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FHIR	
  Genomics	
  
Gil	
  Alterovitz,	
  Track	
  Lead,	
  Connectathon	
  
Harvard	
  Medical	
  School	
  and	
  
Boston	
  Children’s	
  Hospital	
  
 
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	
  
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.	
  
Pharmacogenomics	
  
•  Haplotype	
  representaKon	
  system	
  being	
  designed	
  (terminology	
  
service,	
  codable	
  concept	
  encodings,	
  etc)	
  
•  Integrated	
  pharmacogenomics	
  work	
  into	
  GeneKc	
  ObservaKon	
  
profile	
  with	
  links	
  to	
  Sequence	
  resource	
  
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	
  
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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Genomics connectathon

  • 1. FHIR  Genomics   Gil  Alterovitz,  Track  Lead,  Connectathon   Harvard  Medical  School  and   Boston  Children’s  Hospital  
  • 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. 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. 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. 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. Open  Source  FHIR  Genomics   Server   •  Implemented  in  python   •  Virtual  machine,  docker   •  Will  be  used  in  tutorial  on  Precision  Medicine  FHIR/app   tutorial  on  Thurs