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• TERT rearrangements are frequent in neuroblastoma and identify aggressive tumors

  Whole genome sequencing detected structural rearrangements of TERT in 17/75 high stage neuroblastoma with 5 cases resulting from chromothripsis. Rearrangements were associated with increased TERT expression and targeted immediate up- and down-stream regions of TERT, placing in 7 cases a super-enhancer close to the breakpoints. TERT rearrangements (23%), ATRX deletions (11%) and MYCN amplifications (37%) identify three almost non-overlapping groups of high stage neuroblastoma, each associated with very poor prognosis. This submission contains all newly sequenced samples only.study_refcenter AMC

  Dataset EGAD00001001635

• Indonesian RNA-seq dataset

  This dataset contains 4 batches of Indonesian RNA-seq data from Mentawai, New Guinea and Sumba islands. One RNA-seq batch was prepared without Globin depletion, and three batches were Globin depleted using the Illumina Globin-Zero Gold Kit. There are 179 runs in total, including 119 unique samples. Dataset includes multiple batch control samples.

  Dataset EGAD00001005053

• Low coverage WGS of plasma cfDNA

  This dataset includes FASTQ files of low coverage whole genome sequencing of cell free DNA from plasma samples. The samples include 271 plasma samples of patients with an adnexal mass and 125 plasma samples of healthy individuals.

  Dataset EGAD00001007748

• Whole Transcriptome Analysis + AbSeq + Sample Tag Multiplexing

  Multiomics data for a cohort of 20 COVID-19 patients (10 patients mild, 3 patients moderate, 4 patients severe, 3 patients critical) obtained from peripheral blood mononuclear cells (PBMCs) from longitudinally sampled at hospital admission, discharge, and 1 month thereafter. The data has been obtained a multiwell-based single-cell technology (BD Rhapsody) that includes the analysis of PBMCs' whole transcriptome and a set of 52 surface proteins. The samples of the different patients at different collection times were labelled using a cell hashing strategy with the BD Single-Cell Multiplexing Kit (6 samples for each run).

  Dataset EGAD00001011318

• Whole exome sequencing in multiplex cleft families from a consortium

  Building upon our previous linkage and association studies, we will use whole exome sequencing studies of second and third degree affected relatives drawn from multiplex families. Our specific aims are: 1) To conduct whole exome sequencing on affected members (2° and 3° relatives) drawn from multiplex cleft families from a consortium to identify novel genes causing non-syndromic oral clefts; 2) To confirm and test the role of rare variants in these novel genes through confirmatory Sanger sequencing, plus linkage information using additional members available in these multiplex families. This whole exome sequencing approach will combine evidence from linkage studies and large scale sequencing to identify novel genes causing oral clefts in multiplex cleft families.

  Study phs000459

• scRNA-seq of patient-derived PDAC organoids

  We derived PDAC organoids from primary tumors of 18 patients, together with two matched samples from liver metastases. By single-cell RNA sequencing, we show that PDAC organoids consist of ductal cells with patient-specific expression of several gene groups, including genes which encode cell surface proteins. We report ‘classical’ and ‘basal-like’ cells coexisting within single primary tumors or metastases, with greater intratumor subtype heterogeneity linked to higher tumor grade. Single-cell transcriptome analysis of PDAC organoids and primary PDAC identified distinct tumor cell states shared across patients, including a cycling progenitor cell state and a differentiated secretory state. We show that these cell states are connected by a differentiation hierarchy, with ‘classical’ subtype cells concentrated at the endpoint of this hierarchy.

  Study EGAS00001004661

• Whole Genome Sequencing of clonal expansions of single healthy somatic cells (human, female)

  HSC73_clone: Bone marrow mononuclear cells from the healthy 73 years old female were thawed and labeled with Alexa-Fluor 488-conjugated anti-CD34 (581, Biolegend), Alexa-Fluor 700-conjugated anti-CD38 (HIT2, eBioscience), a cocktail of APC-conjugated lineage antibodies consisting of anti-CD4 (RPA-T4), anti-CD8 (RPA-T8), anti-CD11b (ICRF44), anti-CD20 (2H7), anti-CD56 (B159, all BD Biosciences), anti-CD14 (61D3), anti-CD19 (HIB19) and anti-CD235a (HIR2, all eBiocience) and 1 micro-gram/ml propidium iodide (Sigma). Using a BD FACSAria cell sorter, single Lin-CD34+CD38-PI- cells were individually sorted into low-adhesion 96-well tissue culture plates (Corning) containing 100micro-litre of StemSpan Serum-Free Expansion Medium (Stemcell technologies) supplemented with 100ng/ml of human SCF and FLT-3L, 50ng/ml of human TPO, 20ng/ml of human IL-3, IL-6 and G-CSF (all cytokines from Peprotech) and 50U/ml of penicillin and 50μg/ml of streptomycin (Sigma). Cells were incubated at 37 degrees C in a humidified atmosphere with 5% CO2 in air. After 5 days in culture, another 100micro litres of cytokine-containing medium were added. 13 days after seeding, clones B6 and G2 had expanded to approx. 105 cells and were selected for whole genome sequencing (2x101bp, paired-end, Illumina HiSeq2500) after tagmentation-based library preparation (see Extended Experimental Procedures) for clone B6 and standard library preparation for clone G2. For germline-control ~106 unsorted bone marrow mononuclear cells from the same donor were used for sequencing. An average of 30-fold sequence coverage for each the clones and the matching control were obtained.L4clone: A progenitor cell clone was raised from a peripheral blood sample of the 39 year old healthy female. Frozen peripheral blood mononuclear cells (PBMCs) were isolated from 2 ml heparinised peripheral blood via Ficoll Paque density centrifugation. A methylcellulose assay was performed as described earlier (Weisse et al., 2012). In brief, non-adherent mononuclear cells were incubated in the presence of the recombinant human cytokines IL-3, IL-5 and GM-CSF (R&D systems) over 14 days to induce colony formation. Colonies were detected under an inverted light microscope, and plucked by a pipette when colonies had approximately 10,000 cells/CFU. Each colony was washed three times in PBS and finally frozen as a cell pellet in -80 degrees C. Genomic DNA was isolated using the QIAamp DNA micro kit according to the instructions of the manufacturer (Qiagen, Hilden, Germany). Whole genome sequencing (2x101bp, paired-end, Illumina HiSeq2500) was performed for colony 4 after tagmentation-based library preparation and resulted in 15-fold sequence coverage for each the colony and the matching whole blood.

  Dataset EGAD00001000666

• Investigation of the keratinocytic gene expression pattern in Hidradenitis suppurativa

  The underlying pathogenetic factors generating the innate immune signal necessary for T cell activation, initiation and chronification of Hidradenitis suppurativa (HS, also known as Acne inversa) are still poorly understood. Emerging evidence suggests that defective keratinocyte function critically contributes to HS disease development and progression. To elucidate the role of keratinocytes in HS lesion formation, we compared the transcriptomes of isolated lesional and perilesional HS epidermis by RNA sequencing.

  Study EGAS00001005544

• Functional_characterisation_of_CpG_islands_in_human_and_mouse_tissues

  Tissue-specific methylation patterns suggest a role for CpG island (CGI) methylation in differentiation and cell-type-specific gene regulation. We have applied CXXC affinity purification (CAP), MBD affinity purification (MAP) and chromatin immunoprecipitation (ChIP) in combination with solexa sequencing to investigate the extent and functional significance of CGI methylation in sperm, blood, cerebellum and ES cells for both human and mouse.

  Study EGAS00001000075

• RNA-seq on neuroblastoma PDX model COG-N-519 treated with control miR-1283 and test miR-99b-5p mimics

  COG-N-519 primary neuroblastoma cells were innoculated by subcutaneous injection into NSG mice. When tumours reached a size of 100-200mm3 miRNAs conjugated to nanoparticles were injected intratumourally every 2 days for 1 week. 24 hr after the last injection, snap frozen tumour tissue was harvested for RNA extraction and RNA-seq analysis.

  Study EGAS00001005581

• March 2016 update of smRNA-Seq assays data (bam/fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  March 2016 update of smRNA-Seq assays data (bam/fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001959

• March 2016 update of whole genome shotgun sequencing data (bam/fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  March 2016 update of whole genome shotgun sequencing data (bam/fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001958

• March 2016 update of Whole genome bisulfite sequencing assay data (fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  March 2016 update of Whole genome bisulfite sequencing assay data (fastq) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001957

• March 2016 update of Whole genome bisulfite sequencing assay data (bams) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  March 2016 update of Whole genome bisulfite sequencing assay data (bams) for reference epigenomes generated at Centre for Epigenome Mapping Technologies (Canadian Epigenetics, Environment and Health Research Consortium), Genome Sciences Center, B.C. Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001987

• National Eye Institute (NEI) Age-Related Eye Disease Study 2 (AREDS2)

  The Age-Related Eye Disease Study 2 (AREDS2) was a multi-center, randomized Phase III clinical trial designed to assess the effects of oral supplementation of high doses of lutein, zeaxanthin, and omega-3 fatty acids (docosahexaenoic acid [DHA] and eicosapentaenoic acid [EPA]) in reducing the risk of progression to late age-related macular degeneration (AMD), progression to cataract surgery, and/or progression to moderate vision loss in high-risk participants. The effect of the study supplements on cardiovascular outcomes and cognitive function were also examined. Other study goals included evaluation of eliminating beta-carotene and/or reducing zinc in the original AREDS formulation on the progression and development of late AMD. AREDS2 sought to validate the AREDS AMD scale developed from the photographic data obtained from AREDS, (Study Accession: phs000001).Eighty-two clinical sites across the United States enrolled 4,203 participants aged 50 to 85 (mean age 74 years) between October 2006 and September 2008. Enrollment was restricted to people at high risk of progression to late AMD with either bilateral large drusen or large drusen in 1 eye and late AMD in the fellow eye. Follow-up assessments in the clinic occurred on an annual basis for an average of 5 years, with telephone calls every six months during each year. Blood or saliva samples were also collected from 2,000+ AREDS2 participants for genetic research. Of these, samples from 1,800+ AREDS2 participants were included in the International Age-Related Macular Degeneration Genomics Consortium - Exome Chip Experiment, and have exome chip data available in the dbGaP (Study Accession: phs001039). In addition, samples from 1300+ AREDS2 participants were included in the International Age-Related Macular Degeneration Genomics Consortium - Whole Genome Sequencing Study in the dbGaP (Study Accession: TBD). Of 1363 AREDS2 participants with whole genome sequencing, 488 previously participated in AREDS.Please see "The Age-Related Eye Disease Study 2 (AREDS2) Research Group" document for a full list of AREDS2 study contributors.

  Study phs002015

• Transcriptomic intra-tumor heterogeneity of colorectal cancer varies depending on tumor location within the colorectum

  Background; Intra-tumor heterogeneity (ITH) of colorectal cancer (CRC) complicates molecular tumor classification, such as transcriptional subtyping. Differences in cellular states, biopsy cell composition, and tumor microenvironment may all lead to ITH. Here we analyze ITH at the transcriptomic and proteomic levels to ascertain whether subtype discordance between multiregional biopsies reflects relevant biological ITH or lack of classifier robustness. Further, we study the impact of tumor location on ITH.MethodsMultiregional biopsies from stage II and III CRC tumors were analyzed by RNA sequencing (41 biopsies, 14 tumors) and multiplex immune protein analysis (89 biopsies, 29 tumors). CRC subtyping were performed using consensus molecular subtypes (CMS), CRC intrinsic subtypes (CRIS), and TUMOR types. ITH-scores and network maps were defined to determine the origin of heterogeneity. A validation cohort was used with one biopsy per tumor (162 tumors).ResultsOverall, inter-tumor transcriptional variation exceeded ITH, and subtyping calls were frequently concordant between multiregional biopsies. Still, some tumors had high ITH and were classified discordantly. Proximal tumors showed ITH related to differences in the microenvironment, while ITH within distal tumors were cancer-cell related. This subtype discordancy reflected actual molecular ITH within the tumors. The relevance of the subtypes was reflected at protein level where several inflammation markers were significantly increased in immune related transcriptional subtypes, which was verified in an independent cohort (Wilcoxon rank sum test; p<0.05).ConclusionOur transcriptomic and proteomic analyses show that the tumor location along the colorectum influence the ITH of CRC, which again influence the concordance of subtyping.

  Study EGAS00001004668

• Data of the Institute of Pathology, University Medical Center Freiburg, Germany

  DAC for proteomics data deposited in EGA by the proteomics laboratory of the Institute of Pathology, University Medical Center Freiburg, Germany

  Dac EGAC50000000048

• DAC anti-MPO BCR sequences

  DAC for the requests of access to data of anti-MPO BCR sequences in the EGA repository,

  Dac EGAC50000000446

• NGS WGS Data - Unic TDP

  WGS data from the Unicorn-PASS cohort for the Tandem Duplicator Phenotype paper

  Dataset EGAD50000001567

• Detection of causative structural variants using long read whole genome sequencing in patients with non-syndromic autism spectrum disorder

  This study involved performing long read whole genome sequencing using Oxford Nanopore Technology platform on to detect causative structural variants in patients with non-syndromic autism spectrum disorder. This study was performed on 23 such children in whom prior karyotyping, Fragile-X analysis (in males), chromosomal microarray and whole exome sequencing did not identify a causative variant.

  Study EGAS50000000842

• CCA WGS data (16 CCA with matched normal, 4 cell-line)

  Fastq files for WGS for 16 CCAs (with matched normal tissues), and 4 cell lines in an AA-treatment experiment (0, 10, 20, 40ug AA treatment after 180 days; 2 runs each for 10ug and 40ug experiments). Genomic DNA was extracted using DNeasy Blood and Tissue Kit (Qiagen). Sequencing libraries were prepared from DNA extracted using the SureSelect XT2 Target Enrichment System for the Illumina Multiplexed Sequencing platform (Illumina) according to the manufacturer’s instructions. Whole genome sequencing was performed on Illumina HiSeq4000 sequencer with paired-end sequencing.

  Dataset EGAD00001012100

• Small RNA Sequencing across Diverse Biofluids Identifies Optimal Methods for exRNA Isolation

  We tested the efficiency and reproducibility of 10 RNA isolation methods on 5 different biofluids. Pooled human plasma and serum, bile and urine were used along with cell culture supernatants from human embryonic stem cells (hESC), primary neonatal rat ventricular myocytes (NRVM) and human cholangiocarcinoma cells (KMBC). 4 RNA isolation methods designed to isolate total RNA from bio fluids without enrichment of exRNA carriers were used. 6 methods that preferentially enriched for exRNA carriers were also compared. Small RNA libraries were constructed using the NEBNext small-RNA library prep. The efficiency and reproducibility of the different RNA isolation methods was compared using small-RNA seq.

  Study phs002143

• Prime-seq of human term placenta-derived trophoblast organoids

  To study the one of the mechanisms through which obesity could affect placental cells, we used a novel microfluidic organs-on-a-chip device fabricated for co-culturing adipose spheroids and trophoblast organoids. The organoids were derived from the term placenta of a over-weight women. The adipose spheorids were derived from the white adipose tissue of a woman. And we sequenced the RNAs from the trophoblast organoids. The RNA extracted were subjective to Prime-seq library preparation protocol and being sequenced on Illumina NovaSeq 6000 at Novogene.

  Study EGAS50000000833

• Beta values of methylation data of the CUP/reference/validation cohort (H021)

  Beta values of methylation data of the CUP/reference/validation cohort (H021) used for the validation cohort described in the publication

  Dataset EGAD00001008669

• PASCAL-MID Data Access Committee

  DAC for the center of Personalized Approach to Genome Editing of Stem Cells for Autotransplantation of Monogenic Immunodeficiencies (PASCAL-MID) at Aarhus University and Aarhus University Hospital

  Dac EGAC50000000680