docs(#620): update with notes from Aniwaa

hpi-dhc · Sep 22, 2023 · 4241512 · 4241512
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diff --git a/docs/feature-discussion/App-behavior-in-case-of-missing-data.md b/docs/feature-discussion/App-behavior-in-case-of-missing-data.md
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+# 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.**
+
+**TODO (from meeting w/ Aniwaa): gene report should also show genes in**
+**annotations but not in report (“not tested”); case that CPIC does not know**
+**genotypes should not happen, will handle manually for now (pre-processing**
+**script)**
+
+
+## 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 | 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  | <img width="564" alt="diplotypes_list" src="https://github.com/hpi-dhc/PharMe/assets/7488660/1e4bfb4e-a06c-46ec-a58b-240a36735406"> |
+| Lookups list (matched) | <img width="564" alt="matched_lookups" src="https://github.com/hpi-dhc/PharMe/assets/7488660/5f9a2beb-7642-4d17-930c-c47d6fc45266"> |
+| Single diplotype | <img width="458" alt="diplotype" src="https://github.com/hpi-dhc/PharMe/assets/7488660/27ae08c9-f9ee-405d-b838-7a4e3a9461dc"> |
+| Single lookup | <img width="307" alt="lookup" src="https://github.com/hpi-dhc/PharMe/assets/7488660/ee8586c4-9c7c-4b1d-bada-17b721b374b6"> |
+
+## 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"
+        },
+    ]
+}
+```