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Method Detail
Submitter Method Handle: GENOMED
Submitter Method ID: MYSEQ_UDTSEQ_CL1
Submitted method description:
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.

This method was used in the following submission:

Submitter Handle Batch Type Submitter batch id Release build id
GENOMED Assay UDTseq_CL1 146

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