Dawn Kernagis defended her PhD work yesterday. Rubicon founding board member Gene Hobbs attended her presentation and provided a look inside the work through live coverage of the event on twitter. Below is an expanded version of the event filling in some details missed during the live event. The summary below is Hobbs’ notes from the event filling in around what he could not tweet fast enough:
The event took place in the Markee conference room in Duke Hospital South. After securing funding from the US Office of Naval Research, Kernagis was accepted into the Duke University Medical Center Pathology Department’s PhD program in 2008.
#Kernagis #Duke PhD Defense: Evaluation & optimization of the translational potential of array-based molecular diagnostics. #scuba #diving
@gene_hobbs Her work looked at genetic markers in DCS – #Kernagis #scuba #diving
@gene_hobbs #Kernagis – awesome introduction by Co-advisor Dr Dato
I must apologize to Dr. Datto for not noticing the autocorrection of his name. Dr Datto is a clinical pathologist and Director of the clinical molecular diagnostic laboratories at Duke University Medical Center. Dr. Datto’s humorous introduction noted Kernagis’ persistence in seeking out his assistance for the work she was doing. He started by having her look at some of his own cancer data.
@gene_hobbs #Kernagis – Dato – learned techniques on cancer data before application to #diving
The other co-advisor for Kernagis’ work was Dr. Moon from the Duke Center for Hyperbaric Medicine and Environmental Physiology and Department of Anesthesiology.
@gene_hobbs #Kernagis – tested thousands of samples with microarray to find gene signatures
@gene_hobbs #Kernagis – talking about selection of microarray for work. 1 precision of predictors in #breastcancer
I was not able to copy all the bullet points of this slide but the two other points were: 2. bimodal gene expression analysis to identify molecular subtypes and corresponding markers in ovarian cancer, and 3. differential gene expression analysis to identify candidate blood markers of decompression stress. This was to be the format of her presentation as she stepped each of us through her scientific process and methods.
@gene_hobbs #Kernagis – how much variance in genes? Does variance have impact on precision?
@gene_hobbs #Kernagis – can predict tumor recurrence risk per these predictors, not all data sets, looked at intratumor variance
@gene_hobbs Intratum heterogeneity & prec. microarray-based pred. of #breastcancer biol. & clin. outcome. Barry, #Kernagis et al http://www.ncbi.nlm.nih.gov/m/pubmed/20368555/?i=5&from=kernagis
The publication co-first authored by Kernagis above summarized the effect of intratumor heterogeneity on the precision of array-based predictors of breast cancer biology and behavior.
@gene_hobbs #Kernagis – found bimodal expression in malignant serious tumors
@gene_hobbs #Kernagis – created sum score survival predictor performance
@gene_hobbs #Kernagis – testing with external public data sets conducted and data confirmed
@gene_hobbs #Kernagis – future directions for ovarian cancer with bimodal analysis – wow
The “wow” was mine but further directions for this method in the development of cancer treatments are exciting.
@gene_hobbs #Kernagis – differential gene expression to identify decompression stress in #Divers
@gene_hobbs #Kernagis – only endpoint are clinical DCS and bubbles currently so bio marker for stress needed
@gene_hobbs #Kernagis – #divers from @_NEDU_ and NSMRL gave blood samples
Her work was approved by Institutional Review Boards for both Duke and the US Navy Experimental Diving Unit.
@gene_hobbs #Kernagis found 477 probe sets that were differentually expressed
@gene_hobbs #Kernagis – 44 overlapping genes for mixed gas and normoxic dives
@gene_hobbs #Kernagis – hyperoxic controls found 2 overlapping genes, diurnal variation leaves 35 possible genes
@gene_hobbs #Kernagis. – looked at 4 in great detail… These of interest in complement and stress responses
@gene_hobbs #Kernagis – already working on next steps. Can these be diagnostic markers for Decompression Sickness?
At this point I had been in contact with one of Kernagis’ other collaborators Dr. James, who was following my tweets. The following tweets were fun and made me wonder if this was the first time a PhD defense in diving medicine had ever been tweeted live?
@mlukej @gene_hobbs - awesome!….next stop, live streaming on ESPN’s The Ocho “Contact Sport of Doctoral Defense” and real-time betting like jailai
@mlukej @gene_hobbs – #Kernagis trending spike during doctoral defense… http://pic.twitter.com/Eko97uaQ
Once presentation was over, it was time for the questions.
@gene_hobbs #Kernagis – question on increased risk with divers that are older, fatter
@gene_hobbs #Kernagis question on these 4 main genes in normal diving vs the bent diver
@gene_hobbs #Kernagis – still more questions, some are repeats… How could this be used if you would provide #hyperbaric tx anyway
We do have a couple of abstracts on this work in the Rubicon Research Repository now.
Kernagis, D; Datto, M; Moon, R. Genome-wide expression profiling of decompression stress: a new approach to biomarker discovery and validation. Undersea Hyperb Med. 2009 36(4) RRR ID: 9092
Kernagis, DN; Datto, MB; Gerth, WA; Moon, RE. Classification of gene expression changes inherent to normal biological variance versus decompression stress effect. Undersea Hyperb Med. 2011 Sep-Oct;38(5) RRR ID: 9504
Many thanks to Dr. Kernagis for inviting me to her defense and helping me fill in the information I was unable to provide in the live presentation.