Q (sonnet-5.5): download MSK-CHORD study on Non-Small Cell Lung Cancer dataset

▶ list_studies
{
 "search": "MSK-CHORD"
}

◀ result
{"result":[{"cancer_study_identifier":"msk_chord_2024","name":"MSK-CHORD (MSK, Nature 2024)","type_of_cancer_id":"mixed","sample_count":25040,"has_guide":true,"url":"https://www.cbioportal.org/study/summary?id=msk_chord_2024"}]}

▶ get_studyviewfilter_options
{
 "studyId": "msk_chord_2024",
 "attributeIds": [
  "CANCER_TYPE",
  "CANCER_TYPE_DETAILED"
 ]
}

◀ result
{"success":true,"message":"Successfully retrieved StudyView filter options","data":{"studyId":"msk_chord_2024","attributes":[{"attributeId":"CANCER_TYPE","displayName":"Cancer Type","description":"The main cancer type as defined by the Oncotree cancer classification system for precision oncology. Source: MPath","datatype":"STRING","values":["Non-Small Cell Lung Cancer","Colorectal Cancer","Prostate Cancer","Pancreatic Cancer","Breast Cancer"]},{"attributeId":"CANCER_TYPE_DETAILED","displayName":"Cancer Type Detailed","description":"The cancer subtype as defined by the Oncotree cancer classification system for precision oncology. Source: MPath","datatype":"STRING","values":["Colorectal Adenocarcinoma","Pleuropulmonary Blastoma","Intraductal Tubulopapillary Neoplasm","Prostate Adenocarcinoma","Intraductal Papillary Mucinous Neoplasm","Breast Invasive Carcinoma, NOS","Lymphoepithelioma-like Carcinoma of the Lung","Pleomorphic Carcinoma of the Lung","Breast Invasive Ductal Carcinoma","Large Cell Lung Carcinoma","Non-Small Cell Lung Cancer","Colon Adenocarcinoma In Situ","Adenomyoepithelioma of the Breast","Colon Adenocarcinoma","Lung Neuroendocrine Tumor","Basaloid Large Cell Carcinoma of the Lung","Pancreatic Neuroendocrine Carcinoma","Adenoid Cystic Breast Cancer","Spindle Cell Carcinoma of the Lung","Poorly Differentiated Non-Small Cell Lung Cancer","Signet Ring Cell Adenocarcinoma of the Colon and Rectum","Breast Ductal Carcinoma In Situ","Breast Invasive Carcinosarcoma, NOS","Adenosquamous Carcinoma of the Pancreas","Breast Neoplasm, NOS","Metaplastic Carcinosarcoma","Lung Adenosquamous Carcinoma","Osteoclastic Giant Cell Tumor","Lung Adenocarcinoma In Situ","Metaplastic Adenosquamous Carcinoma","Large Cell Neuroendocrine Carcinoma","Acinar Cell Carcinoma of the Pancreas","Sarcomatoid Carcinoma of the Lung","Pancreatic Adenocarcinoma","Prostate Neuroendocrine Carcinoma","Adenoid Cystic Carcinoma of the Lung","Breast Invasive Mixed Mucinous Carcinoma","Pancreatic Neuroendocrine Tumor","Atypical Lung Carcinoid","Metaplastic Adenocarcinoma with Spindle Cell Differentiation","Lung Carcinoid","NUT Carcinoma of the Lung","Pancreatoblastoma","Breast Invasive Lobular Carcinoma","Solid Papillary Carcinoma of the Breast","Juvenile Secretory Carcinoma of the Breast","Undifferentiated Carcinoma of the Pancreas","Lung Adenocarcinoma","Breast Mixed Ductal and Lobular Carcinoma","Paget Disease of the Nipple","Invasive Breast Carcinoma","Solid Pseudopapillary Neoplasm of the Pancreas","Mucoepidermoid Carcinoma of the Lung","Rectal Adenocarcinoma","Medullary Carcinoma of the Colon","Mucinous Adenocarcinoma of the Colon and Rectum","Mucinous Cystic Neoplasm","Breast Invasive Cancer, NOS","Lung Squamous Cell Carcinoma","Prostate Small Cell Carcinoma","Mixed Type Metaplastic Breast Cancer","Metaplastic Squamous Cell Carcinoma","Metaplastic Breast Cancer"]}]}}

▶ navigate_to_study_view
{
 "studyIds": [
  "msk_chord_2024"
 ],
 "filterJson": {
  "clinicalDataFilters": [
   {
    "attributeId": "CANCER_TYPE",
    "values": [
     {
      "value": "Non-Small Cell Lung Cancer"
     }
    ]
   }
  ]
 },
 "tab": "clinicalData"
}

◀ result
{"success":true,"message":"Navigating to https://www.cbioportal.org/study/clinicalData?id=msk_chord_2024#filterJson=%7B%22clinicalDataFilters%22%3A%5B%7B%22attributeId%22%3A%22CANCER_TYPE%22%2C%22values%22%3A%5B%7B%22value%22%3A%22Non-Small%20Cell%20Lung%20Cancer%22%7D%5D%7D%5D%7D","url":"https://www.cbioportal.org/study/clinicalData?id=msk_chord_2024#filterJson=%7B%22clinicalDataFilters%22%3A%5B%7B%22attributeId%22%3A%22CANCER_TYPE%22%2C%22values%22%3A%5B%7B%22value%22%3A%22Non-Small%20Cell%20Lung%20Cancer%22%7D%5D%7D%5D%7D","data":{"studyIds":["msk_chord_2024"],"studies":[{"studyId":"msk_chord_2024","name":"MSK-CHORD (MSK, Nature 2024)","sampleCount":25040}],"tab":"clinicalData","hasFilters":true,"hasPlotsConfig":false,"pageDescription":"Table of clinical attributes per sample."}}

▶ clickhouse_run_select_query
{
 "query": "SELECT count() AS samples, uniqExact(patient_unique_id) AS patients FROM clinical_data_derived WHERE cancer_study_identifier='msk_chord_2024' AND attribute_name='CANCER_TYPE' AND attribute_value='Non-Small Cell Lung Cancer'"
}

◀ result
{"rows":[{"samples":7809,"patients":7809}]}

═ answer (success)
MSK-CHORD (MSK, Nature 2024, `msk_chord_2024`) is a single pan-cancer study. It has no separate NSCLC dataset, so the NSCLC data is a filtered subset of it. Filtering on Cancer Type = "Non-Small Cell Lung Cancer" gives **7,809 samples** out of 25,040 in the whole study.

**To download the NSCLC subset:**
1. Open [MSK-CHORD, NSCLC only (Clinical Data tab)](https://www.cbioportal.org/study/clinicalData?id=msk_chord_2024#filterJson=%7B%22clinicalDataFilters%22%3A%5B%7B%22attributeId%22%3A%22CANCER_TYPE%22%2C%22values%22%3A%5B%7B%22value%22%3A%22Non-Small%20Cell%20Lung%20Cancer%22%7D%5D%7D%5D%7D). The filter is already applied.
2. Click the download icon at the top right of the table to get the clinical data for the filtered samples.
3. To download mutation and other genomic data for these samples, go back to the Summary tab. Click the download icon next to the "Selected" sample count and choose the data files. You can also use "Query" to send the cohort to OncoPrint or the Mutations tab, then use the Download tab there.

The filter uses the top-level Cancer Type. It includes NSCLC subtypes such as lung adenocarcinoma, squamous cell carcinoma and large cell carcinoma, plus some other lung tumors the study groups under this label. To narrow it, add a "Cancer Type Detailed" filter.

The whole study is also available as a full package at [cBioPortal Datasets](https://www.cbioportal.org/datasets). That package is not subset to NSCLC.