分析技术在肿瘤易感性中的应用,介绍了目前人们对于不同人群中的SNP分析、肿瘤易感基因、个体肿瘤易感性的理解,以及研究SNP标记与肿瘤易感性关系时存在的难点。     

TRbase: a database relating tandem repeats to disease genes for the human genome

MOTIVATION: Tandem repeats are associated with disease genes, play an important role in evolution and are important in genomic organization and function. Although much research has been done on short perfect patterns of repeats, there has been less focus on imperfect repeats. Thus, there is an acute need for a tandem repeats database that provides reliable and up to date information on both perfect and imperfect tandem repeats in the human genome and relates these to disease genes. RESULTS: This paper presents a web-accessible relational tandem repeats database that relates tandem repeats to gene locations and disease genes of the human genome. In contrast to other available databases, this database identifies both perfect and imperfect repeats of 1-2000 bp unit lengths. The utility of this database has been illustrated by analysing these repeats for their distribution and frequencies across chromosomes and genomic locations and between protein-coding and non-coding regions. The applicability of this database to identify diseases associated with previously uncharacterized tandem repeats is demonstrated.     

An Update on the Functional Molecular Immunology (FIMM) Database

Data on the major histocompatibility complex, T-cell epitopes, B-cell epitopes, antigens and diseases are heterogeneous and scattered among different databases and the literature. Since it has become increasingly difficult to obtain an integrated view of functional immune response components, we have developed and updated over several years the Functional molecular IMMunology (FIMM) database (http:// research.i2r.a-star.edu.sg/fimm/). FIMM contains integrated expert-curated data on protein antigens, and on human immunological receptors that recognise and bind them in healthy or disease states. Interfaces with multiple, intuitive query options and query reports provide immunologists with prioritised information that aids data interpretation, vaccine target discovery and immune disease research.     

HDAPD: a web tool for searching the disease-associated protein structures

Background

PCR-restriction fragment length polymorphism (RFLP) assay is a cost-effective method for SNP genotyping and mutation detection, but the manual mining for restriction enzyme sites is challenging and cumbersome. Three years after we constructed SNP-RFLPing, a freely accessible database and analysis tool for restriction enzyme mining of SNPs, significant improvements over the 2006 version have been made and incorporated into the latest version, SNP-RFLPing 2.

Results

The primary aim of SNP-RFLPing 2 is to provide comprehensive PCR-RFLP information with multiple functionality about SNPs, such as SNP retrieval to multiple species, different polymorphism types (bi-allelic, tri-allelic, tetra-allelic or indels), gene-centric searching, HapMap tagSNPs, gene ontology-based searching, miRNAs, and SNP500Cancer. The RFLP restriction enzymes and the corresponding PCR primers for the natural and mutagenic types of each SNP are simultaneously analyzed. All the RFLP restriction enzyme prices are also provided to aid selection. Furthermore, the previously encountered updating problems for most SNP related databases are resolved by an on-line retrieval system.

Conclusions

The user interfaces for functional SNP analyses have been substantially improved and integrated. SNP-RFLPing 2 offers a new and user-friendly interface for RFLP genotyping that can be used in association studies and is freely available at http://bio.kuas.edu.tw/snp-rflping2.     

Genome mapping databases: data acquisition, storage and access.

The introduction of the genome database to the human gene mapping community in September 1990 heralded the advent of a new generation of databases to serve the needs of the human genome initiative over the coming years. The databases will act as a fulcrum around which the activities of the human genome initiative can be coordinated at an international level.     

SNPchiMp v.3: integrating and standardizing single nucleotide polymorphism data for livestock species

Background

In recent years, the use of genomic information in livestock species for genetic improvement, association studies and many other fields has become routine. In order to accommodate different market requirements in terms of genotyping cost, manufacturers of single nucleotide polymorphism (SNP) arrays, private companies and international consortia have developed a large number of arrays with different content and different SNP density. The number of currently available SNP arrays differs among species: ranging from one for goats to more than ten for cattle, and the number of arrays available is increasing rapidly. However, there is limited or no effort to standardize and integrate array- specific (e.g. SNP IDs, allele coding) and species-specific (i.e. past and current assemblies) SNP information.

Results

Here we present SNPchiMp v.3, a solution to these issues for the six major livestock species (cow, pig, horse, sheep, goat and chicken). Original data was collected directly from SNP array producers and specific international genome consortia, and stored in a MySQL database. The database was then linked to an open-access web tool and to public databases. SNPchiMp v.3 ensures fast access to the database (retrieving within/across SNP array data) and the possibility of annotating SNP array data in a user-friendly fashion.

Conclusions

This platform allows easy integration and standardization, and it is aimed at both industry and research. It also enables users to easily link the information available from the array producer with data in public databases, without the need of additional bioinformatics tools or pipelines. In recognition of the open-access use of Ensembl resources, SNPchiMp v.3 was officially credited as an Ensembl E!mpowered tool. Availability at http://bioinformatics.tecnoparco.org/SNPchimp.     

The vegetable SNP database: An integrated resource for plant breeders and scientists

Single nucleotide polymorphisms (SNPs) are widely used in genetic research and molecular breeding. To date, the genomes of many vegetable crops have been assembled, and hundreds of core germplasms for each vegetable have been sequenced. However, these data are not currently easily accessible because they are stored on different public databases. Therefore, a vegetable crop SNP database should be developed that hosts SNPs demonstrated to have a high success rate in genotyping for genetic research (herein, “alpha SNPs”). We constructed a database (VegSNPDB, http://www.vegsnpdb.cn/) containing the sequence data of 2032 germplasms from 16 vegetable crop species. VegSNPDB hosts 118,725,944 SNPs of which 4,877,305 were alpha SNPs. SNPs can be searched by chromosome number, position, SNP type, genetic population, or specific individuals, as well as the values of MAF, PIC, and heterozygosity. We hope that VegSNPDB will become an important SNP database for the vegetable research community.     

Loss-of-function mutation in tryptophan hydroxylase-2 identified in unipolar major depression

Dysregulation of central serotonin neurotransmission has been widely suspected as an important contributor to major depression. Here, we identify a (G1463A) single nucleotide polymorphism (SNP) in the rate-limiting enzyme of neuronal serotonin synthesis, human tryptophan hydroxylase-2 (hTPH2). The functional SNP in hTPH2 replaces the highly conserved Arg441 with His, which results in approximately 80% loss of function in serotonin production when hTPH2 is expressed in PC12 cells. Strikingly, SNP analysis in a cohort of 87 patients with unipolar major depression revealed that nine patients carried the mutant (1463A) allele, while among 219 controls, three subjects carried this mutation. In addition, this functional SNP was not found in a cohort of 60 bipolar disorder patients. Identification of a loss-of-function mutation in hTPH2 suggests that defect in brain serotonin synthesis may represent an important risk factor for unipolar major depression.     

Long non-coding RNA Databases in Cardiovascular Research

With the rising interest in the regulatory functions of long non-coding RNAs (lncRNAs) in complex human diseases such as cardiovascular diseases, there is an increasing need in public databases offering comprehensive and integrative data for all aspects of these versatile molecules. Recently, a variety of public data repositories that specialized in lncRNAs have been developed, which make use of huge high-throughput data particularly from next-generation sequencing (NGS) approaches. Here, we provide an overview of current lncRNA databases covering basic and functional annotation, lncRNA expression and regulation, interactions with other biomole-cules, and genomic variants influencing the structure and function of lncRNAs. The prominent lncRNA antisense noncoding RNA in the INK4 locus (ANRIL), which has been unequivocally associated with coronary artery disease through genome-wide association studies (GWAS), serves as an example to demonstrate the features of each individual database.