Additional file 2: of Identification of missing variants by combining multiple analytic pipelines

Table S2. The composition of Tier 1, 2 and 3 variants in BWA-unique, Novo-unique and shared variants. (DOCX 13 kb

Additional file 4: of Identification of missing variants by combining multiple analytic pipelines

Table S4. The genomic location and GC content of multi-unique, single-unique and shared variants. (DOCX 14 kb

Additional file 3: of Identification of missing variants by combining multiple analytic pipelines

Table S3. The percentage of known and novel variants in BWA-unique, Novo-unique and shared variants. (DOCX 13 kb

Additional file 5: of Identification of missing variants by combining multiple analytic pipelines

Table S5. The composition of Tier 1, 2 and 3 variants in multi-unique, single-unique and shared variants. (DOCX 14 kb

Additional file 6: of Identification of missing variants by combining multiple analytic pipelines

Table S6. The percentage of known and novel variants in multi-unique, single-unique and shared variants. (DOCX 13 kb

Additional file 7: of Identification of missing variants by combining multiple analytic pipelines

Table S7. The full list of variants identified in APP, PSEN1 and PSEN2 by each workflow. (XLSX 14 kb

Additional file 1: of Identification of missing variants by combining multiple analytic pipelines

Table S1. The genomic location and GC content of BWA-unique, Novo-unique and shared variants. (DOCX 14 kb

Additional file 1: Figure S1. of Establishing and characterizing patient-derived xenografts using pre-chemotherapy percutaneous biopsy and post-chemotherapy surgical samples from a prospective neoadjuvant breast cancer study

Characterization and utilization of PDX models generated from both pretreatment biopsies and surgical samples in the BEAUTY study. Figure S2. Representative immunohistochemistry shows the change of subtype from luminal B to triple negative. The histology is depicted using H&E staining and the expression of ER, PR, HER2, and Ki-67 is compared between the representative PDX (passage 2) and the corresponding human tumor (M06). Figure S3. Immunohistochemistry shows different subtypes for xenografts derived from the same original patient tumor. The representative PDX tumors at passage 2, and corresponding human tumor (M14) are shown. Figure S4. In vivo taxane response for the other six PDX models tested. Passage 4 tumors were used for the drug tests. (PDF 4901 kb