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
cs.cancer_study_identifier,
cs.name,
COUNT(DISTINCT p.patient_id) AS patient_count,
cs.sample_count
FROM cancer_study cs
LEFT JOIN patient p ON cs.cancer_study_id = p.cancer_study_id
WHERE cs.cancer_study_identifier = 'msk_chord_2024'
GROUP BY cs.cancer_study_identifier, cs.name, cs.sample_count
"
}
◀ 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: Identifier 'p.patient_id' cannot be resolved from table with name p. In scope SELECT cs.cancer_study_identifier, cs.name, COUNTDistinct(p.patient_id) AS patient_count, cs.sample_count FROM cancer_study AS cs LEFT JOIN patient AS p ON cs.cancer_study_id = p.cancer_study_id WHERE cs.cancer_study_identifier = 'msk_chord_2024' GROUP BY cs.cancer_study_identifier, cs.name, cs.sample_count. (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
cs.cancer_study_identifier,
cs.name,
COUNT(DISTINCT p.internal_id) AS patient_count,
cs.sample_count
FROM cancer_study cs
LEFT JOIN patient p ON cs.cancer_study_id = p.cancer_study_id
WHERE cs.cancer_study_identifier = 'msk_chord_2024'
GROUP BY cs.cancer_study_identifier, cs.name, cs.sample_count
"
}
◀ result
{"rows":[{"cancer_study_identifier":"msk_chord_2024","name":"MSK-CHORD (MSK, Nature 2024)","patient_count":24950,"sample_count":25040}]}
═ answer (success)
The database confirms **24,950 patients** in MSK-CHORD (msk_chord_2024). This is the count stored in the cBioPortal database.
It's possible you're thinking of a different MSK dataset or a different version, or perhaps a higher count refers to the total number of cases in the underlying MSK data repository (which may be larger than what's released in cBioPortal). You can browse all MSK studies at https://www.cbioportal.org to see if there's a different cohort you had in mind. Would you like me to help you find another MSK study?