Bioinformatics Pipeline Advances Research into Environmentally-Induced Cancers

Collaborating with a government agency for the past three years, DHMRI’s bioinformatics team is part of an ongoing research project focused on genomic and transcriptomic changes caused by heavy metal carcinogens in human prostate cells as well as the potential metagenomic regulators for these changes.

DHMRI and the collaborator designed a two-step, paired-sample genomic study to elucidate gene expression and methylation status between cancer cells and the normal control samples.  Both RNASeq and BiS-Seq samples were sequenced on one of the HiSeq2500s in the DHMRI’s Genomics laboratory.  After in-depth quality control, the bioinformatics team completed the analysis using a variety of analytical tools including CLC Genomics Workbench, IPA BISMARK, FastQC, and Bowtie2. 

“As with every project, we use multiple packages and workflows to arrive at the deliverable data,” said Garron Wright, bioinformatics project leader. “We have a very robust internal pipeline that allows us to optimize the production of high quality data for every one of our collaborators.”

The RNASeq and BiS-Seq analyses allowed collaborators to go beyond the usual targets of oncogenesis regulation to the identification of a novel subset of methylated sites in the genome. Research since that initial discovery has led to the validation of these specific regions of methylation and an in-depth look at the structural changes occurring within a common oncogene.  These focused studies are on-going, and findings are being prepared for publication.

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