12000 results for "cancer rna-seq"

in 24.42 milliseconds.

• Multi-omics analysis of serial samples from metastatic TNBC patients on PARP inhibitor monotherapy provide insight into rational PARP inhibitor therapy combinations

  In a pilot study, we evaluated the safety and efficacy of olaparib/durvalumab combination treatment in mTNBC patients and the feasibility of real-time deep analysis of serial tumor samples from triple negative breast cancer patients to identify mechanisms of resistance and treatment opportunities. This study used the SMMART analytic platform at OHSU KCI and incorporated comprehensive multi-omic analysis of serial liquid and tumor biopsies. Deep analysis of longitudinal biopsies combined with a robust computational biology pipeline identified multiple PARPi-induced changes in immune activation, DNA damage checkpoint activation, apoptosis and signaling pathways including RTK, PI3K-AKT and RAS-MAPK. These emergent tumor and immune state changes could act as biomarker targets to be used in selecting patient specific combination therapies.

  Study EGAS00001005479

• Whole Genome Sequencing of Liver Cancers

  Genomic alterations driving tumorigenesis result from the interaction of environmental exposures and endogeneous cellular processes. With a diversity of risk factors including viral infection, carcinogenic exposures and metabolic diseases, liver cancer is an ideal model to study these interactions. Whole genome sequencing of liver tumors identified 10 mutational signatures showing distinct relationships with environmental exposures, replication and transcription. Transcription-coupled damage was specifically associated with the liver-specific signature 16 and alcohol intake. Flood of indels were identified in very highly expressed hepato-specific genes, likely resulting from replication-transcription collisions. Reconstruction of sub-clonal architecture revealed mutational signature evolution during tumor development exemplified by the vanishing of aflatoxin-B1 signature in African migrants. These findings shed new light on the natural history of liver cancers

  Study EGAS00001002408

• Microbiota 16S sequencing study in NSCLC patients eligible for surgery without neoadjuvant treatment

  18 non-small cell lung cancer patients eligible for surgery without neaodjuvant treatment were included in the study at Centre Jean Perrin (France). Patients did not take any antibiotics, food supplements or immunostimulants 2 months prior to inclusion. During surgery, patients underwent partial or complete lobectomy where samples of non-malignant lung tissue, peritumoural tissue and tumour were resected from the removed lobe. This was preceeded by the washing of the removed lobe and obtaining the broncho-alveolar lavage fluid. These four sample types were analysed by 16S sequencing in 17 from 18 patients. The study is a part of the project "Characterization of Microbiota (Intestinal, From Lungs, and Upper Airways) in Patients With Non-small Cell Lung Carcinoma: Exploratory Study " which is registered under ref. NCT03068663 (clinicaltrials.gov).

  Study EGAS00001004728

• Persistent Mutation Burden Drives Sustained Anti-Tumor Immune Responses

  Tumor mutation burden is an imperfect proxy of tumor foreignness and has therefore failed to consistently demonstrate clinical utility in predicting responses in the context of immunotherapy. We evaluated mutations in regions of the genome that are unlikely to undergo loss and discovered that clonal mutations in single-copy regions and those present in multiple copies per cell constitute a persistent tumor mutation burden (pTMB) that is linked with therapeutic response to immune checkpoint blockade. Persistent mutations were retained in the context of tumor evolution under selective pressure of immunotherapy and tumors with a high pTMB content were characterized by a more inflamed tumor microenvironment. pTMB imposes an evolutionary bottleneck that cancer cells cannot overcome and may thus drive sustained immunologic tumor control in the context of immunotherapy.

  Study EGAS00001006660

• Single-cell multi-omics of relapse/refractory multiple myeloma patients (Hipo K08K/H067/K43R)

  Therapy resistance in cancers is ingrained in complex clonal dynamics. While the major clonal population in a tumour might respond well to the employed intervention, minor clones will eventually mutate, consequently acquiring a selective advantage and drug resistance. Hence, to improve cancer therapy, it is crucial to understand the mechanisms behind clonal evolution. Here, we applied single-cell transcriptomics and epigenomics, as well as whole-genome sequencing to 15 patients with relapsed/refractory multiple myeloma (RRMM). By profiling longitudinal samples throughout varying treatment regimens, we were able to interrogate patterns of evolution across patients. In particular, by defining clones based on copy number aberrations (CNAs), we found evidence for the majority of clones being diminished but not fully eradicated during treatment.

  Study EGAS00001006538

• A Genome-Wide Association Study in Patients Experiencing Musculoskeletal Adverse Events on NCIC CTG Trial MA.27 Evaluating Aromatase Inhibitors as Adjuvant Therapy in Early Breast Cancer. A Collaboration Between the NIH Pharmacogenetics Research Network and the RIKEN Yokohama Institute Center for Genomic Medicine.

  Source of Patients The source of the patients for this genome-wide case control study was MA.27, which was conducted as a multi-cooperative group effort under the auspices of the NCI Breast Cancer Intergroup of North America. The NCIC Clinical Trials Group (CTG) serves as the coordinating group, with participation by the NCI-sponsored North Central Cancer Treatment Group, Eastern Cooperative Oncology Group (ECOG), Southwest Oncology Group, and Cancer and Leukemia Group B (CALGB). MA.27 involved postmenopausal women with histologically confirmed and completely resected invasive breast cancer with surgical margins clear of invasive carcinoma and DCIS in the following TMN categories (AJCC Version 6): pT1, pT2, pT3; pNx, pN0, pN1, pN2, pN3 (only when the sole basis is presence of 10 or more involved axillary nodes); MO. The primary tumor must have been ER and/or progesterone receptor positive. Patients were stratified by lymph node status at diagnosis, prior adjuvant chemotherapy, and trastuzumab use and were randomized to 5 years of adjuvant therapy with anastrozole or exemestane. The trial was activated on May 26, 2003, and reached its accrual objectives on July 31, 2008, after the randomization of 6827 North American patients, with the majority (79%) providing DNA and consent for genetic testing. Non-North American patients were also entered by the International Breast Cancer Study Group but they did not contribute DNA. From 2003 to December 21, 2004, patients also underwent a second randomization to celecoxib 400 mg twice daily or placebo but, after the entry of 1,622 patients, this treatment was discontinued because of reports of increased cardiovascular risk associated with celecoxib. Case Definition for Musculoskeletal Adverse Events Cases were defined to have had at least one of the following six MSAE): 1. pain - joint, 2. pain - muscle, 3. pain - bone, 4. arthritis, 5. joint - function, 6. musculoskeletal - other. Cases were required to have at least grade 3 toxicity, according to the NCI Common Terminology Criteria for Adverse Events v3.0, or go off treatment for any grade of the six MSAEs; and were required to have had an MSAE within the first two years (i.e., a MSAE occurring after 2 years was not be considered a case). Subjects were excluded from the case group who met the case definition while on celecoxib or in the three months after stopping celecoxib but subjects were allowed to be cases if they developed their first MSAE more than three months after stopping celecoxib. Study Design The design was a nested matched case-control study with two controls selected for each case. Random matching from the potential control group (i.e., risk-set sampling such that controls had at least the same length of followup as the timing of the case event) was done by matching the case on the following factors: 1. treatment arm (exemestane vs. anastrozole, blinded), 2. prior adjuvant chemotherapy (yes vs. no), 3. age at start of treatment (+/- 5 years), 4. Celecoxib allocation (yes vs. no). Attempts were made to exactly match each case with two controls according to the above criteria. If, however, controls could not be exactly matched, "close" matching was used to define a distance between each case and all potential controls in an optimal matching algorithm. Race is a potential confounding factor, and 94% of the MA.27 population is Caucasian, 3% are Black, 1% Asian, 1% American Indian, and 1% are of unknown race. Because there are so few non-Caucasian participants, was restricted to only Caucasians. Following identification of cases and controls, the list was sent to the CALGB Pathology Coordinating Office (PCO) at Ohio State University Medical Center for plating of the samples. Other patient factors that might influence the association of SNP genotypes with a MSAE, either as confounding factors or as effect modifiers, were included as investigational covariates. These include 1. body mass index (BMI), 2. bisphosphonate use, 3. fractures in past 10 years, 4. baseline ECOG performance status, 5. prior hormone replacement therapy, 6. prior adjuvant radiotherapy, and 7. prior taxane treatment. An Honest Broker Process was utilized to ensure patient confidentiality. Genotype Assays and Quality Control A GWAS was performed with the Illumina Human610-Quad at the RIKEN Center for Genomic Medicine. The DNA for all of the samples were adjusted to a concentration of 50 to 100 ng/µL in a final volume of 50 µL. The 96-well plates were designed to have a unique distribution pattern with x duplicates per plate to evaluate genotype concordance. Samples with <98% call rate were removed from analyses. SNPs with ambiguous call will be excluded using the following criteria: 1. low signal intensity of each allele, 2. low cluster separation score, 3. SNP call rate <0.98, 4. SNPs with Hardy Weinberg Equilibrium p-value <0.001 were excluded. X-chromosome SNPs were used to validate female sex and quality control measures were examined across the different submitting centers. For all pairs of subjects, the percentage of matching genotypes were computed to screen for unexpected duplicate samples. All SNPs found to be associated with MSAE were subjected to visual inspection of the cluster plots to verify that the genotype clustering was adequate.

  Study phs000210

• Extreme phenotypes define epigenetic and metabolic signatures in cardiovascular diseases

  Improving the understanding of cardiometabolic syndrome pathophysiology and its relationship with thrombosis are ongoing healthcare challenges. Using plasma biomarkers analysis coupled with the transcriptional and epigenetic characterisation of cell types involved in thrombosis, obtained from two extreme phenotype groups (obese and lipodystrophy) and comparing these to lean individuals and blood donors, the present study identifies the molecular mechanisms at play, highlighting patterns of abnormal activation in innate immune phagocytic cells and shows that extreme phenotype groups could be distinguished from lean individuals, and from each other, across all data layers. The characterisation of the same obese group, six months after bariatric surgery shows the loss of the patterns of abnormal activation of innate immune cells previously observed. However, rather than reverting to the gene expression landscape of lean individuals, this occurs via the establishment of novel gene expression landscapes. Netosis and its control mechanisms emerge amongst the pathways that show an improvement after surgical intervention. Taken together, by integrating across data layers, the observed molecular and metabolic differences form a disease signature that is able to discriminate, amongst the blood donors, those individuals with a higher likelihood of having cardiometabolic syndrome, even when not presenting with the classic features.

  Dataset EGAD00001005197

• Whole exome sequencing of tumors from the Precision Medicine Program in Pediatric and Adolescent Patients with Recurrent Malignancies

  Sequencing libraries were constructed according to standard procedures from 600 ng of tumor and paired constitutional DNA. WES was captured using Agilent SureSelect V5 (50 Mb), Clinical Research Exome (54 Mb) kit, SureSelect XT human All exon CRE version 1 or 2, or Twist Human Core Exome Enrichment System. Sequencing of subsequent libraries was performed using Illumina sequencers (Next-Seq 500 or Hiseq 2000/2500/4000) in 75 bp paired-end mode, aiming for a mean depth of coverage of 100x.

  Dataset EGAD00001010928

• _WGS__Somatic_mutation_in_skin_epidermis__SMS_

  Previously we have sequenced 2mm2 biospies of human epithelia at high depth using a custom bait set. This has identified a range of mutations. Some of the biospies are predicted to be clonal and we would like to perform WGS to give an insight into mutational burden, and CNV which may be associated with these mutations.

  Study EGAS00001004464

• Chondrosarcoma_Targeted_Sequencing_Study

  This Study uses a focused bait pull down library method to target findings of Chondrosarcoma whole genome and whole exome sequencing studies in order to validate findings. This method will also be used on a larger set of tumour only samples in order to find precedence of these finding in a larger set of patients.

  Study EGAS00001000277

• A common single nucleotide variant in T is strongly associated with chordoma

  Chordoma is a rare malignant bone tumor that expresses the transcription factor T. We conducted an association study of 40 patients with chordoma and 358 ancestry-matched, unaffected individuals with replication in an independent cohort. Whole-exome and Sanger sequencing of T exons reveals a strong risk association ( allelic odds ratio (OR) = 4.9, P = 3.3x10-11, CI= 2.9-8.1) with the common (minor allelic frequency >5%) non-synonymous SNP rs2305089 in chordoma, which is exceptional in cancer genetics.

  Dataset EGAD00001000226

• CHEK2 molecular manuscript

  This study investigated the molecular landscape of 17 tumors from 9 individuals with biallelic germline pathogenic variants in CHEK2. Tumors included breast and non-breast cancers, and WES and sWGS bam files from the tumors are included in this submission. WES data was aligned to GRCh37 and sWGS data to GRCh38.

  Study EGAS50000000080

• Anti-tumor and Immune Stimulatory Activity of Iberdomide in Myeloma, Including Patients with Cereblon Dysregulation

  Study showing Iberdomide treatment leads to immune stimulation and shift to effector T cells in triple-class refractory patients and directly after IMiD therapy. This is the first clinical evidence that Iberdomide can overcome Cereblon defects associated with IMiD resistance in late-line myeloma patients.

  Study EGAS50000000265

• PanelSeq IDC samples

  PDX samples of breast cancer IDC mouse models created from patient tumor material of the NKI. Genomescan prepared the samples according to the procedure for Hybridization Capture using an Agilent SureSelect custom 0.5-2.9Mb kit. The prepared libraries were sequenced with Illumina sequencing technology. The samples are in fastq format and consist of the following PDX samples: IDC025, IDC026, IDC029, IDC031, IDC032, IDC038, IDC057, IDC062, IDC065, IDC069, IDC072, IDC090B, IDC092, IDC097, IDC099, IDC107, IDC113, IDC117, IDC143, IDC152, IDC159A, IDC159B, IDC180, IDC186, IDC192, IDC197, IDC198, IDC207, IDC209, IDC216, IDC218, IDC222, IDC229, IDC232, IDC274, IDC282, IDC290, IDC299, IDC307, IDC338, IDC344, IDC346, ILC006, ILC012, ILC083 and ILC248.

  Dataset EGAD50000001149

• Lung cancer Early Molecular Assessment

  This study aimed to validate the potential utility of a clinically accessible, highly sensitive tumor-informed circulating tumor DNA (ctDNA) assay. The study considers a ‘landmark’ time period (between two weeks and four months after definitive treatment), as well as longitudinal sampling (>2 weeks) and compares two independent, retrospectively collected real-world cohorts.

  Study EGAS50000000896

• Development of actionable molecular targets and/or biomarkers for prognostication and patient stratification in gynecological cancer based on whole-exome sequencing and epigenomic analysis

  We collected 92 endometrial hyperplasia lesions (48 non-atypical from 30 cases and 44 atypical from 24 cases) and matched normal tissues/whole blood. The purpose of this study is to develop actionable molecular targets and/or biomarkers for prognostication and patient stratification.

  Study JGAS000642

• WGS data of conditional knockout mouse model mammary tumours

  Deposited here are 56 whole-genome sequencing BAM files from 15 Trp53f/w, 12 Trp53f/f, 14 Brca1f/f Trp53f/w, and 15 Brca1f/f Trp53f/f mouse mammary tumor samples sequenced on Illumina NovaSeq PE150. An additional 6 whole genome sequencing BAM files from corresponding normal tissues of mice are also included as controls (BPC_D666, B1PC_D840, BPTC_D992, PC_D503, PC_D720_Kid, PTC_H531). All samples were used in the study “Insights into BRCA1 and TP53 associated breast cancer development from integrated whole genome analysis of mouse model mammary tumors, Huo et al., 2026.”

  Dataset EGAD50000002036

• Molecular classification of small intestinal adenocarcinomas

  In this study we analyzed genomic and transcriptomic data from 135 small intestinal adenocarcinoma (SIA) patients. Through this analysis, we identified three distinct subtypes based on gene expression patterns, revealing the diverse molecular characteristics among SIA patients. Our findings provide comprehensive insights into the unique features of each subtype.

  Study EGAS50000001238

• Targeted_Sequencing_of_Human_Myeloid_Malignancies

  This study involves targeted sequencing of samples from myeloid malignancies at different timepoints to assess clonal evolution of malignancya.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001001289

• Lymphocyte_LCM_WGS

  Using whole genome sequencing of lymphocytes excised from human tissue using laser capture microscopy (LCM), we identify the mutations arising in these microenvironments. This work will contribute towards developing a catalogue of mutations present in tissue resident lymphocytes across a range of tissues, and will characterize the mutational signatures that result from each microenvironment.

  Study EGAS00001003384

• Somatic_mutation_and_clonal_evolution_in_the_human_pancreas___WGS

  In this study we aim to characterise the landscape of mutation and clonal selection in the human pancreas. The study combines targeted sequencing and whole-genome sequencing of microbiopsies from the pancreas. The range of patients studied will include healthy individuals, both smokers and non-smokers, and patients with pancreatic ductal adenocarcinoma.

  Study EGAS00001002626

• Melanoma_post_mortem_analysis

  This is a targeted pulldown validation in support of the existing whole-genome sequencing study of melanoma metastases (Canapps ID:1888). We are studying the genomic evolution of cutaneous melanoma metastases. In this pulldown analysis we are specifically sequencing the subclonal variants that we believe account for the variability between the metastases.

  Study EGAS00001003531

• Circulating cell-free DNA analyses for Patient Monitoring in Small Cell Lung Cancer

  This study consists of over 200 data files from cfDNA and germline DNA from 69 patients and 32 healthy normal volunteers discussed in this publication.

  Dataset EGAD00001007070

• Development and Validation of a Prognostic and Predictive 32-Gene Signature for Gastric Cancer

  We applied this signature to a 567-patient GC cohort to establish genomic-based molecular subtypes and then used a support vector machine to build a molecular subtype-based risk-scoring model. Both source code and supplementary datasets for risk score prediction are available at https://github.com/hwanglab/Yonsei_gastric_cancer_32genes.

  Dataset EGAD00001008091

• Hubrecht Organoid Technology Colon Cancer Study

  Functional screening on patient-derived organoids identifies a therapeutic bispecific antibody that triggers EGFR degradation in LGR5+ tumor cells

  Dataset EGAD00001008445