| DNA sequencing was performed with an MiSeq (Illumina Inc) sequencer at the Institute of Biomedical Sciences of |
| the School of Medicine of the University of Chile. Breast Cancer Patients were recruited from the Clinical |
| Hospital of the University of Chile and from Fundación Arturo López Pérez. DNA was extracted from blood samples |
| by Wizard Genomic DNA purification kit (Promega). DNA libraries were constructed with The TruSeq Amplicon Cancer |
| Panel (TSACP), following manufacturer's protocols. The produced library targeted 212 amplicons covering >35Kb of |
| target genomic sequence in 48 genes previously associated to Cancer. Sequencing was done with the Miseq reagent |
| kits v2, producing 2 x 150 bp reads. The average coverage was 4230x per sample. Reads were QC's with fastQC and |
| soft trimmed. Alignment to the genome hg19_lite genome was done with bwa (Smith-Waterman). Variant calling and |
| recalibration around INDELs was done with GATK. The workflow was managed with the Mutascope software. |