-- DBMS: bigquery
CREATE TABLE `isb-cgc-bq.pancancer_atlas.Filtered_all_CNVR_data_by_gene`
(
  ParticipantBarcode STRING OPTIONS(description="TCGA barcode identifier for the study participant, eg TCGA-02-0001"),
  SampleBarcode STRING OPTIONS(description="Barcode of the biospecimen sample, eg TCGA-13-1489-02A"),
  AliquotBarcode STRING OPTIONS(description="TCGA aliquot barcode, eg TCGA-12-1089-01A-01D-0517-28"),
  SampleTypeLetterCode STRING OPTIONS(description="Letter code of the sample type using the TCGA standards, eg TPN, EBV. Full list available at https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/sample-type-codes"),
  SampleType STRING OPTIONS(description="There are 10 sample types: Blood Derived Normal, Primary solid Tumor, Solid Tissue Normal, Recurrent Solid Tumor, Metastatic, Additional - New Primary, Primary Blood Derived Cancer - Peripheral Blood, Buccal Cell Normal, Additioanal Metastatic, Bone Marrrow Normal"),
  Study STRING OPTIONS(description="TCGA study abbreviation, eg LAML. Full list available at https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/tcga-study-abbreviations"),
  Gene_Symbol STRING OPTIONS(description="eg TP53, LRP1B, etc (same as Hugo_Symbol field except blank instead of Unknown"),
  Locus_ID INT64 OPTIONS(description="Gene locus ID, eg.  57380, 100616303"),
  Cytoband STRING OPTIONS(description="Full cytoband name, including chromosome. E.g, 17p13.2 See https://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/chrombanding.html"),
  GISTIC_Calls FLOAT64 OPTIONS(description="Gistic Copy Number calls")
)
OPTIONS(
  friendly_name="PanCancer Filtered Copy Number",
  description="Data extracted from the PanCancer Atlas initiative on the GDC in Aug 2016. Contains Copy Number Variation data based on the GISTIC algorithm. \n\nNote: The original data was annotated with ParticipantBarcode, SampleBarcode, AliquotBarcode, SampleTypeLetterCode, SampleType and TCGA Study; and participants were subsequently filtered using the PanCancer Atlas whitelist (table Whitelist_ParticipantBarcodes)  \n\nMore details: https://www.synapse.org/#!Synapse:syn5031907 \nand https://gdc.cancer.gov/about-data/publications/pancanatlas",
  labels=[("category", "processed_-omics_data"), ("status", "current"), ("access", "open"), ("source_0", "gdc"), ("data_type", "copy_number_segment_masked"), ("program", "pancancer_atlas"), ("reference_genome", "hg19"), ("source_1", "literature")]
);

INSERT INTO `isb-cgc-bq.pancancer_atlas.Filtered_all_CNVR_data_by_gene` (ParticipantBarcode, SampleBarcode, AliquotBarcode, SampleTypeLetterCode, SampleType, Study, Gene_Symbol, Locus_ID, Cytoband, GISTIC_Calls) VALUES ('TCGA-04-1331', 'TCGA-04-1331-01A', 'TCGA-04-1331-01A-01D-0428-01', 'TP', 'Primary solid Tumor', 'OV', 'MIR663B', 100313824, '2q21.2', -0.054), ('TCGA-04-1331', 'TCGA-04-1331-01A', 'TCGA-04-1331-01A-01D-0428-01', 'TP', 'Primary solid Tumor', 'OV', 'REG4', 83998, '1p12', 0.13), ('TCGA-04-1331', 'TCGA-04-1331-01A', 'TCGA-04-1331-01A-01D-0428-01', 'TP', 'Primary solid Tumor', 'OV', 'CABIN1', 23523, '22q11.23', -0.715), ('TCGA-04-1331', 'TCGA-04-1331-01A', 'TCGA-04-1331-01A-01D-0428-01', 'TP', 'Primary solid Tumor', 'OV', 'CHRNA7', 1139, '15q13.3', -0.764), ('TCGA-04-1331', 'TCGA-04-1331-01A', 'TCGA-04-1331-01A-01D-0428-01', 'TP', 'Primary solid Tumor', 'OV', 'AOC2', 314, '17q21.31', -0.277);