The legacy implementation seems to have added extra gene panel ids.
Example
Difference found in list at TFRC.matchingGenePanelIds: (Legacy) ['PROV-TSO500HT-V2', 'WAKE-CA-NGSQ3', 'UHN-TSO500-V1', 'PROV-TST170-V1']
!= (New) ['PROV-TSO500HT-V2', 'WAKE-CA-NGSQ3', 'PROV-TST170-V1']
When running the following query. The result will be all samples with mutation events for GENE TFRC.
This also shows the UHN-TSO500-V1 gene_panel was not in the search.
SELECT concat(cs.cancer_study_identifier, '_', sample.stable_id) as sample_unique_id, gene.hugo_gene_symbol as hugo_gene_symbol, gp.stable_id as gene_panel_stable_id, cs.cancer_study_identifier as cancer_study_identifier, g.stable_id as genetic_profile_stable_id, me.mutation_type as mutation_type, mutation.mutation_status as mutation_status FROM mutation LEFT JOIN mutation_event as me on mutation.mutation_event_id = me.mutation_event_id LEFT JOIN sample_profile sp on mutation.sample_id = sp.sample_id and mutation.genetic_profile_id = sp.genetic_profile_id LEFT JOIN gene_panel gp on sp.panel_id = gp.internal_id LEFT JOIN genetic_profile g on sp.genetic_profile_id = g.genetic_profile_id LEFT JOIN cancer_study cs on g.cancer_study_id = cs.cancer_study_id LEFT JOIN sample on mutation.sample_id = sample.internal_id LEFT JOIN gene on mutation.entrez_gene_id = gene.entrez_gene_id where mutation.entrez_gene_id = 7037;
The legacy implementation seems to have added extra gene panel ids.
Example Difference found in list at TFRC.matchingGenePanelIds: (Legacy) ['PROV-TSO500HT-V2', 'WAKE-CA-NGSQ3', 'UHN-TSO500-V1', 'PROV-TST170-V1'] != (New) ['PROV-TSO500HT-V2', 'WAKE-CA-NGSQ3', 'PROV-TST170-V1']
When running the following query. The result will be all samples with mutation events for GENE TFRC. This also shows the UHN-TSO500-V1 gene_panel was not in the search.
SELECT concat(cs.cancer_study_identifier, '_', sample.stable_id) as sample_unique_id, gene.hugo_gene_symbol as hugo_gene_symbol, gp.stable_id as gene_panel_stable_id, cs.cancer_study_identifier as cancer_study_identifier, g.stable_id as genetic_profile_stable_id, me.mutation_type as mutation_type, mutation.mutation_status as mutation_status FROM mutation LEFT JOIN mutation_event as me on mutation.mutation_event_id = me.mutation_event_id LEFT JOIN sample_profile sp on mutation.sample_id = sp.sample_id and mutation.genetic_profile_id = sp.genetic_profile_id LEFT JOIN gene_panel gp on sp.panel_id = gp.internal_id LEFT JOIN genetic_profile g on sp.genetic_profile_id = g.genetic_profile_id LEFT JOIN cancer_study cs on g.cancer_study_id = cs.cancer_study_id LEFT JOIN sample on mutation.sample_id = sample.internal_id LEFT JOIN gene on mutation.entrez_gene_id = gene.entrez_gene_id where mutation.entrez_gene_id = 7037;