7253 results for "canc*"

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• GELATO clinical trial whole exome sequencing data (metastatic lesions)

  Paired-end whole exome sequencing of 19 lobular breast cancer metastatic tumors and matched normal samples obtained from 19 unique patients from the GELATO clinical trial. The included raw sequencing data in fastq format was generated using Illumina NovaSeq 6000 from fresh frozen material.

  Dataset EGAD00001009837

• RNA sequencing

  RNAseq of 45 high-grade serous ovarian cancer tumour samples. Libraries were generated using the NEB Ultra II Directional RNA library Prep kit with polyA enrichment. Libraries were sequenced as paired-end 50 or 100bp on an Illumina NextSeq or NovaSeq.

  Dataset EGAD00001009844

• Mechanism of action and resistance to Trastuzumab Deruxtecan in patients with metastatic breast cancer: the DAISY trial

  198 exome sequencing samples

  Dataset EGAD00001009853

• FinHer Breast Cancer Study

  The purpose of this study is to sequence 500 known cancer genes in 960 newly diagnosed high risk breast cancer patients treated with current standard of care therapies and trastuzumab, for somatic alteration and copy number changes. We will be using next gen sequencing technology to determine the prognostic relevance of these somatic genetic alterations and of teh low frequency events to determine if they are associated with trastuzumab benefit or HER2 positive breast cancer, i.e. treatment interaction. The samples will be analysed adn correlated with clinical variables including outcome.

  Dataset EGAD00001000871

• RNA-Seq files for St. Jude Clinical Pilot

  This dataset contains whole genome sequencing BAM files for 78 tumor-normal pairs (a total of 156 samples) used in the St. Jude Clinical Pilot. Mapping was performed using BWA. This dataset accompanies the paper "Clinical Cancer Genomic Profiling by Three-Platform Sequencing of Whole Genome, Whole Exome and Transcriptome"

  Dataset EGAD00001004280

• Somatic cancer gene mutation screening

  Sequencing of colorectal tumors and normal tissue using Ion AmpliSeq Cancer Hotspot Panel V2

  Dataset EGAD00001001010

• Whole genome sequencing data of high-grade serous ovarian cancer samples (set 3)

  Whole genome sequencing data of 9 high-grade serous carcinoma (HGSC) patients (55 samples) sequenced with HiSeq X Ten.

  Dataset EGAD00001009888

• WGS of peripheral blood leukocytes from patients with Li-Fraumeni syndrome

  We performed whole genome sequencing on 84 LFS family members from 47 families: 22 with wildtype TP53 and 62 with variant TP53. The variant TP53 cohort consists of 49 individuals who developed cancer and 13 individuals who remain cancer-free; 34 were from 13 families with 2-4 individuals sequenced within a given family and the remaining 28 had no family members sequenced. The wildtype cohort consists of 14 individuals who developed cancer and 8 individuals who are cancer-free, from 6 families.

  Dataset EGAD00001010200

• Genome and transcriptome sequence data from a primary unknown- upper GI or pulmonary patient

  Genome and transcriptome sequence data from a primary unknown- upper GI or pulmonary patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001005827

• RNAseq of breast cancer bone metastases PDX treated to IACS

  Fastq files from RNAseq of breast cancer bone metastases PDX of tumor HBC-124 treated by IACS-010759 (4 samples) or not (4 samples).

  Dataset EGAD00001009857

• Highly differentiated, fusion-negative rhabdomyosarcoma.

  Sequencing was performed using OncoPanel v.2 (OPv2), an Agilent SureSelect custom designed bait set consisting of the coding regions of 504 genes, previously linked to human cancer. Sequencing wa sperformed on an Illumina HiSeq 2500. 8 highly differentiated, fusion-negative rhabdomyosarcoma tumor samples were sequenced. BAM files are available for download.

  Dataset EGAD00001003887

• Genome and transcriptome sequence data from a neuroendocrine tumor (GIC) patient

  Genome and transcriptome sequence data from a neuroendocrine tumor (GIC) patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001005866

• Genome and transcriptome sequence data from a pancreatic cancer patient

  Genome and transcriptome sequence data from a pancreatic cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001005868

• PELICAN45 RNAseq Dataset

  RNAseq in cryostat-microdissected metastatic and primary prostate cancer tissues and matched noncancerous tissues from the same study subjects.

  Dataset EGAD00001009997

• Genome and transcriptome sequence data from a transformed diffuse large B cell lymphoma patient

  Genome and transcriptome sequence data from a transformed diffuse large B cell lymphoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001005869

• Genome and transcriptome sequence data from a cervical squamous cell carcinoma patient

  Genome and transcriptome sequence data from a cervical squamous cell carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001005872

• Enhanced Detection of Landmark Minimal Residual Disease in Lung Cancer using Cell-Free DNA Fragmentomics

  The circulating tumor DNA (ctDNA) mutation-based approach shows limited performance in minimal residual disease (MRD) detection, especially for landmark MRD detection at an early-stage cancer after surgery. Here, A total of 87 NSCLC patients, who received curative surgical resections (23 patients relapsed during follow-up), enrolled in this study. A total of 163 plasma samples, collected at 7 days and 6 months postsurgical, were used for high-throughput sequencing.

  Dataset EGAD00001010300

• Whole genome sequencing data of high-grade serous ovarian cancer samples (set 4)

  Whole genome sequencing data of 7 high-grade serous carcinoma (HGSC) patients (32 samples) sequenced with HiSeq X Ten.

  Dataset EGAD00001010066

• Dataset for "Genomic landscape of oral cancers" (CGI WGS)

  Dataset for "Genomic landscape of oral cancers" (CGI WGS)

  Dataset EGAD00001004339

• TGL49 LFS CHARM panel

  Targeted panel sequencing of hereditary cancer syndrome-associated genes (TP53, BRCA1, BRCA2, PALB2, MLH1, MSH2, MSH6, PMS2, EPCAM, and APC) in plasma and buffy coat samples from patients with Li-Fraumeni syndrome.

  Dataset EGAD00001010011

• Integrative genome profiling in AML

  AML emerges as a consequence of accumulating independent genetic aberrations that direct regulation and/or dysfunction of genes resulting in aberrant activation of signalling pathways, resistance to apoptosis and uncontrolled proliferation. Given the significant heterogeneity of AML genomes, AML patients demonstrate a highly variable response rate and poor median survival in response to current chemotherapy regimens. For the past 4 years we have conducted gene expression profiling on purified bone marrow populations equating to normal haematopoietic stem and progenitor cells from healthy subjects and patients with de novo AML in order to identify AML signatures of aberrantly expressed genes in cancer versus normal. We are now applying a series of bioinformatic methodologies combined with clinical and conventional diagnostic data to establish novel genomics strategies for improved prognostication of AML. Additionally, we use our AML signatures to unravel oncogenic signalling pathway activities in AML patients and test inhibitory drugs for these pathways inn preclinical therapeutic programmes. We consider that superimposing GEP and clinical data for our AML patient cohort with additional data on their mutational status will significantly improve the prognostic power of the study as well as unravel yet unknown mutations associated with aberrant signalling activities of oncogenic pathways.

  Dataset EGAD00001001873

• Treated and control Patient Derived Xenografts of colorectal cancer (CRC) samples

  Bank of treateed and control PDXs metastastic colorectal cancer sample RNAseq

  Dataset EGAD00001010022

• WGS of HSPC clones of healthy individual sequenced with Illumina NovaSeq 6000

  Dataset contains WGS sequecing data from clonally expanded hematopoietic stem cells from 7 individual pediatric cancer patients. Samples were taken before (DX - diagnosis) or Follow-up (DX2/REM/FU - Diagnosis 2, remission or follow-up, respectively). In addtion, cord blood clones (Designated CB) treated with X-ray radiation, Cisplatin, Maphosphamide, Vincristine and Doxorubicin and untreated cord blood hematopoietic stem/progenitor cells were have been whole-genome sequenced. (Abbreviations RAD, CISPL, MAPH, VINC, DOX and CTRL, respectively)

  Dataset EGAD00001007078

• Tracking early lung cancer metastatic dissemination in TRACERx using ctDNA dataset

  Whole-exome sequencing of tumour regions and deep targeted sequencing of plasma samples.

  Dataset EGAD00001010031

• Genome and transcriptome sequence data from a metastatic breast cancer patient

  Genome and transcriptome sequence data from a metastatic breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004703

• Genome and transcriptome sequence data from a metastatic breast carcinoma patient

  Genome and transcriptome sequence data from a metastatic breast carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004671

• Genome and transcriptome sequence data from a neuroendocrine carcinoma patient

  Genome and transcriptome sequence data from a neuroendocrine carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004664

• Genome and transcriptome sequence data from a metastatic rectal adenocarcinoma patient

  Genome and transcriptome sequence data from a metastatic rectal adenocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004685

• CCMA-RNA

  This dataset has the raw RNA sequencing data for the cancer models in CCMA.

  Dataset EGAD00001010034

• A case of colorectal cancer with ERBB2 c.2264T>C (p.Leu755Ser) mutation

  This data set contains next generation sequencing (NGS) data of two serial tumor samples (primary and a metastasis) from a patient with colorectal cancer showing an ERBB2 c.2264T>C (p.Leu755Ser). NGS was performed using the Illumina TruSeq Amplicon Cancer Panel (TSACP, Illumina) covering 212 amplicons in 48 cancer associated genes on the Illumina MiSeq sequencing platform. The dataset contains two BAM files.

  Dataset EGAD00001002252

• Trimmed bam-files from whole genome sequencing data from plasma DNA

  Single-end sequencing data (trimmed to 60bp) of 104 plasma samples from donors without tumors (male=50; female=54) were merged and used to establish coverage profiles around the TSS and to establish a gene expression prediction algorithm. Dataset includes merged alignements of low coverage whole genome sequencing from plasma DNA from 50 male, 54 female non-cancer donors. Furthermore, 2 patients with metastasized breast cancer were sequenced on a NextSeq with higher depth.

  Dataset EGAD00001002254

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0020_002

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0020_002 for Triple negative breast cancer patient-derived xenograft SA604X8XB02164

  Dataset EGAD00001011254

• CCMA-WGSraw

  This dataset has the mapped bam files from WGS for the cancer models in CCMA.

  Dataset EGAD00001010035

• Whole-exome sequencing data from head and neck cancer patients

  This dataset contains paired-end whole-exome sequencing data (2x50 bp) from the normal samples, the primary tumors and the recurrences/metastases of 8 head and neck cancer patients.

  Dataset EGAD00001011278

• Detection of human brain cancers using genomic and immune cell characterization of cerebrospinal fluid through CSF-BAM

  Detection of human brain cancers using genomic and immune cell characterization of cerebrospinal fluid through CSF-BAM

  Dataset EGAD00001015645

• The molecular landscape of colorectal cancer reveals genetic mutations（17 cases）

  We collected tumor samples and adjacent nomal mucosae from 17 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.

  Dataset EGAD00001003224

• Genomic Sequencing of Triple Negative Breast Cancer - Exome data

  Exome data for study EGAS00001008261

  Dataset EGAD00001015687

• Molecular analysis of cancer genomes in children with Lynch syndrome: exploring causal associations WXS

  Molecular analysis of cancer genomes in children with Lynch syndrome: exploring causal associations WXS

  Dataset EGAD00001010043

• Prostate WGS data (late onset)

  Whole genome sequencing for 12 late onset prostate cancer tumor/control pairs (ICGC)

  Dataset EGAD00001003290

• oncogenic gene fusions in primary colon cancers

  This dataset represents RNA-sequencing data from 278 primary colon cancers obtained from fresh-frozen tumor sections. RNA-sequencing was performed using TruSeq library preparation and samples were sequenced on Illumina NextSeq and HiSeq. The data are available as Illumina NextSeq and HiSeq fastq files (_R1.fastq and _R2.fastq for each tumor sample, 556 files in total).

  Dataset EGAD00001003291

• Illumina_WXS_T

  Whole-exome sequencing on Illumina HiSeq2000/2500 of colorectal cancer primary tumor sample

  Dataset EGAD00001002099

• Genome and transcriptome sequence data from a metastatic adenoid cystic carcinoma patient

  Genome and transcriptome sequence data from a metastatic adenoid cystic carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001003679

• Plasma methylome of metastatic prostate cancer

  The dataset contains plasma DNA methylation data derived from metastatic prostate cancer patients.

  Dataset EGAD00001005433

• BCG Molecular Subtyping

  Dataset for the paper: Non-muscle Invasive Bladder Cancer Molecular Subtypes Predict Differential Response to Intravesical Bacillus Calmette-Guérin

  Dataset EGAD00001010065

• Somatic copy-number alterations in plasma circulating tumor DNA from advanced EGFR-mutated lung adenocarcinoma patients

  This is the raw data obtained from shallow whole-genome sequencing of plasma DNA (plasma-seq) for calling of somatic copy number alterations as well as focal amplifications from patients with lung cancer.

  Dataset EGAD00001007505

• Genome and transcriptome sequence data from a metastatic large cell neuroendocrine carcinoma likely of lung origin patient

  Genome and transcriptome sequence data from a metastatic large cell neuroendocrine carcinoma likely of lung origin patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001010979

• OT2_Illumina_WGS_T_XEN

  Whole-genome sequencing on Illumina HiSeq2000/2500 of Patient-derived xenograft derived from colorectal cancer primary tumor sample (OT2_cohort)

  Dataset EGAD00001003376

• Whole genome and Whole exome sequencing of patient-derived xenograft models of endometrial cancer

  Whole genome and Whole exome sequencing of patient-derived xenograft models of endometrial cancer

  Dataset EGAD00001008326

• RNAseq analysis on primary sites Colorectal Cancer xenografts (PRX) samples

  Bank of primary sites (PRs) colorectal cancer of Patient Derived Xenografts (PDXs)

  Dataset EGAD00001010101

• MutWP5: CRUK Mutographs of Cancer: Breast: Reduction Mammoplasty (WG)(Novaseq)

  Sequencing of LCM-derived microbiopsies from 10 women who underwent reduction mammoplasty. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Exome data will be used as a driver and clonality screen, highly clonal or driver-containing samples will subsequenctly be sent for whole-genome sequencing. Results from this poriton of the study will be compared to women who are BRCA1/2 germline carriers and those with cancer. . This dataset contains all the data available for this study on 2023-03-08.

  Dataset EGAD00001010113

• Genome and transcriptome sequence data from a squamous cell carcinoma of the alveolar ridge patient

  Genome and transcriptome sequence data from a squamous cell carcinoma of the alveolar ridge patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004934

• OT2_Illumina_WGS_MET

  Whole-genome sequencing on Illumina HiSeq2000/2500 of colorectal cancer metastasis sample (OT2_cohort)

  Dataset EGAD00001003372

• OT2_Illumina_WXS_MET

  Whole-exome sequencing on Illumina HiSeq2000/2500 of colorectal cancer metastasis sample (OT2_cohort)

  Dataset EGAD00001003379

• Recurrent DNMT3B gene rearrangements are associated with unfavorable outcome in dicentric (9;20)-positive pediatric BCP-ALL

  We provide clinical data sets of Array CGH, targeted RNA-seq, total RNA-seq, whole genome bisulfite (WGBS) and whole genome DNA sequencing (WGS) obtained from bone marrow (BM) or peripheral blood (PB) mononuclear cells of 57 pediatric patients with dicentric chromosome dic(9;20) positive Acute lymphocytic leukemia (ALL), from which in 6 cases DNMT3B gene rearrangement was identified. This data is complemented by total RNA-seq and WGBS of samples from 4 additional ALL patients with a t(12;21) translocation and ETV6-RUNX1 gene fusion. DNA was isolated from BM or PB B-lymphocytes using Qiagen QIAamp DNA Blood Midi Kit to perform i) Array CGH of 58 dic(9;20) positive samples by hybridizing 500ng DNA using a Agilent 400K SurePrint G3 Custom CGH Human Genome Microarray (e-Array design 84704) ii) WGBS of 6 DNMT3B rearrangement positive samples and 4 ETV6-RUNX1 positive samples using Tecan TrueMethyl oxBS-Seq module for library preparation and Illumina NovaSeq 6000 platform to run 2x151 cycles iii) WGS of DNMT3B rearrangement positive samples using Illumina Lotus DNA Library Prep Kit followed by sequencing running 2x160 cycles on an Illumina NovaSeq 6000 platform. RNA was isolated from PB B-lymphocytes using the PerkinElmer Chemagic 360 instrument, followed by i) targeted RNA-seq of 56 dic(9;20) positive samples prepared using Illumina TruSight RNA Pan-Cancer Panel and sequenced on an Illumina MiSeq platform running 2x75 cycles ii) total RNA-seq of 6 DNMT3B rearrangement positive samples and 4 ETV6-RUNX1 positive samples utilizing TruSeq Stranded Total RNA Library Prep Gold kit and running 2x100 cycles on an Illumina NovaSeq 6000 platform.

  Dataset EGAD00001011122

• RBWES

  Retinoblastoma is a rare childhood cancer of the retina. We studied retinoblastoma by Whole-Exome-Sequencing.

  Dataset EGAD00001007591

• 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

• 10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0150_001

  10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0150_001 for Triple negative breast cancer sample SA609X5XB03230

  Dataset EGAD00001011212

• Genome and transcriptome sequence data from a metastatic serous ovarian cancer patient

  Genome and transcriptome sequence data from a metastatic serous ovarian cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001003609

• Genome and transcriptome sequence data from a metastatic rectal adenocarcinoma patient

  Genome and transcriptome sequence data from a metastatic rectal adenocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001003623

• Neoantigen Immunogenicity Landscapes and Evolution of Tumor Ecosystems During Immunotherapy with Nivolumab

  We performed Whole Exome (WXS) and RNASeq sequencing on samples obtained from the same site before and during therapy from our prospective clinical trial (CA209-153, NCT02066636) of nivolumab in advanced Non-small cell lung cancer (NSCLC) patients that progressed on chemotherapy. There are 58 pre and 42 on therapy WXS samples and 24 pre and 12 on therapy RNASeq samples. All WXS tumor samples have matching normal samples.

  Dataset EGAD00001011302

• Genome and transcriptome sequence data from a salivary duct carcinoma patient

  Genome and transcriptome sequence data from a salivary duct carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001003627

• Genome and transcriptome sequence data from a metastatic colorectal carcinoma patient

  Genome and transcriptome sequence data from a metastatic colorectal carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001003620

• Genome and transcriptome sequence data from a non-small cell lung cancer patient

  Genome and transcriptome sequence data from a non-small cell lung cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001003682

• Genome and transcriptome sequence data from a metastatic high grade sarcomatous neoplasm nos patient

  Genome and transcriptome sequence data from a metastatic high grade sarcomatous neoplasm nos patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001003683

• Genome and transcriptome sequence data from a cervical cancer patient

  Genome and transcriptome sequence data from a cervical cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001010947

• Genome and transcriptome sequence data from a metastatic breast carcinoma patient

  Genome and transcriptome sequence data from a metastatic breast carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001003684

• Genome and transcriptome sequence data from a locally advanced right breast cancer patient

  Genome and transcriptome sequence data from a locally advanced right breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001003698

• Genome and transcriptome sequence data from a metastatic myoepithelial carcinoma of parotid patient

  Genome and transcriptome sequence data from a metastatic myoepithelial carcinoma of parotid patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001003701

• Genome and transcriptome sequence data from a low-grade serous ovarian cancer patient

  Genome and transcriptome sequence data from a low-grade serous ovarian cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001003713

• Genome and transcriptome sequence data from a metastatic breast carcinoma patient

  Genome and transcriptome sequence data from a metastatic breast carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001003714

• Genome and transcriptome sequence data from a metastatic pancreatic cancer patient

  Genome and transcriptome sequence data from a metastatic pancreatic cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001003718

• Genome and transcriptome sequence data from a metastatic adenocarcinoma of the rectosigmoid patient

  Genome and transcriptome sequence data from a metastatic adenocarcinoma of the rectosigmoid patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001003725

• Genome and transcriptome sequence data from a metastatic breast cancer patient

  Genome and transcriptome sequence data from a metastatic breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001003732

• Genome and transcriptome sequence data from a large-cell neuroendocrine lung cancer patient

  Genome and transcriptome sequence data from a large-cell neuroendocrine lung cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001003726

• Exome sequencing and RNAseq data

  Whole Exome Sequencing of 9 Colorectal Cancer (CRC) samples performed on Illumina HiSeq4000 consisting of aligned paired reads. RNAseq data sequenced on Illumina NextSeq500 consisting of FASTQ single reads from 3 CRC colon samples. A total of 12 samples from five patients (we matched normal tissue or pbmc and tumors) were sequenced on Illumina NextSeq500.

  Dataset EGAD00001003788

• Three large nuclear families in which a single child per family was diagnosed with cancer

  We collected saliva samples from three nuclear families having 4, 5, and 7 children, respectively. One child in each nfamily had been diagnosed with a pediatric tumor, and neither parent had been diagnosed with cancer. Diagnoses included Wilms tumor, low-grade astrocytoma, and Burkitt’s lymphoma, respectively. We used whole-genome sequencing to profile normal cells from each family member and a linked-read technology.

  Dataset EGAD00001007709

• Genome and transcriptome sequence data from a metastatic breast cancer patient

  Genome and transcriptome sequence data from a metastatic breast cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001003070

• Whole exome sequencing of pdx models of 2 patients with metastatic colorectal cancer

  Paired fastq files ( 12 pairs, WES) of EGFR treated and untreated PDX models of mCRCs of 2 patiens sequenced on Illumina HiSeq 2000, the enrichment kit was Agilent SureSelect V5+UTRs.

  Dataset EGAD00001007713

• Genome and transcriptome sequence data from a metastatic pancreatic carcinoma patient

  Genome and transcriptome sequence data from a metastatic pancreatic carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001002647

• Genome and transcriptome sequence data from an ovarian adenocarcinoma patient

  Genome and transcriptome sequence data from an ovarian adenocarcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001003036

• Genome and transcriptome sequence data from a non-small cell lung carcinoma patient

  Genome and transcriptome sequence data from a non-small cell lung carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001001966

• Single cell RNA sequencing of colorectal cancer with diverse tissue dissociation protocols or fresh vs. frozen cell preparations.

  To evaluate 3 different tissue dissociation protocols or fresh vs. frozen cell preparations, we performed single-cell RNA sequencing on cancer or distant normal tissue dissociates from 2 colorectal cancer patients. Total 18,409 cells from 10 sample preparations were analyzed (5 primary colorectal cancer and 5 matched normal mucosa). The results suggest highly consistent cellular proportions were recovered with different sample preparation methods.

  Dataset EGAD00001005191

• Computational approach to discriminate human and mouse sequences in patient-derived tumour xenografts

  Whole Exome Sequencing was performed in a dilution series containing known amounts of human and mouse DNA, 3x 100% human 0% mouse, 2x 90/10, 3x 50/50, 2x 25/75 and 3x 0/100. A set of breast cancer clinical samples, matched normal tissue and matched PDTXs (total number = 14) were also analysed. Paired-end 75bp sequences for the dilution series and paired-end 125bp for the clinical samples were obtained on Illumina HiSeq2500; fastq files are provided. A triplicate analysis of the transcriptome using RNA-seq was also performed for the Universal Human RNA Reference and the Universal Mouse RNA Reference samples. Paired-end 150bp fastq files obtained on Illumina HiSeq4000 are provided.

  Dataset EGAD00001003800

• Common early-life exposure of the colorectal epithelium to the microbiome-derived mutagen colibactin

  Colibactin is a mutagen produced by bacterial strains in the colorectal microbiomes of some healthy people. It generates somatic mutations characterised by the mutational signatures SBS88 and ID18 in normal human colorectal epithelial cells in vivo. Increasing prevalence of colibactin mutagenesis during the 20th century is hypothesised to have caused recent international increases in early-onset colorectal cancer incidence. Here, we establish the early-life prevalence, timing, mutation burdens and distribution through the colon of colibactin mutagenesis by sequencing normal colorectal epithelial cell genomes to detect SBS88 and ID18 in children and adolescents from the UK and Denmark biopsied between 2016 and 2024. Colibactin mutagenesis was found in ~40% individuals. It starts soon after birth and often ceases by age five years, although some children show longer exposures. Mutation burdens are higher in the left than right colon and show substantial variation between exposed individuals, in some causing >100-fold increases in total mutation loads compared to unexposed children of the same age. Therefore, colorectal mutagenesis by colibactin is currently common in some populations, occurs during early childhood and can produce markedly elevated somatic mutation burdens. The future public health implications of this widespread mutagen exposure will depend on clarification of its role in colorectal cancer causation.

  Dataset EGAD00001015830

• MultiOMICS study of a pair of infant monozygotic twins with concordant B-cell ALL (WGS)

  B-cell acute lymphoblastic leukemia (B-cell ALL) is the most common cancer in childhood. Studying identical twins with B-cell ALL provides a unique and tractable model for deciphering the developmental timing of pre- and post-natal mutations contributing to clonal evolution. To date, this has mainly focused on major cytogenetic subgroups of childhood B-cell ALL, including MLL fusions, ETV6-RUNX1, hyperdiploidy, and BCR-ABL1. However, formal demonstration of the prenatal origin and “backtracking” the natural history of the leukemia remains understudied in “B-other”/Normal Karyotype (NK) B-cell ALL. To characterize the genetic landscape of this particular leukemia subtype, we performed whole genome DNA- and B-cell receptor (BCR)- on a pair of 8-month-old monozygotic twins diagnosed with concordant “B-other”/NK B-cell ALL.

  Dataset EGAD00001005017

• sWGS data of Pap test smears and tumor tissues

  Shallow whole-genome sequencing data divided into three groups: - sWGS data from Pap smears of patients with confirmed high grade serous ovarian cancer - sWGS data from matched tumor tissue (at diagnosis) from the same patients - sWGS data from Pap tests smears of healthy women

  Dataset EGAD00001010141

• Genome and transcriptome sequence data from a metastatic colon cancer patient

  Genome and transcriptome sequence data from a metastatic colon cancer patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004607

• BC WGS Dataset 4

  Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells

  Dataset EGAD00001001353

• Latency and interval therapy affect the evolution in metastatic colorectal cancer

  The cohort of 15 patients included ten patients with available tissue from the primary tumor and ≥1 metastatic site, four patients with pairs of metastases only, and one patient with an anastomotic recurrence five years after initial resection of the primary tumor

  Dataset EGAD00001005226

• Genome and transcriptome sequence data from a metastatic breast carcinoma patient

  Genome and transcriptome sequence data from a metastatic breast carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001004688

• Somatic L1 retrotransposition in normal colorectal epthelium

  Throughout an individual’s lifetime, genomic alterations accumulate in somatic cells. However, the mutational landscape induced by retrotransposition of long interspersed nuclear element-1 (L1), a widespread mobile element in the human genome, is poorly understood in normal cells. Here, we explored the whole-genome sequences of 406 normal colorectal clones, 12 MUTYH-associated adenomatous clones, and 19 matched colorectal cancer tissues. In addition, we analyzed promoter DNA methylation status of retrotransposition-competent L1 (in 139 clones) and read-through RNA expression profiles (in 116 clones) to investigate the epigenetic regulation of L1 activity.

  Dataset EGAD00001010183

• RRBS sequencing data of ovarian cancer, breast cancer, control tissues, and white blood cell DNA.

  The dataset comprises 8 breast cancer, 11 ovarian cancer, 1 benign tumour, 18 normal tissue, 2 endometrium, and 23 white blood cell samples. Genome wide methylation analysis was performed by Reduced Representation Bisulfite Sequencing (RRBS) on Illumina HiSeq 2500. Data is provided as FASTQ files

  Dataset EGAD00001003822

• Single-cell profiling of neoantigen-specific T cells in lung cancers treated with neoadjuvant PD-1 blockade

  This dataset includes 406 samples from non small cell lung cancer patients treated with neoadjuvant anti-PD-1. The Single Cell 5’ V(D)J and 5’ DGE kits (10X Genomics) were used to capture immune repertoire information and gene expression from the same cell in an emulsion-based protocol at the single cell level. Libraries were generated and sequenced on an Illumina NovaSeq instrument using 2x150bp paired end sequencing.

  Dataset EGAD00001007728

• DNA methylation sequencing profiles of 1538 breast tumors and 244 normal breast tissues

  DNA methylation sequencing profiles of 1538 breast tumors and 244 normal breast tissues. Libraries were prepared using a custom Reduced Representation Bisulfite Sequencing pipeline. Sequencing was performed on the Illumina HiSeq 2500 (v4 chemistry), with single-end reads of 125 bp length. Multiplexing was conducted at the level of 8 samples per lane. FASTQ files are provided for 1538 breast tumors and 244 normal breast tissues. Reference: Batra et al. (2021). DNA methylation landscapes of 1538 breast cancers reveal a replication-linked clock, epigenomic instability and cis-regulation.

  Dataset EGAD00001007976

• WES and RNA-seq data of 11 cancer patients with multiple cancer types

  This dataset includes WES and RNAseq from 11 patients with metastatic melanoma, lung, kidney, and stomach cancers, enrolled in phase I clinical trials of TIL ACT (NCT03475134 & NCT04643574). WES was performed on matched cancer and healthy samples, whereas RNAseq was performed on cancer tissues, using Illumina HiSeq 2500/4000 and Illumina NextSeq 550 systems. Paired-end reads are provided in fastq format.

  Dataset EGAD00001010169

• NKI-AvL CRC-OVC scTCR RNA-seq

  The dataset “NKI-AvL CRC-OVC scTCR RNA-seq" includes 368 BAM files from paired-end RNA sequencing on Illumina MiSeq for 2 colorectal cancer and 2 ovarian cancer patients.

  Dataset EGAD00001004342

• Germline whole exome sequencing in testicular cancer

  This dataset contains variant call format files generated from whole exome sequencing of germline DNA from indiviudals with diagnosed with testicualr germ cell cancer.

  Dataset EGAD00001004345

• Whole Exome Sequencing

  The Whole Exome Sequencing dataset contains 30 whole exome sequencing files (tumor, germ line DNA) and phenotype metadata for 15 patients on the phase II clinical trial of neoadjuvant immune checkpoint blockade in high-risk resectable melanoma at MD Anderson Cancer Center (NCT02519322). Included are data from baseline samples.

  Dataset EGAD00001004352

• Xenograft BC WGS Dataset

  We propose to definitively characterise the somatic genetics of breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

  Dataset EGAD00001001336

• 71 Whole-exome sequencing of Esophageal Squamous Cell Carcinoma on Chinese Patients

  Esophageal Squamous Cell Carcinoma (ESCC) is one of the deadliest cancers worldwide. We performed 71 Whole-exome sequencing of Esophageal Squamous Cell Carcinoma on Chinese Patients.

  Dataset EGAD00001001926