Trouble with nomenclatures in personalized medicine Asst.-Prof. Mag. Dr. Matthias Samwald CeMSIIS, Medical University of Vienna SUMMER SCHOOL: GENOMIC MEDICINE – Bridging research and the clinic, May 6 2016, Portoroz, Slovenia One man's *1 is another man's *13? Funded by Austrian Science Fund (FWF): [P 25608-N1 This project has received funding from the European Union’s Horizon 2020 research and Innovation programme under grant agreement No 668353 (KB and MS).
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One man's *1 is another man's *13? Trouble with nomenclatures in personalized medicine
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Trouble with nomenclatures in personalized medicine
Asst.-Prof. Mag. Dr. Matthias SamwaldCeMSIIS, Medical University of Vienna
SUMMER SCHOOL: GENOMIC MEDICINE – Bridging research and the clinic, May 6 2016, Portoroz, Slovenia
One man's *1 is another man's *13?
Funded by Austrian Science Fund (FWF): [P 25608-N15]
This project has received funding from the European Union’s Horizon 2020 research and Innovation programme under grant agreement No 668353 (KB and MS).
What‘s the problem?
We simulated the accuracy of various targeted, low-cost assays suitable for pre-emptive testing compared to next-gen sequencing
Venn diagram displaying the numbers and overlaps of polymorphisms covered by constrained views derived from four pharmacogenomic assays. DMET: derived from the Affymetrix DMET™ Plus assay, VERA: Illumina VeraCode® ADME Core Panel, TAQM: TaqMan® OpenArray® PGx Panel, FLOR: University of Florida and Stanford Custom Array.
We simulated the accuracy of various targeted, low-cost assays suitable for pre-emptive testing compared to next-gen sequencing
We simulated the accuracy of various targeted, low-cost assays suitable for pre-emptive testing compared to next-gen sequencing
We simulated the accuracy of various targeted, low-cost assays suitable for pre-emptive testing compared to next-gen sequencing
Fraction of tested genes resulting in aberrations in haplotype calling with restricted assay compared to next-gen sequencing. Based on full genome sequences of 2504 persons. Manuscript currently under review at ‘Pharmacogenomics’.
We simulated the accuracy of various targeted, low-cost assays suitable for pre-emptive testing compared to next-gen sequencing
Fraction of tested genes resulting in aberrations in haplotype calling with restricted assay compared to next-gen sequencing. Based on full genome sequences of 2504 persons. Manuscript currently under review at ‘Pharmacogenomics’.
Where to go from here?
Allele Registry project
From the lab: experimental mnemonic nomenclature
• Idea: Experiment with human-friendly nomenclatureo No human committeeo Less cryptic alphanumeric descriptors
From the lab: experimental mnemonic nomenclature
• Synthetic pseudo-words can encode a lot of information
• Reference: Matthias Samwald, Kathrin Blagec, Sebastian Hofer and Robert R. Freimuth. “Analysing the potential for incorrect haplotype calls with different pharmacogenomic assays in different populations: a simulation based on 1000 Genomes data.” Pharmacogenomics, September 30, 2015. doi:10.2217/pgs.15.108
• Code Availability: The curated resources and the IPython notebooks available at https://gitlab.com/medication-safety/ms-ipython