Rare Cancer Meta-Analysis, pt.2: Collecting kidney cancer data using BaseSpace Correlation Engine
Updated: Mar 16, 2018
These entries are part two in a series of instructional videos detailing a meta-analysis on eight different human gene expression studies looking at papillary renal cell carcinoma (pRCC). In these installments, I give a demonstration on collecting gene expression data from a single disease using Illumina’s BaseSpace Correlation Engine.
I also describe the types of biological information we can obtain from this type of meta-analysis, as well as go over exporting the results to other statistical and visual programs for further work.
Inspiration for this meta-analysis on papillary kidney cancer came from an upcoming ‘Hackathon’ in May that brings together researchers, engineers and computer scientists to try to tackle challenging problems in life sciences. This year they are focusing on papillary renal-cell carcinoma type 1 (p1RCC), a disease that accounts for between 15 to 20% of all kidney cancers. Little is known about the genetic basis of sporadic papillary renal-cell carcinoma, and no effective forms of therapy for advanced disease exist.
The opinions expressed during this video are mine and may not represent the opinions of Illumina. Any uses of Illumina’s products described in this demonstration may be uses that have not been cleared or approved by the FDA or any other applicable regulatory body. I do not get direct compensation from Illumina for these videos, but do receive reimbursement for travel when I speak at Illumina-sponsored events.
Please subscribe to this YouTube channel or sign up to my blog to receive notifications on when the next video in the series is posted.
Special thanks goes out to the biotech companies Illumina (Correlation Engine and Cohort Analyzer), Partek Inc. (Partek Genomics Suite) and Elsevier (Pathway Studio) for donating their platforms and providing technical assistance for this bioinformatics series.
-Michael Edwards PhD, Bioinfo Solutions LLC
*A link to the actual meta-analysis used in the video in can be obtained in Correlation Engine (must have existing account) by typing in your working domain name into the following URL:
https://”your domain name”.ussc.informatics.illumina.com/c/search/adv.nb?ids=853951,14029,79477,152971,56285,14033,451948,153346,14031,153313,451963,14030,14032,451966,451954,451951,13771
*Blog was edited at 9am on 3/16/18 to replace last section of the video series (pt2.3) with one giving a text description in a pop-up window on how to save a meta-analysis using the "Bookmark" function.