Case-oriented pathways analysis in pancreatic adenocarcinoma using data from a sleeping beauty transposon mutagenesis screen

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Background: Mutation studies of pancreatic ductal adenocarcinoma (PDA) have revealed complicated heterogeneous genomic landscapes of the disease. These studies cataloged a number of genes mutated at high frequencies, but also report a very large number of genes mutated in lower percentages of tumors. Taking advantage of a well-established forward genetic screening technique, with the Sleeping Beauty (SB) transposon, several studies produced PDA and discovered a number of common insertion sites (CIS) and associated genes that are recurrently mutated at high frequencies. As with human mutation studies, a very large number of genes were found to be altered by transposon insertion at low frequencies. These low frequency CIS associated genes may be very valuable to consider for their roles in cancer, since collectively they might emerge from a core group of genetic pathways. Result: In this paper, we determined whether the genetic mutations in SB-accelerated PDA occur within a collated group of biological processes defined as gene sets. The approach considered both genes mutated in high and lower frequencies. We implemented a case-oriented, gene set enrichment analysis (CO-GSEA) on SB altered genes in PDA. Compared to traditional GSEA, CO-GSEA enables us to consider individual characteristics of mutation profiles of each PDA tumor. We identified genetic pathways with higher numbers of genetic mutations than expected by chance. We also present the correlations between these significant enriched genetic pathways, and their associations with CIS genes. Conclusion: These data suggest that certain pathway alterations cooperate in PDA development.

Original languageEnglish (US)
Article number16
JournalBMC Medical Genomics
Issue number1
StatePublished - Apr 1 2016

Bibliographical note

Funding Information:
Y-YH is partially supported by NIH/NCI grants: P30-CA077598, P30-DK050456, P50-CA101955, U19-CA157345, R01 CA179246 and American Cancer Society grant 125627-RSG-14-074-01-TBG. TKS is supported by funding from the NIH NCI (5R00CA151672-04) and the Masonic Cancer Center NIH support grant (P30-CA77598). DL is partially supported by P50-CA101955.

Publisher Copyright:
© 2016 Ho et al.


  • CIS
  • Case-oriented gene set analysis
  • Common insertion sites
  • Forward genetic screen
  • Pathways correlations
  • Sleeping Beauty transposon

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