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• Whole-exome sequencing of acute myeloid leukemias with aberrations of chromosome 7

  Deletions and partial losses of chromosome 7 are frequent in acute myeloid leukemia (AML) and are often linked to dismal outcome. However, the genomic landscape and prognostic impact of concomitant genetic aberrations remain incompletely understood. Therefore, we performed whole-exome sequencing of acute myeloid leukemias (N = 60) with aberrations of chromosome 7.

  Study EGAS50000000429

• Analysis of Complex Genomic Rearrangements of Lung Adenocarcinomas

  Lung adenocarcinomas (LADC) are heterogeneous disease with distinct etiology. A majority of tumors are related with tobacco smoking, and some tumors arise from never-smoking or young patients, whose clinical history do not support the environmental carcinogen-induced oncogenes. Here we analyzed complex rearrangements in lung adenocarcinomas including tumors with distinct etiologies.

  Study EGAS00001002801

• Subclonal diversification of primary breast cancer

  Cancers are ecosystems of genetically related clones, competing across space and time for limited resources. To understand the clonal structure of primary breast cancer, we applied genome and targeted sequencing to 295 samples from 49 patients’ tumors. The extent of subclonal diversification varied considerably among patients and encompassed many spatial patterns, including local growth, intraductal dissemination and clonal intermixture. Landmarks of disease progression, such as acquiring invasive or metastatic potential, arose within detectable subclones of antecedent lesions, suggesting that subclonal mutations could be relevant if actionable. No defined temporal order of mutation was evident, with the commonest genes, including PIK3CA, TP53, BRCA2, PTEN and MYC, mutated early in some, late in others, often exhibiting parallel evolution across subclones. Signatures of homologous recombination deficiency correlated with response to neoadjuvant chemotherapy. Thus, the interplay of mutation, growth and competition drives clonal structures of breast cancer that are complex, variable across patients and clinically relevant.

  Dataset EGAD00001000898

• A GWAS in uveal melanoma identifies risk polymorphisms in the CLPTM1L locus.

  Uveal melanoma, a rare malignant tumor of the eye, is predominantly observed in populations of European ancestry. A genome-wide association study of 259 uveal melanoma patients compared to 401 controls all of European ancestry revealed a candidate locus at chromosome 5p15.33 (region rs421284: OR = 1.7, CI 1.43-2.05). This locus was replicated in an independent set of 276 cases and 184 controls. In addition, risk variants from this region were positively associated with higher expression of CLPTM1L. In conclusion, the CLPTM1L region contains risk alleles for uveal melanoma susceptibility, suggesting that CLPTM1L could play a role in uveal melanoma oncogenesis.

  Study EGAS00001002334

• A comprehensive human gastric cancer organoid biobank captures tumor subtype heterogeneity and enables therapeutic screening​

  Gastric cancer displays marked molecular heterogeneity with aggressive behavior and treatment resistance. Therefore, good in vitro models that encompass unique subtypes are urgently needed for precision medicine development. Here, we have established a primary gastric cancer organoid (GCO) biobank that comprises normal, dysplastic, cancer and lymph node metastases (n=63) from 34 patients, including detailed whole-exome and transcriptome analysis. The cohort encompasses most known molecular subtypes (including EBV, MSI, intestinal/CIN, and diffuse/GS, with CLDN18-ARHGAP6 or CTNND1-ARHGAP26 fusions or RHOA mutations), capturing regional heterogeneity and subclonal architecture, while their morphology, transcriptome, and genomic profiles remain closely similar to in vivo tumors, even after long-term culture. Large-scale drug screening revealed sensitivity to unexpected drugs that were recently approved or in clinical trials, including Napabucasin, Abemaciclib, and the ATR inhibitor VE-822. Overall, this new GCO biobank, with linked genomic data, provides a useful resource for studying both cancer cell biology and precision cancer therapy.

  Study EGAS00001003145

• H3Africa AWI-GEN Phase 1 Phenotype

  The phenotypic data for ~12500 samples of the AWI-Gen Phase 1 Population cross-sectional study of older adults (mostly between 40 and 60 years), men and women. Six study sites in four sub-Saharan African counties including Ghana, Burkina Faso, Kenya and South Africa. Some groups are missing data for specific variables. Data includes questionnaire data (demography, health history, family health history, behaviour and infection data); anthropometry; and laboratory assays on blood and urine.

  Dataset EGAD00001006425

• Somatic Mutations and Cell Lineage in the Human Brain

  Genetic mutations causing human disease are conventionally thought to be inherited from one's parents and present in all somatic (body) cells. Increasingly however, somatic mutations are implicated in neurological diseases. Somatic mutations that arise during the cell divisions of prenatal brain development are inherited in clonal fashion and can cause neurodevelopmental diseases, even when present at low levels of mosaicism. In this study we use whole genome, RNA, and ATAC sequencing of single cells and bulk tissue to identify somatic mutations in control, and some disease, brains to: 1) identify and catalogue the mutations which shape the somatic neuronal genome; 2) perform a cell lineage analysis of the human brain using clonal somatic mutations in cortical neurons; 3) determine patterns of somatic mutations at different ages and in aging related disease phenotypes; and 4) relate cell lineage patterns to cell phenotype in the human brain through cell type-specific analyses.

  Study phs001485

• We describe a method to culture organoids from adult human kidney tissue and describe applications for the culture system.

  Adult Stem Cell (ASC)-derived organoids are 3D epithelial structures that recapitulate essential aspects of their organ of origin. We have developed conditions for the long-term growth of primary kidney epithelial organoids. Cultures can be established from mouse and human kidney tissue, as well as from urine and can be expanded for at least 20 passages (> 6 months). Chromosome numbers remain normal. Human organoids represent proximal as well as distal nephron segments, as evidenced by gene expression, immunofluorescence and tubular functional analyses. BK virus infection of organoids recapitulates in vivo phenomena. Organoids can be established from Wilms nephroblastoma. Kidney organoids from Cystic Fibrosis (CF) patient’s urine allowed ex vivo assessment of treatment efficacy. Finally, organoids cultured on microfluidic organ-on-a-chip plates adopt a tubular conformation and display active transport function. Adult kidney-derived organoids allow studies of hereditary, infectious and malignant kidney disease in a personalized fashion.

  Study EGAS00001002729

• Longitudinal profiling of the immune response to Plasmodium vivax in naive hosts by RNA-sequencing

  Plasmodium vivax offers unique challenges for control and elimination, and may prove a tougher hurdle to overcome than Plasmodium falciparum. And yet compared to P. falciparum we know very little about the innate and adaptive immune responses that need to be harnessed to reduce disease and transmission. We recently generated a blood bank of a new clonal field isolate of P. vivax (PvW1) for human challenge studies and used systems immunology tools to track the host response throughout infection and convalescence. As part of this study, RNA-sequencing was used to resolve changes in whole blood gene expression through time in 6 volunteers (7-9 time-points per volunteer). In summary, these data show that P. vivax induces two distinct transcriptional programmes in whole blood during and after infection. During infection, transcriptional profiling reveals the rapid mobilisation of an emergency myeloid response, which leads to systemic inflammation and the recruitment of all major T cell subsets into lymphoid tissues. Six days after infection, this innate response subsides and a transcriptional signature of proliferation is revealed. This most likely represents widespread activation of lymphocytes, which return to the circulation after parasite clearance - transcriptional profiling of T cells at this time-point could therefore reveal the outcomes of critical cell-cell interactions that take place within the spleen during infection. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ .

  Dataset EGAD00001006924

• Defining the metastasome in colorectal cancer: Implications for hypotheses on metastasis evolution and personalized therapy (HIPO-032)

  Personalized cancer therapy aims at individual genetic changes characterizing primary cancers. Still, however, metastasis is the major clinically unmet problem, also due to an incomplete understanding of its molecular evolution.This study is the first to define the metastasis-specific whole genome landscape of human colorectal primary vs. matched metastatic lesions.Protein coding, ncRNA genes and 3’UTRs harbored about a third each of single nucleotide variations (SNVs)/indels, 19% of them being metastasis-specific. We found novel mutational hills among ncRNAs and 3’UTRs, copy number changes able to explain changes in microRNA expression in metastases, and novel metastasis-specific mutations in the 3’UTRs on important cancer signalling genes. Some metastatic lesions showed targetable mutations not detected in the primaries. Analysis of mutual exclusivity patterns supported a model that has progressive alterations in important colorectal cancer genes and revealed new partners. Metastatic lesions were enriched in SNVs, specific structural variations, and alterations in genes affecting cell adhesion and extracellular matrix interaction.Furthermore, a hepatic stellate activation cascade was enriched in metastases, suggesting genetic programs for site-specific colonization. Allele frequency distribution and mutational signature analysis suggests a common ancestor clone to both the primary tumor and the metastasis, with additional mutagenesis ongoing in both sites independently. Taken together, our results significantly add to hypothesis generation on metastasis evolution, and suggest novel metastasis-specific genomic changes which would be missed by current personalized therapy concepts. (HIPO-032)

  Study EGAS00001002717

• Whole-Genome Sequencing of Salivary Gland Adenoid Cystic Carcinoma

  Adenoid cystic carcinomas (ACCs) of the salivary glands are challenging to understand, treat, and cure. To better understand the genetic alterations underlying the pathogenesis of these tumors, we performed comprehensive genome analyses of 25 fresh-frozen tumors, including whole genome sequencing, expression and pathway analyses. In addition to the well-described MYB-NFIB fusion which was found in 11 tumors (44%), we observed five different rearrangements involving the NFIB transcription factor gene in seven tumors (28%). Taken together, NFIB translocations occurred in 15 of 25 samples (60%, 95%CI=41–77%). In addition, mRNA expression analysis of 17 tumors revealed overexpression of NFIB in ACC tumors compared with normal tissues (p=0.002). There was no difference in NFIB mRNA expression in tumors with NFIB fusions compared to those without. We also report somatic mutations of genes involved in the axonal guidance and Rho family signaling pathways. Finally, we confirm previously described alterations in genes related to chromatin regulation and Notch signaling. Our findings suggest a separate role for NFIB in ACC oncogenesis and highlight important signaling pathways for future functional characterization and potential therapeutic targeting.

  Study EGAS00001002812

• Hypoxia acts as an environmental cue for the human TRM differentiation program

  Tissue-resident memory T-cells (TRM) provide frontline defense against infectious diseases and contribute to anti-tumor immunity; however, aside from the necessity of TGF-β, knowledge regarding TRM-inductive cues remains incomplete, particularly for human cells. Oxygen tension is an environmental cue that distinguishes peripheral tissues from the circulation and here, we demonstrate that differentiation of human CD8+ T-cells in the presence of hypoxia and TGF-β1 led to the development of a TRM phenotype, characterized by a greater than five-fold increase in CD69+CD103+ cells expressing human TRM hallmarks and enrichment for endogenous human TRM gene signatures, including increased adhesion molecule expression and decreased expression of genes involved in recirculation. Hypoxia and TGF-β1 synergized to produce a significantly larger population of TRM phenotype cells than either condition alone, and comparison of these cells from the individual and combination conditions revealed distinct phenotypic and transcriptional profiles, indicating a programming response to milieu rather than a mere expansion. Our findings identify a previously unreported cue for the TRM differentiation program and can enable facile generation of human TRM phenotype cells in vitro for basic studies and translational applications such as adoptive cellular therapy.

  Study EGAS00001005286

• Kidney tumour_DNA (2018-09-19)

  This is a bulk DNA and RNA sequencing study of human renal tumours . This dataset contains all the data available for this study on 2018-09-19.

  Dataset EGAD00001004346

• HTAN Pilot Project: Single-Cell Transcriptomics Toolbox for Fresh and Frozen Human Tumors (Lung, Breast, Ovarian, Melanoma, Neuroblastoma, Sarcoma, Glioblastoma, Glioma, and Leukemia)

  Single cell transcriptomics is a powerful tool to map the complex tumor microenvironment, providing unprecedented resolution into cell types, cell states, cell interactions, and tumor heterogeneity. Depending on their tissue site and whether processing begins from a fresh or frozen sample, different tumors require different optimizations in order to obtain high quality single cell transcriptomic data. In this study, we profiled a range of tumor types, varying in cell-of-origin, solid and non-solid forms, patient ages, and transitions. The tumors also further varied in their tissue site and in their sample collection method. To enable profiling of such diverse samples, we developed a systematic toolbox for single cell RNA-Seq and single nucleus RNA-Seq of fresh and frozen clinical tumor samples. We validated this toolbox for 216,490 cells and nuclei extracted from 39 samples across 23 tumors (some tumors were split into multiple samples). The 23 tumors represented eight unique tumor types. This toolbox comprises both experimental and computational protocols as well as guidelines for comparing and selecting protocols for the biological problem of interest.

  Study phs001983

• BCR-ABL is enriched in S- and G2-cell cycle phases

  To address the unusually long duration of imatinib therapy for chronic myelogenous leukemia, we sought to understand the expression of BCR-ABL gene expression with different phases of the cell cycle. A precedent for dynamic fusion oncoprotein expression already exists for the pediatric solid tumor, rhabdomyosarcoma. Quantitative immunocytochemistry was conducted to compare the expression of BCR-ABL with markers of each cell cycle phase: CDK6 for G1, CDK2 for S, phospho-CDC2 for G2, and phospho-HH3 for M phase. BCR-ABL expression was most strongly correlated with the G2 and S cell cycle phases. Low BCR-ABL expression only coincided with high cell cycle marker expression for the G1. BCR-ABL was rarely if at all expressed in M. Our results suggest a possible explanation for the prolonged nature of imatinib therapy, which may be only effective on S- and G2-phase actively replicating leukemia cells.

  Study EGAS00001006769

• Genomic characterization of co-existing biliary tract intraepithelial neoplasia and carcinoma lesions reveals distinct evolutionary paths of gallbladder cancer

  Gallbladder carcinoma is the most common cancer of the biliary tract with dismal survival largely due to delayed diagnosis. Biliary tract intraepithelial neoplasia (BilIN) is the common benign tumor that is suspected to be precancerous lesions. However, the genetic and evolutionary relationships between BilIN and carcinoma remain unclear. Here we performed whole-exome sequencing of coexisting low-grade BilIN (adenoma), high-grade BilIN, and carcinoma lesions, and normal tissues from the same patients.

  Study EGAS00001005402

• Whole Transcriptome Sequencing of Human Tumor Cells and Hematopoietic Stem and Progenitor Cells During Aging and Bone Marrow Disorders

  Whole transcriptome sequencing analyses were performed on human hematopoietic stem and progenitor cells during aging and bone marrow disorders. For this purpose, normal and diseased bone marrow or peripheral blood-derived mononuclear cells were FACS-purified into hematopoietic stem (CD34+CD38-Lin-) or hematopoietic progenitor (CD34+CD38+Lin-) populations. Primary human samples from healthy individuals were used along with comparative analyses in some pre-malignant and malignant conditions, including myelodysplastic syndrome (MDS), acute myeloid leukemia (AML) and plasma cell dyscrasias (e.g., multiple myeloma). Studies were also performed on total mononuclear cell fractions from patients with newly-diagnosed or relapsed multiple myeloma, or plasma cell leukemia. Briefly, RNA was extracted from all samples and quality was assessed using a Bioanalyzer instrument. Only samples with RNA integrity (RIN) values >7 were subjected to library preparation for RNA-sequencing. The SMARTer v4 cDNA amplification kit was used along with library construction by the NEB Ultra DNA kit for Illumina. Paired-end sequencing was performed on Illumina NextSeq instruments (Scripps Next Generation Sequencing Core), with all samples run over two separate flow-cells (to generate additional sequencing reads); >95M reads were generated in total for each sample. The RNA-sequencing data are available as FASTQ files.

  Study phs002291

• Extracorporeal Life Support Survival in a Pediatric Hematopoietic Cellular Transplant Recipient with Presumed Graft Versus Host Disease-Related Fulminant Myocarditis

  We report the case of a 15-year-old female with hypodiploid pre-B acute lymphoblastic leukemia status post allogeneic hematopoietic stem cell transplantation (HCT) from a matched unrelated male donor who presented on transplant day +75 with cardiac arrest due to ventricular fibrillation associated with fulminant myocarditis. Using conventional diagnostics, an exhaustive search for microbial pathogens in the heart biopsy as well as nasopharynx, blood, urine, and endotracheal aspirate was performed but did not uncover a candidate pathogen. The family consented to a research study for the use of unbiased next-generation genomic sequencing for pathogen identification in the myocardial biopsy. DNA sequencing was performed on 1.5 x 108 sequencing pairs and no microbial pathogens were identified. Interestingly, a significant component of Y-chromosomal human DNA was identified, suggesting infiltration of at least 10 donor leukocytes per host cell. This finding is grossly consistent with the lymphocyte:myocyte ratio in the biopsy according to visual inspection at 40x magnification. This case merits discussion due to (1) her survival after 17 days of veno-arterial extracorporeal life support (ECLS) and (2) the possibility of cardiotropic graft versus host disease (GVHD).

  Study phs001336

• Synovial Fibroblast Gene Expression in Response to Fibronectin Fragment

  Osteoarthritis (OA) is a prevalent joint disease characterized by the progressive degradation of articular cartilage, hypertrophy of neighboring bone, and varying degrees of synovial inflammation. Recent research has highlighted the potential role of synovial fibroblasts in the pathogenesis of OA, particularly their inflammatory properties that disrupt cartilage homeostasis. Notably, degraded cartilage matrix components, such as fibronectin fragments (FN-f), have been identified in the synovial fluid of OA patients, suggesting that FN-f signaling influences the synovium where synovial fibroblasts reside. Despite affecting over 500 million individuals globally, our limited understanding of the underlying mechanisms of OA has significantly impeded the development of effective treatment strategies. To investigate this, we obtained deidentified surgical waste material from individuals undergoing knee replacement for OA. Synovial tissue was used to isolate synovial fibroblasts for cell culture studies. We generated bulk RNA-seq data from primary synovial fibroblasts (N=5 individuals) treated at passage 3 with either Phosphate-Buffered Saline (PBS) as control or FN-f for 18h to model the OA synovial fibroblast phenotype. We identified differentially expressed genes at an adjusted p-value of

  Study phs003999

• Cambridge Neoadjuvant Cancer of the Prostate (CANCAP03): A Window Study into the Effects of Olaparib ± Degarelix in Primary Prostate Cancer.

  Study: Cambridge Neoadjuvant Cancer of the Prostate (CANCAP03): A Window Study into the Effects of Olaparib ± Degarelix in Primary Prostate Cancer. EudraCT Number: 2014-004417-86 Clinicaltrials.gov Number: NCT02324998 Purpose: Investigate combined PARP and androgen inhibition in primary prostate cancer. Aim: To understand the biological mechanism(s) underlying clinical efficacy, especially in the absence of mutations in homologous recombination (HR) repair pathways. Dataset: Single-nuclear RNA sequencing data from post-treatment radical prostatectomy tissue cores for six patients, 3 from each of olaparib and olaparib and degarelix cohorts. Samples were processed for nuclear isolation and extraction, prior to single-nuclear RNA sequencing. 10x libraries were constructed using the 10x supplied protocol, briefly: individual nuclei were trapped into droplets with a single bead, and poly A transcripts were barcoded during reverse transcription. Complementary DNA was amplified, and libraries were prepared for sequencing on NovaSeq 6000 using S4 flow cell (100k reads per cell). FASTQ files were processed using CellRanger pipeline (10X Genomics). Outputs from the CellRanger pipeline were analysed using the Seurat package (v4.9.9.9049) in R (v4.2.0). Processed data is provided as a Seurat object.

  Study EGAS50000000880

• Analysis of CD20 loss in patients treated with Mosunetuzumab

  CD20 is an established therapeutic target in B-cell malignancies. The CD20xCD3 bispecific antibody mosunetuzumab has significant efficacy in B-cell non-Hodgkin lymphomas (NHL). Since target antigen loss is a recognized mechanism of resistance, we evaluated the contribution of CD20 expression to clinical response in patients with relapsed and/or refractory NHL in the phase 1/2 GO29781 trial (ClinicalTrials.gov: NCT02500407) investigating mosunetuzumab monotherapy. CD20 was studied using immunohistochemistry (IHC), RNA sequencing, and whole-exome sequencing performed centrally in biopsies collected prior to treatment, or as paired samples at pre-dose and on-treatment, or at-progression. Prior to treatment, most patients exhibited a high proportion of tumor cells expressing CD20; however, the proportion of CD20+ tumor cells in 14/293 (6%) patients was <10%. Analyses of paired biopsies from patients during treatment revealed that CD20 levels were maintained in 29/30 (97%), vs patients with samples at-progression, in which 11/32 (34%) showed CD20 loss. Reduced transcription or acquisition of truncating mutations explained most but not all cases of CD20 loss. In vitro modeling confirmed the effect of CD20 variants identified in clinical samples on reduction of CD20 expression and confirmed missense mutations in the extracellular domain that could block mosunetuzumab binding. This study expands knowledge about the occurrence of target antigen loss after anti-CD20 therapeutics to CD20-targeting bispecific antibodies and elucidates the underlying mechanisms for reduced CD20 expression at disease progression that may be generalizable to other anti-CD20 targeting agents. These results also establish the utility of readily-available IHC staining for CD20 as a tool to inform clinical decisions.

  Study EGAS50000000151

• Multiple migrations to the Philippines during the last 50,000 years

  A key link to understand human history in Island Southeast Asia is the Philippine archipelago and its poorly investigated genetic diversity. We collected and analyzed the most comprehensive set of population-genomic data for the Philippines, 1028 individuals covering 115 indigenous communities. We demonstrate that the Philippines were populated by at least five waves of human migration. The Cordillerans migrated into the Philippines prior to the arrival of rice agriculture, where some remain to be the least admixed East Asians carrying an ancestry shared by all Austronesian-speaking populations; thereby challenging an exclusive Out-of-Taiwan model of joint farming-language-people dispersal. Altogether, our findings portray Philippines as a crucial gateway, with a multilayered history, that ultimately changed the genetic landscape of the Asia-Pacific region.

  Study EGAS00001005083

• Resuscitation Outcomes Consortium (ROC) Prehospital Resuscitation Using an Impedance Valve and Early Versus Delayed Analysis (PRIMED) (ROC-PRIMED-BioLINCC)

  Accessing Data: Please refer to “Authorized Access” below regarding accessing data through the BioData Catalyst ecosystem. The data from this accession is not available for download through dbGaP.Objective: The purpose of this study was to examine two different treatments during a cardiac arrest that occurs outside of the hospital and whether either or both treatments would increase the number of people who lived to hospital discharge with satisfactory functional status. The first treatment involved using a device called the Impedance Threshold Device (ITD). The other treatment involved the amount of CPR given before the emergency medical services (EMS) providers first looked at the heart rhythm to determine if a shock is needed.Background: Out-of-hospital cardiac arrest is a common and lethal problem with a low survival rate, leading to an estimated 330,000 deaths each year in the United States and Canada. The traditional approach to out-of-hospital cardiac arrest has been to emphasize early analysis of cardiac rhythm, with delivery of defibrillatory shocks, if indicated, as quickly as possible. It has been suggested, however, that many participants may benefit from a period of CPR before the first analysis of rhythm.The impedance threshold device (ITD) is designed to enhance venous return and cardiac output during CPR by increasing the degree of negative intrathoracic pressure. Previous studies have suggested that the use of an ITD during CPR may improve survival rates after cardiac arrest. This effect is achieved by preventing the passive inflow of air into the chest during chest recoil between chest compressions without impeding active ventilation. The ITD has been found to improve hemodynamics, the perfusion of vital organs, and neurologically intact survival in studies in animals. The results of small, short-term clinical trials have suggested that the ITD can increase systolic blood pressure during resuscitation and improve short-term survival rates. Participants: In the ITD study, 4,345 participants were assigned to sham ITD and 4,373 to active ITD, while in the early versus later rhythm analysis, 5,290 participants were assigned to early cardiac rhythm analysis, and 4,643 were assigned to later cardiac rhythm analysis. This study qualified for exception from informed consent required for emergency research.Design: Most participants were enrolled simultaneously in both the early analysis versus later analysis component and the active ITD versus sham ITD component of the trial.The use of an active ITD was compared with that of a sham ITD in participants at 10 ROC sites in the United States and Canada. Participants, investigators, study coordinators, and all care providers were unaware of the treatment assignments. EMS personnel were trained in ITD function, proper use of the ITD, and all aspects of protocol implementation, with an emphasis on the optimal performance of CPR according to local guidelines. The first EMS responders to arrive at the scene of the arrest who were equipped with a randomly assigned ITD (active or sham) attached the device between the ventilation bag and face mask or between the bag and an advanced airway. Responders were encouraged to implement use of the device within 5 minutes after their arrival or as soon as clinically possible. Each of the 10 participating ROC centers was also divided into approximately 20 clusters. All episodes of cardiac arrest in a cluster were randomly assigned to one CPR strategy; after a set period of time, ranging from 3 to 12 months, all episodes in that cluster were then assigned to the other strategy. Participants in the early-analysis group were assigned to receive 30 to 60 seconds of chest compressions and ventilations (sufficient time to place defibrillator electrodes) before electrocardiographic (ECG) analysis, and those in the late-analysis group were assigned to receive 3 minutes of chest compressions and ventilations before ECG analysis. The start and stop times for CPR were recorded by the responders, and the information was supplemented by the recording of defibrillator time. Conclusions: All 10 sites halted enrollment in November 2009 when the data and safety monitoring board recommended termination because interim analysis showed that the findings were not likely to change with continuation of the study. Neither use of the ITD nor the amount of CPR given before cardiac rhythm analysis significantly improved survival with satisfactory function (i.e., a score of ≤3 on the modified Rankin scale) among participants with out-of-hospital cardiac arrest receiving standard CPR. There were also no significant differences in the secondary outcomes, including rates of return of spontaneous circulation on arrival at the emergency department, survival to hospital admission, and survival to hospital discharge.

  Study phs003825

• scRNA-seq data of BALF and blood cells from COPD and control

  Chronic obstructive pulmonary disease (COPD) is ranked the third leading cause of death worldwide and hence constitutes a significant burden, both medically and financially. To date, the cellular mechanism underlying COPD is poorly understood and thus no effective therapy is currently available. To broaden the current knowledge of the immune landscape in the alveolar space, we performed scRNA-Seq of CD45-enriched bronchoalveolar lavage fluid (BALF) cells and isolated blood leukocytes obtained from COPD patients and healthy controls using both the Seq-Well and the Chromium (10x Genomics) technology.

  Study EGAS00001004369

• Pancreatitis after Treatment for Acute Lymphoblastic Leukemia (SJIRB XPD04-123 and XPD05-078)

  A complication of acute lymphoblastic leukemia (ALL) treatment is acute pancreatitis, which is one of the common causes of asparaginase intolerance. To determine clinical and genetic risk factors for pancreatitis, we studied a cohort of children and young adults with ALL enrolled on COG trials (9904/9905/9906, AALL0232) and on St. Jude trial Total XV. We performed a genome-wide association study using germline DNA collected from blood in patients at remission in this cohort of 5185 patients and in an independent case-control group of 213 patients on AALL0331. The frequency of pancreatitis in the cohort was 2.3% (117 of 5185). No common variants reached genome-wide significance, but a rare nonsense variant rs199695765 in CPA2, encoding carboxypeptidase A2, was highly associated with pancreatitis (odds ratio = 587, 95% confidence interval 66.8-5166, P = 9.0 x 10-9). A gene-level analysis showed an excess of additional CPA2 variants in patients who did versus those who did not develop pancreatitis (P = 0.018). Sixteen CPA2 SNPs were associated (P < 0.05) with pancreatitis, and 13 of 24 patients who carried at least one of these variants developed pancreatitis. Biological functions that were overrepresented by common variants modestly associated with pancreatitis included purine metabolism and cytoskeleton regulation.

  Study phs001350

• Regulatory Genomics of Human Embryonic Development

  We used epigenetic profiling to map active enhancers in the developing human limb and cortex as described in two published studies: Cotney J, Leng J, Yin J, Reilly SK et al. The evolution of lineage-specific regulatory activities in the human embryonic limb. Cell 2013;154(1):185-96. Reilly SK, Yin J, Ayoub AE, Emera D et al. Evolutionary changes in promoter and enhancer activity during human corticogenesis. Science 2015;347(6226):1155-9. We also used ChIP-seq to map binding sites for the chromatin modifier CHD8 in the developing human brain, as described in one published study: Cotney J, Muhle RA, Sanders SJ, Liu L et al. The autism-associated chromatin modifier CHD8 regulates other autism risk genes during human neurodevelopment. Nat Commun 2015;6:6404. We are also depositing primary human sequence reads related to processed datasets in the Gene Expression Omnibus under the following accession numbers: GSE42413 (Cotney et al. 2013); GSE63649 (Reilly et al. 2015); GSE57369 (Cotney et al. 2015).

  Study phs001226

• Integrative Somatic and Germline Computational Biology to Redefine Clinical Actionability in Solid Tumors

  Neuroendocrine tumors (NETs) are rare cancers that arise in the gastrointestinal tract and pancreas. The fundamental mechanisms driving gastroenteropancreatic NETs (GEP-NETs) growth remain incompletely elucidated; however, the heterogeneous clinical behavior of GEP-NETs suggests that both cellular lineage dynamics and tumor microenvironment influence tumor pathophysiology. Here, we performed single-cell RNA-sequencing (scRNA-seq) of fresh resections of GEP-NETs, including four pancreatic NETs, three small intestinal NETs, and one perigastric NET. We used single-cell sequencing to investigate the tumor and immune cellular landscapes of GEP-NET patients. Malignant GEP-NET gene and regulon expression was compared with normal, gastrointestinal endocrine cell differentiation and fate determination stages. We further characterized immune-immune and immune-tumor interaction networks within GEP-NETs, identifying novel therapeutic opportunities in the myeloid compartment of the microenvironment. Our findings highlight the transcriptomic heterogeneity that distinguishes the cellular landscapes of GEP-NET anatomic subtypes and reveal potential avenues for future precision medicine therapeutics.

  Study phs003141

• Pilot experiment on functional genomics in osteoarthritis_RNA

  The aim of this work is to apply an integrated systems approach to understand the biological underpinnings of large joint (hip and knee) osteoarthritis which culminates in the need for total joint replacement (TJR). In this pilot we will assess the feasibility of the approach in the relevant tissue. We will obtain diseased and non-diseased tissue (cartilage and endochondral bone) following TJR, coupled with a blood sample, from 12 patients. We will characterise the 12 pairs of diseased and non-diseased tissue samples in terms of transcription (RNASeq) The pilot will help assess the feasibility of isolating sufficient levels of starting material for the different approaches, and will instigate the development of analytical approaches to synthesising the resulting data.

  Dataset EGAD00001001331

• Transcriptome study of differential expression in schizophrenia

  Schizophrenia is a common and severe psychotic disorder. While some common SNPs and rare copy number variants have been identified as being significantly associated with disease risk, the biological mechanisms remain undefined. To identify gene expression abnormalities in schizophrenia, we generated whole-genome gene expression profiles using microarrays on lymphoblastoid cell lines from a total of 413 cases and 446 controls. Regression analysis identified 95 transcripts differentially expressed by affection status at a genome-wide false discovery rate of 0.05, while simultaneously controlling for confounding effects. These transcripts represented 89 genes with functions such as neurotransmission, gene regulation, cell cycle progression, differentiation, apoptosis, and immunity. The observed differential expression of extended major histocompatibility complex region genes converges with the genetic evidence from schizophrenia genome-wide association studies, which find the same region to be the most significant schizophrenia susceptibility locus. Our analysis also provides novel candidate genes for further study to assess their potential contribution to schizophrenia.

  Study phs000775

• Chracterising cellur pathways underlying CD3/CD28 activation of human CD4+ cells

  We devised an approach to disentangle the TCR and CD28 pathways upon stimulation in naive and memory primary human CD4+ T cells (Tcons) in response to defined stimulatory signals. Sorted Tcons were activated using a titration of anti-CD3 and anti-CD28 in combination as well as individually. As a control we cultured cells in the same conditions but without the stimuli. In total, we defined seven conditions from four individuals for sequencing. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/.

  Dataset EGAD00001006610

• Chracterising cellur pathways underlying CD3/CD28 activation of human CD4+ cells

  We devised an approach to disentangle the TCR and CD28 pathways upon stimulation in naive and memory primary human CD4+ T cells (Tcons) in response to defined stimulatory signals. Sorted Tcons were activated using a titration of anti-CD3 and anti-CD28 in combination as well as individually. As a control we cultured cells in the same conditions but without the stimuli. In total, we defined seven conditions from four individuals for sequencing. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ .

  Dataset EGAD00001006612

• Single nucleus RNA sequencing of squamous cell carcinoma arising from mature teratoma of the ovary

  Squamous cell carcinoma arising from mature teratoma is one of the rare ovarian cancers. Therefore, the detailed molecular background of this disease has not been elucidated. The purpose of this study is to investigate the single-cell transcriptional landscape of this disease.

  Study JGAS000521

• Molecular sub-classification of hormone receptor-positive breast cancer

  Patients with estrogen and/or progesterone receptor-positive breast cancer benefit from hormonal treatment, yet high global death burdens due to high prevalence and long-term recurrence risk call for biomarkers to guide additional treatment approaches. From a prospective, observational study of postmenopausal early breast cancer patients treated with tamoxifen or aromatase inhibitors gene expression analyses of 612 tumors was performed using the NanoString® Breast Cancer 360 panel. We identified novel gene expression signatures, i.e. BRCAness and Tumor Inflammation Signature (associated with high tumor lymphocyte infiltration), that may aid to select high-risk patients in order to improve adjuvant treatment by targeting DNA repair deficiency or immune-checkpoints in addition to standard chemo-endocrine treatment. The overall goal is to foster novel concepts for a stratified early breast cancer management.

  Study EGAS00001004594

• Evaluating potential drug candidates for the treament of Henamgiopericytoma on patient derived cell line models

  Solitary fibrous tumor/Hemangiopericytoma (SFT/HPC) is a rare subtype of soft tissue sarcoma associated with NAB2-STAT6 gene fusions. This study established and characterized a novel SFT/HPC patient-derived cell line called SFT-S1. Potential drug candidates that could be repurposed for the treatment of SFT/HPC were screened. Screening was performed through RNA-Seq

  Dataset EGAD50000000039

• Circular RNA characterization in functionally distinct brain regions

  Circular RNAs (circRNAs) represent a class of endogenous, non-coding RNAs that are formed when exons back splice to each other and that are both highly conserved and pervasively expressed in the mammalian brain. The goal of this study was thus to systematically identify and characterize circRNA expression and as well as to evaluate the predicted impact on regulatory networks in five functionally distinct cortical regions of healthy aged human brain - cerebellum (BC), inferior parietal lobe (IPL), middle temporal gyrus (MTG), occipital cortex (OC) and superior frontal gyrus (SGF).

  Study EGAS00001003128

• DNA sequencing of sgRNAs enriched from the CRISPR-Cas9 screened HCC organoids

  There are 12 samples. The project aims to find enriched or depleted sgRNAs to identify functional genes in HCC progression and lenvatinib resistance

  Study EGAS50000001130

• METSIM (METabolic Syndrome In Men) Study

  The METSIM Study includes 10,197 men, aged from 45 to 73 years, randomly selected from the population register of the town of Kuopio, Eastern Finland, and examined in 2005-2010. The aim of the study is to investigate genetic and non-genetic factors associated with the risk of type 2 diabetes (T2D), cardiovascular disease (CVD), and insulin resistance-related traits in a cross-sectional and longitudinal setting. Study protocol includes collection of data on CVD risk factors (smoking, exercise, diet, history of chronic diseases including coronary heart disease, stroke, cardiac failure, medication, history of diabetes or early onset coronary heart disease in the family), questionnaire on the FINDRISC Score, measurement of height, weight, waist, hip, blood pressure, and bioimpedance for the evaluation of fat percentage. July 2016 - The first study release (v1) included phenotype and whole exome sequencing (WES) data of n=982 participants in substudy: Type 2 Diabetes Genetic Exploration by Next-Generation Sequencing in Multi-Ethnic Samples (T2D-GENES) Project 1: Metabolic Syndrome in Men Study (METSIM) - phs001100.v2.p1. The second study release (v2) included phenotype data for the entire METSIM cohort and made two additional substudies available, phs000919.v1.p1 and phs000752.v1.p1. The third study release (v3) made three subcutaneous adipose biopsy substudies available, phs003385.v1.p1, phs003386.v1.p1, and phs003387.v1.p1.The fourth study release (v4) added phenotype data for the subcutaneous adipose biopsies, made two additional substudies available, phs01579.v1.p1 and phs004033.v1.p1, and is utilized in the following dbGaP sub-studies. To view genotypes, other molecular data, and derived variables collected in these sub-studies, please click on the following sub-studies below or in the "Sub-studies" section of this top-level study page phs000743 METSIM Study. phs000752 METSIM FinMetSeq Exome Sequencing phs000919 METSIM GWAS and Exome Chip phs001100 METSIM T2D-GENES Exome Sequencingphs001579 METSIM CCDG Whole Genome Sequencingphs003385 METSIM Subcutaneous Adipose Needle Biopsy RNA-Seq phs003386 METSIM Subcutaneous Adipose Needle Biopsy ATAC-Seq phs003387 METSIM Subcutaneous Adipose Surgical Biopsy RNA-Seqphs004033 METSIM Metabolomics

  Study phs000743

• Control iPSC lines with clinically annotated genetic variants for versatile multi-lineage differentiation

  Induced Pluripotent Stem Cells (iPSC) derived from healthy individuals are important controls for disease modeling studies. To create a resource of genetically annotated iPSC, we reprogrammed footprint-free lines from four volunteers in the Personal Genome Project Canada (PGPC). Multilineage directed differentiation efficiently produced functional cortical neurons, cardiomyocytes and hepatocytes. Pilot users further demonstrated line versatility by generating kidney organoids, T-cells and sensory neurons. A frameshift knockout was introduced into MYBPC3 and these cardiomyocytes exhibited a hypertrophic phenotype as expected. WGS annotation of PGPC lines revealed on average 20 coding variants. Importantly, nearly all annotated PGPC and HipSci lines harboured at least one pre-existing or acquired variant with cardiac, neurological or other disease associations. Overall, PGPC lines were efficiently differentiated by multiple users into cell types found in six tissues for disease modelling, and clinical annotation highlighted variant-preferred lines for use as unaffected controls in specific disease settings.

  Study EGAS00001003684

• Cancer Genetic Markers of Susceptibility (CGEMS) Breast Cancer Genome-wide Association Study (GWAS) - Primary Scan: Nurses' Health Study - Additional Cases: Nurses' Health Study 2

  The initial stage of the Cancer Genetic Markers of Susceptibility (CGEMS) breast cancer genome-wide association study (GWAS) included genotyping 528,173 SNPs (Illumina HumanHap550) in 1,145 postmenopausal women of European ancestry with invasive breast cancer and 1,142 controls from the Nurses' Health Study (NHS). Subsequently, incident invasive breast cancer cases from the Nurses' Health Study 2 (NHS2) cohort were genotyped using the Illumina HumanHap 610 quad. The NHS2 cases are younger than the cases in the first stage of the CGEMS breast cancer GWAS, which only included postmenopausal women. The NHS2 cases are a mix of pre- and postmenopausal women

  Study phs000147

• Targeted_Pulldown_Validation_of_mutations_found_in_whole_genome_sequencing

  This experiment is to inform us of the validity of using pre-made library material to perform a bespoke pulldown experiment to validate the mutations found between the whole genome sequencing of the DNA from the same individuals cancer and normal material. This is to identify the valid and informative mutations in cancer genomes.

  Study EGAS00001000260

• Compilation of Aggregate Genomic Data for General Research Use

  This study contains all authorized aggregate genomic data from datasets currently in dbGaP that are approved for general research use (GRU) and have no further limitations beyond those outlined in model Data Use Certification Agreement. Access to this study will be granted for one year and any additional authorized aggregate GRU datasets that become available during this one-year period. This study does not include individual-level data.

  Study phs000501

• Pre-activated anti-viral innate immunity in the upper airways controls early SARS-CoV-2 infection in children

  Children have reduced SARS-CoV-2 infection rates and a substantially lower risk for developing severe COVID-19 than adults. However, the molecular mechanisms underlying protection in younger age groups remain unknown. Here, we characterize the single-cell transcriptional landscape in the upper airways of SARS-CoV-2-negative (n=18) and age-matched SARS-CoV-2–positive children (n=24) and corresponding samples from adults (n=44), covering an age range of four weeks to 77 years. Children displayed higher basal expression of the relevant pattern recognition receptors (PRR) such as MDA5 (IFIH1) and RIG-I (DDX58) in upper airway epithelial cells, macrophages, and dendritic cells, resulting in stronger innate antiviral responses upon SARS-CoV-2 infection than adults. We further detected distinct immune cell subpopulations including KLRC1 (NKG2A)+ cytotoxic T cells and a CD8+ T cell population with a memory phenotype occurring predominantly in children. Our study provides evidence that the airway immune cells of children are primed for virus sensing, resulting in a stronger early innate antiviral responses to SARS-CoV-2 infection than adults.

  Study EGAS00001005461

• Deciphering the genomic, epigenomic and transcriptomic landscapes of pre-invasive lung cancer lesions to determine prognosis

  Background: Lung carcinoma-in-situ (CIS) lesions are the pre-invasive precursor to lung squamous cell carcinoma. However, only half progress to invasive cancer in three years, while a third spontaneously regress. Whether modern molecular profiling techniques can identify those pre-invasive lesions that will subsequently progress and distinguish them from those that will regress is unknown. Methods: Progressive and regressive CIS lesions were laser-captured and their genome, epigenome and transcriptome interrogated. We analysed 83 progressive lesions, 41 regressive and 33 normal epithelial control samples. DNA methylation and gene expression profiles were further validated using publicly available lung cancer data. Results: Somatic mutation burden was higher in progressive lesions than regressive CIS lesions, across base substitutions, rearrangements, and copy number changes. Driver mutations were present in both progressive and regressive CIS lesions, but were more numerous in progressive cases. Progressive and regressive CIS lesions had distinct epigenomic and transcriptional profiles, with a strong chromosomal instability signature. Gene expression, methylation and copy number profiles can all predict accurately which CIS lesions will progress to lung cancer. Conclusion: Pre-invasive CIS lesions that will subsequently progress to invasive lung cancer can be distinguished from those that will regress using molecular profiling. Progression is associated with a strong chromosomal instability signature. These findings inform the development of novel therapeutic targets.

  Dataset EGAD00001003883

• Long-read whole-genome sequencing-based concurrent haplotype phasing and aneuploidy profiling of single cells

  This dataset contains long-read whole-genome sequencing (lrWGS) data from 14 samples. Five lrWGS data are from single-cell (sc, sc_2, sc_3), multi-cell (mc, 10 cells), and bulk samples of HG002. The remaining nine lrWGS data are from two preimplantation genetic testing (PGT) families, including four from blood bulk DNA of the parental pairs and five from trophectoderm biopsies of two embryos from one family and three embryos from another family. The data are provided in raw FASTQ format and were generated using the PromethION device from Oxford Nanopore Technologies.

  Dataset EGAD50000000787

• WGBS files for PCGP NBL_MYCN_ATRX

  WGBS files for PCGP NBL_MYCN_ATRX paper titled "MYCN Amplification and ATRX Mutations are Incompatible in Neuroblastoma"

  Dataset EGAD00001004559

• Multiple Myeloma GWAS Meta-analysis

  Meta-analysis of Multiple Myeloma genome-wide association study datasets. Included are meta-analyses with and without the UK Biobank dataset.

  Study EGAS50000000292

• Detroit Research on Cancer Survivors (ROCS) and Disparities and Cancer Epidemiology - Colorectal Cancer (DANCE)

  The goals for this study were as follows:1. Enroll a total of 5,060 African Americans newly diagnosed with cancer into the Detroit Research on Cancer Survivors (Detroit ROCS) Cohort. These population-based cases will be ascertained through the Detroit Metropolitan Detroit Cancer Surveillance System (MDCSS), a founding member of the NCI SEER Program. Participation at baseline will include a written, web-based, or telephone interview, saliva and/or blood collection, and tumor block retrieval, with detailed cancer-related information coming from the MDCSS registry and medical records.2. Enroll a subgroup of colorectal cancer patients identified through the Louisiana Tumor Registry (LTR). An additional 500 colorectal cancer patients, approximately half non-Hispanic white and half African American, will be identified through the LTR and enrolled into the ROCS protocol. The survey is the same survey administered to the ROCS cohort. The Louisiana (“DANCE-CRC”) cohort will not be followed beyond baseline, and blood will not be collected (tumor tissue, however, will be collected, deidentified, and sent for processing through Dr. Rozek's laboratory at Georgetown University).The proposed cohorts will provide for a broad research agenda evaluating cancer outcomes in African Americans across a variety of factors from individual, provider, health care system and community perspectives. These factors include tumor characteristics driving individualized treatment planning, quality of life after a diagnosis and recurrence. Utilizing the MDCSS registry, we will enroll a large population-based sample of African-American cases with lung, breast, colorectal, and prostate cancers and their caregivers resulting in a cohort that will provide substantial benefit to the cancer research community. KCI has a strong history of research in the African-American community and the faculty represents a breadth of experience that includes clinical oncology, genetic epidemiology, environmental exposures, quality of life, treatment decision making, racism/discrimination, and health behaviors. Drs. Schwartz and Beebe-Dimmer have been and will continue to be generous collaborators with other institutions to ensure that this resource will be extensively utilized. The proposed overall cohort will be the only one of its kind, to our knowledge, filling a substantial gap in our understanding of the determinants driving cancer outcomes in African Americans. In addition to registry data detailing cancer specifics, yearly surveys have collected information about individualized treatment experiences, heath histories, family histories, quality of life after a diagnosis, recurrence and caregiving. Population: Adult cancer survivors (see inclusion criteria in next section) Molecular Technologies: Genotyping: Infinium Expanded Multi-Ethnic Genotyping Array (MEGAEX) DNA Sequencing: Illumina NovaSeq X Plus using XLEAP-SBS (sequencing by synthesis) Whole genome sequencingPrincipal Findings: The preliminary data collected reinforces differences by race in factors affecting cancer outcomes. Variants in DNA damage repair genes and HOXB13 may be important cancer risk factors for Black men diagnosed with prostate cancer, and are more frequently observed in men with a family history of cancer. ROCS participants reported high rates of a family history of cancer. The high rate of eligibility for Cancer genetic counseling among ROCS participants supports the need for interventions to increase referrals and uptake of genetic counseling among African Americans 60% of ROCS participants reported participating in regular physical activity (PA), with 24% reporting ≥150 min/wk. There were no differences by sex, but prostate cancer survivors were the most likely to report participating in regular PA, whereas lung cancer survivors were the least likely. Survivors who reported participating in regular PA reported higher health-related quality of life and lower depression. More African American than White survivors reported financial hardship and limiting care. More White than African American survivors reported utilizing assets, while more African American survivors reported cancer-related debt. Data available in dbGaP: Individual phenotype data Individual genotype data Individual sequencing dataSample types: Germline DNA

  Study phs003116

• Dataset for study Genome-wide gene expression analysis following CRISPRi of transposable elements

  Transposable elements (TEs), once regarded as parasitic genomic remnants, are now recognized as key regulators of gene expression and genome evolution, yet the functional specificity of individual TE subfamilies remains largely unexplored. This dataset investigates the transcriptional consequences of targeted repression of MER57E3 and LTR10B2 elements using CRISPR interference (CRISPRi) in human induced pluripotent stem cells (hiPSCs). hiPSCs expressing CRISPRi machinery (n = 2 biological replicates) were transduced with guide RNAs targeting individual or grouped copies of MER57E3 and LTR10B2, as well as the ZNF678 promoter or a lacZ non-targeting control. Transduced cells were subsequently differentiated into neural progenitor cells (NPCs), and total RNA was extracted for mRNA library preparation and sequencing. The dataset comprises 24 single-end mRNA-seq FASTQ files generated from these NPCs and wild-type controls.

  Dataset EGAD00001015689

• The Mood and Methylation Study (MMS)

  The Mood Methylation Study (MMS) is an observational study designed to understand epigenetic mechanisms underlying major depression symptoms (MDD) using a co-twin control design. Twins enrolled in the MMS were monozygotic (MZ) twin pairs discordant on lifetime history of MDD. All twins were members of the Washington State Twin Registry (WSTR), a community-based twin registry consisting of over 10,000 twin pairs. Lifetime and current MDD diagnoses were determined using the Structured Clinical Interview for DSM-IV Research Version (SCID-4-RV). DNA methylation in blood monocytes was measured using the Infinium HumanMethylationEPIC BeadChip. Monocyte gene expression was quantified by paired end RNA-seq (50 PE). Zygosity of the twin pairs included in the MMS was self-reported and confirmed using the polymorphic SNPs included in the DNA methylation array.

  Study phs002858

• Understanding the Progression of Metastatic Colorectal Cancer

  This study is to understand (1) the clonal evolution of metastatic colorectal cancer using DNA sequencing and (2) long non-coding RNAs associated with metastatic colon cancer using RNA sequencing. Our goal is to better understand the progression of aggressive colorectal cancer.

  Study phs001722