10/05/14
Customer sends on online inquiry describing his interest in identifying the correlation between one gene (denoted as Gene H below)'s expression with multiple other variables for a particular type of cancer patients. He discusses a project involving analyzing TCGA data, and asks for a description of work to be used in a grant proposal.
Thu, 10/09/2014 at 10:55 AM
AccuraScience LB: (Description of Work prepared for Customer): (1) Obtain genotype, phenotype and other associated data patients of the specific cancer type from TCGA. Genotype data include SNP, indel calling results. Phenotype data include expression of Gene H and other protein-coding genes, miRNA expression and MSI status. Other data include DNA methylation measurements. Note: TCGA controlled access data require permission to access. Request needs to be made with AccuraScience personnel listed as "collaborator" in application. AccuraScience will assist in the application process.
(2) Develop methods and carry out the analysis of correlation between Gene H expression and genotype, phenotype and other data listed in (1). Methods will be tried to stratify patients into 2 and more categories based on Gene H expression level, and specific genotype, phenotype and other variables significantly associated with Gene H expression will be identified. Multiple miRNA target prediction tools will be executed for miRNAs significantly associated with Gene H expression.
(3) Perform pathway analysis to "genes of interest" - including genes carrying recurrent mutations (SNPs and indels) significantly associated with Gene H expression, genes whose expression is significantly correlated with Gene H expression, genes whose DNA methylation level is significantly associated with Gene H expression, and predicted target genes of miRNAs whose expression is significantly associated with Gene H expression. GO-based pathway analysis and Ingenuity Pathway Analysis (IPA) suite will be used.
(4) Other bioinformatics work that falls generally along the line of work described in (1) through (3).
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Note: LB stands for Lead Bioinformatician. An AccuraScience LB is a senior bioinformatics expert and leader of an AccuraScience data analysis team.
Disclaimer: This text was selected and edited based on genuine communications that took place between a customer and AccuraScience data analysis team at specified dates and times. The editing was made to protect the customer’s privacy and for brevity. The edited text may or may not have been reviewed and approved by the customer. AccuraScience is solely responsible for the accuracy of the information reflected in this text.