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• DNA sequences from adolescent and young adult patients with melanoma treated with immunotherapy

  Sequencing libraries were prepared and barcoded using the unique molecular identifier and index tagging following the VariantPlex Somatic Protocol (ArcherDx). Pool-library was loaded at 1.2 pM concentration with 20% PhiX and paired-end sequencing was performed using the NextSeq 500 Illumina sequencer using 300 cycle high output reagent kit.

  Dataset EGAD50000000353

• 340 human whole genome sequences from Angola and Mozambique

  CRAM files of 340 human genomes from Angola and Mozambique. Paired-end reads were generated in an Illumina-X Ten and were mapped against the human reference genome build hg19/GRCh37. More details about the sequencing and the samples in Tallman et al. 2023. Nature Communications.

  Dataset EGAD00001011992

• Genetic and Genomic Stability Across Lymphoblastoid Cell Line Expansions

  This study was focused on exploring genetic and genomic stability across cell line expansions. We used DNA and cell lines sampled from six apparently healthy research participants. We assayed genome-wide genetic variants and inferred structural variants for DNA extracted from blood, from transformed cell cultures, and from three generations of expansions.

  Study phs001650

• Breast implant-associated anaplastic large cell lymphoma shallow whole genome sequencing for copy number analysis and Whole exome sequencing data.

  Breast implant-associated anaplastic large cell lymphoma (BIA-ALCL) shallow whole genome sequencing of 29 BIA-ALCL patients for copy number analysis and 24 Alk-negative ALCL samples as control cohort. 7 Whole exome sequencing BIA-ALCL samples.

  Study EGAS00001003962

• Contribution of Retrotransposition to Developmental Disorders

  Variants and WGS data for Gardner et al. 2018 (biorxiv 471375). One VCF each for Alu, L1, and SVA. Flat text file and WGS for processed pseudogenes.

  Dataset EGAD00001004586

• Disease recurrence after pathologic response (Recurrence DNAseq)

  In this study we aim to gain insight into the mechanisms of immune evasion after initial pathologic response to neoadjuvant immune checkpoint inhibition in macroscopic stage III melanoma by pooling data of the neoadjuvant OpACIN, OpACIN-neo and PRADO trials(EGAD00001012116, EGAS00001004832, EGAD00001006730, EGAS50000000268). Therefore we analyzed in-depth paired baseline(n=10) and recurrent tumor samples of the lymph nodes(n=10) and brain metastasis (n=2) through Whole Exome Sequencing (WES) analyses. Additionally we incorporated transcriptome sequencing data from 22 patients (21 paired-end samples and one single end sample)

  Study EGAS50000000488

• RNA Sequencing of ECOG-E1308

  This study reports the RNA sequencing of HPV positive oropharyngeal squamous cell carcinoma samples from patients with HPV-associated stage III or stage IV cancer of the oropharynx that was surgically resectible. These patients participated in the ECOG-E1308 trial, a phase II trial that studied paclitaxel, cisplatin, and cetuximab followed by cetuximab and two different doses of intensity-modulated radiation therapy.

  Study phs003320

• Melanoma_multi_site_metastases

  Despite multiple large-scale sequencing studies offering substantial insight into the genomic landscape of cutaneous melanoma, the molecular events surrounding disease progression and the resulting molecular heterogeneity between metastases have not been fully elucidated. We have been applying whole genome and transcriptome sequencing across metastases collected during post mortem as well as to multi-site metastases during treatment

  Study EGAS00001001348

• Phylogenetic reconstruction of breast cancer

  The aim of this study was to identify the evolutionary trajectories of metastatic breast cancer. We present whole genome sequencing data (primary tumours, axillary lymph nodes, distant metastasis and matched normal tissues) from 16 breast cancer patients. This work sheds light on the routes on which tumour cells metastasize and their role in disease progression in ER-positive breast cancer.

  Study EGAS00001004356

• Blood transcriptome profiling links immunity to disease severity in myotonic dystrophy type 1 (DM1).

  The blood transcriptome was examined in relation to disease severity in type I myotonic dystrophy (DM1) patients who participated in the Observational Prolonged Trial In DM1 to Improve QoL- Standards (OPTIMISTIC) study. This sought to a) ascertain if transcriptome changes were associated with increasing disease severity, as measured by the muscle impairment rating scale (MIRS) and b) es-tablish if these changes in mRNA expression and associated biological pathways were also observed in the Dystrophia Myotonica Biomarker Discovery Initiative (DMBDI) microarray dataset in blood (with equivalent MIRS/DMPK repeat length). The changes in gene expression were compared using a number of complementary pathways, gene ontology and upstream regulator analyses, which suggested that symptom severity in DM1 was linked to transcriptomic alterations in innate and adaptive im-munity associated with muscle wasting. Future studies should explore the role of immunity in DM1 in more detail to assess its relevance to DM1.

  Study EGAS00001006926

• cfRRBS methylation profiling of cfDNA from cerebrospinal fluid from pediatric CNS tumor patients

  In this study, we explore the potential of classifying pediatric brain tumors based on methylation profiling of the cell-free DNA in cerebrospinal fluid (CSF). For this proof-of-concept study, we collected 20 cerebrospinal fluid samples of pediatric brain cancer patients via a ventricular drain placed for reasons of increased intracranial pressure. For 11 patients in this study we collected matched tumor DNA. This cohort contains fastQ files of cfRRBS data of these samples.

  Dataset EGAD50000000554

• Bulk and single-cell AML RNA-seq post ex vivo culture

  Bulk and single-cell RNA-seq performed on primary AML blasts cultured ex vivo for 3 days in standard or niche-like conditions.

  Study EGAS00001006265

• SDH_deficient_renal_tumours___RNA_

  Succinate dehydrogenase (SDH) deficient renal cancers are a rare and understudied subtype of renal cancer. As such they represent an unmet need in kidney cancer research. Here, we seek to describe the genomics and transcriptomics of SDH deficient renal cancers by sequencing five such tumours. We document their mutational burden, define driver mutations, demonstrate typical patterns of structural variants, and estimate the cell of origin and cellular composition.

  Study EGAS00001004103

• Transcriptomic insights into IPMN-associated PDAC progression

  This study investigates the transcriptomic heterogeneity and evolutionary progression of intraductal papillary mucinous neoplasms (IPMNs) and their associated pancreatic ductal adenocarcinomas (PDAC). Multi-region tumour sampling was performed to characterise spatial variation in gene expression and to identify transcriptional changes associated with malignant transformation. The project aims to improve understanding of tumour evolution in pancreatic cancer and to identify molecular pathways involved in IPMN-to-PDAC progression.

  Study EGAS50000001540

• The transcriptomic response of skeletal muscle in life-long high-level trained and untrained men and women after acute exercise

  To investigate the influence of lifelong exercise training on the response of skeletal muscle to a bout of acute exercise we generated global transcriptomic data from long-term endurance (8 men, 8 women) and strength (8 men, 8 women) trained individuals and healthy age-matched untrained controls (8 men, 8 women). Skeletal muscle biopsies were taken from M. vastus lateralis before, directly after, and after 1h and 3hrs following acute exercise. All subjects completed one bout of acute endurance exercise and one bout of acute resistance exercise, separated by 4-8 weeks. All 384 samples were multiplexed in 4 lanes and sequenced (2x250bp paired end) on the Illumina NovaSeq 6000.

  Dataset EGAD00001008663

• Long-term Impact and Intervention with Micronutrients in Brazil, Parque Universitário, Community-Based Study

  The Parque Universitário Zinc-Vitamin A cohort was a prospective, double-blind, randomized placebo-controlled trial with 324 children enrolled between 2000 and 2004 and randomized into 8 treatment arms: Placebo, Vitamin A, Glutamine, Vitamin A + Glutamine, Zinc + Glutamine, Zinc, Vitamin A + Zinc, Vitamin A + Zinc + Glutamine.The Parque Universitário Zinc-Arginine study conducted between 2006 and 2010 enrolled 349 infants from the Parque Universitário favela in Fortaleza. Participants were randomized into Placebo, Zinc, and Zinc + Arginine arms.This submission includes genetic and corresponding anthropometric data on a subset of 210 participants from the Zinc-Vitamin A (96) and Zinc-Arginine cohorts (114). More information on this project and its related projects can be found here: Studies of diarrheal susceptibility, growth, and development, in pediatric populations in Northeastern Brazil

  Study phs003175

• Assessing gene expression profiling from FFPE Patient Samples: A Comparison of Two Library Preparation Approaches and Recommendations

  Next-Generation Sequencing (NGS) has transformed cancer research and clinical practice, with Whole Exome Sequencing (WES) driving advances in mutational profiling and personalized oncology. Yet, transcriptomic signatures remain essential for understanding disease mechanisms, including therapy resistance pathways. RNA sequencing (RNA-seq), however, faces unique challenges when dealing with low-input or degraded RNA, as often found in archival formalin-fixed paraffin-embedded (FFPE) tissues. Although previous studies have compared library preparation protocols, rapidly evolving technologies call for updated evaluations. Here, we present a direct comparison of two FFPE-compatible stranded RNA-seq library preparation kits: TaKaRa™ SMARTer® Stranded Total RNA-Seq Kit v2 (Kit A) and Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus (Kit B). Both kits generated high-quality RNA-seq data, yet important differences emerged. Notably, Kit A achieved comparable gene expression quantification to Kit B while requiring 20-fold less RNA input, a crucial advantage for limited samples, albeit with increased sequencing depth. We critically discuss these results in relation to RNA availability, technical performance, cost-effectiveness, processing time, and automation potential, offering practical guidance for selecting optimal RNA-seq strategies in clinical and translational research settings

  Study EGAS50000001066

• 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

• ESGI - Whole Genome Sequencing of samples from the INGI-Val Borbera genetic isolate (X10) (2019-08-19)

  Whole genome sequencing of sampels from an isolated population from the Val Borbera valley in Italy. The samples are sequenced using the Illumina HiSeq X Ten system. . This dataset contains all the data available for this study on 2019-08-19.

  Dataset EGAD00001005268

• Parallel Detections of Somatic Gene Mutations in Surgically Resected Tumor tissues and Matched Plasma Specimens in Early-Stages of Primary Breast Cancer

  We developed two panel successively, contain 68 and 136 genes respectively. Combination with ultrasound or mammography, it could be used for breast cancer early detection and avoided unnecessary surgery or other invasive detection.

  Study EGAS00001003075

• Phenotype and Genotype determination of 400 individuals from Northern Germany

  Phenotype determination by SNP-Typing using PCR and snapshotPCR with subsequent fragment analysis. We investigated 400 individuals from Northern Germany and detected up to 12 different SNPs to determine eye, hair and skin colour. More than 1000 different runs on a ABI3130 were performedThis dataset includes:- Phenotype information for 400 samples- Summary and complete genotype calls for 12 SNPs on 400 samples.

  Dataset EGAD00001001315

• Massachusetts General Hospital Cancer Center DAC for high-throughput microfluidic enrichment from whole leukopak for CTC-based liquid biopsy

  Whole genome sequencing and whole exome sequencing data of circulating tumor cells isolated from patients with metastatic prostate cancer and liver cancer.

  Dac EGAC50000000423

• Array data for oesophageal and related samples – Ganguli et al (methylation array)

  Array data for oesophageal and related samples – Ganguli et al (methylation array)

  Dataset EGAD00010002682

• Severe acne GWAS meta-analysis

  Summary statistics of a GWAS meta-analysis for severe acne. A total of 7,441,713 genotyped and imputed variants were used for 5,602 European severe acne cases and 21,120 matched population controls.

  Dataset EGAD00001004419

• RNASeq files for Newman MAP3K8 melanoma

  RNASeq files for MAP3K8 melanoma paper titled "Clinical genome sequencing uncovers potentially targetable truncations and fusions of MAP3K8 in spitzoid and other melanomas"

  Dataset EGAD00001004567