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• Genome Wide Association Studies in ECOG 2997 Trial

  The ECOG 2997 trial was a randomized controlled trial for patients with previously untreated CLL comparing fludarabine monotherapy to the combination of fludarabine and cyclophosphamide. The initial clinical findings of this study were published in the Journal of Clinical Oncology in 2007 (JCO 25:793-8). Additional laboratory studies have also published (JCO 25:799-804).

  Study phs000621

• Washington University Coronary Artery Disease Study

  The genetic basis of coronary artery disease in individuals of non-European ancestry is largely unknown. The Washington University Coronary Artery Disease Study (WUCADS) recruited participants of non-European ancestry with and without coronary artery disease to address this question. Whole genome sequencing in WUCADS was performed at the McDonnell Genome Institute at Washington University.

  Study phs001227

• The Genetic Landscape of Mutations in Burkitt Lymphoma

  Burkitt lymphoma (BL) is characterized by deregulation of MYC, but the contribution of other genetic mutations to the disease is largely unknown. We sequenced exomes of 59 BL tumors, 14 of which had paired normal tissue. Our work elucidates commonly occurring gene-coding mutations in Burkitt lymphoma and implicates ID3 as a novel tumor suppressor gene.

  Study phs000562

• Family-Based Study on Ulcerative Colitis with Whole Exome Sequencing

  Genetic risk factors for ulcerative colitis are not well understood. We performed a family-based whole exome sequencing analysis to identify potential causal mutations. In the proband, we found a heterozygous de novo mutation in the gene HSPA1L. Our results indicate that the de novo mutation in HSPA1L is associated with ulcerative colitis.

  Study phs001251

• Exome Sequencing of Pleuropulmonary Blastoma

  Pleuropulmonary blastoma (PPB) is a rare, aggressive pediatric cancer arising from the lung or pleural cavity. In this study, we sequenced and analyzed the exomes of 15 PPB matched tumor and normal pairs. This study is part of a larger effort to characterize pediatric cancers as part of the Slim Initiative for Genomic Medicine (SIGMA) project.

  Study phs000543

• Myelodysplastic Syndrome (MDS) in Humanized Mice

  This study was to develop a faithful pre-clinical MDS patient-derived xenotransplantation model in cytokine-humanized immunodeficient "MISTRG" mice. We performed targeted genome sequencing on bone marrow from patients with MDS or AML and from bone marrow of mice engrafted with the respective patient bone marrow. Cytokine-humanized immunodeficient mice faithfully replicate human MDS.

  Study phs001778

• Somatic Mutational Analysis by Exome Sequencing Late-Stage Endometrioid Endometrial Carcinoma

  The purpose of this study was to identify somatic (tumor-specific) mutations in advanced stage endometrioid endometrial carcinoma tumor exomes. The dataset was generated at the NIH Intramural Sequencing Center (NISC) and NHGRI by next generation sequencing the exomes of 19 de-identified primary tumor DNAs, from advanced stage tumors, and matched non-tumor DNAs.

  Study phs001153

• LungMAP: Molecular Atlas of Lung Development - Human Lung Tissue

  Mammalian fetal lung development is a complex biological process. Despite considerable progress, a comprehensive understanding of the dynamic regulatory networks that govern postnatal alveolar lung development is still lacking. The purpose of this study as part of the LungMAP consortium (www.lungmap.net) is to understand the transcriptional changes in the process of mammalian lung development.

  Study phs001961

• Genomic characterization of a patient with AGS and CdLS transcriptomic comparison of his monocytes against healthy and disease control samples

  In this study, we describe an extreme genetic phenotype of two simultaneous genetic lesions, leading to broad alterations in immunophenotype and transcriptome. Whole Exome Sequencing and RNA-Sequencing of CD14+ monocytes was performed on the case patient, and RNA-sequencing was also performed on disease (Systemic Lupus Erythematosus) and healthy controls.

  Study EGAS00001007829

• Identifying and Reducing Disparities in Patient-Reported Outcomes Among African American Prostate Cancer Survivors

  This research study aimed to identify disparities in prostate cancer symptom burden and their contributors among African American, Hispanic, and non-Hispanic White prostate cancer survivors. We collected patient-reported outcomes data, focusing on various aspects of the survivors' health and well-being, clinical data, demographics data, and germline genomic data.

  Study phs003745

• An epidemiological study examining the relationship among food, health, and genome

  We conducted a cohort-based study to investigate the association between the genetic background and diet/lifestyle in 962 healthy Japanese. We analyzed the Ebetsu cohort and some participants living in Tokyo. The SNP array (Japonica Array v2) was used for genotyping. Shotgun metagenomic sequencing of fecal microbiome and metabolome of feces and blood were analyzed.

  Study JGAS000678

• Pilot study towards the development of a Companion/Complimentary Diagnosis platform using liquid biopsy with cfDNA for immune checkpoint inhibitor therapy in advanced urothelial cancer

  Preliminary analysis was conducted to develop a cfDNA-based platform capable of predicting gene mutation profiles, TMB, gene expression profiles (molecular subtype diagnosis), and immunohistochemical findings (PD-L1 expression) using the primary lesion tissue of bladder cancer and upper urinary tract epithelial cancer, verifying the feasibility of such development.

  Study JGAS000714

• Circulating Biomarker Laboratory within the Division of Cancer of Imperial College London

  The purpose of the Circulating Biomarker Laboratory within the Division of Cancer of Imperial College London (ICL) is to assist ICL researchers working on solid tumours or/and haematological malignancies with a particular interest in the analysis of liquid biopsies. We are focusing on isolating and analysing single circulating tumour cells (CTCs) and cell-free circulating tumour DNA (ctDNA) from cancer patients' blood samples but also pure tumour poulations from heterogeneous Formalin-fixed paraffin-embedded (FFPE) tissue specimens with a view to monitoring tumour-related changes, such as mutations and copy number alterations at a single cell level.

  Dac EGAC50000000768

• RNA sequencing of genetically modified human iPSCs modeling patients with autism spectrum disorders (ASD)

  We generated two genetically modified iPSC lines. In each line, a single promoter variant identified in a patient with autism spectrum disorder (ASD) was introduced by using the CRISPR/Cas9 system. These mutant lines were analyzed by RNA-seq together with control lines to assess the impact of the introduced variant.

  Study JGAS000651

• Comprehensive molecular and clinicopathological profiling of salivary duct carcinoma

  Molecular targets and predictive biomarkers for prognosis in salivary duct carcinoma (SDC) have not fully identified. We conducted comprehensive molecular profiling to discover novel biomarkers for SDC. A total of 67 SDC samples were examined with DNA sequencing of 464 genes and transcriptome analysis in combination with the clinicopathological characteristics of the individuals.

  Study JGAS000534

• Clonal structure and oncogenic potential of liver cirrhosis tissues.

  Hepatocellular carcinoma (HCC) recurrently develops in cirrhotic liver composed of numbers of regenerative nodules (RNs). The biologic or genetic basis of RNs for hepatocarcinogenesis remains unclear at present. Thus, to uncover the basis of cirrhotic liver for multicentric tumorigenesis, we investigated the oncogenic potential of RNs in LC tissues using multi-omics analysis.

  Study JGAS000134

• The prevalence and clinical characteristics of TECTA-associated autosomal dominant hearing loss.

  TECTA is well known as the causative gene for autosomal dominant mid-frequency hearing loss observed in various populations. In this study, we performed next-generation sequencing analysis of a large Japanese hearing loss cohort from unrelated autosomal dominant hearing loss families, to estimate the prevalence and phenotype-genotype correlations in patients with TECTA mutations.

  Study JGAS000201

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

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

  Study JGAS000091

• CAGEKID: Cancer Genomics of the Kidney

  The aim of CAGEKID is to carry out comprehensive detection of DNA markers for conventional (clear cell) renal carcinoma. The project includes complete analysis of somatic and constitutional DNA variation, methylation patterns and expression in a large number of constitutional/tumor pairs. CAGEKID is a part of the International Cancer Genome Consortium, ICGC.

  Study EGAS00001000083

• Prospective Lynch Syndrome Database materials

  The Prospective Lynch Syndrome Database data. These data contain necessary clinical tables to reproduce the previous PLSD papers using the clinical tables for individual level cancer incidence by age, sex and MMR gene affected. The tables contain the demographics, individual cancers at given age, and therapeutic and prophylactic surgeries removing total or partial organs.

  Study EGAS50000001715

• Clonal Evolution of PPM1D Mutations in the Spectrum of Myeloid Disorders

  PPM1D, a central regulator of the DNA damage response, is commonly mutated in therapy-related clonal hematopoiesis (CH), acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS). PPM1D mutations have been shown to expand under selective pressure of DNA-damaging chemotherapy. However, whether PPM1D mutations promote the development of hematologic malignancies remains unclear.

  Study EGAS50000000840

• PD1-targeted delivery of an IL-2 variant induces a multifaceted anti-tumoral T cell response in human lung cancer

  To explore PD1-IL2v-specific effects on CD8 and CD4 T cells at a transcriptomic level, we performed single-cell RNA sequencing of patient-derived tumor fragments (PDTFs) which were treated with either Isotype (DP47), Isotype-IL2v (DP47-IL2v), anti-PD1 (PembroPGLALA) or PD1-IL2v (PembroPGLALA-IL2v) for 48 hours.

  Study EGAS50000000396

• Evaluation of the Efficacy and Safety of a Clinical Grade Human Induced Pluripotent Stem Cell-Derived Cardiomyocyte Patch: A Pre-Clinical Study

  Cardiomyocyte-derived induced pluripotent stem cells (iPSCs) may represent a promising therapeutic strategy for severely damaged myocardium. This study aimed to assess the efficacy and safety of clinical grade human iPSC-derived cardiomyocyte (hiPSC-CM) patches and conduct a pre-clinical proof-of-concept analysis.

  Study EGAS50000000188

• ChIP-seq analysis of clear cell renal cell carcinoma

  In order to understand the epigenetic basis on ccRCC, we performed ChIP-seq on 3 ccRCC cell lines (786-O, A498, UMRC-2), and 1 normal kidney epithelium cell line (HK-2), cultured under normoxic (20% O2) and hypoxic (0.05% O2) conditions. This study analysed data from H3k4me1, H3K4me3, H3K27ac, H3k27me3, H3k36me3, CTCF, and HIF1A

  Study EGAS50000001322

• Copy number analysis of Diamond-Blackfan Anemia (DBA) using SNP array

  Diamond–Blackfan anemia (DBA), is a rare congenital anemia that usually presents in infancy. About fifty percent of DBA patients possess mutations in ribosomal protains (RPs). In this study, we performed genomic copy number analysis using SNP arrays for 27 Japanese DBA patients to detect genomic copy number lesions of the RP genes' loci.

  Study EGAS00000000105