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Esri UC2013 .
2013 Esri International User Conference
July 8–12, 2013 | San Diego, California
Preparing for the Genomic
Data Deluge of Personalized
Medicine
Alice Rathjen, CEO, Founder DNA Guide
Mike Hargreaves, R&D DNA Guide,
DNA Guide, Inc, © 2013
Esri UC2013 .
Preparing for Personalized Medicine
• Deluge vs Managed Mapping Solutions
• Recognizing the First Waves of Data
• Addressing Needs of All Stakeholders
• Genomic Coordinate Sources
• Genome Maps for the Masses
Genomic Data Deluge of Personalized Medicine, Alice Rathjen, DNA Guide, Inc.
Esri UC2013 . Genomic Data Deluge of Personalized Medicine, Alice Rathjen, DNA Guide, Inc.
Fear and Hoarding
Deluge
Esri UC2013 .
Secure Sharing of Genomic Maps
Genomic Data Deluge of Personalized Medicine, Alice Rathjen, DNA Guide, Inc.
Mapping Software:
 Proven Technology
 Rapid Deployment
 Easy Adoption
 Dynamic
Reports/Maps
 Secure
 Scales Indefinitely
Esri UC2013 .
Waves of Patient
Genetic Data
• Cancer Tumor
Analysis (200 genes)
• Carrier Testing
(1-50 points of data)
• Drug Response
(1-15 points of data)
• Disease Risk (1 to 60
points of data per disease)
Esri UC2013 .
Needs of
Stakeholders
• Quality of Science
(A-F, Scientific Peer Review)
• Medical Utility
(5 stars rating - Pathologists, AMA)
• Viewing Risk (E=Everyone,
PG = Physician Guidance, R =
Restricted –via genetic counselors)
Annotation Turf Wars
Patient Engagement
• Real Time Consent
(fine grain control for sharing info)
Esri UC2013 .
Genomic
Coordinate
Sources
• Human Reference
Genome Builds
http://www.ncbi.nlm.nih.gov/projects
/genome/assembly/grc/human
• Human Genes
HUGO www.genenames.org
• SNPs DBSNP
www.ncbi.nlm.nih.gov/SNP
Esri UC2013 .
Genome Maps
for the Masses
Fast, Simple, Mobile
Genomic Data Deluge of Personalized Medicine, Alice Rathjen, DNA Guide, Inc.
• Chromosomes 1-22
• XX = Female
• XY = Male
• MT = Mitochondria
Esri UC2013 .
DNA Bases: A, T, C, G’s.
A T C G
DNA Mapping
Genomes consist of large .txt files full of A, T, C and G’s
Genomic Data Deluge of Personalized Medicine, Alice Rathjen, DNA Guide, Inc.
Esri UC2013 .
Double Helix (A’s & T’s, C’s & G’s)
T A G C
A T C G
DNA Mapping
A’s and T’s bond together, C’s and G’s bond together.
Genomic Data Deluge of Personalized Medicine, Alice Rathjen, DNA Guide, Inc.
Esri UC2013 .
Top Strand is the Plus (+) Strand
T+ A+ G+ C+
A- T- C- G-
Bottom Strand is the Minus(-) Strand
DNA Mapping
The data is .txt files is for one side of the DNA Strand.
Genomic Data Deluge of Personalized Medicine, Alice Rathjen, DNA Guide, Inc.
Esri UC2013 .
DNA Mapping
Sample Dataset
Genomic Data Deluge of Personalized Medicine, Alice Rathjen, DNA Guide, Inc.
• RSID number is the research
ID for the marker.
• The Genotype “AG” means
the person has an “A” at this
location on one of their
Chromosome 1s and a G at
this location on their second
Chromosome 1
# Human Reference Build 36 , + orientation
#rsid chromosome position genotype
rs3094315 1 742429 AG
rs3131972 1 742584 AG
rs11240777 1 788822 AG
rs6681049 1 789870 CC
rs4970383 1 828418 CC
rs4475691 1 836671 CC
rs7537756 1 844113 AA
rs13302982 1 851671 GG
rs1110052 1 863421 GT
rs2272756 1 871896 AG
rs3748597 1 878522 CC
rs13303106 1 881808 AG
rs28415373 1 883844 CC
rs13303010 1 884436 AA
Esri UC2013 .
Patient data often shown in pairs of letters
AT+ CC+ CG+
TT-
(One letter for each chromosome pair)
DNA Mapping
Points in genome where humans vary are called SNPs
Genomic Data Deluge of Personalized Medicine, Alice Rathjen, DNA Guide, Inc.
Esri UC2013 .
DNA Mapping
Calculating x Coordinate
Genomic Data Deluge of Personalized Medicine, Alice Rathjen, DNA Guide, Inc.
• Longest Chromosome , Chr 1,
has 250,000,000 base pairs
• Using WebMercator,
1 base pair = .01 map units
• X Coordinate = genetic marker
position divided by 100
• Example coordinate/position
(1234567 = 12345.67)
Esri UC2013 .
DNA Mapping
Calculating y Coordinate*
Genomic Data Deluge of Personalized Medicine, Alice Rathjen, DNA Guide, Inc.
23 Chromosome Pairs
• Chromosome number times -
200.000.00 = y coordinate
(i.e. chr 22 = -4,400.000.00)
• Chromosome X
coordinate = -4,600,000.00
• Chromosome Y
coordinate = -4,800,000.00
*midline, for diploid browser add .01 and
subtract .01 for each chromosome pair
Esri UC2013 .
Thank You ESRI
Alice Rathjen
CEO, Founder, DNA Guide
alice@dnaguide.com
Key Contributors:
Mike Hargreaves
Saw Yu Wai
Richard Couch

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DNA Guide - Tech Summary Mapping Genomes w GIS

  • 1. Esri UC2013 . 2013 Esri International User Conference July 8–12, 2013 | San Diego, California Preparing for the Genomic Data Deluge of Personalized Medicine Alice Rathjen, CEO, Founder DNA Guide Mike Hargreaves, R&D DNA Guide, DNA Guide, Inc, © 2013
  • 2. Esri UC2013 . Preparing for Personalized Medicine • Deluge vs Managed Mapping Solutions • Recognizing the First Waves of Data • Addressing Needs of All Stakeholders • Genomic Coordinate Sources • Genome Maps for the Masses Genomic Data Deluge of Personalized Medicine, Alice Rathjen, DNA Guide, Inc.
  • 3. Esri UC2013 . Genomic Data Deluge of Personalized Medicine, Alice Rathjen, DNA Guide, Inc. Fear and Hoarding Deluge
  • 4. Esri UC2013 . Secure Sharing of Genomic Maps Genomic Data Deluge of Personalized Medicine, Alice Rathjen, DNA Guide, Inc. Mapping Software:  Proven Technology  Rapid Deployment  Easy Adoption  Dynamic Reports/Maps  Secure  Scales Indefinitely
  • 5. Esri UC2013 . Waves of Patient Genetic Data • Cancer Tumor Analysis (200 genes) • Carrier Testing (1-50 points of data) • Drug Response (1-15 points of data) • Disease Risk (1 to 60 points of data per disease)
  • 6. Esri UC2013 . Needs of Stakeholders • Quality of Science (A-F, Scientific Peer Review) • Medical Utility (5 stars rating - Pathologists, AMA) • Viewing Risk (E=Everyone, PG = Physician Guidance, R = Restricted –via genetic counselors) Annotation Turf Wars Patient Engagement • Real Time Consent (fine grain control for sharing info)
  • 7. Esri UC2013 . Genomic Coordinate Sources • Human Reference Genome Builds http://www.ncbi.nlm.nih.gov/projects /genome/assembly/grc/human • Human Genes HUGO www.genenames.org • SNPs DBSNP www.ncbi.nlm.nih.gov/SNP
  • 8. Esri UC2013 . Genome Maps for the Masses Fast, Simple, Mobile Genomic Data Deluge of Personalized Medicine, Alice Rathjen, DNA Guide, Inc. • Chromosomes 1-22 • XX = Female • XY = Male • MT = Mitochondria
  • 9. Esri UC2013 . DNA Bases: A, T, C, G’s. A T C G DNA Mapping Genomes consist of large .txt files full of A, T, C and G’s Genomic Data Deluge of Personalized Medicine, Alice Rathjen, DNA Guide, Inc.
  • 10. Esri UC2013 . Double Helix (A’s & T’s, C’s & G’s) T A G C A T C G DNA Mapping A’s and T’s bond together, C’s and G’s bond together. Genomic Data Deluge of Personalized Medicine, Alice Rathjen, DNA Guide, Inc.
  • 11. Esri UC2013 . Top Strand is the Plus (+) Strand T+ A+ G+ C+ A- T- C- G- Bottom Strand is the Minus(-) Strand DNA Mapping The data is .txt files is for one side of the DNA Strand. Genomic Data Deluge of Personalized Medicine, Alice Rathjen, DNA Guide, Inc.
  • 12. Esri UC2013 . DNA Mapping Sample Dataset Genomic Data Deluge of Personalized Medicine, Alice Rathjen, DNA Guide, Inc. • RSID number is the research ID for the marker. • The Genotype “AG” means the person has an “A” at this location on one of their Chromosome 1s and a G at this location on their second Chromosome 1 # Human Reference Build 36 , + orientation #rsid chromosome position genotype rs3094315 1 742429 AG rs3131972 1 742584 AG rs11240777 1 788822 AG rs6681049 1 789870 CC rs4970383 1 828418 CC rs4475691 1 836671 CC rs7537756 1 844113 AA rs13302982 1 851671 GG rs1110052 1 863421 GT rs2272756 1 871896 AG rs3748597 1 878522 CC rs13303106 1 881808 AG rs28415373 1 883844 CC rs13303010 1 884436 AA
  • 13. Esri UC2013 . Patient data often shown in pairs of letters AT+ CC+ CG+ TT- (One letter for each chromosome pair) DNA Mapping Points in genome where humans vary are called SNPs Genomic Data Deluge of Personalized Medicine, Alice Rathjen, DNA Guide, Inc.
  • 14. Esri UC2013 . DNA Mapping Calculating x Coordinate Genomic Data Deluge of Personalized Medicine, Alice Rathjen, DNA Guide, Inc. • Longest Chromosome , Chr 1, has 250,000,000 base pairs • Using WebMercator, 1 base pair = .01 map units • X Coordinate = genetic marker position divided by 100 • Example coordinate/position (1234567 = 12345.67)
  • 15. Esri UC2013 . DNA Mapping Calculating y Coordinate* Genomic Data Deluge of Personalized Medicine, Alice Rathjen, DNA Guide, Inc. 23 Chromosome Pairs • Chromosome number times - 200.000.00 = y coordinate (i.e. chr 22 = -4,400.000.00) • Chromosome X coordinate = -4,600,000.00 • Chromosome Y coordinate = -4,800,000.00 *midline, for diploid browser add .01 and subtract .01 for each chromosome pair
  • 16. Esri UC2013 . Thank You ESRI Alice Rathjen CEO, Founder, DNA Guide alice@dnaguide.com Key Contributors: Mike Hargreaves Saw Yu Wai Richard Couch