Search Results - EGA European Genome-Phenome Archive

Combination Immune Checkpoint Inhibition in Australian Rare Cancers_WES

Combination immune checkpoint inhibition (ICI) with anti-CTLA-4 and anti-PD-1 blockade has demonstrated significant clinical activity across tumour types. Rare cancer patients have limited treatment options due to the scarcity of studies of novel treatment options, so they are often offered chemotherapies untested in their disease. ONJ2016-001/CA209-538 is a prospective, multicentre clinical trial of combination ICI (ipilimumab and nivolumab) in patients with advanced rare cancers, including biliary tract, adrenocortical, rare gynaecological and neuroendocrine cancers (https://clinicaltrials.gov/ct2/show/NCT02923934). The primary endpoint is clinical benefit rate (complete response + partial response + stable disease >3 months) by RECIST 1.1. This study involves generation and analysis of pre-treatment formalin fixed paraffin embedded (FFPE) tumour DNA sequencing data, paired with germline DNA sequencing data, to potentially identify genomic biomarkers that may associate with clinical benefit or other clinical efficacy / toxicity metrics.

Dataset EGAD00001015465

A Tumour Organoid Biobank for Mapping Cancer Cell Vulnerabilities - TGS

Targeted gene sequencing data from cancer patient-derived organoids and their matched tumour tissue samples. Part of a study to include genomic and transcriptomic sequencing data, along with CRISPR screening data from cancer patient-derived organoids and matched tumour tissues. Some organoids were developed as part of the Human Cancer Models Initiative (HCMI) in collaboration with Cancer Research UK (CRUK). The study includes organoids derived from colorectal, oesophageal, ovarian, pancreatic, and stomach cancer samples.

Dataset EGAD00001015468

A Tumour Organoid Biobank for Mapping Cancer Cell Vulnerabilities - WGS

Whole genome sequencing data from cancer patient-derived organoids and their matched tumour tissue samples. Part of a study to include genomic and transcriptomic sequencing data, along with CRISPR screening data from cancer patient-derived organoids and matched tumour tissues. Some organoids were developed as part of the Human Cancer Models Initiative (HCMI) in collaboration with Cancer Research UK (CRUK). The study includes organoids derived from colorectal, oesophageal, ovarian, pancreatic, and stomach cancer samples.

Dataset EGAD00001015469

A Tumour Organoid Biobank for Mapping Cancer Cell Vulnerabilities - RNA

RNA sequencing data from cancer patient-derived organoids. Part of a study to include genomic and transcriptomic sequencing data, along with CRISPR screening data from cancer patient-derived organoids and matched tumour tissues. Some organoids were developed as part of the Human Cancer Models Initiative (HCMI) in collaboration with Cancer Research UK (CRUK). The study includes organoids derived from colorectal, oesophageal, ovarian, pancreatic, and stomach cancer samples.

Dataset EGAD00001015470

The earliest stages of neoplastic transformation in Familial Adenomatous Polyposis

The succession of somatic genetic events associated with the conversion of a normal colorectal epithelial cell into a colorectal carcinoma constitutes a paradigmatic model of cancer development. Familial Adenomatous Polyposis (FAP) is caused by constitutional inactivating mutations in APC, the central gatekeeper gene of colorectal cancer, and is associated with a substantially increased lifetime-risk of colorectal cancer. To investigate the earliest stages of neoplastic change due to APC inactivation, we microdissected and individually whole genome sequenced 279 histologically normal and abnormal colorectal crypts from 15 individuals with FAP. Histologically normal crypts generally exhibited similar mutation burdens and mutational signatures to normal crypts from wild-type individuals of the same age, with 1/110 carrying a somatic inactivating APC mutation. By contrast, 9/18 aberrant crypt foci carried somatic APC mutations and exhibited modestly increased burdens of some mutational signatures found in normal crypts. 12/13 diminutive adenomatous polyps (less than 5mm diameter) showed somatic APC mutations and carried substantially increased mutation loads of most mutational signatures present in normal crypts. Phylogenetic trees of crypts from aberrant crypt foci and adenomatous polyps revealed that some had acquired their initiating somatic APC mutations decades previously during the first few years of life. The results catalogue the changes in somatic mutation rates, mutational processes and “driver” mutations in cancer genes during the earliest stages of colorectal neoplastic transformation initiated by APC inactivation and highlight the long periods of clonal evolution required for a cancer to develop.

Dataset EGAD00001015471

The earliest stages of neoplastic transformation in Familial Adenomatous Polyposis

The succession of somatic genetic events associated with the conversion of a normal colorectal epithelial cell into a colorectal carcinoma constitutes a paradigmatic model of cancer development. Familial Adenomatous Polyposis (FAP) is caused by constitutional inactivating mutations in APC, the central gatekeeper gene of colorectal cancer, and is associated with a substantially increased lifetime-risk of colorectal cancer. To investigate the earliest stages of neoplastic change due to APC inactivation, we microdissected and individually whole genome sequenced 279 histologically normal and abnormal colorectal crypts from 15 individuals with FAP. Histologically normal crypts generally exhibited similar mutation burdens and mutational signatures to normal crypts from wild-type individuals of the same age, with 1/110 carrying a somatic inactivating APC mutation. By contrast, 9/18 aberrant crypt foci carried somatic APC mutations and exhibited modestly increased burdens of some mutational signatures found in normal crypts. 12/13 diminutive adenomatous polyps (less than 5mm diameter) showed somatic APC mutations and carried substantially increased mutation loads of most mutational signatures present in normal crypts. Phylogenetic trees of crypts from aberrant crypt foci and adenomatous polyps revealed that some had acquired their initiating somatic APC mutations decades previously during the first few years of life. The results catalogue the changes in somatic mutation rates, mutational processes and “driver” mutations in cancer genes during the earliest stages of colorectal neoplastic transformation initiated by APC inactivation and highlight the long periods of clonal evolution required for a cancer to develop.

Dataset EGAD00001015477

DERMATLAS: Hidradenoma papilliferum_RNAseq

Virtually no other tumour type is associated with so many different forms as skin cancer. Histologically, tumours of the skin may arise from epithelium, including epidermis, hair follicle, sebaceous or sweat gland, melanocytes, dermal-associated mesenchymal structures or tissue resident immune cells, making for a diversity of clinical presentations. Importantly, many skin tumour types have an extremely poor prognosis. Many skin tumour subtypes have never undergone molecular profiling, or if they have, targeted sequencing has been used and the number of cases analyzed has been so limited that deriving firm conclusions about the profile of driver genes, DNA mutational signatures and germline alleles has not been possible.For 70 key skin tumour subtypes defined by the World Health Organization, that have not undergone extensive genetic analysis previously, we propose to perform whole exome and transcriptome sequencing, from a range of body sites, to build a genomic atlas of dermatological tumours, including detailed maps of SNVs, copy number alterations, genome-wide methylation and expression profiles.

Dataset EGAD00001015480

DERMATLAS: Hidradenoma papilliferum_WES

Virtually no other tumour type is associated with so many different forms as skin cancer. Histologically, tumours of the skin may arise from epithelium, including epidermis, hair follicle, sebaceous or sweat gland, melanocytes, dermal-associated mesenchymal structures or tissue resident immune cells, making for a diversity of clinical presentations. Importantly, many skin tumour types have an extremely poor prognosis. Many skin tumour subtypes have never undergone molecular profiling, or if they have, targeted sequencing has been used and the number of cases analyzed has been so limited that deriving firm conclusions about the profile of driver genes, DNA mutational signatures and germline alleles has not been possible.For 70 key skin tumour subtypes defined by the World Health Organization, that have not undergone extensive genetic analysis previously, we propose to perform whole exome and transcriptome sequencing, from a range of body sites, to build a genomic atlas of dermatological tumours, including detailed maps of SNVs, copy number alterations, genome-wide methylation and expression profiles.

Dataset EGAD00001015481

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Combination Immune Checkpoint Inhibition in Australian Rare Cancers_WES

A Tumour Organoid Biobank for Mapping Cancer Cell Vulnerabilities - TGS

A Tumour Organoid Biobank for Mapping Cancer Cell Vulnerabilities - WGS

A Tumour Organoid Biobank for Mapping Cancer Cell Vulnerabilities - RNA

The earliest stages of neoplastic transformation in Familial Adenomatous Polyposis

The earliest stages of neoplastic transformation in Familial Adenomatous Polyposis

DERMATLAS: Hidradenoma papilliferum_RNAseq

DERMATLAS: Hidradenoma papilliferum_WES

Geographic and age-related variations in mutational processes in colorectal cancer - sequence data (Mutographs)

Genome and transcriptome sequence data from a neuroblastoma tumor patient

Genome and transcriptome sequence data from a neuroblastoma tumor patient

Genome and transcriptome sequence data from a neurofibromatosis type 1 (NF1) tumor patient

Genome and transcriptome sequence data from a neuroblastoma tumor patient

Genome and transcriptome sequence data from a CNS sarcoma tumor patient

Genome and transcriptome sequence data from a ocular melanoma tumor patient

Genome and transcriptome sequence data from a osteosarcoma tumor patient

Genome and transcriptome sequence data from a fibrovascular brain tumor tumor patient

Genome and transcriptome sequence data from a angiosarcoma tumor patient

Genome and transcriptome sequence data from a craniopharyngioma tumor patient

Genome and transcriptome sequence data from a NHL large B cell tumor patient

Genome and transcriptome sequence data from a malignant granular cell tumor tumor patient

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

Genome and transcriptome sequence data from a neuroblastoma tumor patient

Genome and transcriptome sequence data from a osteosarcoma tumor patient

Genome and transcriptome sequence data from a aggressive fibromatosis tumor patient

Genome and transcriptome sequence data from a pineoblastoma tumor patient

Genome and transcriptome sequence data from a multifocal glioblastoma multiforme tumor patient

Genome and transcriptome sequence data from a progressive facial plexiform neurofibroma tumor patient

Genome and transcriptome sequence data from a plexiform neurofibroma tumor patient

Genome and transcriptome sequence data from a diffuse intrinsic pontine glioma tumor patient

Genome and transcriptome sequence data from a acute lymphoblastic leukemia tumor patient

Genome and transcriptome sequence data from a ewing sarcoma tumor patient

Genome and transcriptome sequence data from a ependymoma tumor patient

Genome and transcriptome sequence data from a glioblastoma tumor patient

Genome and transcriptome sequence data from a NUT midline carcinoma tumor patient

Genome and transcriptome sequence data from a angiosarcoma tumor patient

Genome and transcriptome sequence data from a pre-B all (2nd relapse in CNS) tumor 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 aggressive fibromatosis tumor patient

Genome and transcriptome sequence data from a aggressive fibromatosis tumor patient

Genome and transcriptome sequence data from a glioblastoma tumor patient

Genome and transcriptome sequence data from a neurofibromatosis type 1 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 relapsed wilms tumor tumor patient