5270 results for "*oma"

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• Acral Melanoma PDXs from the admixed Brazilian Population - filtered PDX sample BAM files - RNAseq

  BAM files containing the whole exome data for the Patient Derived Xenograft samples mapped to build GRCh38. All files have been processed with XenofilteR to remove mouse reads. Acral melanoma (AM) is an aggressive melanoma subtype with limited therapeutic options and poor outcomes. In non-European descent and admixed populations, like in Latin America, it can account for a significant proportion of cutaneous melanoma cases. Here, we performed comprehensive genomic and functional profiling of AM from a uniquely diverse Brazilian cohort. Whole-exome and transcriptome sequencing was performed on both tumours and patient-derived xenograft (PDX) samples. The PDX were obtained from a comprehensive collection of patient-derived xenograft (AM-PDX) models that we established which faithfully retained the histopathological and genomic features of the original tumours.

  Dataset EGAD00001015746

• Acral Melanoma PDXs from the admixed Brazilian Population- Human RNA expression data from Patient Derived Xenograft samples - htseq count files

  Files containing the read counts obtained with obtained with HTSeq for all the genes in Ensembl v103 annotation for GRCh38 human reference genome. This dataset contains the files for all the Patient Derived Xenograft samples. Counting was performed using filtered BAM files after the removal of mouse reads with XenofilteR. Acral melanoma (AM) is an aggressive melanoma subtype with limited therapeutic options and poor outcomes. In non-European descent and admixed populations, like in Latin America, it can account for a significant proportion of cutaneous melanoma cases. Here, we performed comprehensive genomic and functional profiling of AM from a uniquely diverse Brazilian cohort. Whole-exome and transcriptome sequencing was performed on both tumours and patient-derived xenograft (PDX) samples. The PDX were obtained from a comprehensive collection of patient-derived xenograft (AM-PDX) models that we established which faithfully retained the histopathological and genomic features of the original tumours.

  Dataset EGAD00001015747

• Acral Melanoma PDXs from the admixed Brazilian Population - filtered PDX sample BAM files - Whole exome sequencing data

  BAM files containing the whole exome data for the Patient Derived Xenograft samples mapped to build GRCh38. All files have been processed with XenofilteR to remove mouse reads. Acral melanoma (AM) is an aggressive melanoma subtype with limited therapeutic options and poor outcomes. In non-European descent and admixed populations, like in Latin America, it can account for a significant proportion of cutaneous melanoma cases. Here, we performed comprehensive genomic and functional profiling of AM from a uniquely diverse Brazilian cohort. Whole-exome and transcriptome sequencing was performed on both tumours and patient-derived xenograft (PDX) samples. The PDX were obtained from a comprehensive collection of patient-derived xenograft (AM-PDX) models that we established which faithfully retained the histopathological and genomic features of the original tumours.

  Dataset EGAD00001015748

• Acral Melanoma PDXs from the admixed Brazilian Population - Patient Derived Xenograft samples VCF files with somatic SNV and INDELs - Whole exome sequencing data

  Raw, flagged and annotated VCF files with somatic calls made with CavEMan and Pindel for Patient Derived Xenograft samples. Variant effect prediction was run with Ensembl VEP v103. Acral melanoma (AM) is an aggressive melanoma subtype with limited therapeutic options and poor outcomes. In non-European descent and admixed populations, like in Latin America, it can account for a significant proportion of cutaneous melanoma cases. Here, we performed comprehensive genomic and functional profiling of AM from a uniquely diverse Brazilian cohort. Whole-exome and transcriptome sequencing was performed on both tumours and patient-derived xenograft (PDX) samples. The PDX were obtained from a comprehensive collection of patient-derived xenograft (AM-PDX) models that we established which faithfully retained the histopathological and genomic features of the original tumours.

  Dataset EGAD00001015749

• Ancestry and somatic profile predict acral melanoma origin and prognosis – RNA

  Acral melanoma, which is not ultraviolet (UV)-associated, is the most common type of melanoma in several low- and middle-income countries including Mexico. Latin American samples are significantly underrepresented in global cancer genomics studies, which directly affects patients in these regions as it is known that cancer risk and incidence may be influenced by ancestry and environmental exposures. To address this, we characterise the genome and transcriptome of 123 acral melanoma tumours from 92 Mexican patients, a population notable because of its genetic admixture. Compared with other studies of melanoma, we found fewer frequent mutations in classical driver genes such as BRAF, NRAS or NF1. While most patients had predominantly Amerindian genetic ancestry, those with higher European ancestry had increased frequency of BRAF mutations and a lower median number of structural variants. The tumours with activating BRAF mutations have a transcriptional profile more similar to cutaneous non-volar melanocytes, suggesting that acral melanomas in these patients may arise from a distinct cell of origin compared to other tumours arising in these locations. KIT mutations were found in a subset of these tumours, and quadruple wild-type samples (non BRAF/NRAS/NF1/KIT) differed from mutated samples in their structural genomic profile and overall and recurrence-free survival patterns. Transcriptional profiling defined three expression clusters; these characteristics were associated with recurrence-free and overall survival. We highlight potential novel low-frequency drivers, such as PTPRJ, NF2 and RDH5. Our study enhances knowledge of this understudied disease and underscores the importance of including samples from diverse ancestries in cancer genomics studies.

  Dataset EGAD00001015756

• Genomics Define Malignant Transformation in Myeloma Precursor Conditions

  Multiple myeloma (MM) is consistently preceded by monoclonal gammopathy of undetermined significance (MGUS) and smoldering multiple myeloma (SMM). While these precursor conditions are asymptomatic, they are not entirely benign and carry a lifelong risk of progression to MM. Unlike other cancers defined by pathology, malignant transformation from MGUS or SMM to MM has so far relied on demonstration of clinical end-organ damage as morphology and cytogenetics cannot reliably distinguish them. In this study, using genomic data from 374 patients with MGUS or SMM (277 training, 97 validation), to our knowledge, we demonstrate for the first time the ability to identify malignant transformation in MGUS and SMM. We introduce the concept of genomic MM and genomic MGUS to differentiate the subsets of MGUS and SMM that are biologically malignant with genomic features indistinguishable from MM from the subset that is premalignant and unlikely to progress to malignancy. Importantly, we find that most SMM has biological features of malignant transformation indistinguishable from MM. As expected, this subset that we consider having genomic MM is associated with a high risk of progression to MM although some patients remained progression-free beyond 5 years. Conversely, 60% of MGUS and 10% of SMM have no evidence of malignant transformation (genomic MGUS), with no progression during follow-up. Integration of genomic features with the 2/20/20 International Myeloma Working Group model significantly improved the prediction of progression among genomic MM. These findings support the use of genomic criteria to refine the classification and the risk stratification in myeloma precursor conditions.

  Dataset EGAD00001015768

• CcRCC_metabolic_heterogeneity

  Heterogeneity is a hallmark of clear cell renal cell carcinoma (ccRCC). In this study, hyperpolarized [1-13C]pyruvate MRI (HP-13C-MRI) was used to probe metabolic heterogeneity non-invasively in 6 ccRCC patients from which 58 tumor and healthy tissues biopsies were acquired postoperatively. MRI parameters were correlated with 146 metabolite concentrations and the expression of 2523 metabolic genes across 34 metabolic pathways. Using metabologram projections and pathway consensus scoring, several metabolic pathways were correlated with the metabolic MRI, including glycolysis, pentose phosphate pathway, and the TCA cycle. A simple thresholding approach applied to the imaging metrics was sufficient to provide meaningful metabolic pathway information. We also show that tissue metabolic heterogeneity increases in regions with higher pyruvate-to-lactate conversion on imaging. These results provide validation of the biological relevance of HP-13C-MRI and support the possibility of its clinical use to improve disease characterization, stratification, targeting of biopsies, and providing novel methods to monitor treatment response.

  Dataset EGAD00001015780

• A developmental cell atlas of the human thyroid gland

  Thyroid hormones are essential for health, but human thyroid development and cellular heterogeneity are poorly understood. We generated a high-resolution, spatiotemporal transcriptional atlas of human fetal thyroid, and examined its perturbations in trisomy 21 (T21), where aberrant thyroid development is associated with congenital hypothyroidism, and in papillary thyroid carcinoma (PTC). Normal tissue revealed two functional follicular cell states (fTFC1, fTFC2) with divergent PAX8 expression levels, persisting into adulthood. Additionally, the rare C-cell population was comprehensively profiled at single-cell resolution for the first time. T21 fetal thyroid was hypoplastic, with disrupted follicular morphology and altered expression of genes mediating cellular topology and extracellular matrix interactions. Finally, the transcriptional signals of both fetal follicular cell states were found to be perturbed in PTC. Overall, we defined a reference atlas for normal human fetal thyrocyte heterogeneity and provided novel insights into thyroid disorders.

  Dataset EGAD00001015783

• Genome and transcriptome sequence data from a recurrent invasive carcinoma of the right breast patient

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

  Dataset EGAD00001015963

• Genome and transcriptome sequence data from a sweat-gland carcinoma with neuroendocrine differentiation patient

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

  Dataset EGAD00001015965

• 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 EGAD00001015966

• Genome and transcriptome sequence data from a osteosarcoma patient

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

  Dataset EGAD00001015968

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

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

  Dataset EGAD00001015969

• Genome and transcriptome sequence data from a recurrent cholangiocarcinoma patient

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

  Dataset EGAD00001015972

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

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

  Dataset EGAD00001015973

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

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

  Dataset EGAD00001015977

• Genome and transcriptome sequence data from a radiation induced sarcoma patient

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

  Dataset EGAD00001015978

• Genome and transcriptome sequence data from a dedifferentiated uterine leiomyosarcoma patient

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

  Dataset EGAD00001015979

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

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

  Dataset EGAD00001015980

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

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

  Dataset EGAD00001015982

• Genome and transcriptome sequence data from a carcinoma of the rete-testis patient

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

  Dataset EGAD00001015984

• Genome and transcriptome sequence data from a right proximal humerus osteosarcoma patient

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

  Dataset EGAD00001015986

• Genome and transcriptome sequence data from a clear cell carcinoma of the left ovary patient

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

  Dataset EGAD00001015987

• Genome and transcriptome sequence data from a cholangiocarcinoma patient

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

  Dataset EGAD00001015990

• Genome and transcriptome sequence data from a metastatic minor salivary gland adenoid cystic carcinoma of trachea patient

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

  Dataset EGAD00001015992

• Genome and transcriptome sequence data from a metastatic chordoma of the c-spine patient

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

  Dataset EGAD00001015995

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

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

  Dataset EGAD00001015999

• Genome and transcriptome sequence data from a epitheloid angiosarcoma of bone patient

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

  Dataset EGAD00001016000

• Genome and transcriptome sequence data from a esthesioneuroblastoma recurrent patient

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

  Dataset EGAD00001016001

• 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 EGAD00001016002

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

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

  Dataset EGAD00001016003

• Genome and transcriptome sequence data from a dedifferentiated liposarcoma patient

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

  Dataset EGAD00001016008

• Genome and transcriptome sequence data from a sclerosing epithelioid fibrosarcoma patient

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

  Dataset EGAD00001016009

• Genome and transcriptome sequence data from a ewing sarcoma patient

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

  Dataset EGAD00001016011

• Genome and transcriptome sequence data from a clear cell carcinoma of the left ovary patient

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

  Dataset EGAD00001016012

• Genome and transcriptome sequence data from a uterine leiomyosarcoma patient

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

  Dataset EGAD00001015863

• Genome and transcriptome sequence data from a goblet cell adenocarcinoma of the appendix patient

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

  Dataset EGAD00001015865

• Genome and transcriptome sequence data from a small cell carcinoma of the cervix patient

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

  Dataset EGAD00001015868

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

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

  Dataset EGAD00001015870

• Genome and transcriptome sequence data from a astrocytoma patient

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

  Dataset EGAD00001015871

• Genome and transcriptome sequence data from a oligodendroglioma patient

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

  Dataset EGAD00001015874

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

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

  Dataset EGAD00001015875

• Genome and transcriptome sequence data from a metastatic cholangiocarcinoma vs unknown primary patient

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

  Dataset EGAD00001015876

• Genome and transcriptome sequence data from a uterine leiomyosarcoma patient

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

  Dataset EGAD00001015882

• 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 EGAD00001015884

• 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 EGAD00001015886

• Genome and transcriptome sequence data from a metastatic high grade small cell neuroendocrine carcinoma patient

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

  Dataset EGAD00001015887

• Genome and transcriptome sequence data from a metastatic osteosarcoma patient

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

  Dataset EGAD00001015888

• 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 EGAD00001015893

• Genome and transcriptome sequence data from a nasopharyngeal carcinoma patient

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

  Dataset EGAD00001015896