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

▶ resolve_and_route
{
 "studyKeywords": [
  "MSK-CHORD",
  "NSCLC"
 ]
}

◀ result
{"success":false,"error":"No matching studies found","details":{"searchTerms":["MSK-CHORD","NSCLC"]}}

▶ list_studies
{
 "search": "MSK",
 "limit": "20",
 "verbose": "true"
}

✗ error
<tool_use_error>Error: No such tool available: mcp__navigator__list_studies</tool_use_error>

▶ list_studies
{
 "search": "MSK",
 "limit": 20,
 "verbose": true
}

◀ result
{"result":[{"cancer_study_identifier":"msk_impact_50k_2026","name":"MSK-IMPACT 50K Clinical Sequencing Cohort (MSK, Cancer Cell 2026)","description":"MSK-50K (Memorial Sloan Kettering - 50,000 patients) is a pan-cancer clinical sequencing cohort of 54,331 tumors and their matched normal samples, profiled using MSK-IMPACT. The dataset includes somatic mutations, gene-level copy number alterations, structural variants in select genes, genome-wide allele-specific copy number, cancer cell fractions of mutations, derived mutational signatures, whole genome doubling status, and somatic/germline HLA Class I Genotype data. This data is available under the Creative Commons BY-NC-ND 4.0 license. For commercial use, please contact <a href=\"mailto:data@ascproject.org\">datarequests@mskcc.org</a>.","type_of_cancer_id":"mixed","sample_count":54331,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=msk_impact_50k_2026"},{"cancer_study_identifier":"msk_ch_2023","name":"Cancer Therapy and Clonal Hematopoiesis (MSK, Blood Adv 2023)","description":"Targeted sequencing of 47,532 patient samples with mixed tumor types and their matched normals to identify clonal hematopoiesis mutations using MSK-IMPACT.","type_of_cancer_id":"mixed","sample_count":42714,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=msk_ch_2023"},{"cancer_study_identifier":"msk_met_2021","name":"MSK MetTropism (MSK, Cell 2021)","description":"MSK-MET (Memorial Sloan Kettering - Metastatic Events and Tropisms) is a pan-cancer cohort of tumor genomic and clinical outcome data from 25,000 patients. The dataset identifies associations between tumor genomic alterations and patterns of metastatic dissemination across 50 tumor types; showing that chromosomal instability is strongly correlated with metastatic burden in some tumor types, like prostate and lung adenocarcinomas and HR+/HER2+ breast ductal carcinoma, but not in others, such as colorectal MSS, pancreatic adenocarcinoma and high-grade serous ovarian cancer. The study also identifies somatic alterations associated with increased metastatic burden and routes of metastatic spread. Our data offers a resource for the investigation of the biologic basis for metastatic spread and highlights the role of chromosomal instability in cancer progression. This data is available under the <a href=\"https://creativecommons.org/licenses/by-nc-nd/4.0/deed.en\">Creative Commons BY-NC-ND 4.0 license</a>.","type_of_cancer_id":"mixed","sample_count":25775,"has_guide":false,"url":"https://www.cbioportal.org/study/summary?id=msk_met_2021"},{"cancer_study_identifier":"msk_chord_2024","name":"MSK-CHORD (MSK, Nature 2024)","description":"Targeted sequencing of 25040 tumors from 24950 patients and their matched normals via MSK-IMPACT, along with clinical annotations, some of which are derived from natural language processing (denoted NLP). This data is available under the <a href=\"https://creativecommons.org/licenses/by-nc-nd/4.0/deed … (6828 more chars)

▶ get_study_guide
{
 "study_id": "msk_chord_2024"
}

◀ result
# MSK-CHORD (MSK, Nature 2024)

**Study ID:** `msk_chord_2024`

## Overview
Targeted sequencing via MSK-IMPACT panels. Clinical annotations include some derived from natural language processing (denoted NLP).

**Exactly five cancer types** (`CANCER_TYPE`, patients): Non-Small Cell Lung Cancer 7,809, Colorectal Cancer 5,543, Breast Cancer 5,368, Prostate Cancer 3,211, Pancreatic Cancer 3,109. There is **no melanoma** or any other cancer type; say so up front if asked, instead of substituting another type.

**No therapy-response variable.** There is no RECIST, objective response, or best-response attribute or event. For treatment-outcome questions (e.g. immunotherapy response), say this first; the only proxies are `OS_MONTHS`/`OS_STATUS`, or NLP radiology progression events (`Diagnosis` events with `SUBTYPE = 'Progression'`, key `PROGRESSION` = Y/N/Indeterminate), in patients with `Treatment` events of the relevant `SUBTYPE` (e.g. `Immuno`: 3,341 patients). Hand off the comparison to cBioPortal group comparison / survival.

**Nearly one sample per patient: 24,950 patients / 25,040 samples.** Only 90 patients have more than one sample, and all 90 have samples from two different cancer types (second primaries); only 26 have both a `Primary` and a `Metastasis` sample. There is no meaningful same-patient (paired) primary-vs-metastasis cohort. For "same patient" / paired questions, say this up front, then offer the **unpaired** comparison of all `Primary` vs `Metastasis` samples (`SAMPLE_TYPE`), labelled as unpaired.
```sql
SELECT countIf(n > 1) AS multi_sample_patients,         -- 90
       countIf(has_p AND has_m) AS primary_and_met      -- 26
FROM (SELECT patient_unique_id, count() AS n,
             has(groupArray(attribute_value), 'Primary') AS has_p,
             has(groupArray(attribute_value), 'Metastasis') AS has_m
      FROM clinical_data_derived
      WHERE cancer_study_identifier = 'msk_chord_2024' AND attribute_name = 'SAMPLE_TYPE'
      GROUP BY patient_unique_id);
```

## Gene Panels
This study uses multiple MSK-IMPACT panel versions:
- **IMPACT341**: Earlier version, 341 genes
- **IMPACT410**: 410 genes
- **IMPACT468**: 468 genes  
- **IMPACT505**: Latest version, 505 genes

**Important:** Different samples may have different gene coverage. Always use gene-specific denominators when calculating mutation frequencies.

## Clinical Attributes - Semantic Guide

### Cancer Classification
| Attribute | Description | Values |
|-----------|-------------|--------|
| `CANCER_TYPE` | Broad cancer category | e.g., "Non-Small Cell Lung Cancer", "Breast Cancer" |
| `CANCER_TYPE_DETAILED` | Specific subtype | e.g., "Lung Adenocarcinoma", "Invasive Ductal Carcinoma" |
| `ONCOTREE_CODE` | OncoTree classification code | Standardized cancer type codes |

### Sample Information
| Attribute | Description | Values |
|-----------|-------------|--------|
| `SAMPLE_TYPE` | Sample origin | Primary, Metastasis, Local Recurrence, Unknown |
| `SAMPLE_CLASS` | Sample … (5439 more chars)

═ answer (success)
Excellent! Now I have the information you need. Here are your options for downloading the **MSK-CHORD Non-Small Cell Lung Cancer** dataset:

## Study Overview

[**MSK-CHORD (MSK, Nature 2024)**](https://www.cbioportal.org/study/summary?id=msk_chord_2024)  
**Study ID:** `msk_chord_2024`

The study contains **7,809 NSCLC patients** (7,764 samples) profiled via **MSK-IMPACT targeted sequencing** with comprehensive clinical annotations, including NLP-derived data.

---

## Download Options

### **Option 1: Direct cBioPortal Download (Recommended)**
1. Visit the [MSK-CHORD study page](https://www.cbioportal.org/study/summary?id=msk_chord_2024)
2. Click **"Download"** (top-right corner)
3. Select **data types** you need:
   - Clinical data (patient demographics, treatment, outcomes)
   - Mutation data (MAF format)
   - Copy number alterations
   - Structural variants (select genes)
   - Segment files (FACETS copy number)

### **Option 2: Public REST API**
For programmatic access, use cBioPortal's public REST API:

```bash
# Get all NSCLC samples from MSK-CHORD
curl "https://www.cbioportal.org/api/v2/studies/msk_chord_2024/samples?cancerTypeId=nsclc" | jq .

# Download mutations for a specific study
curl "https://www.cbioportal.org/api/v2/studies/msk_chord_2024/molecular-profiles" | jq .
```

### **Option 3: Query via ClickHouse (Advanced)**
For custom queries, I can extract specific subsets (e.g., TP53-mutated NSCLC, specific treatment cohorts). Examples:
- "Download all NSCLC samples with metastatic disease"
- "Get mutation and clinical data for EGFR-mutated adenocarcinomas"
- "Export treatment-outcome data for immunotherapy-treated patients"

---

## Key Data Notes
- **NSCLC samples:** 7,764 tumors (mostly primary + metastatic)
- **Gene coverage:** Multiple IMPACT panel versions (341–505 genes)
- **Treatment data:** Comprehensive, including chemotherapy, immunotherapy, targeted therapy
- **License:** CC BY-NC-ND 4.0 (contact datarequests@mskcc.org for commercial use)

**Would you like me to help you query a specific subset?** For example, I can pull NSCLC samples with particular mutations, clinical features, or treatment history.