Wednesday, 24 March 2010 11:18 UTC
One more important aspect of study design is the selection of variants for studying the association with the phenotype.
You may look into the disease pathways and get the information regarding the genes involved and the variants observed in those genes. Functional studies related to the variants also have to be checked or verified before selection of these variants. If any functional study is not done and the variant is known to change any aminoacid (in exonic region) or it is in the catalytic domain of an enzyme or it is in the important regulatory region controlling the expression of the gene. How get all these information?
With the availability of number of bioinformatics tools and web databases it is easy to access and retrieve the information related to these variants. The beginners mayl look into the below given databases for easy retrieval of the information related to the gene variants mostly SNPs (information related to the location, it’s impact, details of studies across different ethnic groups, functional studies and allele frequencies in different populations)
1. You may explore the information on variants and the detailed procedure for phenotyping and detailed procedures followed by disease or study wise from genome wide association studies available in database on genotype-phenotype association studies (dbGaP) available at: http://www.ncbi.nlm.nih.gov/gap/2. Another database by NCBI is dbSNP database contains all the required information for a particular variant on a gene which may be obtained by using a reference SNP iD (rsID) or by using search terms with the use of limits. If you know the rsID and know the flanking sequence or have an idea before hand, your job become s easy .This database gives more information about the SNP and easy to access if you have a prior information about the variant. You may also find the links to different companies giving the information on the genotyping assay kits or microarray chips with the inclusion of that variant.
http://www.ncbi.nlm.nih.gov/projects/SNP/
3.Another interesting database is pharmgkb database where you may retrieve the information based on pathway, orgene,or drug or bydisease. Here links are also available to corresponding literature. You may start finding the information about the variants without any prior knowledge.
http://www.pharmgkb.org/
4. Database of genomic variants is another database with upto date information on variants including copy number variants. Here you may find the variants by chromosome number or by giving age ne name or symbol as a search query.
http://projects.tcag.ca/variation/
6.ALFRED is another database where you can get the information about allele frequencies from different populations. http://alfred.med.yale.edu/alfred/index.asp
7.HGV database is another one where you may find information related to genotype-phenotype association studies
http://www.hgvbaseg2p.org/index
8.In addition to these databases the rearesome specific databases fore.g.SNP500 cancer database or variants related cancer (http://snp500cancer.nci.nih.gov/home_1.cfm), CYP allele nomenclature committee website (http://www.cypalleles.ki.se/), GPCR genes variant database(http://nava.liacs.nl/),Alzheimer’s disease variant database (http://www.alzgene.org/), Brain gene expression database (http://genome.mc.pref.osaka.jp/BGED/), Lipid associated disease variants database (https://gold.tugraz.at/), Functional SNPs database (http://compbio.cs.queensu.ca/F-SNP/),etc.
Thus information can be retrieved based on his/her interest, expertise, prior information about the variants and his/her convenience with the database. One more simple but tedious way of finding the variants is from NCBI gene database, PUBMED, ENSEMBL database (www.ensembl.org/) and HapMap project web site (www.hapmap.org )
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