Reads mapped to the MET gene locus after exome-capture-sequencing of a tumor-adjacent normal pancreas tissue
Genomic DNA was extracted from the blood and tumor samples using the E.Z.N.A. SQ DNA/RNA Protein Kit (Omega Bio-Tek, Norcross GA). Genomic DNA from matched normal and cancer tissue were then used for creating sequencing libraries. From each sample, we fragmented 4 µg of genomic DNA with a Covaris instrument (Covaris, Woburn MA). Illumina TruSeq Paired End libraries were constructed from double stranded fragmented DNA preparation per Illumina’s standard protocol (Illumina, San Diego CA). For exome capture hybridization, we used Nimblegen SeqCap version 2 enrichment assay (Roche-Nimblegen, Madison WI). The methods were according to the NimbleGen’s SeqCap EZ Exome Library SR User’s Guide v2.2. Sequencing libraries were run on a Illumina HiSeq 2000 with 100 base paired end reads and aligned with BWA. Using samtools the reads mapping to the MET gene locus were then extracted and are being reported here.