title: HiSeq X Ten paired end sequencing; Whole exome sequencing of Lung Squamous Carcinoma Patients of Indian Origin
design: Whole exome sequencing of Lung Squamous Carcinoma Patients of Indian Origin
library_construction_protocol: Tumor samples from 20 lung squamous carcinoma patients were procured retrospectively from the tumor tissue repository at the Tata Memorial Hospital (TMH), Mumbai during the year 2011-2016. All the tumor tissues were stored as formalin fixed paraffin embedded (FFPE) blocks. The sample cohort and the study protocols were approved by Institutional Review Board and Ethics Committee of Tata Memorial Centre-ACTREC. Genomic DNA extraction from FFPE tumor blocks was performed according to standard protocol of QIAmp DNA FFPE Tissue Kit. DNA concentration and quality was assessed using Qubit 3.0 fluorometer and Tape Station respectively.  Whole exome sequencing was performed on 20 lung squamous carcinoma DNA samples using a minimum of 100ng input DNA (based on Qubit quantification) for library preparation. Exome capture was performed using the SureSelect Human All Exon V6 (target size 60Mb) as per manufacturer's instructions..