8213 results for "canc*"

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• Dataset_for_linked_WES_and_WGS_data_from_EGAS00001004813 which belong also to EGAS00001005537 for germline controls of rare cancers

  WES/WGS sequencing data of 37 germline runs, which were uploaded to umbrella studies. The sequencing was always paired. The WGS sequencing was on HiSeq X Ten using the Illumina TruSeq DNA Nano Kit. The WES Sequencing was on HiSeq4000 with Agilent Sureselect V5+UTR.

  Dataset EGAD00001010046

• Germline variants in patients with rare cancers - control samples WGS and WES

  The control samples (mostly blood) of 351 samples (paired WGS and WES sequencing) are in this dataset. The WGS was in nearly all cases at an Illumina HighSeq X Ten with the Illumina TruSeq Nano DNA Kit. The WES mostly on Illumina HighSeq 4000 with the Agilent SureSelect V5 plus UTRs Kit.

  Dataset EGAD00001010047

• BCG Molecular Subtyping

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

  Dataset EGAD00001010065

• 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

• FFPE, buffycoat and cell free DNA from N. German esophagus cancer patients - 2021

  28 patients. Cell-free DNA and leukocyte DNA, both from before any neoadjuvant treatment. Tumor FFPE tissue (plus metastasic tissue for some patients) from after any neoadjuvant treatment. Some cfDNA from follow-up time points (e.g. after neodj. treatment or in the clinical course). IDT xgen Pan-Cancer panel for hybridisation capture. Illumina TruSeq library prep for cfDNA and leukocyte DNA, Illumina DNA Prep for FFPE DNA. n=150 libraries in total.

  Dataset EGAD00001010081

• untargeted whole genome sequencing - Evaluation and correction of GC biases in cell-free DNA at the fragment level

  These are aligned paired-end reads from Illumina NovaSeq 6000 whole-genome sequencing of 4 cfDNA samples extracted from blood plasma (plasma-Seq). Three samples from patients with breast cancer, prostate cancer, or colorectal cancer and one sample from a healthy individual were aligned to GRCh38 (GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set). The observed GC bias is different in each of these cfDNA samples which leads to different average GC content per sample. This bias is corrected using the GCparagon commandline tool.

  Dataset EGAD00001010100

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

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

  Dataset EGAD00001010101

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

  198 exome sequencing samples

  Dataset EGAD00001009853

• Germline WES data of children with pathogenic mutations in cancer predisposing genes

  This data set includes bam files (aligned to hg38) from the germline of children who have pathogenic mutations in cancer predisposing genes

  Dataset EGAD00001009854

• 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

• Dynamics of sequence and structural cell-free DNA landscapes in small-cell lung cancer

  The dataset for the study “Dynamics of sequence and structural cell-free DNA landscapes in small-cell lung cancer” includes 171 bam files from targeted next-generation sequencing (TEC-Seq) from plasma cell-free DNA and matched white blood cell DNA from 33 individuals with small cell lung cancer, alongside 10 bam files from whole exome sequencing of tumor and matched normal DNA for 5 individuals with small cell lung cancer.

  Dataset EGAD00001009860

• Genomic profiling of subcutaneous patient derived xenograft models of solid childhood cancer

  The pediatric cancer cohort in this study included 70 PDX models from 65 different individuals. This cohort included a total of 16 different pediatric solid tumor subtypes, including fourteen Wilms tumors, thirteen hepatoblastomas, thirteen osteosarcomas, ten germ cell tumors, four neuroblastomas, three clear cell sarcomas, two adrenal cortical carcinomas, two leydig cell tumors, two medulloblastomas, one embryonal rhabdomyosarcoma (ERMS), one Ewing sarcoma, one pleomorphic sarcoma, one adenocarcinoma, one glioblastoma, one mesothelioma and one ovarian tumor. Notably, we have five samples with multiple PDX models from same patient, including two cases with duplicates (564 and 564-Dup, 1796 and 1796-Dup), one case with two different metastasis (560-SM, 560-LM), one case with two blocks from same tumor (1939 and 1939-Dup), and one case with different primary tumor from same patient (2264 and 1932). We have a total of 353 sequencing data, including 82 RNA sequencing data (RNA-seq), 138 whole-exome sequencing (WES) and 135 low-pass whole-genome sequencing (WGS). For RNA-seq data, we have 61 PDXs and 21 PTs; for WES, we have 67 PDXs, 30 PTs and 40 matched normal germlines; for WGS, we have 64 PDXs, 30 PTs and 40 matched normal germlines. Of which, 19 PT-PDX paired RNA-seq, 28 paired PT-PDX paired WES and WGS were included.

  Dataset EGAD00001009863

• Prostate cancer m6A epitranscriptome

  Using meRIP-sequencing, we profiled N-6 methyladenosine (m6A) in a cohort of 148 primary prostate cancer samples as part of the Canadian Prostate Cancer Genome Network project (CPC-GENE). Paired-end sequencing of 150 bp reads were mapped to GRCh38.p13 using annotations from gencode.v34.chr_patch_hapl_scaff.annotation.gtf. Peaks were called using MeTPeak, joint peaks were identified and IP reads were quantitated, normalized and adjusted using Input reads to obtain estimates of m6A abundance.

  Dataset EGAD00001009869

• GELATO clinical trial RNA-Seq data (primary tumors and local recurrences)

  RNA-Seq data of 10 lobular breast cancer primary tumors and 3 local recurrences obtained from 11 unique patients from GELATO clinical trial. The included raw transcriptome sequencing data in fastq format was generated using Illumina NovaSeq 6000 from archived FFPE material.

  Dataset EGAD00001009835

• Tumor/Normal WXS and RNASeq from patients dosed with neoTCR T-cell therapy

  Sixteen patients with refractory solid cancers received up to three distinct neoTCR-transgenic cell products, each expressing a patient-specific neoTCR, in a cell dose-escalation, first-in-human phase 1 clinical trial (NCT03970382). Included are the tumor and normal WXS and tumor RNAseq for dosed patients.

  Dataset EGAD00001009830

• GELATO clinical trial RNA-Seq data (metastatic lesions)

  RNA-Seq data of 46 matched lobular breast cancer metastatic samples obtained from 21 unique patients from GELATO clinical trial assayed at three timepoints: at baseline (directly after patient randomization), pre-atezolizumab (after induction treatment with carboplatin for two weeks) and on atezolizumab (after two cycles of atezolizumab combined with carboplatin). The included raw transcriptome sequencing data in fastq format was generated using Illumina NovaSeq 6000 from fresh frozen material.

  Dataset EGAD00001009834

• GELATO clinical trial whole exome sequencing data (primary tumors and local recurrences)

  Paired-end whole exome sequencing of 10 lobular breast cancer primary tumors, 3 local recurrences and matched normal samples obtained from 10 unique patients from the GELATO clinical trial. The included raw sequencing data in fastq format was generated using Illumina NovaSeq 6000 from archived FFPE material (tumor data) and fresh frozen material (matched normal data).

  Dataset EGAD00001009836

• 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

• 15 Healthy controls, 25 conlonrectal cancer patients without liver metastasis and 24 conlonrectal cancer patients with liver metastasis (target capture)

  15 Healthy controls, 25 conlonrectal cancer patients without liver metastasis and 24 conlonrectal cancer patients with liver metastasis (target capture)

  Dataset EGAD00001009838

• 18 plasma samples and their paired 18 urinary cfDNA samples without cancer

  18 plasma samples and their paired 18 urinary cfDNA samples without cancer

  Dataset EGAD00001009839

• whole genome sequence of liver cancer

  There are six samples with three blood samples and three organids

  Dataset EGAD00001009841

• ChIPseq sequence of liver cancer

  There are 61 samples

  Dataset EGAD00001009842

• 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

• Sequencing of longitudinal glioma pairs

  Clonal evolution drives cancer progression and therapeutic resistance. Recent studies revealed divergent longitudinal trajectories in gliomas, but early molecular traits steering post-treatment cancer evolution remain unclear. We analyzed sequencing data of 544 initial-recurrent adult diffuse glioma pairs to identify genomic and transcriptomic early predictors of tumor evolution in each molecular subtype.

  Dataset EGAD00001009845

• 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

• Sequencing data for the manuscript "Early on-treatment changes in circulating tumor DNA fraction and response to enzalutamide or abiraterone in metastatic castration-resistant prostate cancer"

  This submission contains gzipped fastq files from paired-end targeted sequencing.

  Dataset EGAD00001010105

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

  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. Whole-genome sequencing will be conducted on samples identified as promising from the initial targeted data. Results from this portion of the study will be compared to women who had breast cancer and those who are BRCA 1/2 carriers. This dataset contains all the data available for this study on 2023-03-08.

  Dataset EGAD00001010109

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

  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 subsequently be sent for whole-genome sequencing. Results from this portion 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 EGAD00001010110

• MutWP5: CRUK Mutographs of Cancer: BRCA Carriers (WG)(Novaseq)

  Sequencing of LCM-derived microbiopsies from 20 women who underwent risk-reducing reduction mastecomies due to germline BRCA1/2. 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 had cosmetic breast reduction surgeries and those with cancer. . This dataset contains all the data available for this study on 2023-03-08.

  Dataset EGAD00001010112

• MutWP5: CRUK Mutographs of Cancer: Lung: PD43291_Novaseq (WG)

  Sequencing of LCM-derived microbiopsies from explanted lung from COPD patient. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Deep sampling throughout multiple regions of the lung will determine whether there are differences in smoking-related mutaiton burden in different portions of the lung. Whole-genome sequencing will be conducted on samples identified as promising from the initial targeted data. Results from this poriton of the study will be compared to other individuals with smoking-related diseases (COPD, pulmonary fibrosis, lung cancer), and normal, non-smoking lungs. . This dataset contains all the data available for this study on 2023-03-08.

  Dataset EGAD00001010111

• 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

• MutWP5: CRUK Mutographs of Cancer: Cancer Mastectomy (WG)(Novaseq)

  Sequencing of LCM-derived microbiopsies from 40 women who underwent mastecomies due to breast cancer. LCM and sequencing will be conducted on both normal, unaffected breast, and, where possible, tumour tissue. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue, and compare findings between the normal and associated cancer tissues. Whole-genome sequencing will be conducted on samples identified as promising from the initial targeted data. Results from this poriton of the study will be compared to women who had cosmetic breast reduction surgeries and those who are BRCA carriers. . This dataset contains all the data available for this study on 2023-03-08.

  Dataset EGAD00001010114

• MutWP5: CRUK Mutographs of Cancer: BRCA Carriers (Exome)(Novaseq)

  Sequencing of LCM-derived microbiopsies from 20 women who underwent risk-reducing reduction mastecomies due to germline BRCA1/2. 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 had cosmetic breast reduction surgeries and those with cancer. . This dataset contains all the data available for this study on 2023-03-08.

  Dataset EGAD00001010115

• MutWP5: CRUK Mutographs of Cancer: Breast: Reduction Mammoplasty (Exome)(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 EGAD00001010116

• MutWP5: CRUK Mutographs of Cancer: Cancer Mastectomy (Exome)(Novaseq)

  Sequencing of LCM-derived microbiopsies from 40 women who underwent mastecomies due to breast cancer. LCM and sequencing will be conducted on both normal, unaffected breast, and, where possible, tumour tissue. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue, and compare findings between the normal and associated cancer tissues. Whole-genome sequencing will be conducted on samples identified as promising from the initial targeted data. Results from this poriton of the study will be compared to women who had cosmetic breast reduction surgeries and those who are BRCA carriers. . This dataset contains all the data available for this study on 2023-03-08.

  Dataset EGAD00001010117

• RNA sequencing data of 257 samples from the CORALLEEN trial

  Early-stage Luminal B breast cancer is frequent and is a major cause of breast cancer death due to its poor prognosis. Our proposal aims to study the biology behind the sensitivity and resistance of Luminal B breast cancer to chemotherapy (CHT) or a non-CHT regimen composed of hormone therapy in combination with ribociclib, a CDK4/6 inhibitor. To accomplish this, we first completed the SOLTI-1402 CORALLEEN phase II trial, a study where 106 patients with early-stage Luminal B breast cancer were randomized to standard neoadjuvant CHT for 6 months, or neoadjuvant letrozole and ribociclib for 6 months. After treatment, patients underwent surgery. The primary results of the study, which showed that the response rate to letrozole+ribociclib was similar to CHT, was reported (Prat et al; Lancet Oncol). Tumor biopsies were available at baseline, week 3 and surgery. A total of 257 samples were analyzed using the Illumina TruSeq Stranded Total RNA w/Ribo Zero Gold with MiSeq in TGL (Sequencer NovaSeq S4/PE/100x)

  Dataset EGAD00001010121

• Somatic mutation and clonal evolution normal breast tissue WGS

  Cancer is a genetic disease caused by an accumulation of mutations, however many of these mutations have been identified in pathologically normal tissue. We aim to use laser-capture microscopy (LCM) to sample individual clones from breast tissue to identify whether cancer-associated mutations appear in this normal tissue, assess the mutational burden present, and identify the mutational processes causing these mutations. We will sample from a wide age range of individuals (<20 to >70 years old) to determine whether these processes differ in pre- and post-menopausal women. We will also be comparing the tissue from healthy individuals (samples from breast reduction surgery) to those at elevated risk of breast cancer (mastectomy from BRCA1/2 patients) and those who have breast cancer (adjacent normal, distal normal, and tumour tissue from mastectomy). This will allow us to determine how these processes are different between these groups of individuals, and gain insight into the earliest stages of tumour development. . This dataset contains all the data available for this study on 2023-03-09.

  Dataset EGAD00001010123

• Breast cancer topographs

  Whole genome sequencing to identify subclonal variants for subsequent mapping back to fixed tissue specimens. . This dataset contains all the data available for this study on 2023-03-09.

  Dataset EGAD00001010124

• Genomics of acral lentiginous melanoma

  Melanoma is the most aggressive type of skin cancer, causing about 75% of dermatological cancer deaths. Acral lentiginous melanoma (ALM) is the most common subtype of melanoma in admixed Latin American populations, but very few tumour genomes and exomes, all from European-descent individuals, have been analysed across several studies. Because of this, the genomic landscape of ALM is mostly unknown. Our aim in this project is to define this landscape and identify driver somatic alterations by whole-exome sequencing a collection of ALM germline/tumour paired FFPE samples from the National Cancer Institute of Mexico. . This dataset contains all the data available for this study on 2023-03-09.

  Dataset EGAD00001010126

• patient-derived head and neck cancer organoids

  patient-derived head and neck cancer organoids

  Dataset EGAD00001010134

• WGS of high grade serous ovarian tumours and matched blood normals

  FASTQ reads for 34 matched tumour-normal WGS pairs for high grade serous ovarian cancer patients. Scottish HGSOC samples were collected via local Bioresource facilities at Edinburgh, Glasgow, Dundee and Aberdeen and stored in liquid Nitrogen until required. HGSOC patients were determined from pathology records and were included in the study where there was matched tumour and whole blood samples. Tumour samples were divided into two for DNA and RNA extraction and slivers of tissue were taken, fixed in formalin and embedded in paraffin wax (FFPE). Samples were only included if they were confirmed as HGSOC and there was greater than 40% tumour cellularity throughout the tumour, determined using H&sE staining of the FFPE sections and pathology review. Somatic DNA was extracted from the tumour and germline DNA was extracted from whole blood. Somatic DNA was extracted using the Qiagen DNeasy Blood and tissue kit (cat no 69504). The tissue was initially homogenised using a Qiagen Bioruptor, followed by the manufacturers recommended protocol (including RNase digestion step). Germline DNA was extracted from 1-3ml whole blood using the Qiagen FlexiGene kit (cat no 51206) following the manufacturers recommended protocol. The resulting DNA underwent quality control as follows: firstly, A260 and A280nm were measured on a Denovix DS-11 Fx to qualitatively illustrate A260/280nm and A260/230nm ratios as surrogate measures of DNA purity. A260/280 had to be 1.8 or greater and A260/230 had to be 2.0 or greater. Then, DNA was quantified using LifeTechnologies Qubit dsDNA BR kit (cat no Q32850) and we required a minimum of 50ul at 25ng/ul for WGS. Thirdly, DNA was diluted to 25ng/ul and a representative sample was loaded onto a 0.8% TAE gel, ran at 100v for 60mins and then imaged using a BioRad ChemiDoc imaging system to visualise the DNA quality.

  Dataset EGAD00001010135

• 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

• Differential methylation positions

  This dataset includes an analyzed DMP file that provide the information about differential methylation positions based on Illumina Infinium MethylationEPIC BeadChip. All samples (5 lung cancer cases vs. 5 benign lung disease controls) were obtained from bronchial washings at the site of the lesion under bronchoscopy manipulation. Of the five lung cancer cases, 3 are adenocarcinoma and 2 are squamous carcinoma.

  Dataset EGAD00001010147

• NCCS-NSCLC-ITH2-WES

  NCCS-NSCLC-ITH2 dataset of 185 sectors from 48 patients with early-stage non-small cell lung cancer diagnosed in National Cancer Centre Singapore; these are paired-end, whole-exome and bulk RNA sequencing data, sequenced by Illumina HiSeq 4000/2000.

  Dataset EGAD00001010158

• 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

• Ither2 WXS dataset - Implementation of pediatric precision oncology into clinical practice: The individualized Therapies for Children with cancer program “iTHER”

  iTHER is a prospective national precision oncology program aiming to define tumor molecular profiles in children and adolescents with primary very high-risk, relapsed, or refractory pediatric tumors in order to identify relevant aberrations to inform treatment.

  Dataset EGAD00001010178

• Ither2 RNA-Seq dataset - Implementation of pediatric precision oncology into clinical practice: The individualized Therapies for Children with cancer program “iTHER”

  iTHER is a prospective national precision oncology program aiming to define tumor molecular profiles in children and adolescents with primary very high-risk, relapsed, or refractory pediatric tumors in order to identify relevant aberrations to inform treatment.

  Dataset EGAD00001010179

• 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

• CRUK-ICGC Prostate DNA Methylation Sequencing Dataset (Prostatectomy Batches 1-6)

  This dataset includes Illumina EPIC Capture Sequencing Data of 376 samples from 188 men with prostate cancer. Samples were taken from primary tissue obtained at prostatectomy, with matched pathologically assessed non-cancer control material. This DNA methylation data includes donors and samples included in previously published WGS datasets (from CRUK-ICGC batches 1 to 3 [EGAD00001001116] and batches 4 to 6 [EGAD00001003225]; including the majority of donors used in Wedge et al, Nature Genetics 2018 [PMID: 29662167]). The targeted DNA methylation sequencing data in this EGA dataset were generated using the Illumina TruSeq methyl capture method (EPICseq), covering over 3.3 million CpGs in the human genome, representing a total targeted hybridisation capture panel of 107Mbp. According to the EPICseq protocol, DNA samples extracted from prostatectomy tissue samples were enriched for target regions using hybridisation capture, prior to bisulfite conversion, amplification and sequencing in pools of 12 samples (150 single end reads over two Illumina HiSeq4000 lanes). This approach generated DNA methylation profiles from prostate cancer and control samples at base-pair resolution across millions of CpGs in the human genome.

  Dataset EGAD00001010184

• RCRF release 1

  Transcriptome sequencing from the Rare Cancer Research Foundation: leiomyosarcoma, large cell neuroendocrine carcinoma, clear cell carcinoma

  Dataset EGAD00001010198

• RCRF release 1

  Rare Cancer Research Foundation: leiomyosarcoma, large cell neuroendorcrine carcinoma, clear cell carcinoma

  Dataset EGAD00001010199

• 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

• RNAseq of GEPARSIXTO

  294 formalin-fixed paraffin-embedded (FFPE) tissue samples were sent to the UNC Lineberger Comprehensive Cancer Center Translational Genomics Lab (TGL) for RNA isolation using the Maxwell 16 MDx Instrument (Promega AS3000) and the Maxwell 16 LEV RNA FFPE Kit (Promega AS1260) following the manufacturer’s protocol (Promega 9FB167). 279 total RNA sequencing libraries were prepared at TGL using a Bravo Automated Liquid-Handling Platform (Agilent G5562A) and the TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina 20020599) following the manufacturer’s protocol (Illumina 1000000040499). RNAseq library quality and quantity were measured using a TapeStation 4200 (Agilent G2991AA) and Qubit 3.0 fluorometer (Life Technologies Q33216), pooled at equal molar ratios, and denatured following the manufacturer’s protocol (Illumina 1000000106351). 271 total RNA sequencing libraries were sequenced at TGL on NovaSeq 6000 (Illumina 20012850) S4 flow cells (Illumina 20028313) following the manufacturer’s protocol (Illumina 1000000019358) using a 2x50 bp paired-end configuration and pool sizes of 91 libraries to target a read depth of 110 million clusters per library on average.

  Dataset EGAD00001010201

• Whole genome sequencing data of high-grade serous ovarian cancer samples (set 6)

  Whole genome sequencing data of 31 high-grade serous carcinoma (HGSC) patients (101 samples) sequenced with HiSeq X Ten and BGISEQ-500

  Dataset EGAD00001010202

• Spatial TCR sequencing in breast cancer

  Spatial characterization by TCR sequencing in tumor core and matched stroma in seven cases of triple negative breast cancer.

  Dataset EGAD00001010203

• lymphoma plasma cfRNA

  Dataset contains total RNA sequencing data from plasma of 65 different human donors: 30 diffuse large B-cell lymphoma (DLBCL) and 13 primary mediastinal large B-cell lymphoma (PMBCL) patients, and 22 cancer-free controls. Samples were sequenced on a NovaSeq 6000 and are provided in FASTQ format.

  Dataset EGAD00001010259

• Tumour evolvability metrics predict recurrence in advanced localised prostate cancer (tumour data)

  There is a need for quantitative measurements of evolutionary metrics in controlled clinical trials with long term follow-up information. This is particularly true in advanced localised prostate cancer, which can recur more than a decade after diagnosis. Here we mapped genomic intra-tumour heterogeneity in 642 tumour samples from 114 patients who took part in the IMRT and DELINEATE clinical trials, for which full clinical information and 12y median follow-up was available. We concomitantly assessed phenotypic (morphological) heterogeneity using Deep Learning in 1,923 histological sections from 250 IMRT patients (fully overlapping with the genetic set). This study shows that combining genomics with AI-aided histopathology in clinical trials leads to novel clinical biomarkers. This EGA repository contains data produced from tumour samples using low coverage whole genome sequencing and a prostate cancer specific gene panel data following compression of unique molecular identifiers.

  Dataset EGAD00001010274

• UCSF-CASCADE analysis of metastatic prostate cancer

  Targeted cancer therapy inevitably selects for tumor cells that harbor some form of therapy resistance. This phenomenon is a principle reason why advanced prostate cancer, which can be treated with agents targeting androgen signaling dependency and DNA repair failure, is a lethal condition. The influence of a patient's clinical history and disease evolution on how their disseminated tumors develop resistance has been difficulty to study, because few autopsy studies have been performed in heavily treated patients with DNA-repair deficient metastatic castration-resistant prostate cancer (mCRPC). Here, we assessed how resistance to targeted cancer therapies evolved in an autopsy cohort of 54 mCRPC tumors from six men. This dataset includes targeted sequencing, exome sequencing, and RNA-seq conducted on these biopsies.

  Dataset EGAD00001010275

• Evaluation of triple negative breast cancer with heterogeneous immune infiltration

  This dataset contains the raw RNA-seq data (FASTQ files) of the samples used in the study title: "Evaluation of triple negative breast cancer with heterogeneous immune infiltration". The dataset is composed of 3 patients with 6 samples per patient (3 with high TILs and 3 with low TILs).

  Dataset EGAD00001010280

• Bulk RNAseq of Neuroblastoma patient's tumors

  This dataset contains 9 bulk RNAseq of neuroblastoma patient's tumors used to compare with derived PDXs and/or single-cell data in the Thirant C et al, Nature Communications, 2023. They were intially produced for the Berlanga P., Cancer Discovery, 2022.

  Dataset EGAD00001010287

• Mutation analysis of 77 genes in cfDNA from metastatic CRC patients

  Aligned NGS data (BAM) of 77 frequently mutated genes in cancer using the AVENIO Expanded platform.

  Dataset EGAD00001010294

• Tumour evolvability metrics predict recurrence in advanced localised prostate cancer (normal data)

  There is a need for quantitative measurements of evolutionary metrics in controlled clinical trials with long term follow-up information. This is particularly true in advanced localised prostate cancer, which can recur more than a decade after diagnosis. Here we mapped genomic intra-tumour heterogeneity in 642 tumour samples from 114 patients who took part in the IMRT and DELINEATE clinical trials, for which full clinical information and 12y median follow-up was available. We concomitantly assessed phenotypic (morphological) heterogeneity using Deep Learning in 1,923 histological sections from 250 IMRT patients (fully overlapping with the genetic set). This study shows that combining genomics with AI-aided histopathology in clinical trials leads to novel clinical biomarkers. This EGA repository contains data produced from tumour samples using low coverage whole genome sequencing and a prostate cancer specific gene panel data following compression of unique molecular identifiers.

  Dataset EGAD00001010295

• 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

• Genome and transcriptome sequence data from a breast cancer patient

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

  Dataset EGAD00001010315

• Genomic data used in "ACT-Discover: identifying karyotype heterogeneity in pancreatic cancer evolution using ctDNA"

  Genomic data used in "ACT-Discover: identifying karyotype heterogeneity in pancreatic cancer evolution using ctDNA"

  Dataset EGAD00001010250

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

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

  Dataset EGAD00001010316

• Genome and transcriptome sequence data from a pancreatic ductal adenocarcinoma patient

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

  Dataset EGAD00001010317

• Genome and transcriptome sequence data from a pancreatic adenocarcinoma patient

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

  Dataset EGAD00001010318

• Processed bam files for the whole exome sequencing of primary lung adenocarcinoma samples

  We performed single cell RNA sequencing (scRNA-seq) for 208,506 cells derived from 58 lung adenocarcinomas from 44 patients, which covers primary tumour, lymph node and brain metastases, and pleural effusion in addition to normal lung tissues and lymph nodes. The extensive single cell profiles depicted a complex cellular atlas and dynamics during lung adenocarcinoma progression which includes cancer, stromal, and immune cells in the surrounding tumor microenvironments.

  Dataset EGAD00001010320

• IL1R1+ cancer-associated fibroblasts drive tumor development and immunosuppression in colorectal cancer

  180502: RNA-Sequencing data of cocultured matched CRC patient (P4) derived normal fibroblasts (NFs), cancer associated fibroblasts (CAFs) and tumor spheroids. 200503_coculture: RNA-Sequencing data of cocultured CRC patient derived normal fibroblasts (NFs) or cancer associated fibroblasts (CAFs) (P16, P19, P22, P32, P41, P42) and tumor spheroids (HT29). 200503_il1b: RNA-Sequencing data of IL-1β stimulated fibroblasts (NFs and CAFs) Cole: scRNA-sequencing of matched CRC tumour samples and normal tissue counterparts derived from 3 patients. 220501: RNA-Sequencing of FACS sorted IL1R1 high and IL1R1 low CT5.3 CAFs

  Dataset EGAD00001010322

• Whole exome and RNA sequencing data from urothelial bladder cancer patients treated with anti-PD-(L)1

  We have generated and analyzed genomic data from a cohort of metastatic urothelial carcinoma patients treated with ICI such as anti-PD-(L)1 monoclonal antibodies. The dataset contains whole exome sequencing data of 27 whole blood samples and 27 FFPE tumor samples. Further, it includes RNA sequencing data from 21 tumor samples. Following the RECIST criteria, 10 patients were classified as non-responders to the treatment, and 17 were responders. The dataset also contains a merged vcf file containing somatic mutations called by Strelka2 and Mutect2 following the gatk best practice pipeline.

  Dataset EGAD00001010324

• WGS short read and 10X linked read sequencing of HR Deficient breast cancers

  A set of tumor/normal paired sequencing experiments, performed in short read WGS and 10X linked read whole genomes. BAM files aligned to hg19 are provided. Sample Alias number and Subject ID reflects patient of origin. T/N distinction discriminates between tumor and normal (peripheral blood) tissue.

  Dataset EGAD00001010326

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

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

  Dataset EGAD00001016567

• Genome and transcriptome sequence data from a clear low grade adenocarcinoma of the lower rectum patient

  Genome and transcriptome sequence data from a clear low grade adenocarcinoma of the lower rectum patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016568

• Genome and transcriptome sequence data from a metastatic high grade small cell neuroendocrine ca nasal cavity patient

  Genome and transcriptome sequence data from a metastatic high grade small cell neuroendocrine ca nasal cavity patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016569

• 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 EGAD00001016570

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

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

  Dataset EGAD00001016571

• Genome and transcriptome sequence data from a mixed histology adenocarcinoma high grade neuroendocrine carcinoma of the ge junction patient

  Genome and transcriptome sequence data from a mixed histology adenocarcinoma high grade neuroendocrine carcinoma of the ge junction patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016572

• Genome and transcriptome sequence data from a peritoneal mesothelioma patient

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

  Dataset EGAD00001016573

• Genome and transcriptome sequence data from a angiosarcoma of right breast patient

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

  Dataset EGAD00001016574

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

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

  Dataset EGAD00001016575

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

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

  Dataset EGAD00001016576

• ICGC Prostate UK EPICSeq methylation sequencing data BAMs

  This dataset contains aligned BAM files generated from DNA methylation sequencing of prostate cancer and morphologically normal tissue samples from the ICGC Prostate UK cohort. Libraries were prepared using the Illumina TruSeq Methyl Capture EPIC (EPIC-Seq) assay and sequenced on the Illumina HiSeq 4000 platform. Sequence reads were aligned to the reference genome using Bismark v0.22.1.

  Dataset EGAD00001016579

• Dataset for Genomic and fragmentomic landscapes of cell-free DNA in aging and disease : MICA Morbidity Cohort

  This dataset contains 570 cram files from whole genome next-generation sequencing on the Illumina NovaSeq 6000 with 1-2x coverage. The samples analyzed include plasma samples from non-cancer patients from MICA cohort.

  Dataset EGAD00001016584

• Genome and transcriptome sequence data from a colon adenocarcinoma patient

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

  Dataset EGAD00001016602

• Genome and transcriptome sequence data from a metastatic chondrosarcoma patient

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

  Dataset EGAD00001016595

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

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

  Dataset EGAD00001016596

• Genome and transcriptome sequence data from a poorly differentiated gastric adenocarcinoma patient

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

  Dataset EGAD00001016597

• Genome and transcriptome sequence data from a gastric adenocarcinoma patient

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

  Dataset EGAD00001016598

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

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

  Dataset EGAD00001016599

• Genome and transcriptome sequence data from a metastatic low grade rectosigmoid adenocarcinoma patient

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

  Dataset EGAD00001016600

• Genome and transcriptome sequence data from a glioblastoma patient

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

  Dataset EGAD00001016601

• Genome and transcriptome sequence data from a malignant peripheral nerve sheath tumour patient

  Genome and transcriptome sequence data from a malignant peripheral nerve sheath tumour patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001016603

• Genome and transcriptome sequence data from a rectosigmoid adenocarcinoma patient

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

  Dataset EGAD00001016604

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

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

  Dataset EGAD00001016605

• Genome and transcriptome sequence data from a metastatic dedifferentiated liposarcoma patient

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

  Dataset EGAD00001016606

• Genome and transcriptome sequence data from a metastatic malignant melanoma patient

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

  Dataset EGAD00001016607

• Genome and transcriptome sequence data from a metastatic small bowel cancer patient

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

  Dataset EGAD00001016608

• Genome and transcriptome sequence data from a prostate adenocarcinoma, and small cell carcinoma of the prostate patient

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

  Dataset EGAD00001016609

• Genome and transcriptome sequence data from a metastatic goblet cell adenocarcinoma patient

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

  Dataset EGAD00001016610