I'm trying to find files containing genotypes and phenotypes for cell lines in COSMIC. On their downloads page I found links for mutation data, which I guess could be converted to genotypes, but I haven't been able to find any phenotype information. I'm specifically interested in drug sensitivity information. Does anyone know if it's possible to get more user friendly genotype files and whether phenotype data exists publicly?
$\begingroup$ The genotype is all DNA of an individual (usually summarized as the variants from the reference genome). AFAIK COSMIC only has mutations of variants related to a disease, so it is not exactly a genotype. The phenotype for each mutation or variant is that of the disease to which is related. $\endgroup$– llrsFeb 1, 2018 at 8:51
$\begingroup$ Thanks. After looking a bit more I realized what I want is both germline and somatic variants for each cell line. I still haven't figured out how to get that though. $\endgroup$– GregFeb 1, 2018 at 16:33
$\begingroup$ Which cell line are you talking about? COSMIC doesn't store information of cell lines. $\endgroup$– llrsFeb 1, 2018 at 16:38
$\begingroup$ This cell line data: cancer.sanger.ac.uk/cell_lines/download $\endgroup$– GregFeb 1, 2018 at 16:49
It seems like I was wrong and COSMIC does store information about cell lines.
You need to download the files from Genotypes:
Files listing the SNP calls for each cell line identified by PICNIC analysis of Affymetrix SNP6.0 array data. Both a simple genotype (AA, BB - homozygous or AB - heterozygous) and a complex interpretation of the genotype are given (for example, in a triploid region of the genome the genotype maybe AAB). 'genotypes/.'
You need to register (and get a license) to be able to download the data. Presumably the cell lines are described in the heading of the file. Then you can sort them out by cell line.
Then once you know the germ line identifier look for the paper describing it to know more about their phenotype. (But maybe there is a database with phenotype of known cell lines)