Search Results - EGA European Genome-Phenome Archive

Acral Melanoma PDXs from the admixed Brazilian Population - Tumour and unfiltered PDX sample CRAM files - Whole exome sequencing data

CRAM files containing the whole exome data for Tumours, and unfiltered Patient Derived Xenograft samples mapped to build GRCh38. 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 EGAD00001015740

Acral Melanoma PDXs from the admixed Brazilian Population - Tumour 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 Acral Tumours. 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 EGAD00001015741

Acral Melanoma PDXs from the admixed Brazilian Population - Tumour and unfiltered PDX sample CRAM files - RNAseq

Patient Derived Xenograft RNAseq sample CRAM files mapped to build GRCh38. 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 EGAD00001015742

Acral Melanoma PDXs from the admixed Brazilian Population- Tumour RNA expression data - 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 Tumour samples. 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 EGAD00001015745

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

Genomic and Functional Profiling of Acral Melanoma from the admixed Brazilian Population Reveals Disease Drivers and Targetable Vulnerabilities

Acral melanoma, a subtype of melanoma characterized by its occurrence on palms, soles, and beneath the nails, presents unique challenges in diagnosis and treatment due to its distinct genetic and environmental factors. Despite recent advancements in targeted therapies for melanoma, the efficacy of treatments in acral melanoma remains limited, emphasizing the urgent need for a deeper understanding of its genetic landscape. CRISPR-based functional genomics screening has emerged as a powerful tool for uncovering genetic dependencies and potential therapeutic targets in various cancers. In this project, we present the results of CRISPR screening performed on acral melanoma cell lines to identify genes essential for cell survival and proliferation collectively termed “fitness". Through this screening approach, we aim to elucidate the molecular mechanisms underlying the pathogenesis of acral melanoma and identify novel therapeutic vulnerabilities. Our findings reveal key genetic drivers and pathways implicated in acral melanoma progression, offering potential targets for the development of precision therapies tailored to this aggressive subtype of melanoma

Dataset EGAD00001015690

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Acral Melanoma PDXs from the admixed Brazilian Population - Tumour and unfiltered PDX sample CRAM files - Whole exome sequencing data

Acral Melanoma PDXs from the admixed Brazilian Population - Tumour VCF files with somatic SNV and INDELs - Whole exome sequencing data

Acral Melanoma PDXs from the admixed Brazilian Population - Tumour and unfiltered PDX sample CRAM files - RNAseq

Acral Melanoma PDXs from the admixed Brazilian Population- Tumour RNA expression data - htseq count files

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

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

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

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

Genomic and Functional Profiling of Acral Melanoma from the admixed Brazilian Population Reveals Disease Drivers and Targetable Vulnerabilities

Genome and transcriptome sequence data from a high grade mucinous endometrial adenocarcinoma patient

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

Genome and transcriptome sequence data from a glioblastoma patient

Genome and transcriptome sequence data from a metastatic pulmonary adenocarcinoma patient

Genome and transcriptome sequence data from a metastatic leiomyosarcoma patient

Genome and transcriptome sequence data from a metastatic neuroendocrine carcinoma of the pancreas patient

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

Genome and transcriptome sequence data from a uterine leiomyosarcoma patient

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

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

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

Genome and transcriptome sequence data from a astrocytoma patient

Genome and transcriptome sequence data from a oligodendroglioma patient

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

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

Genome and transcriptome sequence data from a uterine leiomyosarcoma patient

Genome and transcriptome sequence data from a metastatic melanoma patient

Genome and transcriptome sequence data from a metastatic pancreatic adenocarcinoma patient

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

Genome and transcriptome sequence data from a gliomatosis cerebri anaplastic astrocytoma tumor patient

Genome and transcriptome sequence data from a osteosarcoma tumor patient

Genome and transcriptome sequence data from a neuroblastoma tumor patient

Genome and transcriptome sequence data from a metastatic alveolar rhabdomyosarcoma tumor patient

Genome and transcriptome sequence data from a neuroblastoma tumor patient

Genome and transcriptome sequence data from a minimally invasive adenocarcinoma tumor patient

Genome and transcriptome sequence data from a glioblastoma tumor patient

Genome and transcriptome sequence data from a neuroblastoma tumor patient

Genome and transcriptome sequence data from a papillary thyroid carcinoma tumor patient

Genome and transcriptome sequence data from a plexiform neurofibroma tumor patient

Genome and transcriptome sequence data from a metastatic osteosarcoma tumor patient

Genome and transcriptome sequence data from a embryonal rhabdomyosarcoma of the nasopharynx tumor patient

Genome and transcriptome sequence data from a diffuse aarge B-cell lymphoma (relapse) tumor patient