Evolution and clinical impact of genetic epistasis within EGFR-mutant lung cancers: multi-timepoint exome sequencing of a single patient's disease
This dataset is a time-series of EGFR-mutant NSCLC clinical specimens from an individual patient profiled using tumor-based whole exome sequencing and the data is in BAM format. DNA was extracted from FFPE for primary tumor and frozen tumor tissue samples and matched non-tumor tissue using the Qiagen Allprep DNA/RNA Mini Kit. The library preparation protocol was based on the Agilent SureSelect Library Prep and Capture System. DNA was resuspended in a low TE buffer and sheared (Duty Cycle 5%; Intensity 175; Cycles/Burst: 200; Time: 300s, Corvaris S2 Utrasonicator). Bar-coded exome libraries were prepared using the Agilent Sure Select V5 library kit per manfucaturer’s specifications. The libraries were run on the HiSeq2500. Raw paired end reads (100bp) in FastQ format generated by the Illumina pipeline were aligned to the full hg19 genomic assembly obtained from USCS, gencode 14, using bwa version 0.7.12. Picard tools version 1.117 was used to sort, remove duplicate reads and generate QC statistics. Tumor DNA was sequenced to median depth of 303X (range 114.39-383.41) and the matched germline DNA to average depth of 231.65.
- 02/10/2017
- 8 samples
- DAC: EGAC00001000711
- Technology: Illumina HiSeq 2500
UCSF Bivona lab data access policy.
The primary purpose of this study is to accelerate efforts to elucidate mechanisms of resistance to EGFR TKI treatment. The group anticipates that data generated from the project will be used by others interested in the pathogenesis of NSCLC and understanding mechanisms of resistance and is happy to provide the data for such purposes.
Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.
Study ID | Study Title | Study Type |
---|---|---|
EGAS00001002604 | Other |
This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.
ID | File Type | Size | Located in | |
---|---|---|---|---|
EGAF00001766226 | bam | 12.9 GB | ||
EGAF00001766227 | bam | 16.2 GB | ||
EGAF00001766228 | bam | 15.9 GB | ||
EGAF00001766229 | bam | 9.8 GB | ||
EGAF00001766230 | bam | 17.0 GB | ||
EGAF00001766231 | bam | 20.7 GB | ||
EGAF00001766232 | bam | 17.3 GB | ||
EGAF00001766233 | bam | 18.1 GB | ||
8 Files (128.1 GB) |