How Fast Can We Map A Tumor - Alicemarie G Rathjen
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Presentation Patients 2.0 Panel in Silicon Valley, CA 10-04-2015 - Demo on How Patients Can Map Their Own Tumor Genomes to Crowdsource Information, Project for Pancreatic Cancer Patient Saw Yu Wai, Author: Alicemarie G Rathjen Category: Patient Empowerment, Time Sensitive Genetic Information, Precision Medicine, Rare Disease, Patient Centered Data Model, Internet of Human Beings, IoT Everything, Biological Domains, Evolution of EHRs HL7, GA4GH
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How Fast Can We Map A Tumor - Alicemarie G Rathjen
- 1. How Fast Can We Map A Tumor? Alice Rathjen @dnatimes Alice.Rathjen@gmail.com Saw Yu Wai DNApancreas.com
- 2. Saw Yu’s Goal “I want my raw tumor genome data so I can publish it as a map and make it available to anyone” DNApancreas.com
- 3. The Project • Find information in academic journals on pancreatic cancer doi:10.1038/nature14169 • Build Genome Base Map • Focus on top 50 Genes Pancreatic Cancer • Created Editable Map layer to manage crowd source annotation • Promote via Social Media in the hopes of finding actionable information • Waited for data from Physician/Hospital
- 4. What we learned... Alice Rathjen @dnatimes Alice.Rathjen@gmail.com Saw Yu Wai DNApancreas.com + = ~ 2 weeks
- 5. Step 1. Get a .VCF or .txt File Not a .pdf or “report” from the lab mypersonalgenome.com RS_ID Chr Start Stop Genotype rs80358010 17 43124016 43124016 TA rs80357063 17 43093222 43093222 TA rs80358043 17 43115725 43115725 GA rs80357831 17 43091881 43091882 GA rs80358116 17 43104262 43104262 TA rs80358011 17 43104263 43104263 GA rs80358162 17 43070927 43070927 TA rs1800747 17 43063952 43063952 TA rs80358002 17 43047705 43047705 CA rs80358030 17 43099774 43099774 TA rs80358094 17 43063873 43063873 TA RS_ID = Researcher Genetic Marker Unique ID, Chr = Chromosome, Start/End = DNA base pair position on chromosome where marker starts and ends. Genotype = combination of A,T,C or G that you received – one letter from each of your chromosome pair (i.e. T from Mon, A from Dad).
- 6. Step 2. Create X,Y map coordinates Contact alice.rathjen at gmail or @DNAtimes with ?’s Formulas to convert .vcf into genome map http://bit.ly/dnaMapformulas Chromosome centromere lines up with London DNApancreas.com Map service layers to create genome base map REST API URLs http://arcg.is/1hia6sq ArcGis Online: www.esri.com/software/arcgis/arcgisonline Genome Mapping Group: http://arcg.is/1OtBXVT API: http://resources.arcgis.com/en/help/arcgis-rest-api/
- 7. Step 3. Publish your Genome Map using Standard Mapping Software
- 8. If I Had A Magic Wand… Labs would provide people with a map of their genome as soon as it was assembled - so patients could share it as they saw fit. Alice Rathjen @dnatimes http://www.slideshare.net/dnatimes/internet-of-humanbeings Biological Domain Registrars
- 9. Thank You! Alice Rathjen @dnatimes Alice.Rathjen@gmail.com Saw Yu Wai DNApancreas.com