Q (haiku):
How many patients are in MSK-CHORD?
MSK-CHORD (msk_chord_2024) includes 24,950 patients with 25,040 samples.
Continue this conversation: reply to the user's new message.
That seems low, I'm pretty sure MSK-CHORD has about 50,000 patients.
▶ clickhouse_run_select_query
{
"query": "
SELECT
cancer_study_identifier,
name,
patient_count,
sample_count
FROM cancer_study
WHERE cancer_study_identifier = 'msk_chord_2024'
"
}
◀ result
{"error_message":"Query execution failed: HTTPDriver for https://dl96orhu96.us-east-1.aws.clickhouse.cloud:8443 received ClickHouse error code 47\n Code: 47. DB::Exception: Unknown expression identifier `patient_count` in scope SELECT cancer_study_identifier, name, patient_count, sample_count FROM cancer_study WHERE cancer_study_identifier = 'msk_chord_2024'. (UNKNOWN_IDENTIFIER) (version 26.4.1.2359 (official build))\n"}
▶ clickhouse_list_table_columns
{
"table": "cancer_study"
}
◀ result
{"columns":[{"name":"cancer_study_id","type":"Int64","comment":"Internal numeric ID. Prefer cancer_study_identifier for queries as it is more readable and stable."},{"name":"cancer_study_identifier","type":"Nullable(String)","comment":"Stable string identifier for the study (e.g., \"msk_chord_2024\", \"brca_tcga\"). Use this for filtering, not cancer_study_id."},{"name":"type_of_cancer_id","type":"String"},{"name":"name","type":"String","comment":"Full descriptive name of the study (e.g., \"MSK-CHORD (MSK, Nature 2024)\")."},{"name":"description","type":"String"},{"name":"public","type":"Int32"},{"name":"pmid","type":"Nullable(String)"},{"name":"citation","type":"Nullable(String)"},{"name":"groups","type":"Nullable(String)"},{"name":"status","type":"Nullable(Int64)"},{"name":"import_date","type":"Nullable(DateTime64(6))"},{"name":"reference_genome_id","type":"Nullable(Int64)"},{"name":"sample_count","type":"UInt32","comment":"Samples in the study (members of _all), as shown in the portal study list. Precomputed daily at LLM-prep time."},{"name":"mutation_sample_count","type":"UInt32","comment":"Samples profiled for mutations (_sequenced) — portal \"Data type\" filter: \"Mutations\". 0 = no mutation data."},{"name":"cna_sample_count","type":"UInt32","comment":"Samples profiled for copy-number alterations (_cna) — \"CNA\". 0 = no CNA data."},{"name":"structural_variant_sample_count","type":"UInt32","comment":"Distinct samples with at least one structural variant (fusions etc.). 0 = none."},{"name":"rna_seq_sample_count","type":"UInt32","comment":"Samples with RNA-Seq expression (_rna_seq_v2_mrna) — \"RNA-Seq\"."},{"name":"mrna_microarray_sample_count","type":"UInt32","comment":"Samples with microarray mRNA expression (_mrna) — \"RNA (microarray)\"."},{"name":"mirna_sample_count","type":"UInt32","comment":"Samples with microRNA expression (_microrna) — \"miRNA\"."},{"name":"rppa_sample_count","type":"UInt32","comment":"Samples with RPPA protein levels (_rppa) — \"RPPA\"."},{"name":"mass_spectrometry_sample_count","type":"UInt32","comment":"Samples with mass-spectrometry protein quantification (_protein_quantification) — \"Protein Mass-Spectrometry\"."},{"name":"treatment_patient_count","type":"UInt32","comment":"PATIENTS (not samples) with treatment clinical events — \"Treatment\". 0 = no treatment data."},{"name":"resource_sample_counts","type":"Map(String, UInt32)","comment":"Samples with each linked resource, keyed by display name: imaging and pathology such as 'Slide Microscopy', 'Computed Tomography', 'Magnetic Resonance', 'H&E Slide', 'MxIF Image'. Query with mapKeys(resource_sample_counts) or resource_sample_counts['Slide Microscopy'] > 0."},{"name":"mrna_expression_sample_count","type":"UInt32","comment":"Samples in any mRNA expression profile (RNA-Seq, microarray, TPM, z-scores; from sample_profile). Use this for \"does the study have expression data\" — rna_seq_sample_count and mrna_m … (136 more chars)
▶ clickhouse_run_select_query
{
"query": "
SELECT
COUNT(DISTINCT patient_id) as patient_count,
COUNT(DISTINCT sample_id) as sample_count
FROM patient
WHERE cancer_study_id IN (
SELECT cancer_study_id
FROM cancer_study
WHERE cancer_study_identifier = 'msk_chord_2024'
)
"
}
◀ result
{"error_message":"Query execution failed: HTTPDriver for https://dl96orhu96.us-east-1.aws.clickhouse.cloud:8443 received ClickHouse error code 47\n Code: 47. DB::Exception: Unknown expression or function identifier `patient_id` in scope SELECT COUNTDistinct(patient_id) AS patient_count, COUNTDistinct(sample_id) AS sample_count FROM patient WHERE cancer_study_id IN (SELECT cancer_study_id FROM cancer_study WHERE cancer_study_identifier = 'msk_chord_2024'). (UNKNOWN_IDENTIFIER) (version 26.4.1.2359 (official build))\n"}
▶ clickhouse_list_table_columns
{
"table": "patient"
}
◀ result
{"columns":[{"name":"internal_id","type":"Int64","comment":"Primary key. Unique internal identifier for the patient."},{"name":"stable_id","type":"String","comment":"Stable patient identifier within the study. Combined with cancer_study_identifier forms patient_unique_id."},{"name":"cancer_study_id","type":"Int64","comment":"Foreign key to cancer_study.cancer_study_id. Links patient to their study."}]}
▶ clickhouse_run_select_query
{
"query": "
SELECT
COUNT(*) as patient_count
FROM patient
WHERE cancer_study_id IN (
SELECT cancer_study_id
FROM cancer_study
WHERE cancer_study_identifier = 'msk_chord_2024'
)
"
}
◀ result
{"rows":[{"patient_count":24950}]}
═ answer (success)
The database confirms **24,950 patients** in MSK-CHORD (msk_chord_2024). It's possible you're thinking of:
1. **A different version or broader MSK cohort** — there may be other MSK studies with different patient counts
2. **Total sample count** — MSK-CHORD has 25,040 samples (some patients have multiple samples)
3. **A projected or announced future size** — the cohort may have been planned to grow to ~50,000
Would you like me to search for other MSK studies in the database, or do you have additional context on where the 50,000 figure comes from?