Data Load Summary
Data Load Summary This documents the data load decisions made when loading the TCGA Breast Cancer data. The data loaded is identified, the decisions made to overcome conflict or deficiencies in the data. Also identified is the schema created to support the TCGA Breast Cancer data in BIS. Clinical and Sample Data Loaded the clinical (and sample) files with the X next to them. ...\Clinical\Biotab x x x x x x x nationwidechildrens.org_biospecimen_aliquot_brca.txt nationwidechildrens.org_biospecimen_analyte_brca.txt nationwidechildrens.org_biospecimen_cqcf_brca.txt nationwidechildrens.org_biospecimen_normal_control_brca.txt nationwidechildrens.org_biospecimen_portion_brca.txt nationwidechildrens.org_biospecimen_protocol_brca.txt nationwidechildrens.org_biospecimen_sample_brca.txt nationwidechildrens.org_biospecimen_shipment_portion_brca.txt nationwidechildrens.org_biospecimen_slide_brca.txt nationwidechildrens.org_biospecimen_tumor_sample_brca.txt nationwidechildrens.org_clinical_cqcf_brca.txt nationwidechildrens.org_clinical_drug_brca.txt nationwidechildrens.org_clinical_follow_up_v1.5_brca.txt nationwidechildrens.org_clinical_follow_up_v2.1_brca.txt nationwidechildrens.org_clinical_follow_up_v4.0_brca.txt nationwidechildrens.org_clinical_follow_up_v4.0_nte_brca.txt nationwidechildrens.org_clinical_nte_brca.txt nationwidechildrens.org_clinical_patient_brca.txt nationwidechildrens.org_clinical_radiation_brca.txt There were samples that referred to missing participants (patients), so the following participants were inserted TCGA-A7-A5ZW TCGA-A7-A5ZX TCGA-A7-A6VV TCGA-A7-A6VW TCGA-A7-A6VX TCGA-A7-A6VY TCGA-AC-A2FE TCGA-AC-A3EH TCGA-AC-A3QQ TCGA-AC-A3TM TCGA-AC-A3W7 TCGA-AC-A5EH TCGA-AC-A5EI TCGA-AC-A5XS TCGA-AC-A5XU TCGA-AC-A62V TCGA-AC-A62X TCGA-AC-A6IW TCGA-AC-A6IX TCGA-AC-A6NO TCGA-AC-A7VB TCGA-AC-A7VC TCGA-AC-A8OP TCGA-AQ-A7U7 TCGA-AR-A2LJ TCGA-B6-A3ZX TCGA-B6-A400 TCGA-B6-A401 TCGA-E2-A572 TCGA-E2-A576 TCGA-E9-A6HE TCGA-EW-A6S9 TCGA-EW-A6SA TCGA-EW-A6SB TCGA-EW-A6SC TCGA-EW-A6SD TCGA-HN-A2NL TCGA-HN-A2OB TCGA-LD-A74U TCGA-LD-A7W5 TCGA-LD-A7W6 TCGA-LL-A5YN TCGA-LL-A5YO TCGA-LL-A5YP TCGA-LL-A6FP TCGA-LL-A6FQ TCGA-LL-A6FR TCGA-LL-A73Y TCGA-LL-A73Z TCGA-LL-A740 TCGA-LL-A7SZ TCGA-LL-A7T0 TCGA-LL-A8F5 TCGA-OL-A6VO TCGA-OL-A6VR TCGA-PE-A5DC TCGA-BH-A8G0 TCGA-C8-A8HP TCGA-C8-A8HQ TCGA-C8-A8HR TCGA-D8-A73U TCGA-D8-A73W TCGA-D8-A73X TCGA-B6-A408 TCGA-B6-A409 TCGA-B6-A40B TCGA-B6-A40C TCGA-BH-A5IZ TCGA-BH-A5J0 TCGA-BH-A6R8 TCGA-BH-A6R9 TCGA-BH-A8FY TCGA-BH-A8FZ TCGA-PE-A5DE TCGA-PL-A8LZ TCGA-S3-A6ZF TCGA-S3-A6ZG TCGA-S3-A6ZH TCGA-V7-A7HQ TCGA-W8-A86G TCGA-XX-A899 TCGA-XX-A89A TCGA-B6-A402 TCGA-PE-A5DD Computed survival_time (days) = max(days_to_last_followup, days_to_death) Inserted two Samples referred to by the Experiment data. Participant TCGA-E2-A2P5 TCGA-E2-A2P6 Sample TCGA-E2-A2P5-10B TCGA-E2-A2P6-10B Molecular Data Somatic Mutations Loaded file: \somatic mutation\Somatic_Mutations\WUSM__IlluminaGA_DNASeq\Level_2\ genome.wustl.edu__Illumina_Genome_Analyzer_DNA_Sequencing_level2.maf Added the Amino Acid change field values to Genetic Variant by joining chromosome position, type and mutation. Gene Expression Loaded the 590 files in the …\Expression-Genes\UNC__AgilentG4502A_07_3\Level_3 folder. Removed expression observation with gene symbol Rgr. Copy Number Variant Loaded the *hg19.* files. Duplicate rows in the data were found, so we used the following precedence rule If 1 distinct row with CNVObservation_barcode, load it. If there are multiple rows with the same CNVObservation_barcode, load the row that does not have FFPE in the filename and type=NOCNV. For more information To learn more, contact your TransMed representative or visit: xbtransmed.com. © Copyright TransMed Systems, Inc. 2011 TransMed Systems, 21170 Canyon Oak Way, Cupertino, CA 95014. The information contained in this documentation is provided for informational purposes only and is subject to change without notice. While efforts were made to verify the completeness and accuracy of the information contained in this documentation, it is provided “as is” without warranty of any kind, express or implied. All Rights Reserved.
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