Breast invasive carcinoma

Analysis of batch vs clinical traits

Number of clinical traits: 84

Number of batches based on tumor DNA methylation data (samples retrieved according to this pattern: "TCGA-......-0....D-....-05"): 24

Correlation between center and batches ('two'=center (second field in the patient barcode)):

> table(batchID,two)
       two
batchID A1 A2 A7 A8 AC AN AO AQ AR B6 BH C8 D8 E2 E9 EW GI GM HN
   A00Y  0  3  7 66  0 12  2  0  0  0  4  0  0  0  0  0  0  0  0
   A032  0 22  0 14  0 19 10  1  0 16 10  0  0  0  0  0  0  0  0
   A058  0  2  1  3  0  0 11  0  0  4 26  0  0  0  0  0  0  0  0
   A088  7 14  0  1  0  0  1  0  8  9  7  0  0  0  0  0  0  0  0
   A10A  0 12  0  0  0  9  0  0  5  9  4  0  0  0  0  0  0  0  0
   A10N  0  1  0  0  0  1 12  2  0  1  1  0  0  9  0  0  0  0  0
   A10P  7 16  1  4  0  0 12  0  8 13 32  0  0  0  0  0  0  0  0
   A112  1 11  1  0  0  0  5  0  3  5 18 20  9 15  0  0  0  0  0
   A12E  0  0  0  0  0  0  0  0  1  0 20  2  0 21  0  0  0  0  0
   A12R  0  0  3  0  0  0  0  0 15  0 14  0  0 11  0  0  0  0  0
   A138  0  0  0  0  0  0  0  0  1  0  7  6  0  2  0  0  0  0  0
   A13K  0  7  1  0  0  0  5  2  0  3 18  4 19  6  0  8  0  0  0
   A145  6  0  0  0  0  0  1  0  0  0  0  0  0 10  4 19  0  0  0
   A148  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
   A14H  0  1  0  0  0  0  0  0  0  0  1  0  7  5 10  1  0  0  0
   A14N  0  0  0  0  0  0  0  1  0  1  2  0 20  1  6  1  0  0  0
   A161  0  0  0  0  2  0  0  0  0  1  3  0  3  2 17  0  0  0  0
   A16A  0  4  6  0  1  0  0  0 22  0  1  3  0  0  9  0  0  0  0
   A16G  0  3  0  0  0  0  0  0  0  0  1  8 13  0  3  0  1  0  0
   A17F  0  0  0  0  4  0  0  0  0  0  0  0  1  0  0  3  0  0  0
   A17Z  0  0  0  0  2  0  0  0  4  0  0  0  0  0  1  0  0  6  0
   A18O  0  0  0  0  1  0  0  0  5  1  1  0  0  0  1  0  0  7  1
   A19F  0  2  0  1  0  0  0  0  0  1  0  0  0  1  0  0  0  0  0
   A19Z  0  0  0  0  5  0  0  0  1  0  1  0  0  1  0  0  0  0  0

Significant batch-clinical traits correlations (the entire list can be found here):

Unknown macro: {csv}

"BRCA_clinical_traits","DataType","NumberOfNAs","Test","Pvalue"
"tissue_prospective_collection_indicator","factor",35,"Pearson's Chi-squared test",4.47E-62
"tissue_retrospective_collection_indicator","factor",35,"Pearson's Chi-squared test",4.47E-62
"year_of_initial_pathologic_diagnosis","integer",34,"Kruskal-Wallis rank sum test",3.15E-32
"breast_carcinoma_first_surgical_procedure_name","factor",54,"Pearson's Chi-squared test",5.45E-32
"days_to_last_followup","integer",73,"Kruskal-Wallis rank sum test",3.07E-31
"days_to_form_completion","integer",34,"Kruskal-Wallis rank sum test",5.70E-31
"first_pathologic_diagnosis_biospecimen_acquisition_method_type","factor",123,"Pearson's Chi-squared test",3.39E-28
"breast_tumor_clinical_m_stage","factor",35,"Pearson's Chi-squared test",1.06E-22
"axillary_lymph_node_stage_method_type","factor",223,"Pearson's Chi-squared test",9.33E-19
"breast_tumor_pathologic_n_stage","factor",34,"Pearson's Chi-squared test",2.19E-17
"lab_proc_her2_neu_immunohistochemistry_receptor_status","factor",41,"Pearson's Chi-squared test",6.22E-16
"breast_carcinoma_estrogen_receptor_status","factor",34,"Pearson's Chi-squared test",1.85E-13
"breast_carcinoma_progesterone_receptor_status","factor",34,"Pearson's Chi-squared test",8.87E-13
"vital_status","factor",34,"Pearson's Chi-squared test",2.38E-09
"anatomic_site_location_descriptor","factor",119,"Pearson's Chi-squared test",1.03E-07
"age_at_initial_pathologic_diagnosis","integer",34,"Kruskal-Wallis rank sum test",5.87E-06
"days_to_birth","integer",34,"Kruskal-Wallis rank sum test",6.68E-06
"lab_procedure_her2_neu_in_situ_hybrid_outcome_type","factor",194,"Pearson's Chi-squared test",3.18E-05
"person_menopause_status","factor",161,"Pearson's Chi-squared test",5.70E-05
"breast_tumor_pathologic_grouping_stage","factor",40,"Pearson's Chi-squared test",7.40E-05
"her2_immunohistochemistry_level_result","factor",351,"Pearson's Chi-squared test",1.72E-04
"breast_tumor_pathologic_t_stage","factor",34,"Pearson's Chi-squared test",2.82E-04
"pos_finding_lymph_node_hematoxylin_and_eosin_staining_microscopy_count","integer",177,"Kruskal-Wallis rank sum test",6.49E-04
"cytokeratin_immunohistochemistry_staining_method_micrometastasis_indicator","factor",324,"Pearson's Chi-squared test",8.61E-04
"person_neoplasm_cancer_status","factor",284,"Pearson's Chi-squared test",7.95E-03
"breast_cancer_optical_measurement_histologic_type","factor",34,"Pearson's Chi-squared test",1.47E-02
"disease_surgical_margin_status","factor",82,"Pearson's Chi-squared test",3.70E-02

DNA methylation data

December 21st, 2011: 27k and 450k arrays are available. Downloaded Level 1 450k data. It seems that they started splitting green and red probes into 2 separate files.