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Pipeline publication

[…] according to the manufacturer’s instructions. DNA quality was assessed by spectrophotometry with absorbance at 230, 260 and 280 nm. DNA was quantified using a fluorimetric assay with a Qubit device., Two-hundred nanogram of genomic DNA from normal and cancer cells were fragmented with a Covaris device to obtain fragments around 180-200 bp. Then, libraries were constructed and captured by using SureSelect Human All Exon v5 kit (Agilent), following the manufacturer’s protocol. Paired-end (2 × 151 bases) sequencing was performed on a NextSeq500 device (Illumina). Obtained sequences were aligned and annotated with the human Hg19 genome based on the SureSelect Human All Exon v5 manifest by using Burrows-Wheeler Aligne (BWA) and Genome Analysis toolkit (GATK) algorithms. Only sequences with a read depth of 10 × and a mutation allele frequency superior to 5% were conserved for the analysis. The analysis is fostered on 137 clinically relevant genes related to biological pathways linked to cancer predisposition or available targeted therapies (Supplementary Table 1). Copy number variations were studied by using Control-FREEC software as described[,]., A 58-year-old Caucasian male initially presented with abdominal pain. A CT scan, carried out in June 2011, revealed a metastatic sigmoid cancer with the following metastatic locations: mediastinal and lomboartic lymph nodes, lungs. A lymph node biopsy was performed and the diagnosis of wild-type KRAS, NRAS and BRAF, moderately differentiated Lieberkühn adenocarcinoma was made. From 2011 to 2015, the patient received different chemotherapeutic regimens. In July 2015, the patient’s lung metastases progressed and he started to show symptoms such as breathlessness and a permanent dry cough. As no approved chemotherapy or targeted therapy could be proposed […]

Pipeline specifications

Software tools BWA, GATK, Control-FREEC
Organisms Homo sapiens, Mus musculus
Chemicals Ribonucleotides, Nucleotides, Polynucleotides