Skip to content

Commit

Permalink
STXBP1
Browse files Browse the repository at this point in the history
  • Loading branch information
@pnrobinson
pnrobinson committed Dec 4, 2024
1 parent 0e8c0c6 commit e6e5fb8
Show file tree
Hide file tree
Showing 468 changed files with 9,886 additions and 18,613 deletions.
315 changes: 315 additions & 0 deletions notebooks/STXBP1/STXBP1_DEE4_Xian_2022.ipynb
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,315 @@
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# STXBP1: Developmental and epileptic encephalopathy 4\n",
"[developmental and epileptic encephalopathy-4 (DEE4)](https://omim.org/entry/612164) is caused by heterozygous mutation in the STXBP1 gene.\n",
"\n",
"Here, we have recoded the clinical data from [Xian et al. (2022) Assessing the landscape of STXBP1-related disorders in 534 individuals. Brain](https://pubmed.ncbi.nlm.nih.gov/35190816/). We do not use the diagnosis groups of the authors.\n",
"\n",
"The authors used five diagnostic labels.\n",
"\n",
"- The diagnostic label of Ohtahara Syndrome (OS) was used if individuals had EOEE as well as tonic seizures and suppression-burst EEG. (HPO codes for epileptic encephalopathy, infantile onset; Tonic seizure; EEG with burst suppression)\n",
"- West Syndrome (WS) group included individuals with infantile spasms as the first seizure manifestation of STXBP1-related disorders. (HPO Code for Infantile spasm, infantile onset)\n",
"- Early-Onset Epileptic Encephalopathy (EOEE) included individuals with onset of seizures in the first three months of life and clinical features of developmental and epileptic encephalopathy such as developmental delay, and/or additional neurological features such as spasticity or movement disorders. A more specific phenotypic grouping such as Ohtahara Syndrome or West Syndrome was assigned if this information was available.\n",
"- Other Developmental and Epileptic Encephalopathies (other DEE)individuals that had a developmental and epileptic encephalopathy (DEE) that could not be classified as either EOEE, OS, or WS. This group of seizure phenotypes included severe epilepsies with seizures, which are often drug-resistant, as well as evidence of encephalopathy, including significant developmental delay or even loss of developmental skills.\n",
"- Neurodevelopmental disorders (NDD): This group included individuals with developmental differences including developmental delay, autism, and intellectual disability without evidence of an epileptic encephalopathy. For individuals with NDD and seizures, the NDD rather than a DEE label was used if there was evidence that seizures could be controlled by medication and did not result in an epileptic encephalopathy,\n",
"including prominent EEG findings.\n",
"\n",
"\n",
"According to the authors, patients with R406H and R406C mutations were more likely to have a burst suppression pattern on EEG and spastic tetraplegia, and less likely to have ataxia, compared to the rest of the cohort. Additionally, patients with premature termination mutations or deletions in the STXBP1 gene were more likely to have infantile spasms, hypsarrhythmia on EEG, ataxia, hypotonia, and neonatal seizure onset compared to patients with missense mutations."
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Using pyphetools version 0.9.113\n"
]
}
],
"source": [
"from pyphetools.creation import TemplateImporter, Moi\n",
"from pyphetools.visualization import IndividualTable, QcVisualizer\n",
"from IPython.display import display, HTML\n",
"import pyphetools\n",
"print(f\"Using pyphetools version {pyphetools.__version__}\")"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"template = \"input/STXBP1_DEE4_Xian_2022.xlsx\"\n",
"created_by = \"0000-0002-0736-9199\""
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"HPO version 2024-08-13\n",
"Created encoders for 539 fields\n",
"Importing OMIM:612164, Developmental and epileptic encephalopathy 4, HGNC:11444, STXBP1, NM_001032221.6\n",
"We output 463 GA4GH phenopackets to the directory phenopackets\n"
]
}
],
"source": [
"timporter = TemplateImporter(template=template, created_by=created_by)\n",
"individual_list, cvalidator = timporter.import_phenopackets_from_template()"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<h2>Cohort validation</h2>\n",
"<p>Errors found with 200 of 463 phenopackets.</p>\n",
"<table style=\"border: 2px solid black; align: \"left\">\n",
"<caption>Error counts</caption>\n",
"<tr><th style=\"text-align: left;font-weight: bold;\">Level</th><th style=\"text-align: left;font-weight: bold;\">Error category</th><th style=\"text-align: left;font-weight: bold;\">Count</th></tr>\n",
"<tr><td style=\"text-align: left;\">WARNING</td><td style=\"text-align: left;\">REDUNDANT</td><td style=\"text-align: left;\">322</td></tr>\n",
"</table>\n",
"<p>A total of 322 issues were fixed and no individual was removed from the cohort.</p>"
],
"text/plain": [
"<IPython.core.display.HTML object>"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"qc = QcVisualizer(cohort_validator=cvalidator)\n",
"display(HTML(qc.to_summary_html()))"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"[pyphetools] Ingested 463 GA4GH phenopackets.\n",
"[INFO] Extracted 463 from 463 phenopackets with OMIM:612164\n",
"\n",
"\tDevelopmental and epileptic encephalopathy 4 (OMIM:612164): n=463\n",
"We found a total of 518 unique HPO terms\n",
"Extracted disease: Developmental and epileptic encephalopathy 4 (OMIM:612164)\n",
"Wrote HPOA disease file to OMIM-612164.tab\n"
]
},
{
"data": {
"text/html": [
"<div>\n",
"<style scoped>\n",
" .dataframe tbody tr th:only-of-type {\n",
" vertical-align: middle;\n",
" }\n",
"\n",
" .dataframe tbody tr th {\n",
" vertical-align: top;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: right;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>#diseaseID</th>\n",
" <th>diseaseName</th>\n",
" <th>phenotypeID</th>\n",
" <th>phenotypeName</th>\n",
" <th>onsetID</th>\n",
" <th>onsetName</th>\n",
" <th>frequency</th>\n",
" <th>sex</th>\n",
" <th>negation</th>\n",
" <th>modifier</th>\n",
" <th>description</th>\n",
" <th>publication</th>\n",
" <th>evidence</th>\n",
" <th>biocuration</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>OMIM:612164</td>\n",
" <td>Developmental and epileptic encephalopathy 4</td>\n",
" <td>HP:0000733</td>\n",
" <td>Motor stereotypy</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>56/56</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>PMID:35190816</td>\n",
" <td>PCS</td>\n",
" <td>ORCID:0000-0002-0736-9199[2024-12-04]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>OMIM:612164</td>\n",
" <td>Developmental and epileptic encephalopathy 4</td>\n",
" <td>HP:0012000</td>\n",
" <td>EEG with generalized spikes</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>2/2</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>PMID:35190816</td>\n",
" <td>PCS</td>\n",
" <td>ORCID:0000-0002-0736-9199[2024-12-04]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>OMIM:612164</td>\n",
" <td>Developmental and epileptic encephalopathy 4</td>\n",
" <td>HP:0002376</td>\n",
" <td>Developmental regression</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>50/50</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>PMID:35190816</td>\n",
" <td>PCS</td>\n",
" <td>ORCID:0000-0002-0736-9199[2024-12-04]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>OMIM:612164</td>\n",
" <td>Developmental and epileptic encephalopathy 4</td>\n",
" <td>HP:0200048</td>\n",
" <td>Cyanotic episode</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>1/1</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>PMID:35190816</td>\n",
" <td>PCS</td>\n",
" <td>ORCID:0000-0002-0736-9199[2024-12-04]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>OMIM:612164</td>\n",
" <td>Developmental and epileptic encephalopathy 4</td>\n",
" <td>HP:0010536</td>\n",
" <td>Central sleep apnea</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>1/1</td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td></td>\n",
" <td>PMID:35190816</td>\n",
" <td>PCS</td>\n",
" <td>ORCID:0000-0002-0736-9199[2024-12-04]</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" #diseaseID diseaseName phenotypeID \\\n",
"0 OMIM:612164 Developmental and epileptic encephalopathy 4 HP:0000733 \n",
"1 OMIM:612164 Developmental and epileptic encephalopathy 4 HP:0012000 \n",
"2 OMIM:612164 Developmental and epileptic encephalopathy 4 HP:0002376 \n",
"3 OMIM:612164 Developmental and epileptic encephalopathy 4 HP:0200048 \n",
"4 OMIM:612164 Developmental and epileptic encephalopathy 4 HP:0010536 \n",
"\n",
" phenotypeName onsetID onsetName frequency sex negation \\\n",
"0 Motor stereotypy 56/56 \n",
"1 EEG with generalized spikes 2/2 \n",
"2 Developmental regression 50/50 \n",
"3 Cyanotic episode 1/1 \n",
"4 Central sleep apnea 1/1 \n",
"\n",
" modifier description publication evidence \\\n",
"0 PMID:35190816 PCS \n",
"1 PMID:35190816 PCS \n",
"2 PMID:35190816 PCS \n",
"3 PMID:35190816 PCS \n",
"4 PMID:35190816 PCS \n",
"\n",
" biocuration \n",
"0 ORCID:0000-0002-0736-9199[2024-12-04] \n",
"1 ORCID:0000-0002-0736-9199[2024-12-04] \n",
"2 ORCID:0000-0002-0736-9199[2024-12-04] \n",
"3 ORCID:0000-0002-0736-9199[2024-12-04] \n",
"4 ORCID:0000-0002-0736-9199[2024-12-04] "
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"pmid = \"PMID: 35190816\" # Xian et al (2022) Assessing the landscape of STXBP1-related disorders in 534 individuals\n",
"df = timporter.create_hpoa_from_phenopackets(pmid=pmid, mode_of_inheritance=Moi.AD, target=\"OMIM:612164\")\n",
"df.head()"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "ps24venv",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.12.4"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
Loading

0 comments on commit e6e5fb8

Please sign in to comment.