7825 results for "canc*"

in 39.68 milliseconds.

• Genome and transcriptome sequence data from a colorectal cancer patient

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

  Dataset EGAD00001016033

• 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 EGAD00001016034

• Genome and transcriptome sequence data from a solitary fibrous metastatic tumor patient

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

  Dataset EGAD00001016035

• Genome and transcriptome sequence data from a leiomyosarcoma patient

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

  Dataset EGAD00001016036

• Genome and transcriptome sequence data from a primary unknown patient

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

  Dataset EGAD00001016037

• Genome and transcriptome sequence data from a metastatic large cell neuroendocrine carcinoma of colon patient

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

  Dataset EGAD00001016038

• Genome and transcriptome sequence data from a metastatic anal scc patient

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

  Dataset EGAD00001016039

• 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 EGAD00001016040

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

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

  Dataset EGAD00001016041

• Genome and transcriptome sequence data from a mandible osteosarcoma patient

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

  Dataset EGAD00001016042

• 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 EGAD00001016043

• Genome and transcriptome sequence data from a metastatic high-grade neuroendocrine carcinoma (parotid primary) patient

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

  Dataset EGAD00001016044

• Genome and transcriptome sequence data from a cervical adenocarcinoma patient

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

  Dataset EGAD00001016045

• 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 EGAD00001016046

• Genome and transcriptome sequence data from a metastatic neuroendocrine tumor patient

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

  Dataset EGAD00001016047

• Genome and transcriptome sequence data from a metastatic esophageal adenocarcinoma patient

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

  Dataset EGAD00001016048

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

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

  Dataset EGAD00001016049

• Genome and transcriptome sequence data from a thymoma patient

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

  Dataset EGAD00001016050

• Genome and transcriptome sequence data from a intrahepatic cholangiocarcinoma patient

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

  Dataset EGAD00001016051

• 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 EGAD00001015913

• Genome and transcriptome sequence data from a multifocal hepatocellular carcinoma patient

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

  Dataset EGAD00001015914

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

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

  Dataset EGAD00001015915

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

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

  Dataset EGAD00001015916

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

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

  Dataset EGAD00001015917

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

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

  Dataset EGAD00001015918

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

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

  Dataset EGAD00001015919

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

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

  Dataset EGAD00001015920

• Genome and transcriptome sequence data from a wildtype glioblastoma patient

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

  Dataset EGAD00001015921

• 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 EGAD00001015922

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

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

  Dataset EGAD00001015923

• 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 EGAD00001015924

• Genome and transcriptome sequence data from a metastatic gastroentero-pancreatic well differentiated net patient

  Genome and transcriptome sequence data from a metastatic gastroentero-pancreatic well differentiated net patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001015925

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

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

  Dataset EGAD00001015926

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

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

  Dataset EGAD00001015927

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

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

  Dataset EGAD00001015928

• 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 EGAD00001015929

• 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 EGAD00001015930

• Genome and transcriptome sequence data from a metastatic rectal small cell cancer patient

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

  Dataset EGAD00001015931

• Genome and transcriptome sequence data from a metastatic pancreatic cancer patient

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

  Dataset EGAD00001015932

• Genome and transcriptome sequence data from a recurrent salivary gland (myoepithelial carcinoma) patient

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

  Dataset EGAD00001015933

• 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 EGAD00001015934

• Genome and transcriptome sequence data from a recurrent granulosa tumour patient

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

  Dataset EGAD00001015935

• Genome and transcriptome sequence data from a metastatic well differentiated neuroendocrine tumour patient

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

  Dataset EGAD00001015936

• 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 EGAD00001015937

• Genome and transcriptome sequence data from a advanced endometrioid carcinoma (primary unknown) patient

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

  Dataset EGAD00001015938

• 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 EGAD00001015939

• Genome and transcriptome sequence data from a invasive metastatic adenocarcinoma, originating from extramammary paget’s disease patient

  Genome and transcriptome sequence data from a invasive metastatic adenocarcinoma, originating from extramammary paget’s disease patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001015940

• Genome and transcriptome sequence data from a recurrent high grade serous ovarian cancer patient

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

  Dataset EGAD00001015941

• 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 EGAD00001015942

• 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 EGAD00001015943

• Genome and transcriptome sequence data from a metastatic colon cancer patient

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

  Dataset EGAD00001015944

• Genome and transcriptome sequence data from a histiocytic sarcoma patient

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

  Dataset EGAD00001015945

• Genome and transcriptome sequence data from a astrocytoma li fraumeni syndrome patient

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

  Dataset EGAD00001015946

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

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

  Dataset EGAD00001015947

• 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 EGAD00001015948

• Genome and transcriptome sequence data from a triple negative breast cancer patient

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

  Dataset EGAD00001015949

• Genome and transcriptome sequence data from a primary unknown – possibly lung patient

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

  Dataset EGAD00001015950

• 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 EGAD00001015951

• Genome and transcriptome sequence data from a thymoma patient

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

  Dataset EGAD00001015952

• Genome and transcriptome sequence data from a renal cell carcinoma, non-clear cell patient

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

  Dataset EGAD00001015953

• 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 EGAD00001015954

• Genome and transcriptome sequence data from a synovial sarcoma patient

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

  Dataset EGAD00001015985

• Genome and transcriptome sequence data from a metastatic lung adenocarcinoma patient

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

  Dataset EGAD00001015955

• Genome and transcriptome sequence data from a metastatic adenoid cystic carcinoma patient

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

  Dataset EGAD00001015956

• 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 EGAD00001015957

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

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

  Dataset EGAD00001015958

• 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 EGAD00001015959

• Genome and transcriptome sequence data from a malignant paraganglioma patient

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

  Dataset EGAD00001015960

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

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

  Dataset EGAD00001015961

• Whole genome sequencing data of high-grade serous ovarian cancer samples (set 7a)

  Whole genome sequencing data of 36 high-grade serous carcinoma (HGSC) patients (89 samples) sequenced with HiSeq X Ten.

  Dataset EGAD00001010845

• Ovarian cancer cfDNA dataset

  The dataset contains 23 ovarian cancer and 2 healthy control urine cfDNA samples. Shallow WGS was performed on an Illumina Novaseq S4 PE150bp. Samples are provided as raw reads without any prior processing.

  Dataset EGAD00001010848

• Sequence of breast cancer bone metastases PDX from 2 targeted panels

  Sequence of breast cancer bone metastases PDX obtained by 2 targeted panels

  Dataset EGAD00001010856

• Sequence of breast cancer bone metastases PDX from 2 targeted panels

  Sequence of breast cancer bone metastases PDX obtained by 2 targeted panels

  Dataset EGAD00001010860

• Melanoma PEACE Dataset

  Dataset for the initial melanoma PEACE paper in Cancer Discovery, March 2023.

  Dataset EGAD00001010877

• Molecular risk stratification in patients with T1 colorectal cancer_WES

  The introduction of bowel cancer screening has led to a significant increase in the proportion of patients being diagnosed with asymptomatic, early-stage colorectal cancer (CRC). Although the majority of these patients are successfully treated with surgery alone, a small proportion of patients have 'born-to-be-bad' aggressive lesions with early dissemination leading to distant metastases. Current standard of care histological assessment is unable to distinguish between these aggressive versus non-aggressive early lesions which is essential to provide appropriate clinical management decisions. This study aims to carry out molecular and histological profiling of approximately 300 T1 CRCs in order to develop a molecular stratifier based on the risk of relapse in early-invasive CRC. This novel T1 cohort will represent the world's largest molecularly characterised T1 cohort of samples, with digital pathology assessment alongside whole exome sequencing, copy number variation analysis and 3' RNA-seq. This data will be used to generate a robust panel of molecular and/or histological markers applicable to formalin-fixed paraffin embedded (FFPE) archival tissue which discriminates between T1 lesions based on risk of relapse, which will ultimately be used to inform clinical management of CRC at the earliest stages of the disease.

  Dataset EGAD00001010890

• The dataset for Single molecule genome-wide mutation profiles of cell-free DNA for non-invasive detection of cancer

  The dataset for Single molecule genome-wide mutation profiles of cell-free DNA for non-invasive detection of cancer includes 57 BAM files from whole genome next-generation sequencing on the Illumina HiSeq2500. The samples analyzed include plasma samples from individuals with and without cancer.

  Dataset EGAD00001010891

• WGS/WES analysis refines molecular subtypes of hepatocellular carcinoma

  This work aims to identify homogeneous and robust molecular subtypes in HCC based on a large, homogenous and well-annotated cohort. We performed whole genome/exome sequencing (WGS/WES) on 529 HCC from 461 patients collected mainly in France. Based on the genomic data, we identified 9 robust HCC subtypes primarily driven by key mutations. We further characterized these subtypes using genomic and clinicopathological features. Among the 9 subtypes, 5 belonged to chromosome instable tumors, while 3 belonged to chromosome stable tumors. Our subtypes were associated with prognosis and showed distinct distributions across features like etiology and gender. This study offers a comprehensive molecular classification of HCC, enhancing our understanding of hepatocarcinogenesis and supporting the development of genome-based precision medicine for liver cancer.

  Dataset EGAD00001015428

• SGCC GASCAD-II dataset

  The GASCAD-II dataset from the Singapore Gastric Cancer Consortium includes paired tumor-blood whole exome sequencing data for 209 gastric cancer (GC) patients, along with whole transcriptome sequencing data for 125 GC samples. Whole exome sequencing was conducted using Agilent SureSelect Human All Exon V6 kits. For RNA sequencing, total RNA was isolated using the RNeasy Mini Kit, and libraries were prepared with the TruSeq Stranded Total RNA with Ribo-Zero Gold protocol (Illumina). Aligned BAM files for both exome and RNAseq data are included in this dataset

  Dataset EGAD00001015433

• Sequencing data for oesophageal and related samples - Linossi et al

  Data supporting: "Utility of ctDNA assessment after six weeks of immunotherapy to predict radiological response in advanced oesophageal cancer" Linossi et al

  Dataset EGAD00001015434

• Geographic and age-related variations in mutational processes in colorectal cancer - patient metadata files (Mutographs)

  Geographic and age-related variations in mutational processes in colorectal cancer - patient metadata files (Mutographs)

  Dataset EGAD00001015437

• RNA sequencing of Hepatoblastoma cell lines and drug-treated HepG2 xenograft tumors

  RNA sequencing was performed on 7 pediatric liver cancer cell lines, complementing a panel of 8 cell lines previously described (Hirsch, Cancer Discov. 2021) and on 16 HepG2 xenograft tumors treated with cisplatin, low-dose elimusertib, elimusertib at MTD, or elimusertib/cisplatin compared to vehicle-treated controls.

  Dataset EGAD00001015439

• RNA-Seq Dataset of Organoid drug profiling identifies methotrexate as a therapy for SCCOHT, a rare pediatric cancer

  We generated and characterized tumoroids from small cell carcinoma of the ovary, hypercalcemic type. Furthermore, we identified a drug that is selective and effective against SCCOHT tumoroids.

  Dataset EGAD00001015441

• WGS Dataset of Organoid drug profiling identifies methotrexate as a therapy for SCCOHT, a rare pediatric cancer

  We generated and characterized tumoroids from small cell carcinoma of the ovary, hypercalcemic type. Furthermore, we identified a drug that is selective and effective against SCCOHT tumoroids.

  Dataset EGAD00001015442

• A developmental cell atlas of the human thyroid gland - WGS

  The thyroid gland produces hormones essential for health from embryogenesis to adulthood. Thyroid disorders, including congenital hypothyroidism and thyroid carcinoma, are prevalent and pose significant health challenges. Congenital hypothyroidism often results from thyroid dysgenesis or impaired hormone synthesis, is particularly prevalent in trisomy 21 (T21), while thyroid carcinoma is the most frequent endocrine malignancy, affecting both paediatric and adult populations. Understanding the molecular basis of these conditions requires deeper insights into fetal thyroid development. We generated a spatiotemporal atlas of the human thyroid during early pregnancy, revealing key cell types, including hormone-producing thyrocytes. Thyroid follicular cells are heterogeneous, with two functional cell states (fTFC1, fTFC2) that persist into adulthood, with fTFC2 characterised by elevated PAX8 expression. We demonstrated that T21 thyroids displayed dysgenesis with disrupted follicular morphology, and altered extracellular matrix interactions, and that the fTFC2 signature was enriched in paediatric papillary thyroid cancer compared to adults. These findings uncover thyrocyte heterogeneity across the lifespan, advancing understanding of thyroid development and disease.

  Dataset EGAD00001015447

• A developmental cell atlas of the human thyroid gland - RNA

  The thyroid gland produces hormones essential for health from embryogenesis to adulthood. Thyroid disorders, including congenital hypothyroidism and thyroid carcinoma, are prevalent and pose significant health challenges. Congenital hypothyroidism often results from thyroid dysgenesis or impaired hormone synthesis, is particularly prevalent in trisomy 21 (T21), while thyroid carcinoma is the most frequent endocrine malignancy, affecting both paediatric and adult populations. Understanding the molecular basis of these conditions requires deeper insights into fetal thyroid development. We generated a spatiotemporal atlas of the human thyroid during early pregnancy, revealing key cell types, including hormone-producing thyrocytes. Thyroid follicular cells are heterogeneous, with two functional cell states (fTFC1, fTFC2) that persist into adulthood, with fTFC2 characterised by elevated PAX8 expression. We demonstrated that T21 thyroids displayed dysgenesis with disrupted follicular morphology, and altered extracellular matrix interactions, and that the fTFC2 signature was enriched in paediatric papillary thyroid cancer compared to adults. These findings uncover thyrocyte heterogeneity across the lifespan, advancing understanding of thyroid development and disease.

  Dataset EGAD00001015448

• Somatic mutation in edited cholangiocyte organoids

  Primary human cells cultured in organoid format have great promise as potential regenerative cellular therapies. However, their immunogenicity and mutagenic profile remain unresolved, impeding effective long-term translation to the clinic. In this study we report, for the first time, the generation of human leukocyte antigen (HLA)-I and HLA-II knock-out human expandable primary cholangiocyte organoids (PCOs) using CRISPR-Cas9 as a potential ‘universal’ low-immunogenic therapy for bile duct disorders. HLA-edited PCOs (ePCOs) displayed the same phenotypic and functional characteristics as parental unedited PCOs. Despite minimal off-target edits, duplex sequencing approaches demonstrated that ePCOs and PCOs acquire mutations in culture at similar rates, but without evident selection for cancer-driver mutations. ePCOs induced reduced T cell-mediated immunity and donor-dependent NK cell cytotoxicity in vitro and evaded cytotoxic responses with increased graft survival in humanized mice in vivo. Our findings have important implications for assessment of safety and immunogenicity of primary cell-derived organoid cellular therapies.

  Dataset EGAD00001015455

• Somatic mutation in edited cholangiocyte organoids

  Primary human cells cultured in organoid format have great promise as potential regenerative cellular therapies. However, their immunogenicity and mutagenic profile remain unresolved, impeding effective long-term translation to the clinic. In this study we report, for the first time, the generation of human leukocyte antigen (HLA)-I and HLA-II knock-out human expandable primary cholangiocyte organoids (PCOs) using CRISPR-Cas9 as a potential ‘universal’ low-immunogenic therapy for bile duct disorders. HLA-edited PCOs (ePCOs) displayed the same phenotypic and functional characteristics as parental unedited PCOs. Despite minimal off-target edits, duplex sequencing approaches demonstrated that ePCOs and PCOs acquire mutations in culture at similar rates, but without evident selection for cancer-driver mutations. ePCOs induced reduced T cell-mediated immunity and donor-dependent NK cell cytotoxicity in vitro and evaded cytotoxic responses with increased graft survival in humanized mice in vivo. Our findings have important implications for assessment of safety and immunogenicity of primary cell-derived organoid cellular therapies.

  Dataset EGAD00001015456

• Somatic mutation in edited cholangiocyte organoids

  Primary human cells cultured in organoid format have great promise as potential regenerative cellular therapies. However, their immunogenicity and mutagenic profile remain unresolved, impeding effective long-term translation to the clinic. In this study we report, for the first time, the generation of human leukocyte antigen (HLA)-I and HLA-II knock-out human expandable primary cholangiocyte organoids (PCOs) using CRISPR-Cas9 as a potential ‘universal’ low-immunogenic therapy for bile duct disorders. HLA-edited PCOs (ePCOs) displayed the same phenotypic and functional characteristics as parental unedited PCOs. Despite minimal off-target edits, duplex sequencing approaches demonstrated that ePCOs and PCOs acquire mutations in culture at similar rates, but without evident selection for cancer-driver mutations. ePCOs induced reduced T cell-mediated immunity and donor-dependent NK cell cytotoxicity in vitro and evaded cytotoxic responses with increased graft survival in humanized mice in vivo. Our findings have important implications for assessment of safety and immunogenicity of primary cell-derived organoid cellular therapies.

  Dataset EGAD00001015457

• 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

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

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

  Dataset EGAD00001015485

• Geographic and age-related variations in mutational processes in colorectal cancer - filtered vcf files (Mutographs)

  Geographic and age-related variations in mutational processes in colorectal cancer - filtered vcf files (Mutographs)

  Dataset EGAD00001015486

• Neoantigen Immunogenicity Landscapes and Evolution of Tumor Ecosystems During Immunotherapy with Nivolumab

  We performed Whole Exome (WXS) and RNASeq sequencing on samples obtained from the same site before and during therapy from our prospective clinical trial (CA209-153, NCT02066636) of nivolumab in advanced Non-small cell lung cancer (NSCLC) patients that progressed on chemotherapy. There are 58 pre and 42 on therapy WXS samples and 24 pre and 12 on therapy RNASeq samples. All WXS tumor samples have matching normal samples.

  Dataset EGAD00001011302

• Whole genome sequencing data of high-grade serous ovarian cancer samples (set 8a)

  Whole genome sequencing data of 26 high-grade serous carcinoma (HGSC) patients (87 samples) sequenced with MGISEQ-2000 and HiSeq X Ten.

  Dataset EGAD00001011304