DAC Accession Contact Person Email Access Information
EGAC00001000177 Lin Li lilin@genomics.cn http://www.ebi.ac.uk/ega/dacs/EGAC00001000177

This DAC controls 14 datasets:

Dataset Accessionsort descending Technology Samples Description
EGAD00001000975 Illumina HiSeq 2000; 130 65 prostate cancer cases transcriptome sequencing
EGAD00001000983 Illumina HiSeq 2000; 10 65 prostate cancer cases wgs sequencing
EGAD00001001004 Illumina HiSeq 2000; 130 65 prostate cancer cases wgs sequencing
EGAD00001001006 Illumina HiSeq 2000; 234 Dataset for whole exome sequencing of 113 pairs of tumor and normal DNA samples along with 8 cell lines.
EGAD00001001037 Illumina HiSeq 2000; 188 A total of 395 couples were subjected to IVF-PGD treatment, including 129 couples with NGS-based test and 266 couples with SNP array based test for the detection of embryonic chromosomal abnormalities. The NGS test was performed using low coverage whole genome sequencing with HiSeq 2000 platform. And the SNP array test was using Affymetrix Gene Chip Mapping Nsp I 262K. The average age of patients was 32.1 years (age range 20-44 years).
EGAD00001001397 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 72 We sequenced 292 patients who were suffering NSCLC with Whole genome sequencing or Exome sequencing method.
EGAD00001001398 Illumina Genome Analyzer II;, Illumina HiSeq 2000; 147 We sequenced 205 patients who were suffering NSCLC with Exome sequencing method.
EGAD00001001691 Illumina HiSeq 2000; 208 Esophageal cancer is one of the most aggressive cancers and the sixth leading cause of cancer death worldwide1. Approximately 70% of the global esophageal cancers occur in China and over 90% histopathological forms of this disease are esophageal squamous cell carcinoma (ESCC)2-3. Currently, there are limited clinical approaches for early diagnosis and treatment for ESCC, resulting in a 10% 5-year survival rate for the patients. Meanwhile, the full repertoire of genomic events leading to the pathogenesis of ESCC remains unclear. Here we show a comprehensive genomic analysis in 158 ESCC cases, as part of the International Cancer Genome Consortium (ICGC) Research Projects (http://icgc.org/icgc/cgp/72/371/1001734). We conducted whole-genome sequencing in 14 ESCC cases and whole-exome sequencing in 90 cases.
EGAD00001003278 Illumina HiSeq 4000;ILLUMINA 124 Whole Exome and Target Sequencing Data in 75 Samples from 5 Hepatocellular Carcinoma Patients. The sequencing was performed by Illumina HiSeq 4000. Background and aims: Intratumoral heterogeneity (ITH) challenges identifying mutations with target therapy potential whereas circulating cell-free DNAs (cfDNAs) could reflect nearly the entire mutation spectrum in given tumors. We investigated how to minimize the limit of ITH for profiling hepatocellular carcinoma (HCC).Methods: Thirty-two multi-regional HCC samples from five patients were subjected to whole exome sequencing (WES) and targeted deep sequencing (TDS). ITH extent was measured by the average percentage of non-ubiquitous mutations (present in parts of tumor regions). Matched cfDNAs were also analyzed by WES and TDS. Profiling efficiencies of single tumor specimen and cfDNA were compared and the one better depicted mutational landscape was selected to screen therapeutic targets.Results: We found variable extents of ITH in HCCs and observed branched and parallel evolution patterns. ITH level decreased at higher sequencing depth of TDS than that measured by WES (28.1% vs 34.9%, P < 0.01) but it remained unchanged upon additional samples analyzed. TDS of single tumor specimen detected an average of 70% the total mutations in HCC. Although more mutations were detected in cfDNA under TDS than WES, an average of 47.2% total HCC mutations uncovered by cfDNA suggested tissue outperform cfDNA and the latter may serve as alternative in profiling HCC genome. Consequently, TDS of single tumor tissue in 66 patients and cfDNAs in four unresectable HCCs identified 38.6% (26/66 and 1/4) patients bearing therapeutic targets.Conclusions: TDS of single tumor specimen could largely circumvent ITH to uncover mutations indicative of target therapy in HCC.
EGAD00001003304 Complete Genomics;COMPLETE_GENOMICS 38 We collected tumor samples and adjacent nomal mucosae from 46 patients with colorectal cancer in surgical operation from 2014 to 2016 in the First Affiliated Hospital of Chongqing Medical University (Chongqing, China) and the Research Institute of Surgery, Third Military Medical University (Chongqing, China). the qualified captured library of each sample was then loaded on Illumina HiSeq 2000 (Illumina, San Diego, CA) platforms and subjected to high-throughput sequencing.
EGAD00001003392 Illumina HiSeq 2000;ILLUMINA 102 High-coverage WGS sequencing of DNA samples from 214 GCs was performed on the Illumina HiSeq X Ten System.
EGAD00001003405 Illumina HiSeq 2000;ILLUMINA 46 High-coverage WGS sequencing of DNA samples from 214 GCs was performed on the Illumina HiSeq X Ten System.
EGAD00001003431 Illumina HiSeq 2000 (ILLUMINA) 88 High-coverage WGS sequencing of DNA samples from 214 GCs was performed on the Illumina HiSeq X Ten System.
EGAD00001003456 Illumina HiSeq 2000;ILLUMINA 80 There are 5WGS and 35WES sample pairs from the first affiliated hospital of kunming medical university, which belongs to ICGC projects COCA-CN.

DAC description