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• BLUEPRINT release August 2015, ChIP-Seq for CD8-positive, alpha-beta T cell, on genome GRCh38

  ChIP-Seq data for 5 CD8-positive, alpha-beta T cell sample(s). 26 run(s), 26 experiment(s), 26 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820

  Dataset EGAD00001001513

• Genome-wide cell-free DNA termini in patients with cancer

  The structure, fragmentation patterns and terminal sequences of cell-free DNA (cfDNA) are altered by nucleases and biological mechanisms in the blood of cancer patients. The cfDNA fragment-end composition recovered from low coverage WGS (<1 fold coverage) using a bespoke software (FrEIA) is aberrant in the plasma from cancer patient (n = 418, 655 samples) compared to controls (n = 117). As a standalone test FrEIA allows detection down to ~0.2% tumor fraction in vitro and in silico at 95% specificity, leading to a sensitivity of ~71% for detecting lung cancer (14/22 stage I-II, 27/38 stage III, 92/127 stage IV) and ~68% for detecting esophageal adenocarcinoma (26/44 stage II, 46/62 stage III). Additional cfDNA biological patterns can be combined with FrEIA increasing the diagnostic potential of low coverage WGS at minimal cost (mean AUROC = 0.96). Integrating multiple cfDNA biological signal augments the diagnostic performance of liquid biopsy.

  Study EGAS00001006142

• Chemotherapy induces myeloid-driven spatial T-cell exhaustion in ovarian cancer

  Gene expression profiles of single cells from 26 chemo-naïve and IDS tumor tissue and ascites samples from 17 HGSC patients

  Study EGAS50000000607

• Non-coding mutations reveal cancer driver cistromes in luminal breast cancer

  A dataset of ER+PR+ breast tumor samples that were analyzed in order to identify mutation enrichment in cis-regulatory elements and cistrome. The repository includes sequencing data from 88 patients. 26/88 were sequenced using ATAC-seq

  Dataset EGAD00001007650

• WGS Fastq files from the CPC-Gene project in support of PRAD-CA, DCC Release 26

  PRAD-CA, DCC Release 26 : This dataset contains fastq files with Whole genome sequencing data for the CPC-Gene Project. Data from each sample was generated using multiple whole genome libraries and sequenced across multiple runs

  Dataset EGAD00001003706

• Detection of cancers three years prior to diagnosis using plasma cell-free DNA

  A major goal of early cancer detection is to identify subclinical disease when the tumor burden is low, so that treatments are more effective. But how early can cancers be detected prior to clinical signs or symptoms? This question can be answered only through the evaluation of participants whose clinical course has not been altered by the study itself. We here describe such an evaluation, performed on prospectively collected plasma samples from the Atherosclerosis Risk in Communities (ARIC) study, including 26 participants diagnosed with cancer and 26 matched controls. At the index time point, eight of these 52 participants scored positively with a multicancer early detection (MCED) blood test. All eight of these participants were diagnosed with cancer within 4 months after blood collection. In six of these 8 participants, we were able to assess an earlier plasma sample collected 3.1 to 3.5 years prior to clinical diagnosis. In four of these six participants, the same mutations detected by the MCED test could be identified, but at 8.6 to 79-fold lower levels. These results demonstrate that it is possible to detect circulating tumor DNA (ctDNA) more than three years prior to clinical diagnosis, and provide benchmark sensitivities required for the success of ctDNA-based tests for this purpose.

  Study EGAS00001008068

• Sequencing files for "Transcriptional Mechanisms of Resistance to Anti-PD-1 Therapy"

  Files from whole exome sequencing of 26 tumors and two matched normals from one melanoma patient. The 26 tumors include the untreated primary, cutaneous metastases and distant metastases to internal organs.

  Dataset EGAD00001003200

• Clonal somatic copy number altered driver events inform drug sensitivity in high-grade serous ovarian cancer.

  This dataset consists of shallow whole genome sequencing data and amplicon sequencing data for 26 ovarian cancer patients (21 high-grade serous ovarian cancer, 4 low-grade serous ovarian cancer and 1 clear cell ovarian cancer). The data are provided as single end FASTQ files for the shallow whole genome sequencing data (31 libraries) and paired end FASTQ files for the amplicon sequencing data (98 libraries).

  Dataset EGAD00001008716

• PYDP Papuan Y chromosome Diversity Panel

  The PYDP dataset includes 26 bam files of Y chromosome sequences for Papua New Guinean individuals from different locations, extracted from whole genome sequences. DNA was extrated from saliva samples (Oragen kit). Sequencing libraries were prepared using the TruSeq DNA PCR-Free HT kit. 150 bp paired-end sequencing was performed on the Illumina HiSeq X5 sequencer.

  Dataset EGAD00001008572

• Long-read and short-read isoform sequencing in breast cancer

  The goal of this project was to perform long-read RNA sequencing (LR-seq, PacBio) in combination with short-read RNA-seq for systematic characterization of the isoform diversity in primary breast tumor samples. We sequenced the full-length transcriptomes of 26 breast tumors and 4 normal breast samples.

  Study EGAS00001004819