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• Fragmentomics profiling and quantification of plasma Epstein-Barr virus DNA enhance prediction of future nasopharyngeal carcinoma.

  This study evaluated the clinical utility of fragmentomics analysis of plasma Epstein-Barr virus (EBV) DNA in nasopharyngeal carcinoma (NPC) screening. The first-round EBV-positive blood samples from a two-round large-scale prospective NPC screening cohort were analyzed. The EBV DNA of subjects who developed NPC in the second round displayed a distinctive mononucleosomal size pattern, an NPC-associated end motif profile, and aberrations in methylation deduced by fragmentomics-based methylation analysis (FRAGMA). Subjects with these aberrant fragmentomics features and higher EBV DNA quantity showed a dramatically increased risk of NPC development, demonstrating the potential of plasma DNA fragmentomics in predicting future cancer risk.

  Study EGAS50000000395

• Cross-tissue transcriptomic analysis of human secondary lymphoid organ residing ILC3 reveals a default quiescent state in the absence of inflammation

  A cross tissue transcriptional comparison of human ILC3 isolated from non-inflamed lymph nodes (LN) and spleens, inflamed tonsils and the peripheral blood (PB). Using uniform gating and high-purity cell-sorting, ILC3 were sorted as Lineage(CD3,CD19,CD34,CD14,CD94)-CD45intCD127+CRTH2-CD117+. From LN, spleen, tonsils and PB, NKp44- ILC3 were isolated and, in addition, NKp44+ ILC3 were sorted from spleen and tonsils. RNA quality was measured on a RNA 6000 Pico Kit (Agilent Technologies) using a 2100 Bioanalyzer (Agilent Technologies). 100 pg high-quality RNA was isolated and cDNA was generated using the SMART-Seq (v3) Ultra Low Input RNA Kit (Clontech) with 15 cycles of amplification. Amplified and Covaris-fragmented cDNA was quality-checked on a High Sensitivity DNA chip (Agilent Technologies) and further processed according the TruSeq Nano DNA Library Preparation Kit (Illumina). Data was processed as follows: SMARTer adapters were trimmed with cutadapt and the resulting sequences were aligned to the human RefSeq transcriptome using 14 TopHat2 (Kim et al., 2013). Normalization and quantification was performed using Cufflinks (Trapnell et al., 2012). FPKM counts were determined per gene with HTSeq-count.

  Study EGAS00001002636

• Single-nuclei gene-expression analysis of pheochromocytoma and paraganglioma links tumor subtypes with tumor microenvironment

  This dataset contains raw sequencing reads in FASTQ format from single-nuclei (30 samples) and bulk tissue (40 samples) transcriptome sequencing of pheochromocytoma and paraganglioma tissue specimens. Additionally, data from single-nuclei sequencing of two normal adrenal medulla specimens is included.

  Dataset EGAD00001008403

• The evolution of ovarian high grade serous carcinoma from STIC lesions

  We performed Ampliseq on 11 samples on a targeted panel of 17 genes.

  Study EGAS50000000361

• Germline sequencing

  Detection of SNVs/indels in the germline of pediatric cancer patients with a focus on CHEK2 germline variants.

  Study EGAS00001006254

• Germline sequencing

  Detection of SNVs/ indels in the germline of pediatric cancer patients with a focus on CHEK2 germline variants

  Study EGAS00001006705

• Paired diagnostic and relapse medulloblastoma sequencing

  Whole exome and targeted panel sequencing in a cohort of paired diagnostic and relapse medulloblastoma samples.

  Study EGAS00001007120

• 1M-scBloodNL

  Here we present the 1M-scBloodNL study, in which we performed single-cell RNA-seq on 120 individuals of the Northern Netherlands population cohort Lifelines. For each individual peripheral blood mononuclear cells (PBMCs) were sequenced in an unstimulated condition, and after 3 and 24 hour in vitro stimulation with C. albicans (CA), M. tuberculosis (MTB) and P. aeruginosa (PA), totalling approximately 1.3 million cells. scRNA-seq was conducted with the 10X Genomics 3'-end v2 (72 libraries) and v3 (33 libraries) technology. In general, each library contains PBMCs from 8 donors and 2 different stimulation-timepoint combinations. Donors were demultiplexed using a combination of SoupOrCell (https://www.nature.com/articles/s41592-020-0820-1) and genotype information to assign the correct donor to a donor-specific cell cluster.

  Dataset EGAD00001007764

• Exome data from a high-density melanoma family

  This dataset contains whole-exome sequence data from four individuals in a high-density melanoma family. Sequences were aligned against human reference genome HG19 using BWA.

  Dataset EGAD50000002153

• The_identification_of_genetic_vulnerabilities_in_head_and_neck_cancers_for_the_development_of_novel_therapies

  CRISPR/Cas9 lethality screens in a set of Asian head and neck cancer cell lines to identify novel targets.

  Study EGAS00001002204