From 9b29c078489c99c1ba02ee06da1d0aaba6d940fa Mon Sep 17 00:00:00 2001 From: Bryan Wulf Date: Fri, 9 Dec 2022 14:34:24 -0800 Subject: [PATCH] Add script to compare service-generated SEPIO transformation results --- test_data/sepio-transform-test.py | 65 +++++++++++++++++++++++++++++++ test_data/test-source-1.json | 1 + test_data/test-source-2.json | 1 + test_data/test-source-3.json | 1 + 4 files changed, 68 insertions(+) create mode 100644 test_data/sepio-transform-test.py create mode 100644 test_data/test-source-1.json create mode 100644 test_data/test-source-2.json create mode 100644 test_data/test-source-3.json diff --git a/test_data/sepio-transform-test.py b/test_data/sepio-transform-test.py new file mode 100644 index 0000000..fc8e276 --- /dev/null +++ b/test_data/sepio-transform-test.py @@ -0,0 +1,65 @@ +import argparse +import json +import os +import requests +import subprocess +import sys + +arg_parser = argparse.ArgumentParser() +arg_parser.add_argument('-f', '--source-file', help='Source file to test (takes precedence over source-list)') +arg_parser.add_argument('-l', '--source-list', default='test-source-1.json,test-source-2.json,test-source-3.json', help='Comma-separated list of source files to test') +arg_parser.add_argument('-t', '--test-url', default='https://tych0pbo2f.execute-api.us-west-2.amazonaws.com/default/sepio-transform', help='Service URL to generate test results (defaults to non-production service)') +arg_parser.add_argument('-c', '--control-url', default='https://a61m4glrmf.execute-api.us-west-2.amazonaws.com/default/sepio-transform', help='Service URL to generate control results (defaults to production service)') +args = arg_parser.parse_args() + +source_file_list = [] + +# Determine source file(s) to test +try: + if args.source_file: + source_file_list.append(args.source_file) + elif args.source_list: + source_file_list = args.source_list.split(',') + +except Exception as e: + sys.exit('Failed to process source file(s) argument:\n{}'.format(e)) + +print('\nControl service: {}'.format(args.control_url)) +print('Test service: {}'.format(args.test_url)) + +# Run test on each source file +for source_file in source_file_list: + print('\nComparing SEPIO transformation results for {}:'.format(source_file)) + + try: + # Get request data from source file + source_file_object = open(source_file, 'r') + source_file_data = source_file_object.read() + source_file_object.close() + + # Send request data to control service and if successful, save response in a temporary file + service_result_control = requests.post('{}/vci2cgsepio'.format(args.control_url), headers={'Content-Type': 'application/json'}, data=source_file_data, timeout=10) + service_result_control.raise_for_status() + + service_result_control_file = open('temp-sepio-transform-control-result.json', 'w') + json.dump(service_result_control.json(), service_result_control_file, indent=' ', sort_keys=True) + service_result_control_file.close() + + # Send request data to test service and if successful, save response in a temporary file + service_result_test = requests.post('{}/vci2cgsepio'.format(args.test_url), headers={'Content-Type': 'application/json'}, data=source_file_data, timeout=10) + service_result_test.raise_for_status() + + service_result_test_file = open('temp-sepio-transform-test-result.json', 'w') + json.dump(service_result_test.json(), service_result_test_file, indent=' ', sort_keys=True) + service_result_test_file.close() + + # Use diff to compare results + service_result_comparison = subprocess.run('diff temp-sepio-transform-control-result.json temp-sepio-transform-test-result.json', shell=True, text=True) + + # Delete temporary files + os.remove('temp-sepio-transform-control-result.json') + os.remove('temp-sepio-transform-test-result.json') + + except Exception as e: + print('Test failed:\n{}'.format(e)) + pass diff --git a/test_data/test-source-1.json b/test_data/test-source-1.json new file mode 100644 index 0000000..894c467 --- /dev/null +++ b/test_data/test-source-1.json @@ -0,0 +1 @@ +{"snapshots": ["acbae081-2e95-4122-a539-a9b3da0dbab5", "c2fc7b36-2394-4628-a7ce-026d4728a8c1", "0b44a35d-85c8-401b-98bd-d1d5d1410467", "cc5d077c-d81f-4f34-a32d-c1728b72bf62", "6f1f18ce-40af-44da-b423-cb3dab355a3e", "3f332225-1e55-42ca-b1f1-03bf3a38830e", "c8b459e9-5686-48dd-972e-e61223f88ff5"], "status": "Approved", "provisionalVariant": {"reason": "Setting a modified classification...", "approvalDate": "2022-11-21T21:07:02.598Z", "date_created": "2022-11-21T20:32:50.438Z", "provisionedClassification": true, "approvalSubmitter": "John Doe", "submitted_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "classificationApprover": "Jane Doe", "evidenceSummary": "Evidence summary, no met criteria...", "alteredClassification": "Uncertain significance - conflicting evidence", "provisionalSubmitter": "John Doe", "affiliation": "10004", "classificationDate": "2022-11-21T21:06:53.575Z", "provisionalDate": "2022-11-21T21:06:58.522Z", "modified_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "approvedClassification": true, "classificationStatus": "Approved", "publishClassification": false, "last_modified": "2022-11-21T21:07:02.598Z"}, "submitted_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "modified_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "date_created": "2022-11-21T20:28:28.772464", "item_type": "interpretation", "evaluations": [{"criteriaStatus": "not-met", "affiliation": "10004", "submitted_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "variant": "0372c8d4-bec2-4521-b57d-fc626683956b", "modified_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "date_created": "2022-11-21T20:50:11.123704", "PK": "bd903380-9ab6-406d-bef2-a117e3c08e44", "last_modified": "2022-11-21T20:50:11.123704", "criteria": "PM1", "item_type": "evaluation"}], "affiliation": "10004", "variant": {"variationType": "single nucleotide variant", "clinvarVariantTitle": "NM_000548.5(TSC2):c.451A>T (p.Arg151Ter)", "molecularConsequenceList": [{"hgvsName": "NM_000548.5:c.451A>T", "term": "nonsense", "soId": "SO:0001587"}, {"hgvsName": "NM_001077183.3:c.451A>T", "term": "nonsense", "soId": "SO:0001587"}, {"hgvsName": "NM_001114382.3:c.451A>T", "term": "nonsense", "soId": "SO:0001587"}, {"hgvsName": "NM_001318827.2:c.340A>T", "term": "nonsense", "soId": "SO:0001587"}, {"hgvsName": "NM_001318829.2:c.304A>T", "term": "nonsense", "soId": "SO:0001587"}, {"hgvsName": "NM_001318832.2:c.484A>T", "term": "nonsense", "soId": "SO:0001587"}, {"hgvsName": "NM_001363528.2:c.451A>T", "term": "nonsense", "soId": "SO:0001587"}, {"hgvsName": "NM_001370404.1:c.451A>T", "term": "nonsense", "soId": "SO:0001587"}, {"hgvsName": "NM_001370405.1:c.451A>T", "term": "nonsense", "soId": "SO:0001587"}, {"hgvsName": "NM_021055.3:c.451A>T", "term": "nonsense", "soId": "SO:0001587"}, {"hgvsName": "NM_001318831.2:c.-1-1786A>T", "term": "intron variant", "soId": "SO:0001627"}], "submitted_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "modified_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "date_created": "2022-11-21T20:28:13.180914", "dbSNPIds": ["137854199"], "preferredTitle": "NM_000548.5(TSC2):c.451A>T (p.Arg151Ter)", "hgvsNames": {"others": ["LRG_487:g.10105A>T", "LRG_487t1:c.451A>T", "NG_005895.1:g.10105A>T", "NM_000548.5:c.451A>T", "NP_000539.2:p.Arg151Ter", "NM_001077183.3:c.451A>T", "NP_001070651.1:p.Arg151Ter", "NM_001114382.3:c.451A>T", "NP_001107854.1:p.Arg151Ter", "NM_001318827.2:c.340A>T", "NP_001305756.1:p.Arg114Ter", "NM_001318829.2:c.304A>T", "NP_001305758.1:p.Arg102Ter", "NM_001318832.2:c.484A>T", "NP_001305761.1:p.Arg162Ter", "NM_001363528.2:c.451A>T", "NP_001350457.1:p.Arg151Ter", "NM_001370404.1:c.451A>T", "NP_001357333.1:p.Arg151Ter", "NM_001370405.1:c.451A>T", "NP_001357334.1:p.Arg151Ter", "NM_021055.3:c.451A>T", "NP_066399.2:p.Arg151Ter", "NM_001318831.2:c.-1-1786A>T"], "GRCh38": "NC_000016.10:g.2054410A>T", "GRCh37": "NC_000016.9:g.2104411A>T"}, "item_type": "variant", "communityStandardTitle": "NM_000548.5(TSC2):c.451A>T (p.Arg151Ter)", "clinvarVariantId": "50000", "carId": "CA020595", "PK": "0372c8d4-bec2-4521-b57d-fc626683956b", "last_modified": "2022-11-21T20:28:13.180914"}, "PK": "7906ba28-6ee1-41f6-81b9-1f2c516900eb", "last_modified": "2022-11-21T21:07:03.345881"} diff --git a/test_data/test-source-2.json b/test_data/test-source-2.json new file mode 100644 index 0000000..8e075eb --- /dev/null +++ b/test_data/test-source-2.json @@ -0,0 +1 @@ +{"cspec": {"documentName": "ClinGen Hearing Loss Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for CDH23, COCH, GJB2,\nKCNQ4, MYO6, MYO7A, SLC26A4, TECTA and USH2A Version 2", "cspecUrl": "https://cspec.genome.network/cspec/SequenceVariantInterpretation/id/135637577", "ruleSetIri": "https://cspec.genome.network/cspec/RuleSet/id/135640633", "version": "2.0.0", "cspecId": "135640633"}, "snapshots": ["3890bc00-3d08-490f-ad25-8ed8735d024f"], "status": "Approved", "provisionalVariant": {"autoClassification": "Likely pathogenic", "approvalDate": "2022-11-21T22:12:46.514Z", "date_created": "2022-11-21T22:12:35.126Z", "provisionedClassification": true, "approvalSubmitter": "John Doe", "submitted_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "classificationApprover": "Jane Doe", "evidenceSummary": "Evidence summary, several met/supporting pathogenic criteria...", "provisionalSubmitter": "John Doe", "affiliation": "10007", "classificationDate": "2022-11-21T22:12:35.126Z", "provisionalDate": "2022-11-21T22:12:38.188Z", "modified_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "approvedClassification": true, "classificationStatus": "Approved", "last_modified": "2022-11-21T22:12:46.514Z"}, "submitted_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "diseaseTerm": "uterine ligament adenosarcoma", "modified_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "date_created": "2022-11-21T22:04:41.431864", "item_type": "interpretation", "evaluations": [{"affiliation": "10007", "population": "4e4d6fd7-5d0b-4a01-8d13-232f8fdfcafa", "submitted_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "variant": "5ca2daf8-d209-4a59-8ce5-ade4ec5ef05a", "modified_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "PK": "2227036d-888d-4340-97c1-2555e3e68663", "date_created": "2022-11-21T22:08:11.536Z", "last_modified": "2022-11-21T22:08:11.738854", "criteria": "BA1", "item_type": "evaluation"}, {"criteriaStatus": "not-evaluated", "affiliation": "10007", "population": "4e4d6fd7-5d0b-4a01-8d13-232f8fdfcafa", "submitted_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "variant": "5ca2daf8-d209-4a59-8ce5-ade4ec5ef05a", "modified_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "PK": "32ececc1-bf8c-426b-a057-8fecc6c4063d", "date_created": "2022-11-21T22:08:11.537Z", "last_modified": "2022-11-21T22:08:11.798467", "criteria": "BS1", "item_type": "evaluation"}, {"criteriaStatus": "met", "population": "4e4d6fd7-5d0b-4a01-8d13-232f8fdfcafa", "submitted_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "modified_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "date_created": "2022-11-21T22:08:11.537Z", "item_type": "evaluation", "affiliation": "10007", "variant": "5ca2daf8-d209-4a59-8ce5-ade4ec5ef05a", "PK": "8ffab765-d59c-4df2-92e2-3baca069a10c", "last_modified": "2022-11-21T22:08:11.811200", "criteria": "PM2", "explanation": "PM2 criteria met"}, {"affiliation": "10007", "submitted_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "variant": "5ca2daf8-d209-4a59-8ce5-ade4ec5ef05a", "computational": "c07cf205-fc9f-4d9c-bfec-505b90395fbe", "modified_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "date_created": "2022-11-21T22:09:15.879393", "PK": "cf5abd68-328b-4f5b-b608-f27eb6882d35", "last_modified": "2022-11-21T22:09:15.879393", "criteria": "BP1", "item_type": "evaluation"}, {"affiliation": "10007", "submitted_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "variant": "5ca2daf8-d209-4a59-8ce5-ade4ec5ef05a", "computational": "c07cf205-fc9f-4d9c-bfec-505b90395fbe", "modified_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "date_created": "2022-11-21T22:09:15.976104", "PK": "87011def-6afc-4cd0-b244-a09e76e99db0", "last_modified": "2022-11-21T22:09:15.976104", "criteria": "BP4", "item_type": "evaluation"}, {"affiliation": "10007", "submitted_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "variant": "5ca2daf8-d209-4a59-8ce5-ade4ec5ef05a", "computational": "c07cf205-fc9f-4d9c-bfec-505b90395fbe", "modified_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "date_created": "2022-11-21T22:09:15.915897", "PK": "ee56d161-a770-4182-bfd2-5962871a8046", "last_modified": "2022-11-21T22:09:15.915897", "criteria": "PP2", "item_type": "evaluation"}, {"criteriaStatus": "met", "submitted_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "modified_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "date_created": "2022-11-21T22:09:15.952560", "item_type": "evaluation", "criteriaModifier": "moderate", "affiliation": "10007", "variant": "5ca2daf8-d209-4a59-8ce5-ade4ec5ef05a", "computational": "c07cf205-fc9f-4d9c-bfec-505b90395fbe", "PK": "2057ba16-941e-4cd4-adac-2e9119ab6f8f", "last_modified": "2022-11-21T22:09:15.952560", "criteria": "PP3", "explanation": "PP3 criteria moderate"}, {"criteriaStatus": "met", "submitted_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "modified_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "date_created": "2022-11-21T22:09:51.541843", "item_type": "evaluation", "criteriaModifier": "supporting", "affiliation": "10007", "variant": "5ca2daf8-d209-4a59-8ce5-ade4ec5ef05a", "PK": "79c29731-a840-47c2-89d5-9619ae237f5e", "last_modified": "2022-11-21T22:09:51.541843", "criteria": "PM1", "explanation": "PM1 criteria supporting"}, {"criteriaStatus": "met", "affiliation": "10007", "submitted_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "variant": "5ca2daf8-d209-4a59-8ce5-ade4ec5ef05a", "modified_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "date_created": "2022-11-21T22:10:47.268761", "PK": "808fcc9f-122f-4955-a83b-3f1bef87cfe6", "last_modified": "2022-11-21T22:10:47.268761", "criteria": "PS4", "item_type": "evaluation", "explanation": "PS4 criteria met"}], "pathogenicity": "Likely pathogenic", "affiliation": "10007", "disease": {"term": "uterine ligament adenosarcoma", "PK": "MONDO_0200000", "date_created": "2022-11-21T22:06:25.181941", "last_modified": "2022-11-21T22:06:25.181941", "item_type": "disease"}, "variant": {"variationType": "Deletion", "clinvarVariantTitle": "NM_000249.4(MLH1):c.201del (p.Ile68fs)", "molecularConsequenceList": [{"hgvsName": "NM_000249.4:c.201del", "term": "frameshift variant", "soId": "SO:0001589"}, {"hgvsName": "NM_001167617.3:c.-89del", "term": "5 prime UTR variant", "soId": "SO:0001623"}, {"hgvsName": "NM_001167618.3:c.-523del", "term": "5 prime UTR variant", "soId": "SO:0001623"}, {"hgvsName": "NM_001167619.3:c.-431del", "term": "5 prime UTR variant", "soId": "SO:0001623"}, {"hgvsName": "NM_001258271.2:c.201del", "term": "frameshift variant", "soId": "SO:0001589"}, {"hgvsName": "NM_001258274.3:c.-668del", "term": "5 prime UTR variant", "soId": "SO:0001623"}, {"hgvsName": "NM_001354615.2:c.-426del", "term": "5 prime UTR variant", "soId": "SO:0001623"}, {"hgvsName": "NM_001354616.2:c.-431del", "term": "5 prime UTR variant", "soId": "SO:0001623"}, {"hgvsName": "NM_001354617.2:c.-523del", "term": "5 prime UTR variant", "soId": "SO:0001623"}, {"hgvsName": "NM_001354618.2:c.-523del", "term": "5 prime UTR variant", "soId": "SO:0001623"}, {"hgvsName": "NM_001354619.2:c.-523del", "term": "5 prime UTR variant", "soId": "SO:0001623"}, {"hgvsName": "NM_001354620.2:c.-89del", "term": "5 prime UTR variant", "soId": "SO:0001623"}, {"hgvsName": "NM_001354621.2:c.-616del", "term": "5 prime UTR variant", "soId": "SO:0001623"}, {"hgvsName": "NM_001354622.2:c.-729del", "term": "5 prime UTR variant", "soId": "SO:0001623"}, {"hgvsName": "NM_001354624.2:c.-626del", "term": "5 prime UTR variant", "soId": "SO:0001623"}, {"hgvsName": "NM_001354625.2:c.-529del", "term": "5 prime UTR variant", "soId": "SO:0001623"}, {"hgvsName": "NM_001354626.2:c.-626del", "term": "5 prime UTR variant", "soId": "SO:0001623"}, {"hgvsName": "NM_001354627.2:c.-626del", "term": "5 prime UTR variant", "soId": "SO:0001623"}, {"hgvsName": "NM_001354628.2:c.201del", "term": "frameshift variant", "soId": "SO:0001589"}, {"hgvsName": "NM_001354629.2:c.201del", "term": "frameshift variant", "soId": "SO:0001589"}, {"hgvsName": "NM_001354630.2:c.201del", "term": "frameshift variant", "soId": "SO:0001589"}, {"hgvsName": "NM_001354623.2:c.-723+2813del", "term": "intron variant", "soId": "SO:0001627"}, {"hgvsName": "NM_001258273.2:c.-517+3040del", "term": "intron variant", "soId": "SO:0001627"}], "submitted_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "modified_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "date_created": "2022-11-21T22:04:33.050728", "dbSNPIds": ["587778968"], "preferredTitle": "NM_000249.4(MLH1):c.201del (p.Ile68SerfsTer24)", "hgvsNames": {"others": ["LRG_216:g.8354del", "NM_000249.3:c.201delG", "NG_007109.2:g.8354del", "NG_008418.1:g.1604del", "NM_000249.4:c.201del", "NP_000240.1:p.Ile68fs", "NM_001167617.3:c.-89del", "NM_001167618.3:c.-523del", "NM_001167619.3:c.-431del", "NM_001258271.2:c.201del", "NP_001245200.1:p.Ile68fs", "NM_001258274.3:c.-668del", "NM_001354615.2:c.-426del", "NM_001354616.2:c.-431del", "NM_001354617.2:c.-523del", "NM_001354618.2:c.-523del", "NM_001354619.2:c.-523del", "NM_001354620.2:c.-89del", "NM_001354621.2:c.-616del", "NM_001354622.2:c.-729del", "NM_001354624.2:c.-626del", "NM_001354625.2:c.-529del", "NM_001354626.2:c.-626del", "NM_001354627.2:c.-626del", "NM_001354628.2:c.201del", "NP_001341557.1:p.Ile68fs", "NM_001354629.2:c.201del", "NP_001341558.1:p.Ile68fs", "NM_001354630.2:c.201del", "NP_001341559.1:p.Ile68fs", "NM_001354623.2:c.-723+2813del", "NM_001258273.2:c.-517+3040del"], "GRCh38": "NC_000003.12:g.36996703del", "GRCh37": "NC_000003.11:g.37038194del"}, "item_type": "variant", "communityStandardTitle": "NM_000249.4(MLH1):c.201del (p.Ile68SerfsTer24)", "clinvarVariantId": "90000", "carId": "CA008214", "PK": "5ca2daf8-d209-4a59-8ce5-ade4ec5ef05a", "last_modified": "2022-11-21T22:04:33.050728"}, "PK": "ac7bbd73-138f-4cc7-b47f-93c4d47eac74", "modeInheritance": "Autosomal recessive inheritance (HP:0000007)", "last_modified": "2022-11-21T22:12:46.722016"} diff --git a/test_data/test-source-3.json b/test_data/test-source-3.json new file mode 100644 index 0000000..d2f2dd3 --- /dev/null +++ b/test_data/test-source-3.json @@ -0,0 +1 @@ +{"snapshots": ["c0bfee12-3d63-44eb-ac3d-b93dac10fec3"], "status": "Approved", "provisionalVariant": {"autoClassification": "Uncertain significance - conflicting evidence", "approvalDate": "2022-12-07T00:01:18.562Z", "date_created": "2022-12-06T23:56:21.527Z", "provisionedClassification": true, "approvalSubmitter": "John Doe", "submitted_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "classificationApprover": "RASopathy", "evidenceSummary": "Evidence summary, mix of met and not met criteria...", "provisionalSubmitter": "John Doe", "affiliation": "10021", "classificationDate": "2022-12-06T23:56:21.527Z", "provisionalDate": "2022-12-06T23:56:27.477Z", "modified_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "approvedClassification": true, "classificationStatus": "Approved", "last_modified": "2022-12-07T00:01:18.562Z"}, "submitted_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "diseaseTerm": "Wallerian degeneration", "modified_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "curated_evidence_list": [{"evidenceCriteria": "PVS1", "submitted_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "modified_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "date_created": "2022-12-06T23:51:35.349469", "subcategory": "null-variant-analysis", "item_type": "curated-evidence", "affiliation": "10021", "category": "variant-type", "evidenceDescription": "PVS1 evidence...", "variant": "564f899b-9612-4db1-8ed8-c61c43b0afc0", "articles": [{"date": "1979 Nov;38(5):827-30.", "journal": "Applied and environmental microbiology", "date_created": "2022-12-06T23:51:26.107074", "item_type": "article", "abstract": "Isolants from swine and from humans representing serotypes 1, 2, 4, 8, and 10 of the Mycobacterium avium-Mycobacterium intracellulare complex were compared for heat tolerance in aqueous suspension. The most heat-resistant isolant found was a serovar 10 isolated from a human. This isolant was examined further to determine the rate of kill at various temperatures and pH's, the effect of meat protein and fat, and the effect of nitrite. Kill rates were not significant at 60 degrees C or below. Decimal reduction values were 4 min or less at 65 degrees C and 1.5 min or less at 70 degrees C. Kill rates were slightly higher at pH values of 6.5 and 7.0 than at 5.5 or 6.0. the water-soluble fraction of wiener emulsion did not alter kill rates, but the saline-soluble fraction protected the organism somewhat. Fat did not affect the survival of the organisms except to eliminate the protective effect of saline extract when the suspension contained 50% fat. The addition of sodium nitrite to the suspension did not alter the heat sensitivity of the organisms.", "PK": "44444", "pmid": "44444", "title": "Heat inactivation of Mycobacterium avium-Mycobacterium intracellulare complex organisms in aqueous suspension.", "last_modified": "2022-12-06T23:51:26.107074", "authors": ["Merkal RS", "Crawford JA"]}], "PK": "df03241f-d2e4-430f-8925-18ec568999fe", "last_modified": "2022-12-06T23:51:35.349469"}, {"evidenceCriteria": "PM1", "submitted_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "modified_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "date_created": "2022-12-06T23:45:45.120910", "subcategory": "hotspot-functiona-domain", "item_type": "curated-evidence", "affiliation": "10021", "category": "experimental", "evidenceDescription": "PM1 evidence...", "variant": "564f899b-9612-4db1-8ed8-c61c43b0afc0", "articles": [{"date": "1979 Feb 16;121(7):247-50.", "journal": "MMW, Munchener medizinische Wochenschrift", "date_created": "2022-12-06T23:45:26.412709", "item_type": "article", "abstract": "14 patients from the Allergy Unit of an outpatient clinic suffering from acute exacerbation of chronic bronchitis and 13 outpatients with acute bronchitis were treated with 250 mg cefaclor (Panoral) 3 times daily per os for 5 days. 59% of the organisms isolated from cefaclor-sensitive sputum at the time of prominent clinical symptoms were resistent to tetracycline, 53% of them were resistant to penicillin, and 37% were resistant to ampicillin. 12 out of the 14 patients with acute exacerbation of chronic bronchitis became asymptomatic, and no organisms could be detected in the sputum of 13 out of the same 14 patients two days after cessation of cefaclor treatment. In 12 out of the 13 patients with acute bronchitis, the acute clinical symptoms disappeared and in 11 out of the 13 patients the initial sputum organisms were two days after stopping cefaclor treatment.", "PK": "33333", "pmid": "33333", "title": "[Treatment of bronchitis with cefaclor (Panoral) (author's transl)].", "last_modified": "2022-12-06T23:45:26.412709", "authors": ["Kersten W", "Brade W"]}], "PK": "6173b883-5747-40f1-b1ee-7486747bd433", "last_modified": "2022-12-06T23:45:45.120910"}, {"submitted_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "sourceInfo": {"data": {"num_proband_double_het": "1", "num_proband_double_het_comment": "BP2 evidence...", "hpoData": [], "label": "Sample evidence #2", "comments": "Some more additional comments..."}, "metadata": {"pmid": "22222", "_kind_key": "PMID", "_kind_title": "PubMed"}, "relevant_criteria": ["BP2", "PM3"]}, "modified_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "date_created": "2022-12-06T23:43:59.542180", "subcategory": "allele-data", "item_type": "curated-evidence", "affiliation": "10021", "category": "case-segregation", "variant": "564f899b-9612-4db1-8ed8-c61c43b0afc0", "articles": [{"date": "1977;32(5):569-78.", "journal": "Acta neurologica", "abstract": "", "pmid": "22222", "title": "[Clinico-statistical findings on irreversible chronic tardive dyskinesia caused by psychopharmaceuticals].", "authors": ["Fiorillo A", "Maietta A"]}], "PK": "89588f69-ee98-466e-b0e5-56fc70fe9ac7", "last_modified": "2022-12-06T23:43:59.542180"}, {"submitted_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "sourceInfo": {"data": {"num_probands_relevant_phenotype": "1", "num_probands_relevant_phenotype_comment": "PS4 evidence...", "hpoData": [], "label": "Sample evidence #1", "comments": "Some additional comments..."}, "metadata": {"pmid": "11111", "_kind_key": "PMID", "_kind_title": "PubMed"}, "relevant_criteria": ["PS4"]}, "modified_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "date_created": "2022-12-06T23:41:51.886116", "subcategory": "case-control", "item_type": "curated-evidence", "affiliation": "10021", "category": "case-segregation", "variant": "564f899b-9612-4db1-8ed8-c61c43b0afc0", "articles": [{"date": "1976;12(3-4):149-58.", "journal": "Experimentelle Pathologie", "abstract": "From cells and culture media of embryonic rat fibroblasts (1st subculture) the acid mucopolysaccharides were isolated and fractionated. The per cent calculation of the 6 fractions was based on the content of glucuronic acid. The cultures were maintained as follows: 0.5 X 10(6) to 3 X 10(6) cells were examined in Demeter flasks at pH 7.4 or 6.6; lactate concentration was enhanced to 100 mg%. The amount of each fraction was correlated with the cell density (linear regression). The pH-value and lactate concentration in connection with cell density proved to be important factors in the modification of the MPS distribution pattern.", "pmid": "11111", "title": "Acid mucopolysaccharides in fibroblast cultures. 1. Influence of cell density, pH-value and lactate concentration on the MPS distribution pattern.", "authors": ["Kittlick PD", "Neupert G", "Bolck F"]}], "PK": "c29e3010-6417-49c3-b923-fcc627ecb29a", "last_modified": "2022-12-06T23:41:51.886116"}], "date_created": "2022-11-21T23:03:51.019193", "item_type": "interpretation", "evaluations": [{"criteriaStatus": "not-met", "affiliation": "10021", "submitted_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "population": "d1ae053e-e293-465f-8bad-f588b4990294", "variant": "564f899b-9612-4db1-8ed8-c61c43b0afc0", "modified_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "date_created": "2022-12-06T23:39:13.090067", "PK": "d4a97804-e23d-45a9-88ee-c5f9f65b746b", "last_modified": "2022-12-06T23:39:13.090067", "criteria": "BA1", "item_type": "evaluation"}, {"affiliation": "10021", "submitted_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "population": "d1ae053e-e293-465f-8bad-f588b4990294", "variant": "564f899b-9612-4db1-8ed8-c61c43b0afc0", "modified_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "date_created": "2022-12-06T23:39:13.137181", "PK": "252add1d-4a11-4483-b496-2f665eed30e8", "last_modified": "2022-12-06T23:39:13.137181", "criteria": "BS1", "item_type": "evaluation"}, {"affiliation": "10021", "submitted_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "population": "d1ae053e-e293-465f-8bad-f588b4990294", "variant": "564f899b-9612-4db1-8ed8-c61c43b0afc0", "modified_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "date_created": "2022-12-06T23:39:13.078964", "PK": "afed067f-291b-4a95-a44d-1c1ebdc0751f", "last_modified": "2022-12-06T23:39:13.078964", "criteria": "PM2", "item_type": "evaluation"}, {"criteriaStatus": "met", "affiliation": "10021", "submitted_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "variant": "564f899b-9612-4db1-8ed8-c61c43b0afc0", "modified_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "date_created": "2022-12-06T23:40:04.265552", "PK": "ad5f994e-da93-434d-8a12-97f439dfd7a9", "last_modified": "2022-12-06T23:40:04.265552", "criteria": "PS4", "item_type": "evaluation", "explanation": "Criteria PM1 met..."}, {"criteriaStatus": "met", "submitted_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "modified_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "date_created": "2022-12-06T23:43:07.010457", "item_type": "evaluation", "criteriaModifier": "stand-alone", "affiliation": "10021", "variant": "564f899b-9612-4db1-8ed8-c61c43b0afc0", "PK": "e7ddc5a5-847f-4337-84b4-454ccaf08b51", "last_modified": "2022-12-06T23:43:07.010457", "criteria": "BP2", "explanation": "Criteria BP2 stand-alone..."}, {"affiliation": "10021", "submitted_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "variant": "564f899b-9612-4db1-8ed8-c61c43b0afc0", "modified_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "date_created": "2022-12-06T23:43:07.062205", "PK": "c3056b65-20cf-4b4c-b9a6-8cd4024dad43", "last_modified": "2022-12-06T23:43:07.062205", "criteria": "PM3", "item_type": "evaluation"}, {"criteriaStatus": "not-met", "affiliation": "10021", "submitted_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "variant": "564f899b-9612-4db1-8ed8-c61c43b0afc0", "modified_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "date_created": "2022-12-06T23:45:18.138676", "PK": "6db2e508-a66a-4e56-8516-e7c13cdde51a", "last_modified": "2022-12-06T23:45:18.138676", "criteria": "PM1", "item_type": "evaluation", "explanation": "Criteria PM1 not met..."}, {"functional": "692b76e9-5caa-46d6-b689-67500417376d", "criteriaStatus": "not-met", "submitted_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "modified_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "date_created": "2022-12-06T23:46:16.716759", "item_type": "evaluation", "affiliation": "10021", "variant": "564f899b-9612-4db1-8ed8-c61c43b0afc0", "PK": "e5b337dc-f00e-429b-aaf2-966aa048b57c", "last_modified": "2022-12-06T23:46:16.716759", "criteria": "BS3", "explanation": "Criteria BS3 not met..."}, {"functional": "692b76e9-5caa-46d6-b689-67500417376d", "affiliation": "10021", "submitted_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "variant": "564f899b-9612-4db1-8ed8-c61c43b0afc0", "modified_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "date_created": "2022-12-06T23:46:16.759933", "PK": "6013d7b7-7b7e-44ca-afd6-446919a2216a", "last_modified": "2022-12-06T23:46:16.759933", "criteria": "PS3", "item_type": "evaluation"}, {"affiliation": "10021", "submitted_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "variant": "564f899b-9612-4db1-8ed8-c61c43b0afc0", "computational": "dccfc03a-eb2e-4883-b903-5bc8f6d02acf", "modified_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "date_created": "2022-12-06T23:47:38.748566", "PK": "b9a36e58-21b1-40c2-a36e-4e329cfe8996", "last_modified": "2022-12-06T23:47:38.748566", "criteria": "BP1", "item_type": "evaluation"}, {"affiliation": "10021", "submitted_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "variant": "564f899b-9612-4db1-8ed8-c61c43b0afc0", "computational": "dccfc03a-eb2e-4883-b903-5bc8f6d02acf", "modified_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "date_created": "2022-12-06T23:47:38.806467", "PK": "9a698c55-8381-4597-a411-e7e73040da46", "last_modified": "2022-12-06T23:47:38.806467", "criteria": "BP4", "item_type": "evaluation"}, {"criteriaStatus": "not-met", "submitted_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "modified_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "date_created": "2022-12-06T23:47:38.751438", "item_type": "evaluation", "affiliation": "10021", "variant": "564f899b-9612-4db1-8ed8-c61c43b0afc0", "computational": "dccfc03a-eb2e-4883-b903-5bc8f6d02acf", "PK": "8209c673-f9c8-4cee-a97d-3834861b0538", "last_modified": "2022-12-06T23:47:38.751438", "criteria": "PP2", "explanation": "Criteria PP2 not met..."}, {"affiliation": "10021", "submitted_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "variant": "564f899b-9612-4db1-8ed8-c61c43b0afc0", "computational": "dccfc03a-eb2e-4883-b903-5bc8f6d02acf", "modified_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "date_created": "2022-12-06T23:47:38.750250", "PK": "b2dc0575-1a5b-4375-9395-bf74bf1c364f", "last_modified": "2022-12-06T23:47:38.750250", "criteria": "PP3", "item_type": "evaluation"}, {"criteriaStatus": "met", "submitted_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "modified_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "date_created": "2022-12-06T23:50:56.488538", "item_type": "evaluation", "criteriaModifier": "supporting", "affiliation": "10021", "variant": "564f899b-9612-4db1-8ed8-c61c43b0afc0", "PK": "ee606265-f35f-4dd0-9e7c-f7b56bd71652", "last_modified": "2022-12-06T23:50:56.488538", "criteria": "PVS1", "explanation": "Criteria PVS1 supporting..."}, {"criteriaStatus": "not-met", "affiliation": "10021", "submitted_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "variant": "564f899b-9612-4db1-8ed8-c61c43b0afc0", "modified_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "date_created": "2022-12-06T23:53:54.146773", "PK": "630b461d-a955-4426-a342-435775265f98", "last_modified": "2022-12-06T23:53:54.146773", "criteria": "BP5", "item_type": "evaluation", "explanation": "Criteria BP5 not met..."}], "pathogenicity": "Uncertain significance - conflicting evidence", "affiliation": "10021", "disease": {"term": "Wallerian degeneration", "PK": "MONDO_0043280", "date_created": "2022-12-06T23:38:23.496293", "last_modified": "2022-12-06T23:38:23.496293", "item_type": "disease"}, "variant": {"variationType": "single nucleotide variant", "clinvarVariantTitle": "NM_001130438.3(SPTAN1):c.2438-13T>G", "molecularConsequenceList": [{"hgvsName": "NM_001363759.2:c.2438-13T>G", "term": "intron variant", "soId": "SO:0001627"}, {"hgvsName": "NM_001130438.3:c.2438-13T>G", "term": "intron variant", "soId": "SO:0001627"}, {"hgvsName": "NM_003127.4:c.2438-13T>G", "term": "intron variant", "soId": "SO:0001627"}, {"hgvsName": "NM_001363765.2:c.2438-13T>G", "term": "intron variant", "soId": "SO:0001627"}, {"hgvsName": "NM_001195532.2:c.2438-13T>G", "term": "intron variant", "soId": "SO:0001627"}], "submitted_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "modified_by": "b1f1a7c4-8987-4177-bcd0-c8a94f3b2df0", "date_created": "2022-11-21T23:03:32.617641", "dbSNPIds": ["587784434"], "preferredTitle": "NM_001130438.3(SPTAN1):c.2438-13T>G", "hgvsNames": {"others": ["NG_027748.1:g.37151T>G", "NM_001363759.2:c.2438-13T>G", "NM_001130438.3:c.2438-13T>G", "NM_003127.4:c.2438-13T>G", "NM_001363765.2:c.2438-13T>G", "NM_001195532.2:c.2438-13T>G"], "GRCh38": "NC_000009.12:g.128584708T>G", "GRCh37": "NC_000009.11:g.131346987T>G"}, "item_type": "variant", "communityStandardTitle": "NM_001130438.3(SPTAN1):c.2438-13T>G", "clinvarVariantId": "160000", "carId": "CA173550", "PK": "564f899b-9612-4db1-8ed8-c61c43b0afc0", "last_modified": "2022-11-21T23:03:32.617641"}, "PK": "2bb2b4e9-ae70-4dea-af2f-d2d51c40a5c9", "modeInheritance": "X-linked inheritance (HP:0001417)", "last_modified": "2022-12-07T00:01:18.776303"}