2. dataset.csv bc_terms_results.RData - bcterm$term204[ ] bc-variable.csv (Scraped i2b2 query) bc_qa2.Rmd bc_qa_txform.R bcread_api_key.R bc_fetch.Rmd (Extracts db files) bc_fetch.Rmd (Extracts db files) bc-data-files/*.db dataset.R ‘KUMC’ bc_qa_p1.RPres bc_excl.Rmd (QA for 1 site) bc_excl.Rmd (QA for 1 site) bc_excl_all.Rmd (QA for all sites) bc_excl_all.Rmd (QA for all sites) bc_qa_txform.R bc_excl_all_results.RData - site.survey.sample.size$KUMC - site.survey.sample.size$MCRF bc_fetch_results.Rdata bc_excl_KUMC.html Breast Cancer Master Diagram

3. bc_excl.Rmd (QA for 1 site) bc_excl.Rmd (QA for 1 site) bc_excl_KUMC.html dataset.csv bc_terms_results.RData - bcterm$term204[ ] bc-data-files/*.db dataset.R ‘KUMC’ dataset[ ] – Describes REDCap file tumor.site[ ] – translated enctr-level with.var => tumor.site[P#,E#, Var1, Var2...] sample.size[ ] – pt-level eligibility flags bc_qa_txform.R builder.summary(conn.site)  variable pt, enc & fact cnts check.cases(tumor.site)  survey.sample count.cases  survey.sample.size survey.sample[ ] tumor.site[ ] survey.sample.size[ ] Eligibility

4. GPC Sites KUMC IOWA REDCap

5. BC Expanded Datamart Adds to implemented set of TR variables (v=42) 71 Add’l TR Variables 8 Add’l EMR Variables (~100 Concept Facts) Sites run new query, identified and filter for consented pts

6. Exclusion Criteria used by bc_excl ## Analytic Dataset: Tumors, Inclusion Criteria Data of Dx –0390-Date of Diagnosis If NULL then use ‘Primary Site’, 0400-Primary Site If NULL then use ‘Seer Site Breast’ Exclusion Criteria - Male - <18 yrs - If only tumor morphology was lobular carcinoma in situ? –‘Morphology’==8520/2 Stage 4 –AJCC or SS2000==7

7. bc_random_sample (Generates sampling file for 1 site) bc_random_sample (Generates sampling file for 1 site) bc_qa_txform.R bc_terms_results.RData - bcterm$term204[ ] dataset.R ‘KUMC’ survey.sample[ ] tumor.site[ ] bc.exclusions(conn.site) check.cases tumor.site IN survey.sample randomized.pts.selected[ ]