genie forum question on version 10 TNF

2021-09-07_alishacoll_genie_tnf_no_mutations.sql

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+/* 
+Description: Investigate why 'TNFRSF10B' and 'TNF' have no mutations in
+  the GENIE v10 databse.
+Author: Haley Hunter-Zinck
+Date: September 7, 2021
+Request: 
+	source: GENIE discusssion forum
+	Author: https://www.synapse.org/#!Profile:3432090 (@AlishaColl)
+	url: https://www.synapse.org/#!Synapse:syn7222066/discussion/threadId=8196
+*/
+
+/*
+-- are there assays covering 'TNFRSF10B' or 'TNF': DUKE-F1-T7 and VICC-01-T7 covering TNF
+SELECT DISTINCT hugo_symbol, seq_assay_id
+FROM genie_release_public.genomic_information
+WHERE hugo_symbol IN ('TNFRSF10B', 'TNF')
+	AND release = 10
+--*/
+
+/*
+-- number of mutations recorded in genes 'TNFRSF10B' or 'TNF': 0
+SELECT *
+FROM genie_release_public.mutation
+WHERE hugo_symbol = 'TNF'
+	AND release = 10
+*/
+
+/*
+-- number of samples sequenced with assays that cover TNF: 10,740
+SELECT COUNT(*) AS n_sample
+FROM genie_release_public.genomic_information as gi
+	JOIN genie_release_public.sample AS sam
+		ON gi.seq_assay_id = sam.seq_assay_id
+WHERE hugo_symbol = 'TNF'
+	AND gi.release = 10 AND sam.release = 10
+--*/
+
+/*
+-- number of mutations recorded within TNF regions sequenced: 0
+SELECT *
+FROM genie_release_public.genomic_information AS gi
+	JOIN genie_release_public.mutation AS mut
+		ON mut.chromosome = gi.chromosome 
+			AND mut.start_position >= gi.start_position
+			AND mut.end_position <= gi.end_position
+WHERE gi.hugo_symbol = 'TNF'
+	AND gi.release = 10 AND mut.release = 10
+*/
+
+/*
+-- number of mutations recorded associated with samples sequenced by TNF assays: 29,422
+-- so these samples have recorded mutations at other locations, just not TNF
+SELECT COUNT(*) AS n_sample_tnf
+FROM genie_release_public.mutation AS mut
+	JOIN genie_release_public.sample AS sam
+		ON mut.tumor_sample_barcode = sam.sample_id
+WHERE mut.release = 10 AND sam.release = 10
+	AND sam.seq_assay_id IN ('DUKE-F1-T7', 'VICC-01-T7')
+--*/
+
+/*
+-- is there CNA data covering these regions?  no
+SELECT *
+FROM genie_release_public.genomic_information AS gi
+	JOIN genie_release_public.cna AS cna
+		ON cna.chrom = gi.chromosome 
+			AND CAST(cna.loc_start AS INTEGER) >= gi.start_position
+			AND CAST(cna.loc_end AS INTEGER) <= gi.end_position
+WHERE gi.hugo_symbol = 'TNF'
+	AND gi.release = 10 AND cna.release = 10
+*/
+
+-- looking at VICC-01-07 gene panel, what about 'TNFRSF14' or other variations?: yes: "TNFAIP3", "TNFRSF11A", "TNFRSF14"
+/*
+SELECT hugo_symbol, COUNT(*) AS n_mutation
+FROM genie_release_public.mutation
+WHERE hugo_symbol LIKE 'TNF%'
+	AND release = 10
+GROUP BY hugo_symbol
+ORDER BY COUNT(*) DESC
+*/
+
+/*
+-- is there fusion data covering these regions?  yes, 3 for TNFRSF10B
+SELECT hugo_symbol, COUNT(*)
+FROM genie_release_public.fusion AS fus
+WHERE fus.hugo_symbol IN ('TNF', 'TNFRSF10B')
+	AND fus.release = 10 
+GROUP BY fus.hugo_symbol
+*/
+/*
+SELECT *
+FROM genie_release_public.fusion AS fus
+WHERE fus.hugo_symbol IN ('TNF', 'TNFRSF10B')
+	AND fus.release = 10 
+*/
+