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FHIR	
  Genomics	
  
Gil	
  Alterovitz,	
  Track	
  Lead,	
  Connectathon	
  
Harvard	
  Medical	
  School	
  and	
  
Bost...
 
HLA	
  (Human	
  Leukocyte	
  Antigen)	
  Use	
  Case:	
  	
  
National	
  Marrow	
  Donor	
  Program	
  
•  Scenario	
 ...
HLA	
  Use	
  Case	
  
•  A	
  buccal	
  smear	
  collected	
  on	
  a	
  swab	
  (Specimen)	
  is	
  collected	
  
from	
...
Pharmacogenomics	
  
•  Haplotype	
  representaKon	
  system	
  being	
  designed	
  (terminology	
  
service,	
  codable	...
Testing	
  
•  AEGIS.net	
  migrated	
  scenarios	
  for	
  STU3	
  ballot	
  
•  Uncovered	
  potenKal	
  issues	
  in	
 ...
Open	
  Source	
  FHIR	
  Genomics	
  
Server	
  
•  Implemented	
  in	
  python	
  
•  Virtual	
  machine,	
  docker	
  
...
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Genomics connectathon

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report on genomics track at the Baltimore connectathon

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Genomics connectathon

  1. 1. FHIR  Genomics   Gil  Alterovitz,  Track  Lead,  Connectathon   Harvard  Medical  School  and   Boston  Children’s  Hospital  
  2. 2.   HLA  (Human  Leukocyte  Antigen)  Use  Case:     National  Marrow  Donor  Program   •  Scenario  designed  and  being  implemented   •  Terminology  server  for  HLA  nomenclature  being  enhanced/ migrated  from  DSTU2  to  STU3  
  3. 3. HLA  Use  Case   •  A  buccal  smear  collected  on  a  swab  (Specimen)  is  collected   from  a  potenKal  donor  (PaKent)   •  It  is  sent  to  a  HLA  typing  lab  (OrganizaKon)  and  requests  that   HLA  typing  for  HLA-­‐A,  HLA-­‐B,  and  HLA-­‐DBR1   (DiagnosKcRequest).     •  The  lab  does  DNA  sequencing  for  each  locus  (Sequence)  and   assigns  allele  names  (GeneKcs  ObservaKon  Profile)  and   generates  genotypes  for  each  locus  (GeneKcs  ObservaKon   Profile).     •  These  are  aggregated  into  a  single  report  (DiagnosKcReport)   and  sent  back  to  the  requestor.  
  4. 4. Pharmacogenomics   •  Haplotype  representaKon  system  being  designed  (terminology   service,  codable  concept  encodings,  etc)   •  Integrated  pharmacogenomics  work  into  GeneKc  ObservaKon   profile  with  links  to  Sequence  resource  
  5. 5. Testing   •  AEGIS.net  migrated  scenarios  for  STU3  ballot   •  Uncovered  potenKal  issues  in  fluent  validaKon  engine  on   ObservaKon  resource  constraints-­‐  going  from  May  candidate   to  Sep  ballot  STU3  
  6. 6. Open  Source  FHIR  Genomics   Server   •  Implemented  in  python   •  Virtual  machine,  docker   •  Will  be  used  in  tutorial  on  Precision  Medicine  FHIR/app   tutorial  on  Thurs  

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