7073 results for "canc*"

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• Whole genome sequencing data of high-grade serous ovarian cancer samples (set 0)

  Whole genome sequencing data of 5 High-grade serous carcinoma (HGSC) patients (6 samples) sequenced with BGI.

  Dataset EGAD00001009738

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

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

  Dataset EGAD00001004925

• 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

• Single cell RNA sequencing of tumor and ascites in high grade ovarian cancer

  Fastq files for single cell RNA sequencing of cells from ovarian cancer tumor and ascites (10X chromium 5' v1.1 libraries). Multiple cases are pooled in each sequencing library.

  Dataset EGAD00001006627

• RNA-seq study of a Princess Margaret Cancer Centre human acute myeloid leukemia patient cohort

  The PMCC AML RNAseq dataset consists of 81 AML patient samples (clinical data in Supplemental Table 11 of manuscript), processed in two batches. These patient samples are able to engraft in the NSG (NOD.Cg PrkdcscidIl2rgtm1Wjl /SzJ) mouse model. Five patients (90543, 598, 90240, 110484, 100500) were included in both batches. Viaably frozen material from the Leukemia Tissue Bank at Princess Margaret Cancer Centre/ University Health Network were thawed by dropwise addition of X-VIVO + 50% fetal calf serum supplemented with DNase (100μg/mL final concentration, Roche). RNA was extracted from bulk peripheral blood mononuclear cells (PBMC) using the RNeasy Micro Kit (Qiagen Inc.). A paired-end 76 base-pair flow-cell lane Illumina High seq 2000 yielded an average of 240 million sequence reads aligning to genome per sample at the Genome Sciences Centre, BC Cancer Agency for cohort 1. Cohort 2 was subjected to 125 bp, paired-end RNA-sequencing on the Illumina HiSeq 2500 with an average of 50 million reads/sample at the Centre for Applied Genomics, Sick Kids Hospital.

  Dataset EGAD00001006576

• Normal sample for patient SA668

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA668

  Dataset EGAD00001009254

• sWGS of core biopsies from localized breast cancer patients

  Paired end shallow whole genome sequencing (sWGS) data for the identification of genomewide somatic copy number alterations (SCNA) and the estimation of tumor fractions.

  Dataset EGAD00001008397

• Transcriptomic intra-tumor heterogeneity of colorectal cancer evaluated by RNA sequencing of multi-regional biopsies

  RNA sequencing of a total of 41 tumor biopsies taken from a total of 14 patients with colorectal cancer. Ribosomal RNA was removed using the Ribo-Zero Gold rRNA Removal Kit (Illumina, CA, USA) and Paired-end sequencing were performed using ScriptSeq v2 RNA-seq Library preparation Kit (Illumina). Data processing of the paired raw sequence reads was performed using TopHat2, with mapping to the human reference genome HG19. Forty-one BAM files with reads mapping the the human reference genome (HG19) is enclosed.

  Dataset EGAD00001006636

• High-throughput sequencing data for study of molecular drivers of resistance to castration in localised prostate cancer

  Aligned whole-genome sequencing and RNA-seq of localised prostate cancer for study 'Loss of SNAI2 in prostate cancer correlates with clinical response to androgen deprivation therapy'.

  Dataset EGAD00001006640

• Colorectal cancer samples WES

  The whole exome was sequenced in two cancer-affected members (II:1 and III:1) of the family. The family subject of this study showed an autosomal dominant mode of CRC inheritance, fulfilling the Amsterdam I clinical criteria with three CRCs in two consecutive generations. The exome capture was performed using SureSelectXT Human All Exon V3 (51Mb, Agilent Technologies), and the library was sequenced on an Illumina HiSeq 2000 platform with paired-end reads of 101bp and a 50x average coverage depth.

  Dataset EGAD00001009170

• Combinatorial CRISPR screen identifies fitness effects of paralogues FAM50A and FAM50B

  Genetic redundancy has evolved as a way for human cells to survive the loss of genes that are single copy and essential in other organisms, but also allows tumours to survive despite having highly rearranged genomes. In this study we CRISPR screen 1,191 gene pairs, including paralogues and known and predicted synthetic lethal interactions to identify 105 gene combinations whose co-disruption results in a loss of cellular fitness. 27 pairs influence fitness across multiple cell lines including the paralogues FAM50A/FAM50B, two genes of unknown function. Silencing of FAM50B occurs across a range of tumour types and in this context disruption of FAM50A reduces cellular fitness whilst promoting micronucleus formation and extensive perturbation of transcriptional programmes. This dataset includes CRISPR screening of cancer cell lines, RNA sequencing studies of cancer cell lines and also data from the sequencing of tumour xenografts collected from mice.

  Dataset EGAD00001006648

• RRBS analysis to characterize the epigenomic conservation between species in the context of Aging and Cancer.

  This dataset contains Raw Reduced Representation DNA bisulfite-sequencing data obtained from human brain samples corresponding to 3 Young and 3 Old individuals (aging context), and 3 normal and 3 Glioblastoma samples (tumor context). RRBS libraries were prepared at Diagenode SA and samples were sequenced using the Illumina Novaseq6000 sequencing platform.The accompanying samples from this study (mouse tissues) are located at the ENA database under the accession number PRJEB41460.

  Dataset EGAD00001006650

• UROMOL 2020 - RNA-seq data

  For this project about non-muscle invasive bladder cancer (NMIBC), we analysed total RNA-seq data from 535 patients. Sequencing of total RNA was performed using ScriptSeq-v2 RNA-Seq Library Preparation Kit (Illumina) and KAPA RNA HyperPrep Kit with RiboErase HMR (Roche). RNA input was 500 ng for both kits. The dataset is composed of 1,596 fastq files.

  Dataset EGAD00001006656

• Normal sample for patient SA214

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA214

  Dataset EGAD00001009547

• Whole genome sequencing

  Whole genome sequencing of high-grade serous ovarian cancer (HGSC) tumours and matched normals from 15 patients with homologous recombination deficiencies. The dataset includes fastq files from 56 HGSC tumours (1 primary, 1 relapse, 54 end-stage) and 15 matched normals. Sequence libraries were generated from tumour and matched normal genomic DNA using the KAPA HyperPrep PCR-free library preparation kit (Roche), or the Illumina TruSeq DNA Nano kit according to manufacturer’s instructions. Sequencing was carried out by the Kinghorn Centre for Clinical Genomics Sequencing Laboratory (Sydney, Australia) on the HiSeq X Ten System (Illumina) or by the Australian Genome Research Facility (Melbourne, Australia) on an Illumina NovaSeq to a minimum base coverage of 30-fold for normal DNA and 60-fold for tumour DNA samples.

  Dataset EGAD00001009746

• Dataset for head_and_neck_cancer-EXON

  Rare cancer sequencing data of 86 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008880

• Targeted DNA sequencing

  Targeted DNA sequencing of high-grade serous ovarian cancer (HGSC) tumour and normal samples from 15 patients with homologous recombination deficiencies. The dataset includes fastq files from 243 HGSC tumours (15 primary, 3 relapse, 225 end-stage) and 15 normals from 15 HGSC patients. Following target hybrid capture of 63 genes involved in DNA repair and response to treatment with an Agilent SureSelect XT panel, sequencing libraries were generated using the SureSelect XT Low Input Target Enrichment System (Agilent) as per the manufacturer's protocol. Libraries were sequenced on an Illumina NextSeq 500 at the Peter MacCallum Cancer Centre (Melbourne, Australia).

  Dataset EGAD00001009747

• 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

• Dataset-linking-WGS-samples-in-ega-box-81-via-README-for-study-EGAS00001002923

  This dataset contains 318 Tumor and Control WGS files submitted in another EGA box for samples for Gerhauser et al.,Cancer Cell, 2018, 34:996-1011. WGS and sequencing protocol was earlier described in Weischenfeldt et al, Cancer Cell, 2013.

  Dataset EGAD00001007861

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

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

  Dataset EGAD00001004905

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

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

  Dataset EGAD00001004921

• Multi-region WGS of a RET fusion positive cancer

  high depth WGS sequencing of 8 sites of a RET fusion tumour

  Dataset EGAD00001006878

• RNA of peripheral blood for pancreatic cancer and chronic pancreatitis

  Samples of nucleated cells found in peripheral blood from over 300 patients suffering from resectable pancreatic ductal adenocarcinoma, non-resectable pancreatic cancer, chronic pancreatitis, or none of these. Please cite this article when using data: Al-Fatlawi, A.; Malekian, N.; García, S.; Henschel, A.; Kim, I.; Dahl, A.; Jahnke, B.; Bailey, P.; Bolz, S.N.; Poetsch, A.R.; Mahler, S.; Grützmann, R.; Pilarsky, C.; Schroeder, M. Deep Learning Improves Pancreatic Cancer Diagnosis Using RNA-Based Variants. Cancers 2021, 13, 2654. https://doi.org/10.3390/cancers13112654

  Dataset EGAD00001006915

• Longitudinal single-cell RNA-seq data from metastatic ovarian cancer

  Longitudinal single-cell RNA-seq data of prospectively collected tumor tissue samples before and after chemotherapy from 11 HGSOC patients.

  Dataset EGAD00001006922

• S:CORT Stratification in COloRecTal cancer

  Colorectal cancer samples will be submitted for Illumina sequencing using a custom capture of 116 genes implicated in colorectal tumourigenesis. Driver mutations will be detected and ultimately correlated with phenotypic data.

  Dataset EGAD00001009760

• MutWP5: CRUK Mutographs of Cancer: Lung: PD37920 (Targeted) (2021-02-02)

  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 mutation burden in different portions of the lung. Targeted sequencing will be conducted on samples to identify drivers of interest and clonality of the samples, well-performing samples will be sent for subsequent whole-genome sequencing. Results from this portion 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 2021-02-02.

  Dataset EGAD00001006929

• MutWP5: CRUK Mutographs of Cancer: Lung: PD43291_Novaseq (Exome) (2021-02-02)

  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 2021-02-02.

  Dataset EGAD00001006932

• Bulk tumor RNAseq of bladder cancer patients

  RNAseq fastq files from 611 bulk pre-treatment tumors from two indications: metastatic urothelial bladder cancer patients (IMvigor210) and metastatic renal cell carcinoma (IMmotion150)

  Dataset EGAD00001006960

• Single Cell Genome Sequence for DLP+ library A96141A

  Single Cell Genome Sequence for triple negative breast cancer patient-derived xenograft SA604 passage 8 on DLP+ library A96141A

  Dataset EGAD00001009777

• BCSA_Exome+SmartSeq3

  Multiple regions were cut out of each tumor extracted form breast cancer patients and two experiments were run: - Whole exome sequencing on each of the regions plus an adjacent normal tissue sample - Smart-Seq3 Single cell RNA sequencing on EPCAM+ CD45- sorted cells from different tumor regions

  Dataset EGAD00001009781

• Dataset for breast_cancer-WHOLE_GENOME

  Rare cancer sequencing data of 12 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008867

• Tumor Educated Platelets (TEPs) for breast cancer detection

  The TEP dataset consists of 549 Fastq samples which are divided into two experiments: a training data cohort, used to train the classifier, and a validation data cohort, used to assess classifier performance

  Dataset EGAD00001009790

• Whole genome sequencing data of high-grade serous ovarian cancer samples (set 2)

  Whole genome sequencing data of 8 High-grade serous carcinoma (HGSC) patients (20 samples) sequenced with HiSeq X Ten.

  Dataset EGAD00001009791

• HGSOC-celllines-SmartSeq3

  Smart-seq3 scRNA-seq of cells from primary (OV2295) and metastatic (OV2295R2) high-grade serous ovarian cancer cell-line

  Dataset EGAD00001009798

• Peripheral clonal expansion of T cells (scTCR-seq)

  Single-cell TCR-seq of tumor-infiltrating lymphocytes from 14 cancer patients before treatment, taken from tumor, normal adjacent tissue, and peripheral blood. Dataset consists of paired-end FASTQ files, including replicate libraries and runs.

  Dataset EGAD00001005465

• 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 EGAD00001010951

• Genome and transcriptome sequence data from a merkel cell carcinoma patient

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

  Dataset EGAD00001010955

• 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 EGAD00001010984

• Genome and transcriptome sequence data from a prostate adenocarcinoma patient

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

  Dataset EGAD00001010988

• Genome and transcriptome sequence data from a metastatic lymphoepithelial carcinoma of the parotid gland patient

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

  Dataset EGAD00001010993

• Concatenated long-read single-cell RNA sequencing of momentum biopsies of ovarian cancer patients

  Concatenated long-read single-cell RNA sequencing samples prepared using 10X and the HIT-scIsoSeq protocol. The sequencing was performed on Sequel II Pacbio machine. 3 ovarian cancer patients, 5 omentum biopsies samples: 3 metastasis samples (one per patient), 2 healthy samples (one per patient except Patient2). 4 bam files per metastasis sample, 2 bam files per healthy sample.

  Dataset EGAD00001009814

• Genome and transcriptome sequence data from a metastatic cholangiocarcinoma patient

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

  Dataset EGAD00001011012

• Illumina single-cell RNA sequencing of omentum biopsies of ovarian cancer patients

  Illumina Novaseq paired-end single-cell RNA sequencing samples prepared using 10X Genomics platform. 3 ovarian cancer patients, 5 omentum biopsies samples: 3 HGSOC metastasis samples (one per patient), 2 healthy samples (one per patient except Patient2). 4 paired fastq files per sample.

  Dataset EGAD00001009815

• Sequence of breast cancer bone metastases PDX from 2 targeted panels

  Sequence of breast cancer bone metastases PDX obtained by 2 targeted panels

  Dataset EGAD00001010860

• Genome and transcriptome sequence data from a carcinoma of unknown primary patient

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

  Dataset EGAD00001008945

• The identification of genetic vulnerabilities in head and neck cancers for the development of novel treatments. (2019-06-10)

  Exome Sequencing in a set of Asian Head and Neck cancer cell lines, to identify mutations that can be used to genomically classify the cell lines. . This dataset contains all the data available for this study on 2019-06-10.

  Dataset EGAD00001005082

• Genome and transcriptome sequence data from a urachal adenocarcinoma patient

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

  Dataset EGAD00001011031

• 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 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

• 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

• 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

• 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

• Normal sample for patient SA394

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA394

  Dataset EGAD00001009229

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

  198 exome sequencing samples

  Dataset EGAD00001009853

• 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

• Tumour sample for patient SA274

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA274

  Dataset EGAD00001009180

• 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

• Tumour sample for patient SA275

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA275

  Dataset EGAD00001009181

• Single-cell gene expression data from CD8+ T cells from two Austrian COVID19 patients stimulated with wildtype and mutant SARS-Cov-2 peptides

  The data contains single-cell gene sequencing data (10x Genomics) from FACS-purified CD8 T lymphocytes from two Austrian patients. The cells were stimulated with one MHC class I peptides obtained from a common (wild type) variant and an emerging mutant variant of the SARS-Cov-2 virus. Then the samples were multiplexed using hashtag oligos. We provide the raw and aligned sequence data for: i. The single-cell experiments ii. The PCR-amplified samples for enrichment of the hashtag oligo multiplexing barcodes iii. The PCR-amplified samples for enrichment of the T Cell Receptor (TCR) VDJ region for immuno-profiling. The samples and libraries were processed and obtained in collaboration between St. Anna Children's Cancer Research Institute (CCRI), CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, and the Medical University of Vienna. The cell barcodes and processed data has been submitted to the GEO database with GEO accession GSE166651.

  Dataset EGAD00001006995

• Genome and transcriptome sequence data from a lung adenocarcinoma patient

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

  Dataset EGAD00001005880

• Whole-genome sequencing data for inflammatory breast cancer patients

  This study reports the whole-genome sequencing data for 20 inflammatory breast cancer patients, each of whom has one normal blood sample and one breast tumor sample. Overall, there are 40 files included in this study, in the format of BAM.

  Dataset EGAD00001005749

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

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

  Dataset EGAD00001005903

• 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

• Genome and transcriptome sequence data from a colorectal cancer patient

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

  Dataset EGAD00001008909

• 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

• Colon Cancer Organoid Cultures and Tumors Whole Exome Sequencing Data

  Five hundred fifty nanograms of genomic DNA were input for library preparation after fragmentation by Covaris S2, following the KAPA Hyper Prep Kit (KR0961-V1.14) protocols, with selection for a library size range of 250-450 bp. Three hundred nanograms per library DNA each from 12 samples were normalized and combined into a single pool for exome capture using the xGen Lockdown Probes and Reagents based on their standard protocols

  Dataset EGAD00001005754

• Single Cell Genome Sequence for DLP+ library A118790A

  Single Cell Genome Sequence for triple negative breast cancer patient-derived xenograft SA610 passage 3, patient-derived xenograft SA1096C passage 1 on DLP+ library A118790A

  Dataset EGAD00001009437

• Single Cell Genome Sequence for DLP+ library A96109A

  Single Cell Genome Sequence for triple negative breast cancer patient-derived xenograft SA501 passage 2 on DLP+ library A96109A

  Dataset EGAD00001009452

• Tumour sample for patient SA399

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA399

  Dataset EGAD00001009541

• Tumour sample for patient SA212

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA212

  Dataset EGAD00001009528

• Normal sample for patient SA420

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA420

  Dataset EGAD00001009570

• Normal sample for patient SA1069

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA1069

  Dataset EGAD00001009593

• Tumour sample for patient SA1027

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA1027

  Dataset EGAD00001009610

• Tumour sample for patient SA997

  Whole genome sequencing of tumour sample for triple negative breast cancer patient SA997

  Dataset EGAD00001009621

• 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 EGAD00001011035

• PELICAN45 RNAseq Dataset

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

  Dataset EGAD00001009997

• TGL49_HBC 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 healthy control patients.

  Dataset EGAD00001010001

• PGDx elio™ plasma resolve assay: targeted sequencing analyses of plasma cfDNA

  The dataset "PGDx elio™ plasma resolve assay: targeted sequencing analyses of plasma cfDNA" includes paired end FASTQ reads of 183 cfDNA samples from metastatic colorectal cancer patients. Sequencing was performed using a panel consisting of 33 genes, covering over 237,000 bp, targeting 25,000x depth across the targeted regions.

  Dataset EGAD00001009719

• Genome and transcriptome sequence data from a chromophobe renal cell carcinoma patient

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

  Dataset EGAD00001010952

• 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

• 2 paired WGS samples of peritumour regions of colorectal cancer

  2 paired WGS samples of peritumour regions of colorectal cancer (2 patients). The library was prepared using the Illumina TruSeq Nano FFPE kit and the sequencing was done on NovaSeq6000.

  Dataset EGAD00001009714

• Exome and RNA sequencing of pancreatic cancer biopsies and PDX models

  Pancreatic cancer biopsies and matching normal controls from 10 patients were exome sequenced. The same biopsies and PDX models derived from these were also subject to RNA sequencing.

  Dataset EGAD00001008113

• Bulk BCR NGS data from metastatic breast tumours from donors with therapy-resistant lethal metastatic breast cancer.

  Bulk B Cell Receptor high-throughput sequencing data across 27 metastatic breast tumours obtained from 8 donors with therapy-resistant lethal metastatic breast cancer at the time of a warm autopsy. The 35 samples were sequenced on an Illumina MiSeq instrument and their raw FastQ files deposited here.

  Dataset EGAD00001010023

• 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

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

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

  Dataset EGAD00001010042

• 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

• 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

• 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

• 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

• BCG Molecular Subtyping

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

  Dataset EGAD00001010065

• 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 EGAD00001005911

• 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

• bladder cancer patient data

  This contains H3K27ac ChIP-seq, RNA-seq and HiC fastq files.

  Dataset EGAD00001007052

• 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