We hope you enjoyed our recent webinar “Integrated analysis of copy number, sequence variant and gene expression data in cancer cohort”.To recap, in this webinar we discussed how to prepare, upload and process copy number, expression and sequence variant results for the same samples within a cancer cohort. The RNA-Seq expression data was pre-processed in Nexus Expression to generate single-sample differential expression versus a group of normal tissue samples as a reference. After loading and processing all results in Nexus Copy Number, we were able to identify frequent aberrations across the cohort and identify a new sub-groups with co-occurring copy number alterations using the Concordance Function tool. Integration of expression results allowed us to easily see if any significant copy number alterations also had significance changes in expression. Inclusion of survival analysis revealed that the new subgroup did NOT affect overall survival within the cohort. However, Survival Predictive Power analysis identified several significant regions of copy number alteration with associated expression changes which impact survival and may be of further interest.
As a follow up to this presentation, here are a few frequently asked questions and answers:
Q: You only showed one type of input for each kind of data. Can I only import one type for my integrated analysis?
A: Nexus Copy Number accepts a variety of different input data for copy number estimation, including microarray (SNP and CGH) and NGS results (whole genome, whole exome, and targeted panel), and methylation array. These sources (and the platforms within them) can be mixed and matched within the Nexus project. The only requirement is that the results all belong to the same organism and genome build.
Annotated MAF or VCF files can be uploaded for sequence variant analysis. For single-sample expression analysis, a .txt file of the differentially regulated gene lists, along with significance and fold change is needed for analysis. This can be easily generated within Nexus Expression for microarray or RNA-Seq results.
Q: You mentioned copy number from NGS – can you explain that further?
A: Sure! Nexus Copy Number can use your post-aligned BAM files to estimate copy number alterations from your whole genome, whole exome or targeted sequencing panel results. This can be done using matched tumor-normal pairs or using tumor samples with an unmatched normal pool. For germline analysis, each sample can be analyzed using a user-created pooled reference. For more information on NGS copy number estimation specifically, check out our related webinar and white paper.
Q: This is great, but we use animal models in our lab. Can we still use this software?
A: Of course! As long as the organism has a mapped genome, you can use Nexus Copy Number and Nexus Expression to evaluate your results. A list of our most common genome downloads and annotation files can be found here. If you don’t see your organism of interest, just let us know.
This is just a recap of the most frequent questions asked. If you have any other questions not answered here or would like to learn more about Nexus Copy Number or Nexus Expression, please feel free to email us at firstname.lastname@example.org.