Table S1. Number of patients for breast cancer subtype in the TCGA dataset according to IHC status. Sample sizes of the initial dataset, and for samples that were able to be included at each stage (mutation burden calling, neoepitope load estimation, and then gene expression analysis), are reported for each of the three breast cancer subtype categories (ER/PR(+)HER-2(â), HER-2(+), TNBC) (PDF 56 kb
The Cancer Genome Atlas (TCGA) and Molecular Taxonomy of Breast Cancer International Consortium (MET...
Table S1. Gene membership of the immune cell type metagenes and the immune function metagenes. (XLSX...
Table S5. Contains allele sets tested and associated epitope counts from analysis on overlap of epit...
Table S3. Number of neoepitopes predicted for HLA class I alleles in all the breast cancer samples a...
Table S2. Patient and tumor characteristics. Demographic data for patients and clinical measurements...
Figure S5. Expressed neoepitopes (FPKM≥5) in subtypes of breast cancer. The range of expressed neoep...
Figure S1. Frequently mutated genes in TCGA breast cancer data. Here we show the mo for: (A) ER/PR(+...
Figure S11. Kaplan-Meier estimates based on mutation burden and neoepitope load. KS curves of (A) di...
Figure S3. Correlation of number of potential binding neoepitopes with number of nonsynonymous mutat...
Figure S8. Distribution of neoepitopes binding to HLA class I alleles in the three subtypes of breas...
Figure S6. Correlation of number of potential binding neoepitopes with number of expressed (FPKM≥2) ...
Figure S10. Kaplan-Meier estimates by neoepitope load. KM curves of (A) disease-free survival and (B...
Figure S7. Expression analysis for the high affinity neoepitopes (FPKM ≥2). (A) The number of the ex...
Figure S2. Comparison of mutations called by the current protocol versus cBioportal ( http://www.cbi...
Figure S4. Length of potential binding neoepitopes in breast cancer. The number of potential binding...
The Cancer Genome Atlas (TCGA) and Molecular Taxonomy of Breast Cancer International Consortium (MET...
Table S1. Gene membership of the immune cell type metagenes and the immune function metagenes. (XLSX...
Table S5. Contains allele sets tested and associated epitope counts from analysis on overlap of epit...
Table S3. Number of neoepitopes predicted for HLA class I alleles in all the breast cancer samples a...
Table S2. Patient and tumor characteristics. Demographic data for patients and clinical measurements...
Figure S5. Expressed neoepitopes (FPKM≥5) in subtypes of breast cancer. The range of expressed neoep...
Figure S1. Frequently mutated genes in TCGA breast cancer data. Here we show the mo for: (A) ER/PR(+...
Figure S11. Kaplan-Meier estimates based on mutation burden and neoepitope load. KS curves of (A) di...
Figure S3. Correlation of number of potential binding neoepitopes with number of nonsynonymous mutat...
Figure S8. Distribution of neoepitopes binding to HLA class I alleles in the three subtypes of breas...
Figure S6. Correlation of number of potential binding neoepitopes with number of expressed (FPKM≥2) ...
Figure S10. Kaplan-Meier estimates by neoepitope load. KM curves of (A) disease-free survival and (B...
Figure S7. Expression analysis for the high affinity neoepitopes (FPKM ≥2). (A) The number of the ex...
Figure S2. Comparison of mutations called by the current protocol versus cBioportal ( http://www.cbi...
Figure S4. Length of potential binding neoepitopes in breast cancer. The number of potential binding...
The Cancer Genome Atlas (TCGA) and Molecular Taxonomy of Breast Cancer International Consortium (MET...
Table S1. Gene membership of the immune cell type metagenes and the immune function metagenes. (XLSX...
Table S5. Contains allele sets tested and associated epitope counts from analysis on overlap of epit...