Search Results - EGA European Genome-Phenome Archive

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 EGAD00001015847

Genome and transcriptome sequence data from a metastatic endometrial cancer patient

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

Dataset EGAD00001015848

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 EGAD00001015849

Genome and transcriptome sequence data from a melanoma (history of cll) patient

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

Dataset EGAD00001015850

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 EGAD00001015851

Genome and transcriptome sequence data from a metastatic rectal cancer patient

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

Dataset EGAD00001015852

Genome and transcriptome sequence data from a metastatic colorectal cancer patient

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

Dataset EGAD00001015853

Genome and transcriptome sequence data from a suspected radiation induced retroperitoneal sarcoma patient

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

Dataset EGAD00001015854

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 EGAD00001015855

Genome and transcriptome sequence data from a invasive ductal carcinoma of the breast patient

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

Dataset EGAD00001015856

Genome and transcriptome sequence data from a extranodal nk/t-cell lymphoma patient

Genome and transcriptome sequence data from a extranodal nk/t-cell lymphoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

Dataset EGAD00001015857

Genome and transcriptome sequence data from a metastatic colorectal cancer patient

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

Dataset EGAD00001015858

Genome and transcriptome sequence data from a cervical cancer- hpv independent gastric type adenocarcinoma patient

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

Dataset EGAD00001015859

Genome and transcriptome sequence data from a metastatic breast cancer patient

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

Dataset EGAD00001015860

Genome and transcriptome sequence data from a large cell neuroendocrine carcinoma of prostate patient

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

Dataset EGAD00001015861

Genome and transcriptome sequence data from a metastatic low grade stromal sarcoma endometrial cancer patient

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

Dataset EGAD00001015862

Ancestry and somatic profile predict acral melanoma origin and prognosis – WXS

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 EGAD00001015755

Aneuploidy in Pancreatic Cancer

WGS of pancreatic lesions

Dataset EGAD00001015734

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

PEACE (Posthumous Evaluation of Advanced Cancer Environment) whole exome sequencing data

Dataset EGAD00001015763

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

Single-cell RNA sequencing of breast cancer lung metastasis and adjacent normal tissue

This dataset contains single-cell RNA sequencing data from two samples: L1 (breast cancer metastasis to lung) and N3 (adjacent normal lung tissue) from a female patient. The samples were processed using 10X Chromium 3' technology and sequenced on Illumina NextSeq 500. This data supports the study "Endocrine therapy reprogramming of breast cancer facilitates metastatic escape via upregulation of P-Rex1/Rac1 signalling" which investigates how endocrine therapy reprograms breast cancer cells, leading to upregulation of P-Rex1/Rac1 signalling pathways that facilitate metastatic escape. The single-cell analysis reveals cellular reprogramming mechanisms in endocrine therapy-resistant breast cancer cells that form metastases in the lung.

Dataset EGAD00001015769

Resolution of tumour cell populations enhances specificity of treatment options for precision cancer medicine

This dataset comprises FASTQ files for single-cell RNA-seq and single-cell ATAC-seq data. These data were generated using 10x Genomics' multiome kit. In this cohort, there are 25 samples from 17 human cancer patients.

Dataset EGAD00001015782

Genome and transcriptome sequence data from a metastatic breast cancer patient

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

Dataset EGAD00001015962

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 de novo metastatic triple negative breast cancer patient

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

Dataset EGAD00001015964

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 metastatic breast cancer patient

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

Dataset EGAD00001015967

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 primary unknown –looks like lung with nodes and pleural disease. prior breast cancer patient

Genome and transcriptome sequence data from a primary unknown –looks like lung with nodes and pleural disease. prior breast cancer patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

Dataset EGAD00001015970

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Genome and transcriptome sequence data from a pancreatic cancer patient

Genome and transcriptome sequence data from a metastatic endometrial cancer patient

Genome and transcriptome sequence data from a pancreatic cancer patient

Genome and transcriptome sequence data from a melanoma (history of cll) patient

Genome and transcriptome sequence data from a astrocytoma patient

Genome and transcriptome sequence data from a metastatic rectal cancer patient

Genome and transcriptome sequence data from a metastatic colorectal cancer patient

Genome and transcriptome sequence data from a suspected radiation induced retroperitoneal sarcoma patient

Genome and transcriptome sequence data from a metastatic melanoma patient

Genome and transcriptome sequence data from a invasive ductal carcinoma of the breast patient

Genome and transcriptome sequence data from a extranodal nk/t-cell lymphoma patient

Genome and transcriptome sequence data from a metastatic colorectal cancer patient

Genome and transcriptome sequence data from a cervical cancer- hpv independent gastric type adenocarcinoma patient

Genome and transcriptome sequence data from a metastatic breast cancer patient

Genome and transcriptome sequence data from a large cell neuroendocrine carcinoma of prostate patient

Genome and transcriptome sequence data from a metastatic low grade stromal sarcoma endometrial cancer patient

Ancestry and somatic profile predict acral melanoma origin and prognosis – WXS

Aneuploidy in Pancreatic Cancer

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

PEACE (Posthumous Evaluation of Advanced Cancer Environment) whole exome sequencing data

Genomics Define Malignant Transformation in Myeloma Precursor Conditions

Single-cell RNA sequencing of breast cancer lung metastasis and adjacent normal tissue

Resolution of tumour cell populations enhances specificity of treatment options for precision cancer medicine

Genome and transcriptome sequence data from a metastatic breast cancer patient

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

Genome and transcriptome sequence data from a de novo metastatic triple negative breast cancer patient

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

Genome and transcriptome sequence data from a metastatic melanoma patient

Genome and transcriptome sequence data from a metastatic breast cancer patient

Genome and transcriptome sequence data from a osteosarcoma patient

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

Genome and transcriptome sequence data from a primary unknown –looks like lung with nodes and pleural disease. prior breast cancer patient

Genome and transcriptome sequence data from a metastatic gyne vs. breast cancer patient

Genome and transcriptome sequence data from a recurrent cholangiocarcinoma patient

Genome and transcriptome sequence data from a metastatic renal carcinoma patient

Genome and transcriptome sequence data from a metastatic colorectal cancer patient

Genome and transcriptome sequence data from a metastatic breast cancer patient

Genome and transcriptome sequence data from a metastatic colon cancer patient

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

Genome and transcriptome sequence data from a radiation induced sarcoma patient

Genome and transcriptome sequence data from a dedifferentiated uterine leiomyosarcoma patient

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

Genome and transcriptome sequence data from a colon cancer patient

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

Genome and transcriptome sequence data from a transformed mycosis fungoides patient

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

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

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

Genome and transcriptome sequence data from a metastatic gallbladder cancer patient

Genome and transcriptome sequence data from a metastatic solitary fibrous tumour of the left proximal thigh patient