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#Your nameYour emailDate created
OPERATIONS |
REF IMPLEMENTATION
BUG |
ENHANCEMENT |
OTHER		OperationTitleDescriptionStatus
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THIS IS A LEGACY LIST OF ISSUES. PLEASE LOG NEW ISSUES AT https://github.com/FHIR/genomics-operations/issues
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1Bob Dolinbdolin@elimu.io2022-03-08OPERATIONSENHANCEMENTapplicable to many operationsVersioning of operationsSpecify how versioning works (e.g. current version is '/find-subject-variants' and past version is '/STU2/$find-subject-variants'). See also the zulip discussion.
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2Bob Dolinbdolin@elimu.io2022-03-08OPERATIONSENHANCEMENTfind-subject-specific-variantsLarge amount of input dataHow will this operation work if thousands to millions of variants are being sought (e.g. for polygenic risk score calculation)? Do we need to define a POST method?
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3Bob Dolinbdolin@elimu.io2022-03-08REF IMPLEMENTATIONOTHERapplicable to many operationsTest with other data modelsCreate reference implementations for other data models (OMOP, vector-based, Amazon OMICS, FHIR, Jupyter notebook, etc)Active
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5Bob Dolinbdolin@elimu.io2022-03-08OPERATIONSENHANCEMENTapplicable to many operationspHGVS capabilities- Find DNA variants predicted to have BRAF V600E (NP_001341538.1:p.Val600Glu, NP_001365397.1:p.Val600Glu, NP_001365403.1:p.Val600Glu, NP_004324.2:p.Val600Glu)
- (Resolution of this issue is related to https://jira.hl7.org/browse/FHIR-40320)
- 1- vs. 3-letter AA abbreviations for search
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6Bob Dolinbdolin@elimu.io2022-03-08OPERATIONSENHANCEMENTfind-study-metadataAlign study metadata with IGstudy metadata - align with latest resolution (related to https://jira.hl7.org/browse/FHIR-35864)
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7Bob Dolinbdolin@elimu.io2022-03-08OPERATIONSENHANCEMENTapplicable to many operationsOther parameters to consider - implications - filter for clinical significance (e.g. don't want to get back benign variants);
- gene;
- variantType;
- logical NOT parameter
- size, gene content threshold (relevant for determination of SV pathogenicity)
- other parameters needed for diagnostic oddysey pipeline
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8Bob Dolinbdolin@elimu.io2022-03-08OPERATIONSENHANCEMENTapplicable to many operationsOther operations to consider - GWAS;
- microbiology;
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11Bob Dolinbdolin@elimu.io2022-03-15REF IMPLEMENTATIONENHANCEMENTapplicable to many operationsEnhance search to include representative cHGVS, pHGVSIn cases where normalization fails, we can potentially also search against representative cHGVS and pHGVS fields. Relates to issue #5 and https://jira.hl7.org/browse/FHIR-40320) (May not be necessary, given issue #12)
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17Bob Dolinbdolin@elimu.io2022-04-18OPERATIONSENHANCEMENTapplicable to many operationscomparisons - comparison testing (e.g. trio, siblings, results from 2 tests);
- 'compare-patient-to-patient' send in two patient Ids and get back a similarity score and ability to request the difference and similarity. (or same patient, over time)
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19Bret Heale
bheale@humanizedhealthconsulting
2022-04-19REF IMPLEMENTATIONENHANCEMENTapplicable to many operationsFHIR importerImport FHIR genomics data into MongoDB (overlaps with #49, #52, #55)
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20Bob Dolinbdolin@elimu.io2022-04-22OPERATIONSENHANCEMENTapplicable to many operationsRNA-seqCreate IG proposal and operations update to model and query for RNA-Seq data
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24Bob Dolinbdolin@elimu.io2022-05-03REF IMPLEMENTATIONENHANCEMENTapplicable to many operationsAdd a FHIR CapabilityStatementServer can include a FHIR capability statement
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25Bret Heale
bheale@humanizedhealthconsulting
2022-05-03OPERATIONSBUGapplicable to many operationsValidate operationDefinition 'subject' IN parameterShould the subject IN parameter include a target profile, to be clear that this is a patient reference?
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26Kim Peifer
kim.peifer@flatiron.com
2022-05-03OPERATIONSENHANCEMENTapplicable to many operationsspecimen collection dateWhere testDateRange is a parameter, a more applicable parameter could be specimenCollectionDateRange. I can see how test date range is useful, but from what I understand the critical factor is when the specimen was collected, especially with increasing use of testing at different points in time for new mutations which might again alter treatment course.
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28Bob Dolinbdolin@elimu.io2022-08-05OPERATIONSENHANCEMENTfind-subject-tx-implicationsImplication range-based searchRange-based searching currently only retrieves tx-implications of simple and structural variants, but should possibly also retrieve implications of genotypes / haplotypes
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29Jamie Jones
james.jones.bch@gmail.com
2022-08-15OPERATIONSENHANCEMENTfind-subject-variantsCollapse similar operationsMerge find-subject-specific-variants into find-subject-variants (similar to how phenotype oeprations include both a variants and a ranges parameter. Likewise, merge find-subject-specific-haplotypes into find-subject-haplotypes operation.
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30Bob Dolinbdolin@elimu.io2022-10-04OPERATIONSENHANCEMENTapplicable to many operationsVersion based on FHIR R5/6Make updates as needed to align with FHIR R5/6. Create new operation for MolDef.
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31Bob Dolinbdolin@elimu.io2022-10-17REF IMPLEMENTATIONENHANCEMENTapplicable to many operationsChange parameter output to bundleIf we change the parameter output to a bundle, we can enable direct import of operations output into a FHIR server.
Alternatively, we can add an identifier to each variant, and then implications can reference the identifier, like this:
"derivedFrom": {"reference": "Practitioner?identifier=http://hl7.org/fhir/sid/us-npi|9999999391"}
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32Bob Dolinbdolin@elimu.io2022-10-28OPERATIONSENHANCEMENTapplicable to many operationsexplicit negationHow do operations return pertinent negatives? How do operations (or an app) enable inferring other negatives (Negatives: infer wildtype based on studied and uncallable regions; explicit variant - absent; explicit wildtype - present). How does this overlap with gVCF?
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33Bob Dolinbdolin@elimu.io2022-11-20OPERATIONSENHANCEMENTapplicable to many operationsstructural variant molec conseq pipelineOur current molec conseq pipeline isn't working for SVs - need to debug and possibly do code revisions to sure up the steps. can't run SV files through vcfPrepper and then vcf2json; need to create valid examples and test end to end pipeline;
vcfPrepper: Some rows have huge annotations (e.g. for inv); some of our SV files aren't parsing correctly (e.g. END is less than POS)
vcf2json: if(record.INFO['SVTYPE'][0].upper() not in list(SVs)) - change to if(record.INFO['SVTYPE'] not in list(SVs)); if genomicSourceClass input parameter is 'mixed', just don't output a genomicSourceClass
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34Bob Dolinbdolin@elimu.io2022-12-02OPERATIONSENHANCEMENTapplicable to many operationsexplore dynamic annotation of structural variantsDevelop designs and implementations that show dynamic annotation of SVs (consider CQL as in clinical trials matching)
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35Rohan Gupta
rohaninjmu@gmail.com
2022-12-03REF IMPLEMENTATIONENHANCEMENTapplicable to many operationsRefactor the code to isolate the data access layerWould be nice to 'unplug' Mongo, and plug in some other database, and be able to just update the data query layer without needing to alter or carefully review the entire code base
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37Bob Dolinbdolin@elimu.io2023-03-06OPERATIONSENHANCEMENTapplicable to many operationsreturn additional provenanceConsider additional provenance of annotations - how to distinguish static vs. dynamic, source of knowledge, etc. (related to issue #22)
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39Bob Dolinbdolin@elimu.io2023-03-16REF IMPLEMENTATIONENHANCEMENTapplicable to many operationsImport family history into variant filtration app
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40Bob Dolinbdolin@elimu.io2023-03-31REF IMPLEMENTATIONENHANCEMENTapplicable to many operationsVariant discovery app - use of MMEAfter the fact Matchmaker Exchange for further exploration of LOF variants not found in ClinVar, etc.
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41Bob Dolinbdolin@elimu.io2023-04-04OPERATIONSENHANCEMENTapplicable to many operationsComprehensive bundle operationPull in everything known about a variant (dx/tx implications, molec conseq) - saves a number of calls. Implications can still be static or dynamic. (workflow might be similar to fhir bulk query api)
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42Bob Dolinbdolin@elimu.io2023-04-04OPERATIONSENHANCEMENTapplicable to many operationsstatic vs. dynamic phenotype callsallow phenotype operations to differentially pull in static and/or dynamically computed dx/tx implications
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44Bob Dolinbdolin@elimu.io2023-05-19OPERATIONSENHANCEMENTfind-subject-dx-implicationsadd Haplotypes parameterHaplotypes such as HLA are associated with disease risk
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45Bob Dolinbdolin@elimu.io2023-06-02REF IMPLEMENTATIONENHANCEMENTapplicable to many operationscreate multiple environmentsNeed an environment that reflects what has been balloted and another for what is in build, possibly an experimentation environment (e.g. for microbiology operation development) etc. Need Dev and Prod for each.
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46Bob Dolinbdolin@elimu.io2023-06-09OPERATIONSENHANCEMENTapplicable to many operationsPopulation range-based searchAdd ranges parameter to population queries (e.g. 'find all patients have a LDLR variant associated with FH). (Does it even make sense to have a Variants parameter for find-pop-mol-conseq?)
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47Bob Dolinbdolin@elimu.io2023-06-09OPERATIONSENHANCEMENTapplicable to many operationsFHIR Search capabilitiesFHIR Search defines a number of patterns (e.g. the 'above' modifier) that might be of value to incorporate into operations
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48Bret Heale
bheale@humanizedhealthconsulting
2023-06-29OPERATIONSENHANCEMENTapplicable to many operationsJSON / FHIR / TTLBe clear on expectations around response format (e.g. at least JSON, but can also include other formats?)
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49Bob Dolinbdolin@elimu.io2023-09-18REF IMPLEMENTATIONENHANCEMENTapplicable to many operationsClinical trial txImplicationsRevise mongo schema to capture additional information about clinical trials (e.g. title; tumor type / solid tumor; ...) (overlaps with #19, #52, #55)
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50Bob Dolinbdolin@elimu.io2023-09-25REF IMPLEMENTATIONENHANCEMENTapplicable to many operationsPGx outputClean up responses that include haplotypes and genotypes based on latest PGx guidance.
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51Bob Dolinbdolin@elimu.io2023-09-26REF IMPLEMENTATIONBUGapplicable to many operationsdate formatsAre operations returning correct dateTime datatype? (e.g. MTB - study-metadata); looks at all uses of date/time for QA
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52Bob Dolinbdolin@elimu.io2023-10-05REF IMPLEMENTATIONENHANCEMENTapplicable to many operationscentralize FHIR generationCentralize the code that converts Mongodb objects into FHIR. This will make it easier to, say, add new fields into Mongo and then have them correctly surfaced in FHIR. Make sure we have a uniform approach to nulls (e.g. if no value is present in Mongo, then don't emit the component) (overlaps with #19, #49, #55)
Consider refactoring code into layers: API Interpreter --> Normalization --> Query Factory --> FHIR Generation Factory
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53Bob Dolinbdolin@elimu.io2024-01-17OPERATIONSENHANCEMENTapplicable to many operationsPopulation operations need a way to limit the denominatorConsider something like the FHIR Group resource, stored in GACS (or referenceable in a FHIR server)
under consideration
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54Bob Dolinbdolin@elimu.io2024-04-12REF IMPLEMENTATIONENHANCEMENTapplicable to many operationsExperiment with gVCFgVCF has wild type alleles and is being used for polygenic scores. Experiment with gVCF in reference implementation.active
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55Bob Dolinbdolin@elimu.io2024-05-05REF IMPLEMENTATIONENHANCEMENTapplicable to many operationsRevise internal data structuresOther than Variants collection, why not have all other collections, except perhaps Test, as native FHIR objects?? (overlaps with #19, #49, #52)
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56Bob Dolinbdolin@elimu.io2024-05-19REF IMPLEMENTATIONBUGapplicable to many operationsvcf2json is not generating phase data for VCF rows with multiple ALT allelesvcf2json.add_phase_records uses the raw VCF row to construct phase relationship, which doesn't work for multi ALTs. (Also, for variant calls in gvcf, we aren't parsing the row because of the presence of the unrecognized ALT token).
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57Bob Dolinbdolin@elimu.io2024-05-19REF IMPLEMENTATIONBUGapplicable to many operationsvcf2json is not generating molec conseq data for VCF rows with multiple ALT allelessnpEff output for multi ALT rows includes predicted consequences for each ALT allele - so would need to grab the correct set of consequences depending on the relevant allele.
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58Bob Dolinbdolin@elimu.io2024-05-22REF IMPLEMENTATIONBUGfind-subject-structural-intersecting-variantsSV output is missing CNCheck SV pipeline, from loading the VCF to Mongo representation to FHIR output
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59Bob Dolinbdolin@elimu.io2024-06-14REF IMPLEMENTATIONBUGapplicable to many operationsNon-conformant outputValidate output of each operation for IG conformance
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60Bob Dolinbdolin@elimu.io2024-07-16REF IMPLEMENTATIONENHANCEMENTapplicable to many operationsInconsistent dataEnhance loading script to ensure certain fields are populated - e.g. gene, SPDI, etc.
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61Bob Dolinbdolin@elimu.io2024-12-12REF IMPLEMENTATIONENHANCEMENTapplicable to many operationsInclude quality data in outputgvcf files may emit everything, regardless of quality. How do we enable quality criteria as filters on the data?
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62Bob Dolinbdolin@elimu.io2025-04-24REF IMPLEMENTATIONENHANCEMENTapplicable to many operationsAdd CQL engine, for advanced annotation capabilitiesDeploy the Cat-VRS to CQL logic and show its use in reference implementation
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in progress
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