Q (sonnet):
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, sample_count, name FROM cancer_study WHERE cancer_study_identifier = 'msk_chord_2024'"
}
◀ result
{"rows":[{"cancer_study_identifier":"msk_chord_2024","sample_count":25040,"name":"MSK-CHORD (MSK, Nature 2024)"}]}
▶ clickhouse_run_select_query
{
"query": "SELECT count(DISTINCT patient_unique_id) AS patient_count FROM patient_derived 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 60\n Code: 60. DB::Exception: Unknown table expression identifier 'patient_derived' in scope SELECT countDistinct(patient_unique_id) AS patient_count FROM patient_derived WHERE cancer_study_identifier = 'msk_chord_2024'. (UNKNOWN_TABLE) (version 26.4.1.2359 (official build))\n"}
▶ clickhouse_list_tables
{}
◀ result
{"tables":[{"name":"allele_specific_copy_number"},{"name":"alteration_driver_annotation"},{"name":"cancer_study"},{"name":"cancer_study_query_preferences"},{"name":"cancer_study_tags"},{"name":"cbioportal_sequence_state"},{"name":"clinical_attribute_counts"},{"name":"clinical_attribute_meta"},{"name":"clinical_data_derived"},{"name":"clinical_event"},{"name":"clinical_event_data"},{"name":"clinical_event_data_derived"},{"name":"clinical_event_derived"},{"name":"clinical_patient"},{"name":"clinical_sample"},{"name":"cna_event"},{"name":"cna_panel_gene_coverage"},{"name":"cna_wes_coverage"},{"name":"co_altered_genes_in_study"},{"name":"copy_number_seg"},{"name":"copy_number_seg_file"},{"name":"gene"},{"name":"gene_alias"},{"name":"gene_alteration_frequency_by_cancer_type"},{"name":"gene_cna_distribution_in_study"},{"name":"gene_mutation_frequency_by_cancer_type"},{"name":"gene_mutation_frequency_in_studies"},{"name":"gene_mutation_frequency_in_study"},{"name":"gene_mutation_variants_in_study"},{"name":"gene_pair_coexpression"},{"name":"gene_panel"},{"name":"gene_panel_list"},{"name":"gene_panel_to_gene_derived"},{"name":"generic_assay_data_derived"},{"name":"generic_assay_meta_derived"},{"name":"generic_assay_profile_entity_derived"},{"name":"generic_entity_properties"},{"name":"geneset"},{"name":"geneset_gene"},{"name":"geneset_hierarchy_leaf"},{"name":"geneset_hierarchy_node"},{"name":"genetic_alteration"},{"name":"genetic_alteration_derived"},{"name":"genetic_entity"},{"name":"genetic_profile"},{"name":"genetic_profile_link"},{"name":"genetic_profile_samples"},{"name":"genomic_event_derived"},{"name":"gistic"},{"name":"gistic_to_gene"},{"name":"info"},{"name":"mut_sig"},{"name":"mutation"},{"name":"mutation_count_by_keyword"},{"name":"mutation_derived"},{"name":"mutation_event"},{"name":"mutation_panel_gene_coverage"},{"name":"mutation_wes_coverage"},{"name":"patient"},{"name":"reference_genome"},{"name":"reference_genome_gene"},{"name":"resource_definition"},{"name":"resource_patient"},{"name":"resource_sample"},{"name":"resource_study"},{"name":"sample"},{"name":"sample_cna_event"},{"name":"sample_derived"},{"name":"sample_list"},{"name":"sample_list_list"},{"name":"sample_profile"},{"name":"sample_to_gene_panel_derived"},{"name":"structural_variant"},{"name":"sv_panel_gene_coverage"},{"name":"sv_wes_coverage"},{"name":"top_cna_genes_in_study"},{"name":"top_mutated_genes_in_cohort"},{"name":"top_mutated_genes_in_study"},{"name":"top_sv_genes_in_study"},{"name":"treatment_counts_in_study"},{"name":"treatment_regimens_in_study"},{"name":"type_of_cancer"}]}
▶ clickhouse_run_select_query
{
"query": "
SELECT
(SELECT count(DISTINCT patient_unique_id) FROM patient p JOIN cancer_study cs ON p.cancer_study_id = cs.cancer_study_id WHERE cs.cancer_study_identifier = 'msk_chord_2024') AS patient_count,
(SELECT count(DISTINCT sample_unique_id) FROM sample s JOIN cancer_study cs ON s.cancer_study_id = cs.cancer_study_id WHERE cs.cancer_study_identifier = 'msk_chord_2024') AS 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: Unknown expression or function identifier `patient_unique_id` in scope (SELECT countDistinct(patient_unique_id) FROM patient AS p INNER JOIN cancer_study AS cs ON p.cancer_study_id = cs.cancer_study_id WHERE cs.cancer_study_identifier = 'msk_chord_2024') AS patient_count. (UNKNOWN_IDENTIFIER) (version 26.4.1.2359 (official build))\n"}
▶ clickhouse_list_table_columns
{
"table": "patient"
}
▶ clickhouse_list_table_columns
{
"table": "sample"
}
◀ 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."}]}
◀ result
{"columns":[{"name":"internal_id","type":"Int64","comment":"Primary key. Unique internal identifier for the sample."},{"name":"stable_id","type":"String","comment":"Stable identifier for the sample within the study. Combined with cancer_study_identifier forms sample_unique_id."},{"name":"patient_id","type":"Int64","comment":"Foreign key to patient.internal_id. Links sample to its patient."}]}
▶ clickhouse_run_select_query
{
"query": "
SELECT count(DISTINCT p.internal_id) AS patient_count
FROM patient p
JOIN cancer_study cs ON p.cancer_study_id = cs.cancer_study_id
WHERE cs.cancer_study_identifier = 'msk_chord_2024'
"
}
◀ result
{"rows":[{"patient_count":24950}]}
═ answer (success)
I re-verified directly against the database, and the number holds: **MSK-CHORD (msk_chord_2024)** contains **24,950 patients** and 25,040 samples.
A couple of notes on the discrepancy you may be thinking of:
- The MSK-CHORD publication (Jonsson et al./Nature 2024, and related preprints) drew from a broader institutional cohort during development, but the **public cBioPortal release** of MSK-CHORD is the ~25,000-patient dataset.
- If you're thinking of a different MSK cohort — e.g., **MSK-IMPACT (MSKCC, ~50,000+ samples across multiple releases)** — that's a separate, larger pan-cancer targeted sequencing dataset and could be the source of the ~50,000 figure.
You can browse the MSK-CHORD cohort directly here: [MSK-CHORD Study View](https://www.cbioportal.org/study/summary?id=msk_chord_2024)
If you meant MSK-IMPACT instead, let me know and I can pull the patient/sample counts for that study as well.