Search Results - EGA European Genome-Phenome Archive

3D-GSC_expression_profiles

In this study, we used RNA-sequencing gene expression profiling in order to characterize specific phenotypic traits in DIPG-derived glioma stem cell (GSC) models. Twenty-two primary GSC models derived from biopsies collected at diagnosis were cultured in an ECM-mimicking compound before for RNA extraction and subsequent rRNA-depletion and sequencing .

Study EGAS00001007182

Myasthenia gravis-specific aberrant neuromuscular gene expression by medullary thymic epithelial cells in thymoma

Myasthenia gravis (MG) is a neurological disease caused by autoantibodies against neuromuscular-associated proteins. While MG is frequently developed in thymoma patients, the etiologic factors for MG are not well understood. Here, by constructing a comprehensive atlas of thymoma using bulk and single-cell RNA-seq, we identified ectopic expression of neuromuscular molecules in MG-associated thymoma (MG-thymoma). These molecules were originated from a distinct subpopulation of medullary thymic epithelial cells (mTECs), which we named neuromuscular mTECs (nmTECs). MG-thymoma also exhibited microenvironments dedicated to autoantibody production, including ectopic germinal center formation, T follicular helper cell accumulation, and type 2 conventional dendritic cell migration. Cell-cell interaction analysis also predicted the interaction between nmTECs and T/B cells via CXCL12-CXCR4. The enrichment of nmTECs presenting neuromuscular molecules within MG-thymoma was further confirmed by immunohistochemically and by cellular composition estimation from MG-thymoma transcriptome. Altogether, this study suggests that nmTECs play a significant role in MG pathogenesis via ectopic expression of neuromuscular molecules.

Study JGAS000482

ICGC prostate cancer RNA sequencing

Dataset EGAD00001000305

Pseudogene_RNAseq

RNA sequencing to validate findings of somatic pseudogenes acquired during cancer development

Study EGAS00001000606

Cross-site Concordance Evaluation of Tumor DNA and RNA Sequencing Platforms of CIMAC-CIDC Network

The Cancer Immune Monitoring and Analysis Centers (CIMACs) and the Cancer Immunologic Data Commons (CIDC)  has engaged in efforts to harmonize Whole-exome (WES) and RNA-sequencing (RNA-seq) data from three different experimental platforms (MD Anderson, NCI MoCha lab, and Broad Institute) and are using a series of developed pipelines to process the early trial samples. To evaluate the consistency of tumor WES and RNA-seq profiling platforms across different centers, the CIMACs-CIDC conducted a systematic harmonization study. DNA and RNA were centrally extracted from fresh frozen (FF) and formalin-fixed paraffin-embedded (FFPE) non-small cell lung carcinoma (NSCLC) tumors and distributed to three centers for WES and RNA-seq profiling

Study phs002295

Small RNA sequencing of human oocytes and early embryos

This study looks at small RNA expression in human oocytes (n=12), zygotes (n=5), and embryos (n=10). The sample preparation and sequencing were done in two batches.

Study EGAS50000000157

Single-cell RNA-sequencing for peripheral blood mononuclear cells and plasma proteomics data from COVID-19 patients and healthy controls of Japanese

We performed single-cell RNA-sequencing of peripheral blood mononuclear cells and measured plasma protein expression from COVID-19 patients and healthy controls.

Study JGAS000783

Long read mRNA sequencing of human neural retinal samples - Usher syndrome transcript landscape

Long-read (PacBio) RNA sequencing dataset of three neural retinal samples. Three PacBio libraries were prepared according the 'standard workflow' optimized for sequencing transcripts centered around 2kb. Additionally one Library (input HNR_S2) was prepared according an optimized 'long workflow' to enrich for larger transcripts up to >10kb. To further enhance the capture of full-length transcripts for USH2A and ADGRV1 (USH2C) genes, we also employed a targeted enrichment approach using the Samplix Xdrop System, followed by PacBio long-read sequencing. USH2A and ADGRV1 enrichment was performed by targeting '5- mid and 3' targets of the respective genes. Finally, we also added ONT (Oxford Nanopore technology) long-read mRNA sequencing of three independent neural retina samples. These data were used for the validation of events observed from the Iso-Seq and Samplix data. The ONT datasets contain sequencing data of the Usher-associated genes. Files are raw BAM, and CRAM format files generated by a Sequel II machine. Additionally, the ccs3 BAM format files are included.

Dataset EGAD50000000720

The Institute for Genomic Medicine at Nationwide Children's Hospital Pediatric Cancer and Blood Disorder Project

The aim of this study is to enable the unification of the clinical and research arms of comprehensive genomic profiling in the setting of cancer and hematologic disease. Increasingly, studies of the genomic etiology of cancer and hematologic diseases are being utilized for patient management, including prognostication, informing diagnosis, and evaluating eligibility for targeted therapeutics and clinical trials. Clinically available testing can be limited in scope and follow-up, and thus assessment of the impact on patient outcomes is difficult to ascertain. N-of-1 studies have the ability to more broadly impact our understanding of the mechanisms of cancer and hematologic disease, and can have benefit for the individual as well as the larger population of patients with these diseases. Thus, we seek to study and characterize the genomic underpinnings of cancer and hematologic disease through genomic profiling studies bridging both clinical and research components. We will rigorously perform and vet research sequencing and genomic studies protocols for the purpose of transitioning these assays to clinically valid testing for use in clinical patient care. We have been enrolling patients onto this comprehensive genomic profiling study since January 2018. As part of the genomic workup for these patients, we have been performing tumor and normal whole genome sequencing, whole exome sequencing and RNA-Seq. The project is largely supported by the Nationwide Children's Foundation, and we anticipate adding another 50-70 cases per year. This protocol is significant in that it expands our understanding of the etiology of cancer and hematologic disease through a comprehensive analysis aimed at detecting a broad scope of genomic aberrations. Additionally, it improves our understanding of the clinical utility of genomic profiling and has the potential to ultimately improve patient management and surveillance at both level of an individual and general populations of patients affected by these diseases. Primary Objectives: Aim 1: Use diagnostic, relapse, and/or germline samples for augmented whole exome sequencing to characterize the spectrum of germline and somatic genomic alterations in pediatric malignancies and hematologic disease. Aim 2: Examine gene expression and fusion events using whole RNA-seq "transcriptome" analysis or targeted RNA-seq analysis such as the Archer FusionPlex technology. Aim 3: Compare the results of our enhanced molecular profiling vs. that which is detectable by traditional methods as related to cytogenetic, molecular, and minimal residual disease analyses performed as part of standard of care. Aim 4: Examine the utility of comprehensive genomic profiling by collection and evaluation of outcomes data as related to enhancement/alteration in diagnosis, prognosis, treatment management, and clinical benefit. Secondary Objective: Aim 1: Use and clinically validate expanded laboratory methodologies and bioinformatic approaches to more broadly assess genomic complexity (e.g. whole genome sequencing, transcriptome sequencing, in vitro analyses, minimal residual disease testing, clonality assays, proteomics) in the setting of hematologic and oncologic disease. In so doing, we aspire to make novel discoveries and associations, as related to disease phenotypes and subtypes, variant causality, therapeutic targeting, and cancer biology.

Study phs001820

Transcriptome profiling of megakaryocytes and platelets: application to GP9- and IKZF5-related thrombocytopenia

Platelets are anucleate cells produced in the bone marrow and derived from large progenitor cells called megakaryocytes (MKs). Platelets receive RNA transcripts from their progenitorial MKs during thrombopoiesis. However, the correspondence between platelet and MK transcriptomes is poorly understood, particularly in the context of germline mutations that cause platelet formation defects or thrombocytopenia. We have studied the effects of two such mutations on MK and platelet transcriptomes. We generated immortalized MK cell line (imMKCL)-based models of Bernard-Soulier syndrome and IKZF5-related thrombocytopenia. MKs derived from imMKCLs with either a homozygous deletion of GP9 (GP9-/-) or a heterozygous Y121F variant in IKZF5 (IKZF5WT/Y121F) exhibited reduced proplatelet formation (reductions of 96% and 57%, respectively). Platelets from patients with either GP9-/- or IKZF5WT/Y121F genotypes had broad transcriptomic dysregulation, suggesting that (pro)platelet formation defects due to mutations in glycoprotein receptor and transcription factor genes such as GP9 and IKZF5 affect the trafficking of transcripts from MKs into platelets. RNA-seq data from MKs at four stages of differentiation revealed widespread but distinct changes in expression over time between the GP9-/- and the IKZF5WT/Y121F genotypes. Dysregulated genes in GP9-/- MKs were enriched for RNA metabolism and actin/tubulin folding pathways while those in IKZF5WT/Y121F MKs were enriched for cell cycle pathways. Most of these genes were also dysregulated in the platelets of patients with the corresponding diseases. Our results suggest that patients with inherited forms of thrombocytopenia present with a transcript trafficking defect during platelet formation.

Study EGAS50000001276

Pilocytic Astrocytoma ICGC PedBrain RNA sequencing

Dataset EGAD00001000617

HipSci - Battens Disease - RNA Sequencing - July 2017

Dataset EGAD00001003533

HipSci - Hypertrophic Cardiomyopathy - RNA Sequencing - July 2017

Dataset EGAD00001003540

HipSci - Macular Dystrophy - RNA Sequencing - July 2017

Dataset EGAD00001003541

HipSci - Usher Syndrome - RNA Sequencing - July 2017

Dataset EGAD00001003543

HipSci - Kabuki Syndrome - RNA Sequencing - July 2017

Dataset EGAD00001003535

HipSci - Alport Syndrome - RNA Sequencing - July 2017

Dataset EGAD00001003532

HipSci - Retinitis Pigmentosa - RNA Sequencing - July 2017

Dataset EGAD00001003542

RNA sequencing data from glioblastoma primary cell lines treated with indisulam data access committee

Four glioblastoma primary cell lines (BT592/pt1, BT1007/pt2, BT1009/pt3; BT1012/pt4) were derived from glioblastoma Cavitron Ultrasonic Aspirator (CUSA) material and cultured as neurospheres (GB-NS) in DMEM/F12+Glutamax medium containing B27 supplement (Thermofisher, Waltham, MA, USA) and the mitogenic factors epidermal growth factor (EGF) and fibroblast growth factor b (bFGF) (Peprotech, Rocky Hill, NJ, USA). GB-NS were confirmed mycoplasma-free by PCR Test. Cells were seeded in triplicate in 6-well plates, treated with 5 μM indisulam (Sigma Aldrich, Merk), or vehicle control, and collected after 6 and 16 hours for RNA extraction. Total RNA was extracted using TRIzol Reagent (Life Technologies, Thermo Fisher, cat n. 15596026), RNeasy Mini Kit, and RNase-Free DNase Set (Qiagen, cat n. 74104 and 79254). Sample QC, RNA library preparations, and sequencing reactions were conducted at GENEWIZ (Germany GmbH). The concentration of RNA was quantified using a Qubit Fluorometer (Life Technologies, Carlsbad, CA) and RNA integrity was assayed using a TapeStation. Sequencing libraries were prepared with RNA with PolyA selection and ERCC spike-in with standard ERCC kit (ERCC RNA Spike-In Mix,Thermo Fisher 4456740). Final libraries (Illumina, RNA with PolyA selection) were sequenced on a NovaSeq platform, producing 2×150 base paired-end reads.

Dac EGAC50000000407

Comparison of capture-based method for transcriptome profiling of formalin-fixed paraffin embedded tumor samples

Background: The need for fresh frozen (FF) tissue limits implementing RNA sequencing (RNA-seq) in the clinic. The majority of clinical samples are stored as formalin-fixed, paraffin-embedded (FFPE) tissues. Exome capture platforms have been developed for RNA-seq from FFPE samples. However, these methods have not been systematically compared. Methods: Transcriptomic analysis of 32 FFPE tumor samples from 11 patients was performed using three exome capture-based methods: Agilent SureSelect V6, TWIST NGS Exome, and IDT XGen Exome Research Panel. We compared these methods to TruSeq RNA-seq of fresh frozen (FF-TruSeq) tumor samples from the same patients. We assessed the recovery of clinically relevant biological features. Results: The Spearman's correlation coefficients between the global expression profiles of the three capture-based methods from FFPE and matched FF-TruSeq were high (rho = 0.72-0.9, p < 0.05). A significant correlation between the expression of key immune genes between individual capture-based methods and FF-TruSeq (rho = 0.76-0.88, p < 0.05) was observed. All exome capture-based methods reliably detected outlier expression of actionable genes, including ERBB2, MET, NTRK1, and PPARG. In urothelial cancer samples, the Agilent assay was associated with the highest molecular subtype concordance with FF-TruSeq (Cohen's k = 0.7, p < 0.01). Both Agilent and IDT detected all the clinically relevant fusions that were initially identified in FF-TruSeq. Conclusion: All exome capture-based methods had comparable performance and concordance with FF-TruSeq. By enabling the interrogation of FFPE tumor samples, our findings will enable the implementation of RNA-seq in the clinic to guide precision oncology approaches.

Study EGAS00001005255

Chromatin run-on and RNA sequencing of fibrolamellar carcinoma

Fibrolamellar carcinoma (FLC) is a rare, therapeutically intractable liver cancer that disproportionately affects youth. Here we used chromatin run-on sequencing to characterize the enhancer landscape in FLC and RNA sequencing to identify dysregulated genes in FLC.

Study EGAS00001004169

Genomic Analysis of Nucleic Acid Sequences from Pancreatic Cancer

Our study aims to perform multi-omics analysis of pancreatic ductal adenocarcinoma. We performed dual single-cell RNA sequencing and whole genome sequencing on fresh tumor specimens and dual bulk RNA-sequencing and 16S amplicon sequencing on frozen tumor specimens to identify human and non-human nucleic acid sequences. Additionally, we identified microbial sequences and found that bacterial taxonomic profiles from the same sample strongly correlated across technologies.

Study phs003035

Genetic and transcriptional landscape of plasma cells in POEMS syndrome

POEMS syndrome is a rare paraneoplastic disease, associated with monoclonal plasma cells whose pathogenic importance remains unclear. We performed comprehensive genetic analyses of plasma cells in 20 patients with POEMS syndrome. Whole exome sequencing and targeted sequencing identified 7 recurrently mutated genes: KLHL6, LTB, EHD1, EML4, HEPHL1, HIPK1, and PCDH10. None of the driver gene mutations frequently found in multiple myeloma (MM) such as NRAS, KRAS, BRAF, and TP53 was detected. Copy number analysis showed chromosomal abnormalities shared with monoclonal gammopathy of undetermined significance (MGUS). RNA sequencing revealed a transcription profile specific to POEMS syndrome, especially in terms of tumorigenesis. Unexpectedly, disease-specific VEGFA expression was not increased in POEMS syndrome. Our study illustrates that the genetic and transcriptional profiles of plasma cells in POEMS syndrome are distinct from MM and MGUS, indicating its unique pathogenesis.

Study JGAS000150

Reference Epigenomes and Regulatory Landscape of CLL

Analysis of the reference epigenomes and regulatory landscape of CLL as a whole and its major clinico-biological subtypes (with mutated and unmutated IGHV) in the light of the normal B-cell differentiation. We have extensively characterized the reference epigenomes of seven primary chronic lymphocytic leukemia samples (CLLs) with mutated (n=5) and unmutated IGHV (n=2) as well as several mature B-cell subpopulations (naive B cells from blood and tonsil, germinal center B cells, memory B cells and plasma cells from tonsil) using genome-wide maps of six histone marks (H3K4me3, H3K4me1, H3K27ac, H3K36me3, H3K9me3 and H3K27me3), DNA accessibility (ATAC-seq), DNA methylation (whole-genome bisulfite sequencing) and gene expression (RNA-seq). Furthermore, we have mapped the regulatory chromatin landscape of 100 additional CLL cases using chIP-seq of H3K27ac and ATAC-seq and linked these data to additional layers of information (whole-genome and/or whole-exome sequencing (WGS/WES), RNA-seq and DNA methylation microarrays) studied in the context of the International Cancer Genome Consortium (ICGC).

Dataset EGAD00001004046

RNA sequencing of colon tumor/normal sample pairs

Dataset EGAD00001000215

Deep RNA sequencing in CLL

Dataset EGAD00001000258

HipSci - Monogenic Diabetes - RNA Sequencing - January 2016

Dataset EGAD00001001955

HipSci - Monogenic Diabetes - RNA Sequencing - April 2015

Dataset EGAD00001001953

Genomic Analysis of Relapsed/Refractory DLBCL

Molecular phenotyping techniques have established a landscape of genomic variants in diagnostic Diffuse Large B Cell Lymphoma (DLBCL), however these have not yet been applied in large scale studies of relapsed/refractory DLBCL resulting in incomplete characterization of mechanisms driving tumor progression and treatment resistance. Here, we performed an integrated multiomic analysis on relapsed/refractory DLBCL samples. Tumors from 87 relapsed/refractory DLBCL patients were included in this study and were available for data deposition [Tumor whole exome sequencing (WES): n=75, Germline WES: n=73, RNA sequencing (RNA-Seq): n=72]. Tumor DNA was extracted from formalin-fixed, paraffin embedded (FFPE) tissue sections, germline DNA was extracted from blood, and WES of all samples was performed using the Agilent SureSelect XT All Exon v6 kit and sequencing was carried out on an Illumina NovaSeq, 100 x 2 paired end reads. Tumor RNA was extracted from FFPE tissue sections and RNA-Seq was performed using the Illumina TruSeq RNA Exome Kit (Illumina) for library preparation, sequencing platform HiSeq 4000, 100 x 2 paired end reads.

Study phs003868

Single cell RNA sequencing of cerebrospinal fluid

Single-cell RNA sequencing of cells isolated from cerebrospinal fluid from 81 individuals with multiple sclerosis (n=33) or other neurological disease (n=48) using 10x Genomics 3’ expression (v2 chemistry).

Study EGAS00001007478

Whole genome sequencing, SNP array and RNA-seq of uveal melanomas

We conducted whole genome sequencing and DNA SNP array of 12 uveal melanoma genomes and their matched DNA from blood. We also conducted RNA-seq of the 12 tumour samples.

Study EGAS00001000472

HipSci - Primary Immune Deficiency - RNA Sequencing - July 2017

Dataset EGAD00001003536

HipSci - Hereditary Spastic Paraplegia - RNA Sequencing - July 2017

Dataset EGAD00001003537

HipSci - Bardet-Biedl Syndrome - RNA Sequencing - April 2015

Dataset EGAD00001001952

HipSci - Hereditary Cerebellar Ataxias - RNA Sequencing - July 2017

Dataset EGAD00001003538

HipSci - Bardet-Biedl Syndrome - RNA Sequencing - January 2016

Dataset EGAD00001001954

Single Cell RNA Transcriptomics of Mantle Cell Lymphoma Reveals the Presence of Treatment-Resistant Subclones at the Time of Diagnosis

Mantle cell lymphoma is a chronically relapsing B cell neoplasm characterized by clonal heterogeneity. We implemented single cell RNA sequencing of paired tumor samples from four patients with an aggressive nodal MCL at diagnosis and after failure of standard immunochemotherapy. Clustering the cells based on the inferred CNVs showed small subclones present at diagnosis with a CNV profile similar to the major subclone at relapse. Comparison of these subclones to major subclones present at diagnosis revealed 119 upregulated pathways common for the four patient with an aggressive MCL, including NF-kappaB and PTEN signaling pathways. Additionally, we sequenced a patient with an indolent to blastoid MCL transformation with intestinal tissue involvement. In contrast to other compartments at relapse, the cells in the intestine showed strikingly different CNV profile and presence of new driver mutations including NOTCH1. In conclusion, our study demonstrates that scRNAseq can potentially detect therapy resistant subclones at diagnosis.

Study EGAS50000000825

Differential expression in clear cell renal cell carcinoma

To investigate the levels of gene expression in clear cell renal cell carcinoma (ccRCC), we performed an RNA-seq analysis in 786-O, A-498, UM-RC-2 clear cell renal carcinoma cell lines, as well as HK-2 normal renal epithelium cell line, cultured under normoxic (20% O2) and hypoxic (0.05% O2) conditions. Data are provided in raw fastq files and csv files with the differential expression results. Differential expression was calculated by the RNAflow pipeline (DEseq2), and log fold changes are calculated with respect to the normal cell line (HK-2), with separate results between normoxic and hypoxic datasets.

Dataset EGAD50000001883

RNAseq of blood, fat and muscle samples from 45,X, 46,XX, 46,XY and 47,XXY

Samples of blood, muscle and fat were collected from individuals with TS (n = 33) and KS (n = 22) and from male (n = 16) and female (n = 44) controls. The RNA-seq libraries were multiplexed paired-end sequenced on an Illumina Novaseq 6000 (100 bp) and subjected to initial quality control using FastQC (BAbraham Bioinformatics). In addition to trimming of low-quality ends, adaptor removal was conducted using Trim Galore with default settings (BAbraham Bioinformatics).

Dataset EGAD00001010052

Colorectal adenomas and carcinomas NKI-AvL TGO series Gut2009

Colorectal cancer (CRC) develops from normal epithelium, through a benign precursor lesion called adenoma, by accumulation of genetic alterations affecting oncogenes and tumour suppressor genes. These CRC-related genomic alterations often result in specific RNA-expression patterns. RNA isolated from fresh frozen specimen of 32 adenomas and 29 CRCs was obtained from the previously published study (Carvalho et al. 2009) and RNA-sequencing was performed with the aim to examine RNA expression changes in colorectal adenoma-to-carcinoma progression.

Study EGAS00001002758

Single nucleus and bulk transcriptomics in prefrontal cortex of individuals with alpha synucleinopathies

We explore cell-specific changes in gene expression across different α-synucleinopathies. We perform single nucleus RNA sequencing using 10X Genomics, and bulk RNA sequencing from the prefrontal cortex of individuals with alpha synucleinopathies - Parkinson's Disese (PD), monogenic LRRK2 PD, and multiple system atrophy (MSA), together with neurologically healthy controls.

Study EGAS50000000301

Comprehensive Genomic Characterization of Acral Melanoma

In this study, we performed paired tumor/normal long insert whole genome and exome sequencing and tumor RNA sequencing on primary or metastatic acral melanoma tumors collected from 34 patients. Patients were enrolled from either Vanderbilt University or the Memorial Sloan-Kettering Cancer Center. We report an integrated analysis of DNA and RNA sequencing data to describe genomic and transcriptomic characteristics of acral melanoma.

Study phs001036

Multi-omics profiling of PSCCE

We performed whole-exome sequencing, RNA sequencing and immunohistochemistry profiling of primary small cell carcinomas of the esophagus.

Study EGAS00001004889

Kidney_tumour_RNA

This is a bulk DNA and RNA sequencing study of human renal tumours

Study EGAS00001002487

A single-cell multi-omic atlas of nodal B-cell non-Hodgkin lymphomas

CITE-Seq (cellular indexing of transcriptomes and epitopes) of 51 lymph node (LN) samples from including mantle cell lymphoma (MCL, n = 8), follicular lymphoma (FL, n = 12), germinal center (GCB, n = 5) or activated B-cell (non-GCB/ABC, n = 7) diffuse large B-cell lymphoma (DLBCL), and marginal zone lymphomas (MZL, n = 11), in addition to non-malignant reactive lymph nodes (rLN, n = 8). Of the malignant LN samples, 20 were collected at the time of initial diagnosis and 23 were from patients who had previously undergone one or more lines of systemic treatment. Relapse samples were collected at least 3 months after cessation of systemic treatment. This dataset also includes 5 prime RNA sequencing and immune receptor sequencing (10X Genomics) for 11 of these samples (2 rLN, 2 MCL, 3 FL, 2 DLBCL (GCB) and 2 MZL).

Dataset EGAD50000000497

Single cell RNA sequencing of mononuclear cells from synovial fluid of patients with rheumatoid arthritis

Mononuclear cells were collected from synovial fluid of anti-citrullinated positive antibodies (ACPA)-positive rheumatoid arthritis patients (n=8) and ACPA-negative RA patients (n=8). Global cell types (i.e., no enrichment) were obtained from these cryopreserved synovial fluid mononuclear cells (SFMC) samples and immediately fixed and processed using the GEM-X Flex Gene Expression Reagent Kits (10x Genomics) according to protocol. Following Gel Bead-in Emulsion (GEM) generation, samples were processed using the standard manufacturer’s protocol. Once sequencing libraries passed standard quality control metrics, libraries were sequenced on an Illumina NextSeq2000 P4 100 cycle reagent kit with the following read structure: R1: 28, R2: 90, I1: 10, I2: 10. Libraries were sequenced to obtain a read depth greater than 10,000 reads/cell for gene-expression (GEX). FASTQ files are made available. More detailed information can be obtained in Argyriou A. et al, Annals of the Rheumatic Disease, 2025.

Dataset EGAD50000001801

Somatic L1 retrotransposition in normal colorectal epthelium

Throughout an individual’s lifetime, genomic alterations accumulate in somatic cells. However, the mutational landscape induced by retrotransposition of long interspersed nuclear element-1 (L1), a widespread mobile element in the human genome, is poorly understood in normal cells. Here, we explored the whole-genome sequences of 406 normal colorectal clones, 12 MUTYH-associated adenomatous clones, and 19 matched colorectal cancer tissues. In addition, we analyzed promoter DNA methylation status of retrotransposition-competent L1 (in 139 clones) and read-through RNA expression profiles (in 116 clones) to investigate the epigenetic regulation of L1 activity.

Dataset EGAD00001010183

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