From 1e7d0845ebcbba87a78a584a39e0e4d55327bf6f Mon Sep 17 00:00:00 2001 From: Peter Robinson Date: Wed, 13 Dec 2023 08:33:23 +0100 Subject: [PATCH] ISCA2 --- docs/collections.md | 1 + notebooks/ISCA2/ISCA2_cohort.ipynb | 463 ++++++++++++++++++ notebooks/ISCA2/input/ISCA2_curation.xlsx | Bin 0 -> 15331 bytes .../PMID_25539947_25539947_P1.json | 171 +++++++ .../PMID_29122497_29122497_P1.json | 159 ++++++ .../PMID_29122497_29122497_P10.json | 159 ++++++ .../PMID_29122497_29122497_P2.json | 165 +++++++ .../PMID_29122497_29122497_P3.json | 165 +++++++ .../PMID_29122497_29122497_P4.json | 165 +++++++ .../PMID_29122497_29122497_P5.json | 173 +++++++ .../PMID_29122497_29122497_P6.json | 173 +++++++ .../PMID_29122497_29122497_P7.json | 179 +++++++ .../PMID_29122497_29122497_P8.json | 159 ++++++ .../PMID_29122497_29122497_P9.json | 171 +++++++ .../PMID_29297947_29297947_P1.json | 225 +++++++++ .../PMID_29297947_29297947_P2.json | 221 +++++++++ .../PMID_29359243_29359243_P1.json | 220 +++++++++ .../PMID_31279336_31279336_P1.json | 159 ++++++ .../PMID_32424628_32424628_P1.json | 248 ++++++++++ 19 files changed, 3376 insertions(+) create mode 100644 notebooks/ISCA2/ISCA2_cohort.ipynb create mode 100644 notebooks/ISCA2/input/ISCA2_curation.xlsx create mode 100644 notebooks/ISCA2/phenopackets/PMID_25539947_25539947_P1.json create mode 100644 notebooks/ISCA2/phenopackets/PMID_29122497_29122497_P1.json create mode 100644 notebooks/ISCA2/phenopackets/PMID_29122497_29122497_P10.json create mode 100644 notebooks/ISCA2/phenopackets/PMID_29122497_29122497_P2.json create mode 100644 notebooks/ISCA2/phenopackets/PMID_29122497_29122497_P3.json create mode 100644 notebooks/ISCA2/phenopackets/PMID_29122497_29122497_P4.json create mode 100644 notebooks/ISCA2/phenopackets/PMID_29122497_29122497_P5.json create mode 100644 notebooks/ISCA2/phenopackets/PMID_29122497_29122497_P6.json create mode 100644 notebooks/ISCA2/phenopackets/PMID_29122497_29122497_P7.json create mode 100644 notebooks/ISCA2/phenopackets/PMID_29122497_29122497_P8.json create mode 100644 notebooks/ISCA2/phenopackets/PMID_29122497_29122497_P9.json create mode 100644 notebooks/ISCA2/phenopackets/PMID_29297947_29297947_P1.json create mode 100644 notebooks/ISCA2/phenopackets/PMID_29297947_29297947_P2.json create mode 100644 notebooks/ISCA2/phenopackets/PMID_29359243_29359243_P1.json create mode 100644 notebooks/ISCA2/phenopackets/PMID_31279336_31279336_P1.json create mode 100644 notebooks/ISCA2/phenopackets/PMID_32424628_32424628_P1.json diff --git a/docs/collections.md b/docs/collections.md index 4fc8ab765..da38de128 100644 --- a/docs/collections.md +++ b/docs/collections.md @@ -15,6 +15,7 @@ were mainly created using the Python library [pyphetools](https://github.com/mon | [FBN1](https://github.com/monarch-initiative/phenopacket-store/tree/main/notebooks/FBN1){:target="_blank"} | 103 phenopackets ;[Ectopia lentis, familial](https://omim.org/entry/129600){:target="_blank"}, [Marfan lipodystrophy syndrome](https://omim.org/entry/616914){:target="_blank"}, [Marfan syndrome](https://omim.org/entry/154700){:target="_blank"}, [Geleophysic dysplasia 2](https://omim.org/entry/614185){:target="_blank"},[Acromicric dysplasia](https://omim.org/entry/102370){:target="_blank"} | | [FLXB4](https://github.com/monarch-initiative/phenopacket-store/tree/main/notebooks/FBXL4/FBXL4-curation.ipynb){:target="_blank"}|30 phenopackets; [Mitochondrial DNA depletion syndrome 13 (encephalomyopathic type)](https://omim.org/entry/615471){:target="_blank"} | | [GLI3](https://github.com/monarch-initiative/phenopacket-store/tree/main/notebooks/GLI3){:target="_blank"} | 77 phenopackets; [Greig cephalopolysyndactyly syndrome](https://omim.org/entry/175700){:target="_blank"}, [Pallister-Hall syndrome](https://omim.org/entry/146510){:target="_blank"}, [Polydactyly, postaxial, types A1 and B](https://omim.org/entry/174200){:target="_blank"} | +| [ISCA2](https://github.com/monarch-initiative/phenopacket-store/tree/main/notebooks/ISCA2/ISCA2-curation.ipynb) | 16 phenopackets; [Mitochondrial DNA depletion syndrome 4](https://omim.org/entry/616370){:target="_blank"} | | [Jacobsen syndrome](https://github.com/monarch-initiative/phenopacket-store/blob/main/notebooks/11q_terminal_deletion/grossfield_11q_2002.ipynb){:target="_blank"} |69 phenopackets; [Jacobsen syndrome](https://omim.org/entry/147791){:target="_blank"} | | [KDM6B](https://github.com/monarch-initiative/phenopacket-store/blob/main/notebooks/KDM6B/KDM6B_PMID_37196654.ipynb){:target="_blank"} |73 phenopackets; [Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities](https://omim.org/entry/618505){:target="_blank"} | | [LIRICAL](https://github.com/monarch-initiative/phenopacket-store/blob/main/notebooks/LIRICAL/LIRICAL.ipynb){:target="_blank"} | 384 phenopackets, various diseases | diff --git a/notebooks/ISCA2/ISCA2_cohort.ipynb b/notebooks/ISCA2/ISCA2_cohort.ipynb new file mode 100644 index 000000000..071162673 --- /dev/null +++ b/notebooks/ISCA2/ISCA2_cohort.ipynb @@ -0,0 +1,463 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "e230d3c7-7f17-48fc-b09e-e141cdd8b943", + "metadata": {}, + "source": [ + "# ISCA2\n", + "\n", + "Pathogenic variants in ISCA2 cause [Multiple mitochondrial dysfunctions syndrome 4 ](https://omim.org/entry/616370). This notebook contains information from several publications." + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "id": "718cb83d-6fe7-4724-a04c-f263a137378e", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Using pyphetools version 0.9.15\n" + ] + } + ], + "source": [ + "import pandas as pd\n", + "pd.set_option('display.max_colwidth', None) # show entire column contents, important!\n", + "from collections import defaultdict\n", + "from IPython.display import display, HTML\n", + "import pyphetools\n", + "from pyphetools.creation import *\n", + "from pyphetools.visualization import *\n", + "from pyphetools.validation import CohortValidator\n", + "print(f\"Using pyphetools version {pyphetools.__version__}\")" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "f99da07a-1900-4e72-9d7a-d9aacde210f9", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "HPO version 2023-10-09\n" + ] + } + ], + "source": [ + "import ssl\n", + "ssl._create_default_https_context = ssl._create_unverified_context\n", + "parser = HpoParser()\n", + "hpo_cr = parser.get_hpo_concept_recognizer()\n", + "hpo_version = parser.get_version()\n", + "hpo_ontology = parser.get_ontology()\n", + "metadata = MetaData(created_by=\"ORCID:0000-0002-0736-9199\")\n", + "metadata.default_versions_with_hpo(version=hpo_version)\n", + "print(f\"HPO version {hpo_version}\")" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "id": "2324589c-8e83-435c-9763-90a1910534bb", + "metadata": {}, + "outputs": [], + "source": [ + "df = pd.read_excel('input/ISCA2_curation.xlsx')\n", + "#df.head(2)" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "id": "82a64764-da34-411b-b2fc-86dc27a403a6", + "metadata": {}, + "outputs": [], + "source": [ + "df['patient_id'] = df['ID']\n", + "df.set_index('patient_id', inplace=True)" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "id": "ad92b264-2c69-4086-b3dd-db64f8629c23", + "metadata": {}, + "outputs": [], + "source": [ + "def extract_cdna(variant):\n", + " \"\"\"\n", + " split strings like c.772G>T(p.Gly258*) on the open-parenthesis symbol and return the first part\n", + " \"\"\"\n", + " v = variant.split(\"(\")[0]\n", + " v = v.replace(\" \", \"\").replace(\"p.\",\"\")\n", + " return v\n", + " \n", + "def extract_variant_1(variants):\n", + " \"\"\"\n", + " Split on the slash (\"/\") and return the first part (or entire string for homozygous)\n", + " \"\"\"\n", + " v1 = variants.split(\"/\")[0]\n", + " return extract_cdna(v1)\n", + "\n", + "def extract_variant_2(variants):\n", + " \"\"\"\n", + " Split on the slash (\"/\") and return the second part (or entire string for homozygous)\n", + " \"\"\"\n", + " fields = variants.split(\"/\")\n", + " if len(fields) == 2:\n", + " return extract_cdna(fields[1])\n", + " else:\n", + " # there was only one variant\n", + " return extract_cdna(variants)" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "id": "b16e288b-ee17-4e12-b152-13191d0d2333", + "metadata": {}, + "outputs": [], + "source": [ + "df[\"var1\"] = df['Variant annotation'].apply(lambda x: extract_variant_1(x))\n", + "df[\"var2\"] = df['Variant annotation'].apply(lambda x: extract_variant_2(x))" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "id": "3cdad651-5642-45d5-a11d-9c59d316f9d9", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "c.355G>A\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_194279.3%3Ac.355G>A/NM_194279.3?content-type=application%2Fjson\n", + "c.229G>A\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_194279.3%3Ac.229G>A/NM_194279.3?content-type=application%2Fjson\n", + "c.413C>G\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_194279.3%3Ac.413C>G/NM_194279.3?content-type=application%2Fjson\n", + "c.295delT\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_194279.3%3Ac.295delT/NM_194279.3?content-type=application%2Fjson\n", + "c.5C>A\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_194279.3%3Ac.5C>A/NM_194279.3?content-type=application%2Fjson\n", + "c.334A>G\n", + "https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_194279.3%3Ac.334A>G/NM_194279.3?content-type=application%2Fjson\n", + "extracted 6 variants with VariantValidator\n" + ] + } + ], + "source": [ + "from time import sleep\n", + "var1_list = df[\"var1\"].unique()\n", + "var2_list = df[\"var2\"].unique()\n", + "var_set = set()\n", + "var_set.update(var1_list)\n", + "var_set.update(var2_list)\n", + "variant_d = {}\n", + "hg38 = \"hg38\"\n", + "inca2_transcript = \"NM_194279.3\"\n", + "vvalidator = VariantValidator(genome_build=hg38, transcript=inca2_transcript)\n", + "for v in var_set:\n", + " print(f\"{v}\")\n", + " var = vvalidator.encode_hgvs(v)\n", + " variant_d[v] = var\n", + " sleep(1)\n", + "print(f\"extracted {len(variant_d)} variants with VariantValidator\")" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "id": "dddc1175-1d9a-4279-a15b-1369bf33bc20", + "metadata": {}, + "outputs": [], + "source": [ + "df['age in months']= df['Age of diagnosis'].apply(lambda x: x.split(\" \")[0])\n", + "ageMapper = AgeColumnMapper.by_month(column_name='age in months')\n", + "#ageMapper.preview_column(df['age in months'])" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "id": "4004f71c-512f-44f2-97b6-d9bf8e884622", + "metadata": {}, + "outputs": [], + "source": [ + "sexMapper = SexColumnMapper(male_symbol=\"M\", female_symbol=\"F\", unknown_symbol=\"nan\", column_name=\"Gender\")\n", + "#sexMapper.preview_column(df['Gender']).head()" + ] + }, + { + "cell_type": "markdown", + "id": "e6e91aea-f0f7-42ac-aeff-d9ea2c617505", + "metadata": {}, + "source": [ + "# Mapping phenotypic features" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "id": "3d122094-b717-43ea-9d2f-da98e1fc286c", + "metadata": {}, + "outputs": [], + "source": [ + "mapper_d = {}\n", + "phenotypeColumnMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d={})\n", + "phenotypeColumnMapper.preview_column(df['Phenotype'])\n", + "mapper_d['Phenotype'] = phenotypeColumnMapper\n", + "# phenotypeColumnMapper.preview_column(df['Phenotype'])" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "id": "213cf061-ab8b-4e5c-b578-31fd95ff69ee", + "metadata": {}, + "outputs": [], + "source": [ + "# This column conttains no data in the original file\n", + "prenatalUSmapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d={})\n", + "#prenatalUSmapper.preview_column(df['Prenatal ultrasound phenotype'])\n", + "#mapper_d['Prenatal ultrasound phenotype'] = prenatalUSmapper" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "id": "f2193d60-7f6d-4743-96e2-bcc78df7e46d", + "metadata": {}, + "outputs": [], + "source": [ + "mriMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d={})\n", + "mriMapper.preview_column(df['MRI phenotype'])\n", + "mapper_d['MRI phenotype'] = mriMapper" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "id": "9671ae99-fffa-4e1a-b360-30ff25376d27", + "metadata": {}, + "outputs": [], + "source": [ + "# This column conttains no data in the original file\n", + "cardiacMapper = OptionColumnMapper(concept_recognizer=hpo_cr, option_d={})\n", + "#cardiacMapper.preview_column(df['Cardiac phenotype'])\n", + "#mapper_d['Cardiac phenotype'] = cardiacMapper" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "id": "caa1a579-f063-466a-bb28-76cbe17f54bd", + "metadata": {}, + "outputs": [], + "source": [ + "aod_d = {\n", + " \"9 months\": \"P9M\",\n", + " \"3 months\": \"P3M\",\n", + " \"28 months\": \"P2Y4M\",\n", + " \"26 months\": \"P2Y2M\",\n", + " \"16 months\": \"P1Y4M\",\n", + " \"11 months\": \"P11M\",\n", + "}\n", + "aodMapper = AgeOfDeathColumnMapper(column_name='Age at death', string_to_iso_d=aod_d)" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "id": "0eab24c3-0336-4475-9a37-63d0a7c3b1bd", + "metadata": {}, + "outputs": [], + "source": [ + "mdds4 = Disease(disease_id=\"OMIM:616370\", disease_label=\"Mitochondrial DNA depletion syndrome 4\")\n", + "disease_d = {\"616370\": mdds4}\n", + "diseaseMapper = DiseaseIdColumnMapper(column_name=\"omim_id\", disease_id_map=disease_d)" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "id": "2991b248-459a-4e63-b883-7e3d90a74e9d", + "metadata": {}, + "outputs": [], + "source": [ + "encoder = MixedCohortEncoder(df=df,\n", + " hpo_cr=hpo_cr,\n", + " column_mapper_d=mapper_d,\n", + " individual_column_name=\"patient_id\",\n", + " disease_id_mapper=diseaseMapper,\n", + " pmid_column=\"PMID\",\n", + " title_column=\"title\",\n", + " sexmapper=sexMapper,\n", + " agemapper=ageMapper,\n", + " age_of_death_mapper=aodMapper,\n", + " metadata=metadata\n", + " )" + ] + }, + { + "cell_type": "code", + "execution_count": 17, + "id": "297872d5-3bc5-40ca-92c3-1257bb452ee3", + "metadata": {}, + "outputs": [], + "source": [ + "individuals = encoder.get_individuals()\n", + "# retrieve the variant strings and add Variant objects to each individual\n", + "# the individual id (i.id) is also the index of the pandas dataframe\n", + "for i in individuals:\n", + " row = df.loc[i.id] \n", + " v1 = row['var1']\n", + " v2 = row['var2']\n", + " #print(f\"{i.id}: v1={v1} and v2={v2}\")\n", + " if v1 == v2:\n", + " var1 = variant_d.get(v1)\n", + " var1.set_homozygous()\n", + " i.add_variant(var1)\n", + " else:\n", + " var1 = variant_d.get(v1)\n", + " var2 = variant_d.get(v2)\n", + " var1.set_heterozygous()\n", + " var2.set_heterozygous()\n", + " i.add_variant(var1)\n", + " i.add_variant(var2)" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "id": "2e2ace81-4532-400d-a32b-9d468796de72", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "

Cohort validation

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Errors found with 1 of 16 phenopackets.

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Error counts
LevelError categoryCount
WARNINGREDUNDANT1
\n", + "

A total of 1 issues were fixed and no individual was removed from the cohort.

" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "cvalidator = CohortValidator(cohort=individuals, ontology=hpo_ontology, min_hpo=1, allelic_requirement=AllelicRequirement.BI_ALLELIC)\n", + "qc = QcVisualizer(cohort_validator=cvalidator)\n", + "display(HTML(qc.to_summary_html()))" + ] + }, + { + "cell_type": "code", + "execution_count": 19, + "id": "2a1e1f5b-085f-43e0-8e3c-9409b819b314", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "
16 phenopackets - PMID:29297947 (n=2); PMID:29359243 (n=1); PMID:31279336 (n=1); PMID:32424628 (n=1); PMID:25539947 (n=1); PMID:29122497 (n=10)
IndividualDiseaseGenotypePhenotypic features
29297947_P1 (MALE; P3M)Mitochondrial DNA depletion syndrome 4 (OMIM:616370)NM_194279.3:c.229G>A (homozygous)Postnatal growth retardation (HP:0008897); Failure to thrive (HP:0001508); Diffuse optic disc pallor (HP:0012512); Visual impairment (HP:0000505); Low-set ears (HP:0000369); Wide nasal bridge (HP:0000431); Nasogastric tube feeding (HP:0040288); Global developmental delay (HP:0001263); Developmental regression (HP:0002376); Generalized hypotonia (HP:0001290); Spasticity (HP:0001257); Increased CSF glycine concentration (HP:0500230); Increased CSF glutamate concentration (HP:0500200); Increased CSF lactate (HP:0002490); Hyperglycinuria (HP:0003108); Leukodystrophy (HP:0002415); Hyperintensity of cerebral white matter on MRI (HP:0030890); Hyperintensity of MRI T2 signal of the spinal cord (HP:0040272)
29297947_P2 (FEMALE; P6M)Mitochondrial DNA depletion syndrome 4 (OMIM:616370)NM_194279.3:c.229G>A (homozygous)Nystagmus (HP:0000639); Leg muscle stiffness (HP:0008969); Motor regression (HP:0033044); Postnatal growth retardation (HP:0008897); Macrocephaly (HP:0000256); Diffuse optic disc pallor (HP:0012512); Visual impairment (HP:0000505); Feeding difficulties in infancy (HP:0008872); Generalized joint laxity (HP:0002761); Short 4th metacarpal (HP:0010044); Cutaneous syndactyly of toes (HP:0010621); Global developmental delay (HP:0001263); Hypotonia (HP:0001252); Spasticity (HP:0001257); Leukodystrophy (HP:0002415); Hyperintensity of cerebral white matter on MRI (HP:0030890)
29359243_P1 (FEMALE; P2M)Mitochondrial DNA depletion syndrome 4 (OMIM:616370)
  • NM_194279.3:c.297del (heterozygous)
  • NM_194279.3:c.334A>G (heterozygous)
Severe muscular hypotonia (HP:0006829); Nystagmus (HP:0000639); Motor regression (HP:0033044); Feeding difficulties (HP:0011968); Brisk reflexes (HP:0001348); Respiratory failure requiring assisted ventilation (HP:0004887); Increased CSF lactate (HP:0002490); Abnormal cerebral cortex morphology (HP:0002538); Abnormal diffusion weighted cerebral MRI morphology (HP:0032615); Abnormality of the internal capsule (HP:0012502)
31279336_P1 (MALE; P7M)Mitochondrial DNA depletion syndrome 4 (OMIM:616370)NM_194279.3:c.355G>A (homozygous)Malaise (HP:0033834); Insomnia (HP:0100785); Irritability (HP:0000737); Muscle stiffness (HP:0003552); Hypotonia (HP:0001252); Abnormal periventricular white matter morphology (HP:0002518); Abnormal cerebellum morphology (HP:0001317)
32424628_P1 (MALE; P11M)Mitochondrial DNA depletion syndrome 4 (OMIM:616370)
  • NM_194279.3:c.5C>A (heterozygous)
  • NM_194279.3:c.413C>G (heterozygous)
Spastic tetraparesis (HP:0001285); Optic atrophy (HP:0000648); Cognitive impairment (HP:0100543); Developmental regression (HP:0002376); Poor appetite (HP:0004396); Vomiting (HP:0002013); Nystagmus (HP:0000639); Encephalopathy (HP:0001298); Arm dystonia (HP:0031960); Abnormal pyramidal sign (HP:0007256); Increased serum lactate (HP:0002151); Increased CSF lactate (HP:0002490); Hyperreflexia (HP:0001347); Periventricular white matter hyperintensities (HP:0030891); Thick corpus callosum (HP:0007074); Central nervous system cyst (HP:0030724)
25539947_P1 (FEMALE; P7M)Mitochondrial DNA depletion syndrome 4 (OMIM:616370)NM_194279.3:c.229G>A (homozygous)Developmental regression (HP:0002376); Irritability (HP:0000737); Insomnia (HP:0100785); Spasticity (HP:0001257); Optic atrophy (HP:0000648); Hyperreflexia (HP:0001347); Periventricular white matter hyperintensities (HP:0030891); Abnormal corpus callosum morphology (HP:0001273); Abnormal midbrain morphology (HP:0002418)
29122497_P1 (FEMALE; P6M)Mitochondrial DNA depletion syndrome 4 (OMIM:616370)NM_194279.3:c.229G>A (homozygous)Developmental regression (HP:0002376); Optic atrophy (HP:0000648); Nystagmus (HP:0000639); Axial hypotonia (HP:0008936); Lower limb spasticity (HP:0002061); Upper limb spasticity (HP:0006986); Confluent hyperintensity of cerebral white matter on MRI (HP:0040330)
29122497_P2 (FEMALE; P7M)Mitochondrial DNA depletion syndrome 4 (OMIM:616370)NM_194279.3:c.229G>A (homozygous)Developmental regression (HP:0002376); Optic atrophy (HP:0000648); Nystagmus (HP:0000639); Axial hypotonia (HP:0008936); Lower limb spasticity (HP:0002061); Upper limb spasticity (HP:0006986); Confluent hyperintensity of cerebral white matter on MRI (HP:0040330); Hyperintensity of MRI T2 signal of the spinal cord (HP:0040272)
29122497_P3 (FEMALE; P4M)Mitochondrial DNA depletion syndrome 4 (OMIM:616370)NM_194279.3:c.229G>A (homozygous)Developmental regression (HP:0002376); Optic atrophy (HP:0000648); Nystagmus (HP:0000639); Axial hypotonia (HP:0008936); Lower limb spasticity (HP:0002061); Upper limb spasticity (HP:0006986); Confluent hyperintensity of cerebral white matter on MRI (HP:0040330); Hyperintensity of MRI T2 signal of the spinal cord (HP:0040272)
29122497_P4 (FEMALE; P5M)Mitochondrial DNA depletion syndrome 4 (OMIM:616370)NM_194279.3:c.229G>A (homozygous)Developmental regression (HP:0002376); Optic atrophy (HP:0000648); Nystagmus (HP:0000639); Axial hypotonia (HP:0008936); Lower limb spasticity (HP:0002061); Upper limb spasticity (HP:0006986); Confluent hyperintensity of cerebral white matter on MRI (HP:0040330); Hyperintensity of MRI T2 signal of the spinal cord (HP:0040272)
29122497_P5 (FEMALE; P6M)Mitochondrial DNA depletion syndrome 4 (OMIM:616370)NM_194279.3:c.229G>A (homozygous)Developmental regression (HP:0002376); Optic atrophy (HP:0000648); Nystagmus (HP:0000639); Axial hypotonia (HP:0008936); Lower limb spasticity (HP:0002061); Upper limb spasticity (HP:0006986); Confluent hyperintensity of cerebral white matter on MRI (HP:0040330); Hyperintensity of MRI T2 signal of the spinal cord (HP:0040272)
29122497_P6 (FEMALE; P3M)Mitochondrial DNA depletion syndrome 4 (OMIM:616370)NM_194279.3:c.229G>A (homozygous)Developmental regression (HP:0002376); Optic atrophy (HP:0000648); Nystagmus (HP:0000639); Axial hypotonia (HP:0008936); Lower limb spasticity (HP:0002061); Upper limb spasticity (HP:0006986); Confluent hyperintensity of cerebral white matter on MRI (HP:0040330); Hyperintensity of MRI T2 signal of the spinal cord (HP:0040272)
29122497_P7 (MALE; P5M)Mitochondrial DNA depletion syndrome 4 (OMIM:616370)NM_194279.3:c.229G>A (homozygous)Developmental regression (HP:0002376); Optic atrophy (HP:0000648); Nystagmus (HP:0000639); Axial hypotonia (HP:0008936); Lower limb spasticity (HP:0002061); Upper limb spasticity (HP:0006986); Seizure (HP:0001250); Confluent hyperintensity of cerebral white matter on MRI (HP:0040330); Hyperintensity of MRI T2 signal of the spinal cord (HP:0040272)
29122497_P8 (MALE; P3M)Mitochondrial DNA depletion syndrome 4 (OMIM:616370)NM_194279.3:c.229G>A (homozygous)Developmental regression (HP:0002376); Optic atrophy (HP:0000648); Nystagmus (HP:0000639); Axial hypotonia (HP:0008936); Lower limb spasticity (HP:0002061); Upper limb spasticity (HP:0006986); Seizure (HP:0001250)
29122497_P9 (MALE; P6M)Mitochondrial DNA depletion syndrome 4 (OMIM:616370)NM_194279.3:c.229G>A (homozygous)Developmental regression (HP:0002376); Optic atrophy (HP:0000648); Nystagmus (HP:0000639); Axial hypotonia (HP:0008936); Lower limb spasticity (HP:0002061); Upper limb spasticity (HP:0006986); Seizure (HP:0001250); Confluent hyperintensity of cerebral white matter on MRI (HP:0040330); Hyperintensity of MRI T2 signal of the spinal cord (HP:0040272)
29122497_P10 (MALE; P6M)Mitochondrial DNA depletion syndrome 4 (OMIM:616370)NM_194279.3:c.229G>A (homozygous)Developmental regression (HP:0002376); Optic atrophy (HP:0000648); Nystagmus (HP:0000639); Axial hypotonia (HP:0008936); Lower limb spasticity (HP:0002061); Upper limb spasticity (HP:0006986); Confluent hyperintensity of cerebral white matter on MRI (HP:0040330)
" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "individuals = cvalidator.get_error_free_individual_list()\n", + "table = PhenopacketTable(individual_list=individuals, metadata=metadata)\n", + "display(HTML(table.to_html()))" + ] + }, + { + "cell_type": "code", + "execution_count": 20, + "id": "9581607e-8913-4ada-b44b-d96306e3361f", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "We output 16 GA4GH phenopackets to the directory phenopackets\n" + ] + } + ], + "source": [ + "MixedCohortEncoder.output_individuals_as_phenopackets(individual_list=individuals)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "b3ad6d6b-3738-4f37-826b-26342d90596d", + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "ps2venv", + "language": "python", + "name": "ps2venv" + }, + "language_info": { + 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