5032 results for "*oma"

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• Genome and transcriptome sequence data from a metastatic melanoma patient

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

  Dataset EGAD00001004931

• 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 EGAD00001004932

• Genome and transcriptome sequence data from a metastatic sarcomatoid carcinoma of the lung patient

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

  Dataset EGAD00001004933

• 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

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

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

  Dataset EGAD00001004936

• RNA-sequencing of adult T-cell leukemia/lymphoma sample

  This dataset includes 10 RNA-sequencing (RNA-seq) data for 9 primary tumors and 1 cell line from adult T-cell leukemia/lymphoma (ATL).

  Dataset EGAD00001004937

• Tumor-derived cell lines as pharmacogenomic models to predict therapeutic vulnerabilities in hepatocellular carcinoma

  Hepatocellular carcinoma (HCC) is a heterogeneous aggressive malignancy with low efficacy of current therapies at advanced stages. We integrated molecular and pharmacological profiling of a large panel of liver cancer cell lines (LCCL) to assess their clinical relevance as HCC preclinical models and identify new effective therapies and biomarkers of response. Here, we performed multi-omic analysis including whole-exome, RNA and microRNA sequencing in a series 34 LCCL. Molecular profiles of LCCL and primary HCC were compared and we searched for molecular features associated with drug response. Our panel of LCCL faithfully recapitulated the most aggressive molecular “proliferation class” of HCC.

  Dataset EGAD00001004938

• Mucoepidermoid carcinoma- normals

  Whole exome sequencing data for 18 mucoepidermoid carcinoma samples. The samples were used for Illumina TruSeq library construction and captured using Agilent V4 exome panel. The PE fastq files are provided.

  Dataset EGAD00001004946

• Whole genome sequencing data of lung adenocarcinomas

  This dataset includes the whole-genome sequencing data from a study entitled "Tracing Oncogene Rearrangements in the Mutational History of Lung Adenocarcinoma". Whole-genome sequencing libraries were generated by PCR-free methods, and sequencing run was made in HiSeq X Ten machines. PCR duplicates-marked, indel-realigned, and base-recalibrarted BAM files are provided in our dataset.

  Dataset EGAD00001004793

• RNA-seq dataset of lung adenocarcinomas

  This dataset includes the RNA-seq data from a study entitled "Tracing Oncogene Rearrangements in the Mutational History of Lung Adenocarcinoma". PolyA tails were captured by Oligo-dT beads, and sequencing run was made in HiSeq 2500 machines. Paired-end FASTQ files are provided in our dataset.

  Dataset EGAD00001004794

• Frequent germline mutations of HAVCR2 in sporadic subcutaneous panniculitis-like T-cell lymphoma.

  Subcutaneous panniculitis-like T-cell lymphoma (SPTCL) is a rare subtype of peripheral T-cell lymphoma affecting younger cases and associated with hemophagocytic lymphohistiocytosis. To clarify the molecular pathogenesis of SPTCL, we analyzed paired tumor and germline DNAs from 13 patients by whole exome sequencing.

  Dataset EGAD00001004795

• 24 Chordoma samples (WES,WGS)

  Case series of the rare tumor entity chordoma. 9 cases sequenced with Whole Exome Sequencing (WES) and 2 cases sequenced with Whole Genome Sequencing (WGS) were recruited from the personalized oncology program NCT-MASTER/DKTK-MASTER at the German Cancer Research Center. One of the WES patients was re-sequenced at a later time point when he relapsed, this resequencing was done by WGS. Therefore there are 11 patients, one of which with two samples, all of which were sequenced with matched normal controls, amounting to a total number of 24 NGS samples.

  Dataset EGAD00001004825

• Genomic stratification and liquid biopsy in a rare adrenocortical carcinoma (ACC) case, with dual lung metastases

  Dataset consisting of three WGS BAM files, representing the two dual lung metastases with matched germline control, for a 37 year old female patient, with primary adrenocortical carcinoma. Work conducted at Garvan Institute of Medical Research, Sydney, Australia.

  Dataset EGAD00001004833

• Presentation and relapse myeloma

  Series of 56 paired presentation, relapse and control samples from newly diagnosed, uniformly treated myeloma patients. Deep of treatment response and maintenance allocation (active observation or lenaldiomide) was determined for all. All samples underwent whole exome sequencing with additional baits to cover the myc and immunoglobulin loci. There are 168 (56 presentation, 56 relapse and 56 control) samples in this study. 131 are available as part of this dataset. The remaining 37 are available with dataset accession id EGAD00001001358.

  Dataset EGAD00001004846

• Deciphering Intratumoral Molecular Heterogeneity in Clear Cell Renal Cell Carcinoma with a Radiogenomics Platform

  We used 200 ccRCC samples from 51 tumors to simultaneously isolate DNA, RNA, and protein according to established protocol. RNA quality was assessed using an Agilent Bioanalyzer, and total RNA with RIN>7 was used for further RNA sequencing. 184 ccRCC samples from 49 tumors passing initial quality control underwent RNA sequencing at Admera Health Inc. (Genohub Inc., Austin, TX). RNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA high throughput (HT) sample preparation kit following the manufacturers’ protocol. Pair-end RNA Seq data was deposited in this cohort.

  Dataset EGAD00001005356

• 110 "KOREAN" never-smoker female adenocarcinoma RNA-seq

  All sequencing was performed within the DNAlink (Korea) by using the Solexa sequencing technology (Illumina, San Diego, CA). mRNA was isolated from total RNA using poly-T oligo-attached magnetic beads and was fragmented with fragmentation buffer to an average size of 300 bp. The libraries were prepared by using TruSeq RNA Library Prep Kit v2 (Illumina) and were sequenced on the Illumina HiSeq2000 using the manufacturer’s recommended protocols

  Dataset EGAD00001005358

• WGS data of patients diagnosed with angiosarcoma

  Whole-genome sequencing (WGS) was performed for 13 pairs of tumor-normal and 5 tumor-only samples from patients diagnosed with angiosarcoma. Genomic DNA from tumor tissue was extracted with QIAamp DNA Mini Kit. The DNA for the matching normal was obtained from blood or buccal swabs and purified by Blood and Cell Culture DNA Mini kit or E.Z.N.A. Tissue DNA Kit (Omega Bio-tek) according to manufacturer’s instructions. The quantity and quality were assessed by Quant-iT PicoGreen dsDNA Assay Kit (Invitrogen) and agarose gel electrophoresis. All sequencing libraries were prepared using TruSeq Nano DNA Library Prep Kit (Illumina). Paired-end sequencing was performed on Illumina HiSeq X Ten as 2x151 bp.

  Dataset EGAD00001005366

• WTS data of patients diagnosed with angiosarcoma

  Whole-transcriptome sequencing (WTS) of 6 tumor-normal and 6 tumor-only samples from patients diagnosed with angiosarcoma. Total RNA from snap frozen EITL tumor samples was extracted using TRIzol (Invitrogen) and purified with RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions. The integrity of RNA was determined by electrophoresis using 2100 Bioanalyzer (Agilent Technologies). 500 ng of total RNA was reverse transcribed with iScript cDNA Synthesis Kit (Bio-Rad, Hercules, CA, USA). Quantification was performed using SsoFast EvaGreen Supermix and CFX96 Real-Time PCR System (both Bio-Rad). Sequencing libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero (Illumina) and WTS was performed on HiSeq 2500 and HiSeq 3000 (Illumina) with 2x101 bp and 2x151 bp read length, respectively.

  Dataset EGAD00001005367

• Single Cell RNA Seq GBM

  Single Cell RNA sequencing for 4 high grade glioma samples. NovaSeq6000 was used for snRNA Seq. The files uploaded are bam files created with grch38 reference.

  Dataset EGAD00001005369

• Single Cell RNA Seq LGG

  Single Cell RNA sequencing for 5 low grade glioma samples. NovaSeq6000 was used for scRNA Seq. The files uploaded are bam files created with grch38 reference.

  Dataset EGAD00001005368

• WES from two human osteosarcoma with two samples each from the corresponding cell line

  WES from two human osteosarcoma with two samples each from the corresponding cell line, BAM files

  Dataset EGAD00001005370

• Paired-end RNA-seq analysis of the Hypermutation and Malignant Progression in Low-grade Glioma Patients

  44 DNA samples were derived from the tumors of the low grade glioma patients and sequenced using Illumina RNAseq paired-end technology. Dataset contains 44 BAM files aligned to hg19 using Tophat 2.

  Dataset EGAD00001005387

• WGS datasets of pediatric glioblastoma

  WGS with linked reads of pediatric glioblastoma. For each patient, blood and tumor tissue were sequenced. For two patients, we also provide sequencing data for the blood of their parents.

  Dataset EGAD00001005212

• Polyomavirus-positive Merkel cell carcinoma derived from a trichoblastoma suggests an epithelial origin of Merkel cell carcinoma

  Tricholastoma (TB): Exome Merkel cell carcinoma (MCC): Genome and Exome Healthy tissue (HT): Exome

  Dataset EGAD00001005223

• Leeds Paired Primary and Recurrent GBM RNAseq

  Whole transcriptome, strand-directional RNAseq data for paired primary dn recurrent samples from patients with glioblastoma

  Dataset EGAD00001005224

• Melanoma post mortem analysis

  We have been applying whole genome and transcriptome sequencing across metastases collected during post mortem. Herein we show the findings for the first such patient.

  Dataset EGAD00001005072

• Melanoma post mortem analysis

  Despite multiple large-scale sequencing studies offering substantial insight into the genomic landscape of cutaneous melanoma, the molecular events surrounding disease progression and the resulting molecular heterogeneity between metastases have not been fully elucidated. We have been applying whole genome and transcriptome sequencing across metastases collected during post mortem. Herein we show the findings for the first such patient. This is a targeted pulldown validation in support of the whole-genome sequencing analysis of the metastatic tumours and targeted pulldown of the primary tumour.

  Dataset EGAD00001005073

• Hospital for Sick Children Infant Glioma RNA Sequencing

  Whole transcriptome (n=4) and targetted RNA sequencing (n=15) .bam files of infantile glioma samples reported on at the Hospital for Sick Children

  Dataset EGAD00001005092

• Cancer and germline exomes, and cancer RNA-seq consisiting of FASTQ paired-end reads from melanoma and lung cancer samples

  Cancer and germline exomes, and cancer RNA-seq consisiting of FASTQ paired-end reads from melanoma and lung cancer samples

  Dataset EGAD00001005097

• Genomic profiling of patient-derived xenograft models of myxoid liposarcoma either sensitive or resistant to trabectedin

  The dataset consists of two patient-derived xenograft model of myxoid liposarcoma one sensitive and one resistant to trabectedin. Both models underwent the same treatment schedule with trabectedin (tree time points and one treatment with doxorubicin). We performed genomic profiling using Agilent OneSeq assay.

  Dataset EGAD00001005099

• Sporadic and endemic Burkitt lymphoma have frequent FOXO1 mutations but distinct hotspots in the AKT recognition motif

  Sample set of 74 whole-exome sequencing samples from sporadic Burkitt lymphoma patients from the UK. 33 of these samples have matched constitutional data, giving a total number of 107 samples

  Dataset EGAD00001005105

• Histone and transcriptome profiling of glioblastoma initiating cells

  ChIP-seq and RNA-seq of glioblastoma initiating cells and their differentiated counterparts with and without inhibition/knockdown of KDMs.

  Dataset EGAD00001005124

• 112 "KOREAN" never-smoker female adenocarcinoma exome-seq

  All sequencing was performed within the DNAlink (Korea) by using the Solexa sequencing technology (Illumina, San Diego, CA). 1 ug of genomic DNA was sheared to an average size of 150 bp by using the Covaris System. The libraries were prepared by using TruSeq DNA Sample Prep Kit (Illumina). The purified DNA library was hybridized with the SureSelect Human All Exon V3 probe set (Agilent Technologies) to capture 50 Mb of targeted exons following the manufacturer’s instructions. Exome capture was carried out using the Agilent SureSelect Human All Exon 50Mb Kit. The captured exome libraries were sequenced on the Illumina HiSeq2000 using the manufacturer’s recommended protocols.

  Dataset EGAD00001005126

• Human tumor bulk RNA-seq

  We profiled 186 patient tumor samples by bulk RNA-seq. These includes 38 embryonal brain tumors, 101 high-grade gliomas, 24 low-grade gliomas, 10 medulloblastoma and 13 matched normals. The raw fastqs are provided.

  Dataset EGAD00001005131

• Human tumor single-cell

  We profiled 11 patient tumor samples by single-cell and single-nuclei RNA-seq using 10X Chromium 3'. These include samples from the following entities: WNT-subtype medulloblastoma (N=3), embryonal tumors with multilayered rosettes (N=3), and atypical teratoid-rhabdoid tumors (N=5). The BAM files are provided.

  Dataset EGAD00001005129

• Gene expression profile of mesothelial-derived carcinoma-associated fibroblasts

  RNA-sequencing was carried out on ascetic fluid-isolated mesothelial cells from low-grade serous ovarian cancer patients, high-grade serous ovarian cancer patients, chemotherapy-treated high-grade serous ovarian cancer patients and control mesothelial cells obtained from non-oncologic patients to identify differentially expressed genes associated to mesothelial-to-mesenchymal transition process. The dataset contains 18 samples: - Control mesothelial cells: 4 samples - Group 1, high-grade serous ovarian cancer patients: 3 samples - Group 2, chemotherapy-treated high-grade serous ovarian cancer patients: 5 samples - Group 3, low-grade serous ovarian cancer patients: 6 samples

  Dataset EGAD00001005133

• Exome and RNA seq data for female patient

  Exome and RNA sequencing data for EGAS00001003776 - one female patient with neurofibroma/schwannoma hybrid nerve sheath tumor (N/S HNST)

  Dataset EGAD00001005249

• Next gen seq of eye cancers (2019-08-14)

  Retinoblastoma (RB), the commonest eye cancer in children was the first cancer for which a genetic cause was identified: the Rb1 gene is a tumour suppressor gene that is mutated in RB. The Rb1 gene defect alone does not predict the clinical outcome. We propose to study other possible mechanisms: 1. Stepwise further mutations occur in RB, increasing its carcinogenesis. We will sequence the whole genome in RB tissue, and relate the different genes expressed to the treatments used. 2. Extracellular matric proteins contribute to a tumour permissive environment for RB to continue to grow. This includes Samll Leucine Rich Proteoglycans (SLRP), a family of 15 secreted extracellular matrix proteins involved in eye development. 3. Cancer stem cells (CSC), a subpopulation of treatment resistant cells, drive RB tumours, and whether these stem cells can be manipulated for new therapies. The aim of this study is to assist finding targeted diagnostic techniques and treatments for RB. . This dataset contains all the data available for this study on 2019-08-14.

  Dataset EGAD00001005251

• Predictor_ChemoNEAR_TNBC (2019-08-14)

  In this study a collection of core biopsies from breast cancer patients receiving neoadjuvant chemotherapy as part of the ChemoNEAR trial will be investigated. The study is intended to detect early acquired resistance in women with diagnosed breast carcinoma. Samples will undergo whole genome sequencing and analysis, including use of HR Predict. . This dataset contains all the data available for this study on 2019-08-14.

  Dataset EGAD00001005255

• Analysis of resistance to PLX4032 (2019-08-21)

  We have collected material from a patient who had BrafV600E mutant melanoma that was treated with PLX4032. We have germline DNA from the patient and DNA and RNA from distinct lesions before and after treatment with PLX4032. We would like to exome sequence these samples to gain a snap shot of the mechanisms of resistance that are operative. . This dataset contains all the data available for this study on 2019-08-21.

  Dataset EGAD00001005278

• Genetic landscape of SMM

  Identifying high risk smoldering myeloma patients and progression mechanism is a prerequisite to implement effective inception strategies and curve myeloma related morbidity and mortality. We hypothesize that genomics may help identify determinants of progression that may help predict outcome and offer effective chemo preventive targets. Eighty-two patients underwent a custom targeted panel sequencing with an additional capture for the translocation loci. These results were compared to 223 newly diagnosed patients (EGAS00001003223 and EGAD00001004117) and 17 MGUS and 10 early myeloma patients. DNA was obtained from either CD138+ cells from the bone marrow of multiple myeloma patients (tumor) or from stem cell harvests or peripheral blood cells from the same patient (control). 100 ng of DNA was fragmented, end-repaired, and adapters ligated using the HyperPlus kit (KAPA Biosystems). After PCR amplification the libraries were hybridized with probes against either a targeted panel consisting of 140 genes and chromosomal regions (Nimblegen) using SeqCap reagents (Nimblegen). Hybridized libraries underwent further amplification before being sequenced on a NextSeq500 (Illumina) using 75 bp paired end reads. Overall, these data highlight the importance of dysregulation of the MAPK pathway in the progression to MM.

  Dataset EGAD00001005285

• Deep multi-region WGS of lung cancer tumours

  Deep WGS (germline and 2-5 tumour regions) was performed on 20 patients: 13 lung adenocarcinoma, 5 squamous cell carcinoma, 2 small-cell lung cancers. A total of 68 BAM files are provided, where tumours were sequenced to 60x or 150x depth.

  Dataset EGAD00001005287

• CRISPR screen M14, NCI-H3122 (2019-08-28)

  Genome wide CRISPR screen was performed to find resistance to targeted drugs for melanoma and lung . This dataset contains all the data available for this study on 2019-08-28.

  Dataset EGAD00001005296

• RNA sequencing and whole-genome mate-pair sequencing of osteosarcoma

  This data set includes 72 mate pair sequenced osteosarcomas (36 as part of a discovery cohort and 36 as part of a validation cohort). It also includes RNA-sequencing data on 67 osteosarcomas (mostly overlapping with the above mate pair sequenced cases) and 13 osteoblastomas used as controls for gene expression levels.

  Dataset EGAD00001005307

• SF11956 scRNA-Seq GBM IDHR132H Wildtype Male

  SF11956 IDHR132H WT GBM. Male, 63. Single Cell RNA seq from high grade glioma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference through Cellranger count (10xGenomics.)

  Dataset EGAD00001005392

• Paired-end Whole Exome-seq analysis of the Hypermutation and Malignant Progression in Low-grade Glioma Patients

  113 DNA samples were derived from the tumors of the low grade glioma patients and sequenced using Illumina WES (exome seq) paired-end technology. Dataset contains 113 BAM files aligned to hg19 using BWA v.0.5.9. After mapping duplicated reads were removed, reads were re-aligned around InDels and read base quality score was re-calibrated.

  Dataset EGAD00001005386

• Whole genome sequencing of osteosarcoma from patients seen at UT MD Anderson Cancer Center.

  Whole genome sequencing of 35 osteosarcoma patients (primary, relapsed, and metastatic) with matched normals. Tumors were sequenced at target 60X and matched normals at target 30X.

  Dataset EGAD00001005389

• SF11979 scRNA-Seq Primary GBM IDHR132H Wild-type Female

  Single Cell-RNA Seq IDHR132H Wild-type Primary GBM Female, 76. Single Cell RNA seq from high grade primary glioma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference through cellranger count (10xGenomics.)

  Dataset EGAD00001005390

• SF11977 scRNA-Seq Primary GBM IDHR132H Wildtype Female

  SF11977 single cell RNA-seq IDHR132H Wild-type GBM Female, 61 Single Cell RNA seq from high grade primary glioma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference through Cellranger count (10xGenomics.)

  Dataset EGAD00001005391

• SF11644 scRNA-Seq primary GBM

  SF11644 Primary GBM Gender Male age 57. Single Cell RNA seq from high grade primary glioma sample. NovaSeq6000 was used for RNA seq. The files uploaded are bam files created with grch38 reference through Cellranger count (10xGenomics.)

  Dataset EGAD00001005393