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WES data (cfTrack study) from NSCLC patients and OC patients

We also collected samples from 8 NSCLC patients and 4 ovarian cancer patients and. For all 8 NSCLC patients, a tumor biopsy sample, a WBC sample, and three plasma samples were collected. For all 4 ovarian cancer patients, a WBC sample and two serum samples were collected. We collected tumor tissue sample from one ovarian cancer patient (OV4). The cfDNA was extracted from their plasma samples using the QIAamp circulating nucleic acid kit from QIAGEN (Germantown, MD). For serum cfDNA, ampure XP beads size selection was further performed to eliminate gDNA contamination. In brief, 0.5 volume of beads were first added to the cfDNA samples. After incubation, the supernatant was transferred to a new tube and an additional 2.0 volume of beads were added. After 80% ethanol wash, cfDNA was eluted from the beads. FA assays (Agilent Technologies) were performed to rule out the contamination of gDNA in the size selected samples. The cfDNA WES library of all patients and the genomic DNA WES library of the 4 ovarian cancer patients were constructed with the SureSelect XT HS kit from Agilent Technologies (Santa Clara, CA) according to the manufacturer’s protocol. In brief, 10ng of cfDNA was used as input material. After end repair/dA-tailing of cfDNA, the adaptor was ligated. The ligation product was purified with Ampure XP beads (Beckman-Coulter, Atlanta, GA) and the adaptor-ligated library was amplified with index primer in 10-cycle PCR. The amplified library was purified again with Ampure XP beads, and the amount of amplified DNA was measured using the Qubit 1xdsDNA HS assay kit (ThermoFisher, Waltham, MA). 700-1000 ng of DNA sample was hybridized to the capture library and pulled down by streptavidin-coated beads. After washing the beads, the DNA library captured on the beads was re-amplified with 10-cycle PCR. The final libraries were purified by Ampure XP beads. The library concentration was measured by Qubit, and the quality was further examined with Agilent Bioanalyzer before the final step of 2x150bp paired-end sequencing at an average coverage of 200. Whole-exome capture libraries of genomic DNA from the 8 NSCLC patients were constructed via Roche SeqCap EZ Exome V6 (Roche). Enriched exome libraries were sequenced on the Illumina HiSeq 3000 platform (Illumina) to generate 2x100bp paired-end reads at an average coverage of 200.

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the data usage policy (cfTrack study) for WES data from NSCLC and OC patients

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
EGAS00001005906 Other
ID File Type Size Located in
EGAF00005758741 fastq.gz 7.5 GB
EGAF00005758742 fastq.gz 8.4 GB
EGAF00005758743 fastq.gz 8.2 GB
EGAF00005758744 fastq.gz 8.9 GB
EGAF00005758745 fastq.gz 5.7 GB
EGAF00005758746 fastq.gz 6.3 GB
EGAF00005758747 fastq.gz 10.1 GB
EGAF00005758748 fastq.gz 10.9 GB
EGAF00005758749 fastq.gz 8.5 GB
EGAF00005758750 fastq.gz 9.2 GB
EGAF00005758751 fastq.gz 7.5 GB
EGAF00005758752 fastq.gz 8.3 GB
EGAF00005758753 fastq.gz 6.6 GB
EGAF00005758754 fastq.gz 7.2 GB
EGAF00005758755 fastq.gz 7.8 GB
EGAF00005758756 fastq.gz 8.5 GB
EGAF00005758757 fastq.gz 9.1 GB
EGAF00005758758 fastq.gz 9.9 GB
EGAF00005758759 fastq.gz 6.0 GB
EGAF00005758760 fastq.gz 6.6 GB
EGAF00005758761 fastq.gz 7.9 GB
EGAF00005758762 fastq.gz 8.6 GB
EGAF00005758763 fastq.gz 7.4 GB
EGAF00005758764 fastq.gz 7.9 GB
EGAF00005758765 fastq.gz 6.6 GB
EGAF00005758766 fastq.gz 7.3 GB
EGAF00005758767 fastq.gz 7.7 GB
EGAF00005758768 fastq.gz 8.3 GB
EGAF00005758769 fastq.gz 7.6 GB
EGAF00005758770 fastq.gz 8.1 GB
EGAF00005758771 fastq.gz 9.7 GB
EGAF00005758772 fastq.gz 10.5 GB
EGAF00005758773 fastq.gz 8.6 GB
EGAF00005758774 fastq.gz 9.2 GB
EGAF00005758775 fastq.gz 8.1 GB
EGAF00005758776 fastq.gz 8.7 GB
EGAF00005758777 fastq.gz 6.8 GB
EGAF00005758778 fastq.gz 7.7 GB
EGAF00005758779 fastq.gz 7.9 GB
EGAF00005758780 fastq.gz 8.3 GB
EGAF00005758781 fastq.gz 8.0 GB
EGAF00005758782 fastq.gz 8.6 GB
EGAF00005758783 fastq.gz 7.8 GB
EGAF00005758784 fastq.gz 8.6 GB
EGAF00005758785 fastq.gz 4.6 GB
EGAF00005758786 fastq.gz 4.9 GB
EGAF00005758787 fastq.gz 4.8 GB
EGAF00005758788 fastq.gz 5.2 GB
EGAF00005758789 fastq.gz 4.7 GB
EGAF00005758790 fastq.gz 5.1 GB
EGAF00005758791 fastq.gz 7.2 GB
EGAF00005758792 fastq.gz 7.7 GB
EGAF00005758793 fastq.gz 7.8 GB
EGAF00005758794 fastq.gz 8.4 GB
EGAF00005758795 fastq.gz 7.2 GB
EGAF00005758796 fastq.gz 7.7 GB
EGAF00005758797 fastq.gz 2.7 GB
EGAF00005758798 fastq.gz 2.9 GB
EGAF00005758799 fastq.gz 12.0 GB
EGAF00005758800 fastq.gz 12.7 GB
EGAF00005758801 fastq.gz 15.0 GB
EGAF00005758802 fastq.gz 16.1 GB
EGAF00005758803 fastq.gz 8.3 GB
EGAF00005758804 fastq.gz 9.2 GB
EGAF00005758805 fastq.gz 7.0 GB
EGAF00005758806 fastq.gz 7.6 GB
EGAF00005758807 fastq.gz 6.9 GB
EGAF00005758808 fastq.gz 7.5 GB
EGAF00005758809 fastq.gz 8.5 GB
EGAF00005758810 fastq.gz 9.0 GB
EGAF00005758811 fastq.gz 7.5 GB
EGAF00005758812 fastq.gz 8.1 GB
EGAF00005758813 fastq.gz 7.6 GB
EGAF00005758814 fastq.gz 8.2 GB
EGAF00005758815 fastq.gz 6.6 GB
EGAF00005758816 fastq.gz 7.0 GB
EGAF00005758817 fastq.gz 11.9 GB
EGAF00005758818 fastq.gz 11.9 GB
EGAF00005758819 fastq.gz 6.0 GB
EGAF00005758820 fastq.gz 6.0 GB
EGAF00005758821 fastq.gz 9.3 GB
EGAF00005758822 fastq.gz 10.3 GB
EGAF00005758823 fastq.gz 5.9 GB
EGAF00005758824 fastq.gz 6.2 GB
EGAF00005758825 fastq.gz 12.1 GB
EGAF00005758826 fastq.gz 12.9 GB
EGAF00005758827 fastq.gz 8.5 GB
EGAF00005758828 fastq.gz 8.5 GB
EGAF00005758829 fastq.gz 6.3 GB
EGAF00005758830 fastq.gz 6.3 GB
EGAF00005758831 fastq.gz 12.0 GB
EGAF00005758832 fastq.gz 13.5 GB
EGAF00005758833 fastq.gz 8.4 GB
EGAF00005758834 fastq.gz 8.3 GB
EGAF00005758835 fastq.gz 10.1 GB
EGAF00005758836 fastq.gz 10.2 GB
EGAF00005758837 fastq.gz 6.7 GB
EGAF00005758838 fastq.gz 6.8 GB
EGAF00005758839 fastq.gz 8.5 GB
EGAF00005758840 fastq.gz 9.4 GB
EGAF00005758841 fastq.gz 7.4 GB
EGAF00005758842 fastq.gz 7.9 GB
EGAF00005758843 fastq.gz 5.3 GB
EGAF00005758844 fastq.gz 5.3 GB
EGAF00005758845 fastq.gz 8.2 GB
EGAF00005758846 fastq.gz 8.2 GB
106 Files (861.0 GB)