From d93a36f3448d48ffaeb15a78d1d7793fbd611df9 Mon Sep 17 00:00:00 2001 From: Tamara Slosarek Date: Thu, 28 Sep 2023 12:05:17 +0200 Subject: [PATCH] chore(docs): remove old file version --- .../App-behavior-in-case-of-missing-date.md | 91 ------------------- 1 file changed, 91 deletions(-) delete mode 100644 docs/feature-discussion/App-behavior-in-case-of-missing-date.md diff --git a/docs/feature-discussion/App-behavior-in-case-of-missing-date.md b/docs/feature-discussion/App-behavior-in-case-of-missing-date.md deleted file mode 100644 index 1bffb7e7..00000000 --- a/docs/feature-discussion/App-behavior-in-case-of-missing-date.md +++ /dev/null @@ -1,91 +0,0 @@ -# App Behavior in Case of Missing Data - -Missing data with regards to PharMe can occur when there is a mismatch -between genes or diplotypes in the lab report, in the annotations, -and in CPIC lookups. - -Lookups are fetched from CPIC and matched with users' diplotypes from the lab. -Sometimes, genes or diplotypes might be unknown. - -This page collects the app's current and desired behavoir in such cases for -further discussion, as of August 28, 2023. - -**Baseline: this should not happen, we will test the lab results before, but** -**need to define what happens especially if missing genotype.** - -## App Behavior - -**Biggest question: should we overwrite (known) lab phenotypes with** -**Indeterminate? We will not be able to map to CPIC guidelines currently** - -**Also test: can we get different annotations for "Indeterminate" vs.** -**"No Result" in app?** - -☑️ TODO: split up cases by examples - -| Page | Case | Desired behavior | Current behavior | TODO | -| ---- | --- | ----------------- | ---------------- | ---- | -| Gene report | Gene in lab results not in lookups (e.g., APOE) | Not shown in gene results | ✅ | – | -| Gene report | Gene in lookups not in lab results | Should show in list but with "not tested" | Not shown in gene results | – | -| Gene report | Unknown diplotype | Shown in results with "Indeterminate" phenotype | Not shown in gene results | (1) Show known genes with unknown diplotype as Indeterminate; (2) Overwrite lab phenotype as "Indeterminate" if CPIC lookup not present | -| Gene detail | Unknown diplotype | As in report, diplotype shown; drugs with guidelines only for this gene should map to "Indeterminate" status | Not shown in gene results, so not getting here | Fix (1) in report and come back here; will probably need to overwrite lab phenotype with "Indeterminate", might be directly fixed by (2) | -| Drug search | Unknown gene (only guideline gene) | Not sure if it makes sense to publish such guidelines we cannot show; if there, should show "Indeterminate" status | Warning shown in script that maps FDA guidenlines to CPIC lookups; "Amifampridrine" currently staged and shown, showing as "Indeterminate" (but will probably be removed, as NAT2 not inclued in new test) | – | -| Drug search | Unknown or missing diplotype | Should show "Unknown" status | ✅ | – | -| Drug search | Unknown or missing diplotype (multiple guideline genes) | Should show status based on guideline for present gene (or "Unknown", if all are not known) | **Cannot test currently, as no such guidelines; test indeterminate and missing** | ? | -| Drug detail | Unknown or missing gene (only guideline gene) | Guideline should be shown as "Unknown"; if unknown, maybe instead of gene, "no guidelines present" should be shown; if missing, this should be shown | Guideline is "Indeterminate", phenotype is not; need to test for missing | See (2); maybe shown "no guidelines present" | -| Drug detail | Unknown diplotype | Guideline and phenotype should be shown as "Indeterminate" | Guideline is "Indeterminate", phenotype is not | See (2) | -| Drug detail | Unknown or missing gene or diplotype (multiple guideline genes) | See drug search; if unknown gene, hide in "your genome"; if missing, this should be shown | **Cannot test currently, as no such guidelines; test indeterminate and missing** | ?; probably will need to hide unknown gene and overwrite unknown diplotype phenotype | - -## Data Examples - -| Description | Screenshot | -| ----------- | ------------ | -| Diplotypes list | diplotypes_list | -| Lookups list (matched) | matched_lookups | -| Single diplotype | diplotype | -| Single lookup | lookup | - -## Test Data for Cases Above - -See the example below. User is `???`, password `1234`. - -* `CYP2D6`: all good, gene known, diplotype known -* `CYP2C19`: gene known, diplotype unknown (second star allele made up) -* `APOE`: gene not known (also, no guideline in Anni) -* `NAT2`: gene not known (but guideline in Anni; should be no difference to - no guideline in Anni, but for testing) - -```json -{ - "diplotypes": [ - { - "gene": "CYP2D6", - "resultType": "Diplotype", - "genotype": "*1/*17", - "phenotype": "Normal Metabolizer", - "allelesTested": "*xN.*3.*4.*5.*6.*8.*9.*10.*14A.*14B.*17.*41" - }, - { - "gene": "CYP2C19", - "resultType": "Diplotype", - "genotype": "*1/*101", - "phenotype": "Intermediate Metabolizer", - "allelesTested": "*2.*3.*4A.*4B.*5.*6.*8.*9.*10.*17.*101" - }, - { - "gene": "APOE", - "resultType": "Diplotype", - "genotype": "ε3/ε3", - "phenotype": "Normal APOE function", - "allelesTested": "ε4" - }, - { - "gene": "NAT2", - "resultType": "Diplotype", - "genotype": "*6/*6", - "phenotype": "Poor Metabolizer", - "allelesTested": "*6" - }, - ] -} -```