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• Multiple paralogues and recombination mechanisms contribute to the high incidence of 22q11.2 Deletion Syndrome

  To enable haplotype-specific assembly and rearrangement mapping in LCR22 clusters, we combined fiber-FISH optical mapping with whole genome (ultra-)long read sequencing or rearrangement-specific long-range PCR on 254 duos families (22q11.2DS patient and parent-of-origin) comprising several different LCR22-mediated rearrangements.

  Study EGAS50000000601

• DAC for human-derived clonal organoid studies

  This is the DAC for human-derived clonal organoid culture studies. It includes the study to investigate the clonal evolution of metastatic CRC at the single-cell level, where we performed WGS in 58 clonal organoids and 18 fresh-frozen (FT) bulk-tissue samples from surgically resected primary and metastatic tumors before and after anticancer therapies in 6 patients. This approach enabled detailed phylogenetic reconstruction of individual clones. We discovered the timing and burden of treatment-related mutations as well as the heterogeneous evolution in driver mutations and genomic rearrangements in late-stage clonal evolution under anticancer therapies in metastatic CRC.

  Dac EGAC50000000628

• Identification of genetic mutations characteristic for recurrence and metastasis of lymphoma.

  We collected the cancerous tissues of the primary and recurrence tumors from the same patient with recurrent B cell lymphoma, and the purpose of this study is to find the characteristics of recurrent B cell lymphoma by carrying out a "molecular profiling", mainly the exome sequence analysis of these tissues.

  Study JGAS000087

• Identification of genetic mutations characteristic for recurrence and metastasis of gastric cancer.

  We collected the cancerous tissues of the primary and recurrence tumors from the same patient with recurrent / metastatic gastric cancer, and the purpose of this study is to find the characteristics of recurrent / metastatic gastric cancers by carrying out a "molecular profiling", mainly the exome sequence analysis of these tissues.

  Study JGAS000086

• Variant calling for IMMU-SCCHN1 cohort

  The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence this interaction. This cohort includes patients with confirmed locally recurrent and/or metastatic squamous cell carcinoma of the head and neck (SCCHN) who receive first-line treatment with immune checkpoint inhibitors (ICI) or ICI combined with chemotherapy. This dataset contains whole exome sequencing data from tumor and matching germline samples processed with the Vegan pipeline. It includes SNP and CNV calling.

  Dataset EGAD50000002205

• Whole-genome and transcriptome sequencing of tumor-stage mycosis fungoides

  Mycosis fungoides (MF) is the most common cutaneous T-cell lymphoma (CTCL), a group of malignancies derived from skin-homing malignant T cells. We subjected tumor biopsies from MF patients to whole-genome sequencing and RNA-sequencing to investigate genomic alterations and deregulated gene expression in the disease.

  Study EGAS00001002860

• Whole Exome Sequencing of cohorts of Mutant Braf mouse model melanoma DNA and germline DNA.

  Whole Exome Sequencing of cohorts of Mutant Braf mouse model melanoma DNA and germline DNA. The cohorts are (1) Mutant Braf mouse model melanomas, (2) Mutant Braf mouse model melanomas from UVR exposed mice and (3) Mutant Braf mouse model melanomas from UVR exposed, sunscreen protected mice.

  Study EGAS00001000729

• Cerebrospinal fluid circulating tumour DNA allows the characterisation and monitoring of medulloblastoma

  The molecular characterisation of medulloblastoma, the most common paediatric brain tumour, is crucial for the correct management and treatment of this heterogenous disease. In this study we show that CSF ctDNA allows the molecular characterisation and monitoring of medulloblastoma. This can ultimately facilitate the clinical management of medulloblastoma patients.

  Study EGAS00001004651

• Multi-region RNA sequencing of tumour regions and tumour-adjacent normal lung tissue

  TRACERx (TRAcking Cancer Evolution through therapy (Rx)) is a prospective cohort study designed to investigate intratumor heterogeneity (ITH) in relation to clinical outcome, and to determine the clonal nature of driver events and evolutionary processes in early stage non-small cell lung cancer (NSCLC).

  Study EGAS00001006517

• Smart-seq3 scRNA-seq of cells from primary (OV2295) and metastatic (OV2295R2) high-grade serous ovarian cancer cell-line

  In this project, single cells extracted from two high-grade serous ovarian cancer cell-lines, one primary (OV2295) and one metastatic (OV2295R2), where split into two 384 well plates and libraries were prepared using Smart-seq3 single cell RNA sequencing (Hagemann-Jensen et al, 2020).

  Study EGAS00001006868