Submit SNP Array Data

PharmGKB defines SNP array data as data regarding genomic alternations within the genome, such as single nucleotide polymorphisms (SNPs) that are detected with high-density arrays (e.g., Affymetrix 100K arrays) which may also detect deletions, amplifications, and loss-of-heterozygosity on a genome scale.

Currently, PharmGKB accepts data from the following platforms:

• Affymetrix
• Illumina

In addition to the raw data files, PharmGKB also requires that the SNP Array Template is completed for each submission. The data in this template ensure that there is minimal meta-data associated with the data so that it will be appropriately indexed on the website. Please note that existing fields in the templates, including the instructions, must not be altered. Altering templates will cause your submission to be rejected.

PharmGKB subject and sample IDs can be obtained from submission@pharmgkb.org.

For Affymetrix data, PharmGKB requires the Affymetrix .CEL file. This file is generated from the .dat file by the Affymetrix MAS 5 or Affymetrix GeneChip Operating Software (GCOS). The native .cel file format for GCOS is a proprietary binary format. To upload GCOS .cel files into the database, open the GCOS Manager program and export the .cel file. This converts it into a text file the database can understand.

For Illumina data, PharmGKB requires the Illumina FinalReport file exported from the Illumina software as a .txt file. The output file must be produced from the Illumina software; please do not try to engineer this file, as it will cause errors in the system and delays in your submission.

If the submission passes validation it will be given a Submission ID and will put in the queue to be processed by PharmGKB. Once processed, it will be uploaded to the PharmGKB preview site and an email will be sent to let you know of its availability for review.

If you have any further questions, comments, or need assistance, please contact the PharmGKB team.