title: Illumina HiSeq 2500 paired end sequencing; Whole exome sequencing of human tumours and cell lines to investigate how ERBB2 and KRAS Alterations mediate response to EGFR inhibitors in early stage Gallbladder Cancer
design: Whole exome sequencing of human tumours and cell lines to investigate how ERBB2 and KRAS Alterations mediate response to EGFR inhibitors in early stage Gallbladder Cancer
library_name: AD0758_p
library_construction_protocol: A total of 27 fresh frozen samples (10 tumor-normal paired and 7 orphan tumors) were utilized for whole exome sequencing. An additional set of 27 FFPE samples were utilized as a validation set. Tumor-normal paired samples were collected at Tata Memorial Hospital and Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Mumbai. Sample set and (ACTREC-TMC) Internal Review Board (IRB) --IRB Project Number # 104-- approved study protocols. Formalin-fixed paraffin-embedded tissue blocks were collected from the tissue repository of Tata memorial hospital (TMH-TTR) in compliance with the guidelines. These tissues were examined for tumor content and the tumor content was in the range of 40-90%.  Genomic DNA was extracted from fresh frozen samples by using Qiagen Blood and Cell culture DNA kit. The extracted DNA yield and quality were assessed using Nanodrop ND2000 (Thermo scientific). The extracted DNA (about 1µg) from the fresh-frozen tissue specimens were sent to Genotypic Technology Pvt Ltd, Bangalore for exome sequencing. Genomic DNA from FFPE blocks was extracted using Qiagen QiAmp DNA FFPE Tissue kit as per manufacturer instructions. The extracted DNA yield and quality were assessed using Nanodrop ND2000 (Thermo scientific).  Exome capture and sequencing were performed as described previously 58. Briefly, Agilent Sure select in-solution (low-input capture-500ng) were used to capture ~62Mb region of human genome comprising of ~201,121 exons representing ~20,974 gene sequences, including 5'UTR, 3'UTR, microRNAs and other non-coding RNA.
attributes.tag: Experimental Factor: cell line
attributes.value: not applicable
attributes.tag: Experimental Factor: sampling site
attributes.value: neoplasm