FHIR Genomics Use Case: Reporting HLA Genotyping Consensus-Sequence-Block & Observation-genetics-Sequence Cardinality
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1 FHIR Genomics Use Case: Reporting HLA Genotyping Consensus-Sequence-Block & Observation-genetics-Sequence Cardinality Bob Milius, PhD Bioinformatics NMDP/Be The Match
2 Outline Background MIRING, & HML FHIR Profiles Created for HLA Diagnostic Report > Profile for HLA Genotyping Results Sequence > Profile for Consensus Sequence Blocks Proposal #1 Delete Sequence > Profile for Consensus Sequence Blocks Proposal #2 Change cardinality of Observation-genetics-Sequence from 0..1 to 0..* 2
3 3
4 4
5 HML 1.0 Header Typing Method Allele Assignment Consensus Sequence
![.* ] [ 0.](/docs-images/75/72382246/images/6-3.jpg ".* ] hmlid reporting-center sample typing-test-names")
![[ 0..* ] collection-method typing [ 1.](/docs-images/75/72382246/images/6-5.jpg ".* ] gene-family * date * typing-test-name name * [ 1.")
6 hml version * project-name element required attribute * optional attribute [ 0..1 ] [ 0..1 ] [ 1..* ] [ 0..* ] hmlid reporting-center sample typing-test-names root * extension reporting-center-id * reporting-center-context id * center-code test-id * [ 0..* ] collection-method typing [ 1..* ] gene-family * date * typing-test-name name * [ 1..* ] [ 1 ] [ 0..* ] [ 0..* ] Typing Method Allele Assignment Consensus Sequence
![.1 ] [ 0.](/docs-images/75/72382246/images/7-3.jpg ".* ] sso ssp sbt-sanger sbt-ngs locus test-id")
![test-id-source [ 0..* ] [ 1 ] [ 0..* ] [ 0.](/docs-images/75/72382246/images/7-6.jpg ".* ] raw-reads amplification registered-name *")
7 typing-method element required attribute * optional attribute [ 0..1 ] [ 0..1 ] [ 0..1 ] [ 0..* ] sso ssp sbt-sanger sbt-ngs locus test-id test-id-source scores * locus test-id test-id-source scores * locus test-id test-id-source locus test-id test-id-source [ 0..* ] [ 1 ] [ 0..* ] [ 0..* ] raw-reads amplification registered-name * sequence sub-amplification registered-name * sequence gssp registered-name primer-sequence primer-target sequence uri * format * paired * pooled * availability adapter-trimmed quality-trimmed
8 allele-assignment date * allele-db allele-version element required attribute * optional attribute [ 0..* ] [ 0..* ] [ 0..* ] locus * method * type * haploid genotype-list [ 1..* ] diploid-combination uri glstring string [ 1..2 ] diploid-combination locus-block [ 1..* ] allele-list [ 1..* ] allele present [ 1..* ] string
![.* ] reference-sequence date * [ 0.](/docs-images/75/72382246/images/9-3.jpg ".* ] consensus-sequence-block reference-sequence-id * start")
![.* ] element required attribute * optional attribute [ 0.](/docs-images/75/72382246/images/9-6.jpg ".* ] id * name description start end accession strand uri")
9 consensus-sequence reference-database name description version availability * curated uri [ 1..*] [ 1..* ] reference-sequence date * [ 0..* ] consensus-sequence-block reference-sequence-id * start end strand phase-set continuity expected-copy-number description [ 1 ] [ 0..* ] element required attribute * optional attribute [ 0..* ] id * name description start end accession strand uri sequence iupac-bases variant id name start * end * reference-bases * alternate-bases * quality-score filter uri sequence-quality sequence-start * sequence-end * quality-score * [ 0..* ] variant-effect term * hgvs uri
10 Two FHIR Profiles were created for the HLA reporting use case Diagnostic Report > Profile for HLA Genotyping Results Sequence > Profile for Consensus Sequence Blocks 10
11 HLA Profiles Diagnostic Report > Profile for HLA Genotyping Results Diagnostic Report > Profile for HLA Genotyping Results hla-genotyping-resultsalleledatabase Allele Database : Allele Database. hla-genotyping-resultsalleleasignmentdate AlleleAsignment-data : AlleleAsignment-data. hla-genotyping-resultsglstring glstring : glstring. hla-genotyping-resultshaploid haploid : haploid. hla-genotyping-resultsconsensussequenceblock ConsensusSequenceBlock : ConsensusSequenceBlock. hla-genotyping-resultsmethod The platform, methodology and software applied at the time of the genotyping : The platform, methodology and software applied at the time of the genotyping. 11
12 HLA Profiles Sequence > Profile for Consensus Sequence Blocks sequence-consensus-sequence-blockexpectedcopynumber Expected Copy Number : To indicated how many copies of the sequence block was expected. May be satisfied with observation-geneticsallelicstate sequence-consensus-sequence-blockstrand Strand : Strand. May be satisfied with Sequence.referenceSeq.strand sequence-consensus-sequence-blockcontinuity Continuity : A continuity flag to indicate whether a gap exists between blocks. May be calculated with coordinates to a reference and calculated indels 12
13 Sequence Continuity Two consensus sequence blocks (contigs) that are phased but without a bridging sequence between them. We use a continuity attribute in HML to indicated if two sequence blocks are separated by a gap or if they are suspected to be continuous. Consensus Sequence Blocks Raw reads We can calculate this using sequence coordinates relative to a reference (taking into account any indels), so perhaps we don t need this. 13
14 First Proposal Remove a Profile Sequence > Profile for Consensus Sequence Blocks Why? Almost all the extensions found in this profile can now be met using existing elements in Sequence and Observation for Genetics, The one remaining extension (continuity) may be calculated, and it doesn t make sense and in its current structure (continuity describes the relationship between two sequences, not an attribute of a single sequence). 14
15 Observation-genetics-Sequence Cardinality Observation-genetics-Sequence currently 0..1 Why not 0..*? 15
16 Need to report genotypes of a panel of HLA loci in a single report Patient/Donor HLA-A HLA-B HLA-C HLA-DRB1 HLA-DQB1 Profile Diagnostic Report Each locus is a separate observation 16
17 Breaking down a genotype for a single locus, e.g. HLA-A Patient/Donor Specimen HLA-A*01:01:01:01 Exon 2 phaseset 1 HLA-A*01:01:01:01 Exon 3 phaseset 1 HLA-A*01:02 Exon 2 phaseset 2 HLA-A*01:02 Exon 3 phaseset 2 Sequence blocks HLA-A*01:01:01:01 HLA-A HLA-A*01:01:01:01+HLA-A*01:02 HLA-A*01:02 Genotype Individual alleles Profile Diagnostic Report 17
18 Observation-genetics-Sequence 0..1 Patient/Donor Specimen Sequence Genetics Profile phaseset 1 Observation Sequence Sequence Sequence Genetics Profile phaseset 1 Observation Genetics Profile phaseset 2 Observation Genetics Profile phaseset 2 Observation Sequence blocks Profile Observation Profile Observation Profile Diagnostic Report Genotype Profile Observation Individual alleles If sequencing 2 exons per locus, then need 11 resource instances per locus 4 Sequences 7 Observations 18
19 Reducing the number of Observations needed by changing cardinality of Observation-genetics-Sequence to 0..* Patient/Donor Specimen Sequence Sequence Sequence Sequence Genetics Profile phaseset 1 Observation Genetics Profile phaseset 2 Observation Individual alleles Genetics Profile Observation Profile Diagnostic Report Genotype for a locus If sequencing 2 exons per locus, then need 7 resource instances per locus 4 Sequences 3 Observations 19
20 Summary: Two Proposals 1. Remove a Profile Sequence > Profile for Consensus Sequence Blocks 2. Change cardinality of Observation-genetics-Sequence from 0..1 to 0..* 20
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