I am asked to add the frequency of a locus (cyclin A2) as a control against my own copy number results revealed by real-time PCR. Is there a database where I can extract out this information? And is it possible to find what "normal changes" are in both human cancer cells/ tissue and in normal cells/tissue? I am defending my thesis in a couple of weeks, and would like to know this before that day!
Your question is a little difficult to understand, but the following information may help.
The database of genomic variation holds all copy number variation (CNV) data (http://projects.tcag.ca/variation/) derived from phenotypically normal individuals. You can search this database for your genes of interest and see if they are targeted by CNV. It is not an exhaustive list but is relatively comprehensive now. In principle, this database holds CNV data from numerous studies drawn from phenotypically normal individuals. However, you will need to look at each specific study to ensure this is correct. The data was initially from array-based comparative genomic hybridization or SNP array studies, but nom includes data from other sources such as high-throughput sequencing. You also need to understand the platform used to investigate CNV because the resolution with vary dramatically. This data is also included into several genomic databases, such as ensembl and the NCBI. The 1000 genome project may also be useful (http://www.1000genomes.org/home) and is based of high-throughput sequencing data.
For somatic copy number aberrations (CNA) you can look at the specific tumour type of interest in the literature, but there are also some repositories. The NCBI have one (http://www.ncbi.nlm.nih.gov/sky/), and there is also the Progenetix database (http://www.progenetix.net/cgi-bin/pgHome.cgi) and the Japanese CGH database (http://www.cghtmd.jp/CGHDatabase/index_e.jsp). Cytogenetic and fusion gene information is stored in the Mitelman Database (http://cgap.nci.nih.gov/Chromosomes/Mitelman). The same caveats apply to somatic changes as they did above for germ-line variation.
There are numberous resources to find information about specific genes, that may include some CNV/ CNA data and whether your gene is targeted by chromosomal changes, such as AGCOH (http://atlasgeneticsoncology.org/)
There are so many resources now, but these are some of them. Good luck.
Thank you very much for your thorough response. The information you gave was exactly what I was looking for. I will go through the databases mentioned above and search for the specific gene. Thank you!
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