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• Data Access Commitee to XP skin study

  Dac EGAC00001002945

• Genetic predisposition to cancer, University of Tampere

  Dac EGAC00001000488

• Data access commitee to RUBY study

  Dac EGAC00001001775

• dummy DAC, to be replaced with EGAC00001000055

  Dac EGAC00001000846

• DAC for present-day Central Asia genotype data at the Centre for GeoGenetics, Natural History Museum of Denmark.

  Dac EGAC00001000894

• DAC for "The application of RNA sequencing for the diagnosis and genomic classification of pediatric acute lymphoblastic leukemia"

  Dac EGAC00001001501

• Leukemia Data Access committee for the deposited data. The committee consists of the principal investigators for the data set.

  Dac EGAC00001003565

• DATA FILES FOR SJTALL

  DATA FILES FOR SJTALL

  Dataset EGAD00001001052

• DATA FILES FOR PCGP Dyer_iPSC TEBS

  DATA FILES FOR PCGP Dyer_iPSC TEBS

  Dataset EGAD00001001416

• DATA FILES FOR PCGP Dyer_iPSC 5hmc

  DATA FILES FOR PCGP Dyer_iPSC 5hmc

  Dataset EGAD00001001418

• DATA FILES FOR SJMEL-WGS

  DATA FILES FOR SJMEL-WGS

  Dataset EGAD00001001032

• DATA FILES FOR PCGP Dyer_iPSC WGS

  DATA FILES FOR PCGP Dyer_iPSC WGS

  Dataset EGAD00001001415

• Genomic Landscape of Human Skin at a Single-Cell Resolution

  Every cell in the human body has a unique set of somatic mutations, yet it remains difficult to comprehensively genotype an individual cell. Here, we developed solutions to overcome this obstacle in the context of normal human skin, thus offering the first glimpse into the genomic landscapes of melanocytes at single-cell resolution. We comprehensively genotyped 133 melanocytes from 19 sites across 6 donors. As expected, sun-shielded melanocytes had fewer mutations than sun-exposed melanocytes. However, within sun-exposed sites, melanocytes on chronically sun-exposed skin (e.g. the face) displayed a lower mutation burden than melanocytes on intermittently sun-exposed skin (e.g. the back). Melanocytes from donors with a history of skin cancer had higher mutation burdens than melanocytes from donors without skin cancer, implying that the mutation burden of normal skin can be harnessed to measure cumulative sun damage and skin cancer risk. Moreover, melanocytes from healthy skin commonly harbor pathogenic mutations, likely explaining the origins of the melanomas that arise in the absence of a pre-existing nevus. Phylogenetic analyses identified groups of related melanocytes, suggesting that melanocytes spread throughout skin as fields of clonally related cells, invisible to the naked eye. Overall, our study offers an unprecedented view into the genomic landscapes of individual melanocytes, revealing key insights into the causes and origins of melanoma.

  Study phs001979

• Inherited chromosomally-integrated human herpesvirus 6A/B (HHV-6A/B) genome sequences in the Japanese population

  The deposited sequences represent inherited chromosomally-integrated human herpesvirus 6 (iciHHV-6) genomes identified from 10 BioBank Japan (BBJ) subjects based on the analysis of the whole-genome sequencing (WGS) data. In brief, we re-aligned unmapped reads from the WGS to HHV-6A genome (Genbank accession number: KJ123690.1) using BWA-MEM algorithm. Ten out of 3,256 subjects were identified with high depth of coverage of HHV-6. We further distinguished subjects with integrated HHV-6A subtypes from those with integrated HHV-6B based on phylogenetic analysis of concatenated sequences of three viral genes (U27/U43/U83, which show high divergence between viral species). We reconstructed the HHV-6 viral genome of 10 subjects. First, reads that mapped to a reference HHV-6A genome (KJ123690.1) were further aligned against the integrated HHV-6A genome derived from a Japanese individual NA18999 (GenBank Accession number: KY316047.1) using BWA-MEM. Based on the alignment, variant calling was performed using freebayes (version: v1.2.0-2-g29c4002) with parameters ploidy = 1 and min-alternate-fraction = 0.8 {Garrison, 2012}. We generated subject-specific iciHHV-6 viral sequences by applying the resulting variants to the KY316047.1 reference genome using the FastaAlternateReferenceMaker function in the Genome Analysis Toolkit (GATK) v3.7. Please note that HHV-6B-specific variants are unlikely to be sensitively reconstructed using this method.

  Study JGAS000240

• Mutational Landscape of Grey Zone Lymphoma

  The mutational landscape of grey zone lymphoma (GZL) has not yet been established and differences to related entities are mostly unknown. Here, we studied coding sequence mutations of 50 EBV-negative GZL and 20 polymorphic EBV-positive DLBCL NOS (poly-EBV-L) in comparison to classical Hodgkin lymphoma (cHL), primary mediastinal B cell lymphoma (PMBCL), and diffuse large B cell lymphoma (DLBCL). Paired exomes of 21 GZL and 7 poly-EBV-L cases were analyzed as a discovery cohort followed by targeted sequencing of 217 genes in an extension cohort of 29 GZL and 13 poly-EBV-L cases. GZL cases with thymic niche involvement displayed a mutation profile closely resembling cHL and PMBCL, with SOCS1 (45%), B2M (45%), TNFAIP3 (35%), GNA13 (35%) and NFKBIA (29%) being the most recurrently mutated genes. In contrast, GZL cases without thymic niche involvement (N=18) had a significantly distinct pattern, enriched in mutations related to apoptosis defects (TP53 (39%), BCL2 (28%), BIRC6 (22%)) and depleted in GNA13, XPO1 or NFKB signaling pathway mutations (TNFAIP3, NFKBIE, IKBKB, NFKBIA). Poly-EBV-L cases presented a distinct mutational profile including STAT3, PRKDC mutations and a significantly lower coding-mutation load in comparison to EBV-negative GZL. Our study highlights characteristic mutational patterns in GZL associated with presentation in the thymic niche suggesting a common cell of origin and disease evolution with related anterior mediastinal lymphomas.

  Study EGAS00001004482

• Structural variant analysis of homologous recombination-deficient genomes

  Homologous recombination (HR) deficiency causes DNA breaks and cytogenetic aberrations. Paradoxically, the types of DNA rearrangements specifically associated with HR-deficient cancers only minimally impact chromosomal structure. Addressing this, we combined a genome graph analysis of short-read whole genome sequencing (WGS) profiles across thousands of tumors with deep linked-read (LR) WGS of 46 BRCA1 or BRCA2 mutant breast cancers to discover a distinct class of HR deficiency-enriched rearrangements called reciprocal pairs. LR WGS showed that reciprocal pairs with identical rearrangement orientations gave rise to one of two distinct chromosomal outcomes, distinguishable only with long molecule data. While one (cis) outcome corresponded to the copy and pasting of a small segment to a distant site, a second (trans) outcome was a quasi-balanced translocation or multi-megabase inversion with substantial (10kb) duplications at each junction. The full spectrum of reciprocal pair outcomes could be explained by an HR-independent replication restart repair mechanism. LR WGS additionally identified single-strand annealing (SSA) as a BRCA2-deficiency specific repair pathway in human cancers. Replication restart- and SSA-associated SVs improved BRCA1- vs. BRCA2- deficiency classification and identified metastatic cancer cases with favorable chemotherapy responses. Our data reveal classes of BRCA1- and BRCA2-deficiency specific rearrangements as drivers of cytogenetic aberrations in HR deficient cells.

  Study EGAS00001007186

• Diagnosis of pediatric central nervous system tumors using methylation profiling of cfDNA from cerebrospinal fluid

  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.

  Study EGAS50000000377

• Genomewide copy number alteration screening of circulating plasma DNA

  Early cancer diagnosis might improve survival rates. As circulating tumor DNA (ctDNA) carries cancer-specific modifications, it has great potential as a noninvasive biomarker for detection of incipient tumors. We collected cell-free DNA (cfDNA) samples of 1002 elderly without a prior malignancy, carried out whole-genome massive parallel sequencing and scrutinized the mapped sequences for the presence of (sub)chromosomal copy number alterations (CNAs) predictive for a malignancy. When imbalances were detected, 6-monthly clinical follow-up was carried out.

  Study EGAS00001006031

• scEC&T-seq manuscript data

  This dataset includes all data produced in the study describing "scEC&T-seq", a method for parallel sequencing of extrachromosomal circular DNA and transcriptome in single cells. This dataset includes: - Illumina scEC&T-seq Circle-seq data (scCircle-seq) for a total of 626 single cells / nuclei - bam files - Illumina scEC&T-seq RNA-seq data (scRNA-seq-Illumina) for the same single cells / nuclei - bam files - Nanopore scCircle-seq data for 18 single cells - bam files - Nanopore bulk WGS for 2 cell lines and 2 primary tumor samples - bam files - Illumina bulk WGS for 2 cell lines - bam files - Illumina bulk Circle-seq data from 1 cell line - bam file - Illumina ChIP-seq H3K27me3 data from 1 cell line - fasta files + peaks bed file + coverage bw file

  Dataset EGAD00001010071

• Genomic Analysis of Pediatric Low Grade Gliomas

  Pediatric low-grade gliomas (PLGGs) are among the most common solid tumors in children but, apart from mutations or duplications in the BRAF kinase in specific subclasses, few genetic driver events are known. Diffuse PLGGs compose a set of uncommon subtypes that exhibit invasive growth and are therefore especially challenging clinically. These tumors are particularly poorly understood. We performed high-resolution copy-number analysis of 44 diffuse PLGGs to identify recurrent alterations. Diffuse PLGGs exhibited fewer such alterations than adult low-grade gliomas, but we identified several significantly recurrent events. The most significant event, 8q13.1 gains, was observed in 28% of diffuse astrocytoma WHO grade II (DA2) and resulted in partial duplication of the transcription factor MYBL1 with truncation of its C-terminal negative-regulatory domain. A similar recurrent deletion-truncation breakpoint was identified in two angiocentric gliomas in the related gene MYB on 6q23.3. Whole genome sequencing of a MYBL1-rearranged diffuse astrocytoma grade II demonstrated MYBL1 tandem duplication and few other events. Two truncated MYBL1 transcripts identified in this tumor induced anchorage-independent growth when expressed in 3T3 cells and tumor formation in nude mice. Truncated transcripts were also expressed in two additional tumors with MYBL1 partial duplication. Our results define clinically relevant molecular subclasses of diffuse PLGGs and highlight a potential role for the MYB family in the biology of low-grade gliomas. "Reprinted from www.pnas.org/cgi/doi/10.1073/pnas.1300252110 with permission from PNAS."

  Study phs000614

• Single cell RNA sequencing of co-culture of human organoids with polarized pro-inflammatory (M1) or anti-inflammatory (M2) macrophages

  Human intestinal organoids co-cultured with pro-inflammatory (M1) or anti-inflammatory (M2) human macrophages for 48 hours. 3 days after the co-culture alive cells were sorted and processed for single cell RNA sequencing

  Study EGAS50000000467

• Single-nucleus transcriptome sequencing of the ALS-FTD motor cortex after sorting by TDP-43

  Single-nucleus RNA-sequencing of NeuN+ nuclei of the post-mortem human primary motor cortex from patients with ALS-FTD confirmed for TDP-43 pathology, after sorting for TDP-43 signal, TDP-43 Low vs. TDP-43 High

  Study EGAS50000001566

• ATAC-seq data in normal colon mucosa

  This dataset includes ATAC-seq data generated in normal colon mucosa obtained in four healthy volunteers during colonoscopy indicated for colorectal cancer screening. Subjects had no lesions in the colon. Also includes one frozen sw480 colon adenocarcinoma cell line sample for piloting the protocol

  Study EGAS00001005281

• Integrative and comparative genomic analyses identify clinically relevant groups of pulmonary carcinoids and unveil the supra-carcinoids

  Multi-omic data for lung neuroendocrine neoplasms, including the first multi-omic sequencing data for the understudied lung atypical carcinoids. The data includes Whole-exomes, whole-genomes, RNA-seq, and EPIC 850K methylation array data.

  Study EGAS00001003699

• Genome-wide association data on male-pattern baldness

  The study comprises 1000Genomes imputed data for 581 MPB cases and 416 male controls. Cases are selected for age<40 and Hamilton-Norwood grade V-VII. Control include 270 males >60 years no signs of AGA (Hamilton-Norwood grade I).

  Study EGAS00001001354

• August 2020 data update (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.

  August 2020 data update (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 EGAD00001006383

• August 2019 data update (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.

  August 2019 data update (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 EGAD00001005335

• May 2019 data update (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.

  May 2019 data update (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 EGAD00001005060

• September 2016 data update (bam/fastq/vcf) 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.

  September 2016 data update (bam/fastq/vcf) 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 EGAD00001002724

• January 2018 data update (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.

  January 2018 data update (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 EGAD00001003962

• June 2017 data update (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.

  June 2017 data update (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 EGAD00001003414

• Strand-specific mRNA-Seq assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, as part of the International Human Epigenome Consortium.

  Strand-specific mRNA-Seq assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001227

• 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

• ChIP-Seq (Input) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, as part of the International Human Epigenome Consortium.

  ChIP-Seq (Input) assays for reference epigenomes generated by Centre for Epigenome Mapping Technologies at Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada as part of the International Human Epigenome Consortium.

  Dataset EGAD00001001235

• KiCS cancer panel data for academic and for-profit use

  This data set contains KiCS cancer panel data for academic and for-profit use.

  Dataset EGAD00001009734

• Whole Genome Sequencing for Korean Diffuse Gastric Cancer

  Fastq files for the whole genome sequencing data (Illumina HiSeq 2500; 32.6-fold) for two diffuse gastric cancers revealing the fusion breakpoints. 2102T: CTNND1-ARHGAP26 gene fusion (g.chr11:57,578,103-g.chr5:142,358,707) 354T: ANXA2-MYO9A gene fusion (g.chr15:60,656,550-g.chr15:72,157,966)

  Dataset EGAD00001003953

• Metastatic breast cancer targeted gene screen (2014-09-24)

  The samples will be sequenced for a targeted panel of cancer relevant genes (n ~ 370) and analysed for somatic mutations. This dataset contains all the data available for this study on 2014-09-24

  Dataset EGAD00001001018

• Metastatic breast cancer targeted gene screen (2017-05-11)

  The samples will be sequenced for a targeted panel of cancer relevant genes (n ~ 370) and analysed for somatic mutations. This dataset contains all the data available for this study on 2017-05-11.

  Dataset EGAD00001003330

• The application of RNA sequencing for the diagnosis and genomic classification of pediatric acute lymphoblastic leukemia

  RNA-seq data for ALL patients as described in "The application of RNA sequencing for the diagnosis and genomic classification of pediatric acute lymphoblastic leukemia"

  Dataset EGAD00001006335

• Hyperpolarized carbon-13 MRI for very early response assessment of neoadjuvant chemotherapy in breast cancer patients

  Transcriptomic data for five patients with breast cancer undergoing neoadjuvant chemotherapy and hyperpolarised 13C-MRI for early response assessment

  Dataset EGAD00001008141

• Data access committee for genomic and clinical data produced by the Institute for Biomedical Technology.

  Dac EGAC00001000110

• DAC for the BCTL

  DAC for submissions from the BCTL (Hopital Jules Bordet, Université LIbre de Bruxelles)

  Dac EGAC50000000323

• DATA FILES FOR PCGP SJETP WXS

  DATA FILES FOR PCGP SJETP WXS

  Dataset EGAD00001001248

• BiSeqS

  Runs that contain data for the sensitivity and specificity experiments for BiSeqS.

  Dataset EGAD00001003323

• dataset for BGI bladder cancer project

  dataset for BGI bladder cancer project

  Dataset EGAD00001000758

• To reveal the spectrum of gene mutations in grade II/III gliomas, whole exome sequencing of 52 samples including 4 multi-regional and 10 multi-time points sampling cases and 293 SNP-array were performed.

  To reveal the spectrum of gene mutations in grade II/III gliomas, whole exome sequencing of 52 samples including 4 multi-regional and 10 multi-time points sampling cases and 293 SNP-array were performed. Our analysis revealed high degrees of temporal/spatial heterogeneity generated during tumor expansion and relapse.

  Study EGAS00001001045

• We performed whole-exome sequencing and whole epigenome sequencing (RRBS) of samples collected from different time points during radiotherapy from thirty-four ESCC patients. We compared the genetic and epigenetic features of the different time biopsy samples to reveal the changes in ESCC received radiotherapy.

  We performed whole-exome sequencing and whole epigenome sequencing (RRBS) of samples collected from different time points during radiotherapy from thirty-four ESCC patients. We compared the genetic and epigenetic features of the different time biopsy samples to reveal the changes in ESCC received radiotherapy.

  Study EGAS00001002718

• RoCK and ROI single-cell transcriptome of one acute lymphoblastic leukemia patient

  Whole-transcriptome single-cell RNA sequencing (scRNA-seq) was performed following the manufacturer’s protocol (BD Rhapsody, BD Biosciences). Targeted enrichment of BCR::ABL1 transcripts was conducted using the RoCK and ROI-seq approach, based on the barcoded bead technology of the BD Rhapsody platform. In the RoCK and ROI-seq workflow, the template-switch oligonucleotides (TSOs) attached to BD Rhapsody beads were modified with one or multiple capture sequences specific to transcripts of interest, enabling targeted transcript capture during reverse transcription. ROI primers that are added during library preparation to direct amplification and sequencing toward these defined regions of interest (ROIs). Resulting libraries were sequenced on an Illumina sequencer.

  Dataset EGAD50000001976

• We performed whole-exome sequencing and whole epigenome sequencing (RRBS) of samples collected from different time points during radiotherapy from thirty-four ESCC patients. We compared the genetic and epigenetic features of the different time biopsy samples to reveal the changes in ESCC received radiotherapy.

  We performed whole-exome sequencing and whole epigenome sequencing (RRBS) of samples collected from different time points during radiotherapy from thirty-four ESCC patients. We compared the genetic and epigenetic features of the different time biopsy samples to reveal the changes in ESCC received radiotherapy.

  Study EGAS00001002719

• Application of Hi-C sequencing to detect structural variants in B-cell acute lymphoblastic leukemia

  Large structural variants are easily detected by Hi-C sequencing as strong, distant signals on a Hi-C contact map. Translocations are frequently evident in B-ALL and accurate identification of these translocations can guide clinical treatment options. Here were apply shallow Hi-C sequencing as an unbiased, cost-effective approach to identify translocations among B-ALL patients.

  Study EGAS00001005605

• Genomic characterisation of SDH deficient renal cell carcinoma - RNA

  SDH deficient renal cell carcinomas are a rare and recently defined subtype of kidney cancer, often associated with an inherited mutation in one of the SDH gene subunits. This dataset sought to understand the genomic events that underpin tumour formation, from putative cell of origin, characterisation of the tumour microenvironment, to the genomic evolution of these rare tumours. We performed whole genome and RNA sequencing of 4 patients with SDH deficient renal cell carcinomas, including one patient who had an additional paraganglioma. An addition patient in this cohort had the initial diagnosis revised to a clear cell renal cell carcinoma.

  Dataset EGAD00001008470

• Pharmacogenomic profiling reveals molecular features of chemotherapy resistance in IDH wild type primary glioblastoma

  We stratified 69 primary IDH-wt GBM patients into TMZ-resistant (n = 29) and sensitive (n = 40) groups, using TMZ screening of the corresponding patient-derived glioma stem-like cells (GSCs). Genomic and transcriptomic features were then examined to identify TMZ-associated molecular alterations. Subsequently, we developed a machine learning (ML) model to predict TMZ response from combined signatures. Moreover, TMZ response in multisector samples (52 tumor sectors from 18 cases) was evaluated to validate findings and investigate the impact of intra-tumoral heterogeneity on TMZ efficacy.

  Dataset EGAD00001010156

• Whole Genome, RNA, and ChIP Sequencing of matched brain tumor-normal pairs (ICGC)

  Whole Genome Seq: Illumina HiSeq sequence data (with >30x coverage) were aligned to the hg19 human reference genome assembly using BWA (Li and Durbin, 2009);duplicate reads were removed from the final BAM file. No realignment or recalibration was performed. Paired-end RNA sequencing reads were mapped to the hg19 assembly of the human reference genome using BWA.Each ChIP-seq library was sequenced with two complete lanes on the Illumina HiSeq 2500 in the 101-bases paired-end rapid mode and aligned to hg19 using bwa.This resulted in the following coverage values (genome-wide, after deduplication, including all uniquely mapping reads):GBM103 macroH2A1: 17x H3K36me3: 20xMB59 macroH2A1: 11x H3K36me3: 11x

  Dataset EGAD00001000664

• Inherited Predisposition to Cancer Projects Data Access Committee

  Dac EGAC00001001565

• Board considering access to BELOB RNA-seq data

  Dac EGAC00001001686

• Data access committee for white blood cell and cell-free DNA analyses for detection of residual disease in gastric cancer

  Dac EGAC00001001435

• DATA FILES FOR SJEPD

  DATA FILES FOR SJEPD

  Dataset EGAD00001000162

• WGS DATA FILES FOR SJCBF

  DATA FILES FOR SJCBF

  Dataset EGAD00001000268

• DATA FILES FOR SJEPD

  DATA FILES FOR SJEPD

  Dataset EGAD00001000853

• CGMH data access committee for the CGMH-OCCC-WES data

  CGMH data access committee for the CGMH-OCCC-WES data

  Dac EGAC50000000028

• The data access committee for Genome-wide analyses of cell-free DNA for therapeutic monitoring of patients with pancreatic cancer

  Dac EGAC50000000588

• DAC for pediatric AML genomic sequences

  DAC for dataset containing matched tumor-healthy genomic sequences from patients with pediatric AML

  Dac EGAC50000000666

• DAC for DLBCL dataset

  Data Access Committee for cfDNA sequencing dataset from 290 samples from patients with DLBCL and HGBL.

  Dac EGAC50000000257

• Metastatic_Prostate_Follow_Up_2

  Validation/deeper sequencing for metastatic prostate cancer samples

  Study EGAS00001000756

• Metastatic_Prostate_Follow_Up

  Validation/deeper sequencing for metastatic prostate cancer samples

  Study EGAS00001000730

• Nrf2 transcript alterations

  WGS and RNA-seq data for Nrf2 study

  Study EGAS00001001740

• Targeted Gene Panel for 171 PTCLs

  Targeted Gene Panel for 171 PTCLs

  Dataset EGAD00001003967

• DATA FILES FOR PCGP SJMEL WXS

  DATA FILES FOR PCGP SJMEL WXS

  Dataset EGAD00001001246

• DATA FILES FOR PCGP SJMEL RNASEQ

  DATA FILES FOR PCGP SJMEL RNASEQ

  Dataset EGAD00001001247

• WGS data for NRF2 study

  WGS data for cell lines and clinical samples

  Dataset EGAD00001002244

• Single-cell transcriptome analysis of B-cell development in the ABO platform

  The dataset includes samples from four individual donors, pooled at each cell-harvesting time point (days 21, 28, and 35). Single-cell RNA sequencing was performed on the 10x Genomics Chromium platform using GEM-X Single Cell 5′ v3 and GEM-X Single Cell V(D)J v3 for BCR profiling. For each timepoint, paired libraries were constructed: a 5′ GEX library and a V(D)J-B library. Per reaction 350,000-400,000 cells were loaded, aiming for 60,000 cells per reaction. Pooled libraries were sequenced on an Illumina NovaSeq X sequencer. 50,000 read pairs per cell for GEX and 5,000 read pairs per cell for V(D)J were targeted.

  Dataset EGAD50000002433

• Normal brain controls for ICGC PedBrain DNA methylation sequencing

  DNA methylation profiling of 8 control samples from adult (4) and fetal brain (4) used, for example, for the following studies: Mack, Witt, et al. Epigenomic alterations define lethal CIMP-positive ependymomas of infancy. Nature 506(7489):445-450, 2014 (see EGAS00001000443) Hovestadt, et al. Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing. 510(7506):537-541, 2014 (see EGAS00001000561)

  Study EGAS00001000909

• Mosaic Chromosomal Aneuploidies Detection in Clinical Samples

  Mosaic chromosomal aneuploidy occurs when only a subset of cells carries an abnormal number of chromosomes. Mosaic aneuploidy has been reported in multiple types of diseases. Here we have developed a new sequencing-based approach to identify, characterize and quantify mosaic aneuploidy events in human tissue samples. This ongoing study has begun with results from sequencing data from two clinical patients, one with autism spectrum disorder (ASD) and the other with hemihyperplasia (OMIM 235000). We captured ~100,000 common SNPs from the samples to identify the nature of the mosaic aneuploidy events in each of the samples.

  Study phs001557

• OCD Collaborative Genetic Association Study (OCGAS)

  The OCD Collaborative Genetics Association Study Group (OCGAS) was funded by NIMH to conduct a genome-wide association study to identify disease susceptibility loci of early-onset obsessive-compulsive disorder (OCD). Collaborators at Johns Hopkins, Brown, Columbia, MGH, UCLA, and NIMH evaluated 2,000 individuals with OCD and collected DNA from these individuals and both their parents. The genotyping and analyses was performed in two stages. In the first stage 1,065 families (comprising 1406 patients with OCD and 2895 individuals in total) were genotyped on the Illumina OmniExpress GWA (SNPs) panel at the JHU SNP Center.

  Study phs000903

• FinaleMe: Predicting DNA Methylation by the Fragmentation Patterns of Plasma Cell-Free DNA

  Analysis of DNA methylation in cell-free DNA (cfDNA) reveals clinically relevant biomarkers but requires specialized protocols and sufficient input material that limits its applicability. Millions of cfDNA samples have been profiled by genomic sequencing. To maximize the gene regulation information from existing datasets, we developed FinaleMe, a non-homogeneous Hidden Markov Model (HMM), to predict DNA methylation of cfDNA and, therefore, tissues of origin directly from plasma whole genome sequencing (WGS). We validated the performance with 80 pairs of deep and shallow coverage WGS and whole genome bisulfite sequencing (WGBS) data from both cancer patients and healthy controls.

  Study phs003287

• Combination pembrolizumab and radiotherapy induces systemic anti-tumor immune responses in immunologically-cold non-small cell lung cancer

  The abscopal effects of radiation may sensitize immunologically “cold” tumors to immune checkpoint inhibition (ICI). We investigated the immunostimulatory effects of radiotherapy leveraging multi-omic analyses of serial tissue and blood biospecimens (n=293) from a phase 2 clinical trial of stereotactic body radiation therapy (SBRT) followed by pembrolizumab in metastatic non-small cell lung cancer (NSCLC; NCT02492568). Patients with immunologically-cold tumors (low tumor mutation burden, null PD-L1 expression, WNT-pathway mutated) in the SBRT arm had significantly longer progression-free survival compared to ICI alone (P<0.05). Induction of interferon-gamma, interferon-alpha, and antigen processing and presentation gene sets was significantly enriched post SBRT in non-irradiated tumor sites (FDR adjusted P<0.01). Significant on-therapy expansions of new and pre-existing TCR clones in both the tumor and blood compartments were noted in the SBRT arm (P<0.05). These findings support the systemic anti-tumor effects of immuno-radiotherapy and may open a therapeutic window of opportunity to overcome resistance to ICI.

  Dataset EGAD50000000404

• Oncogene activated human breast luminal progenitors contribute basally located myoepithelial cells

  Basal-like breast cancer originates in luminal progenitors, frequently with an altered PI3K pathway, and focally in close association with genetically altered myoepithelial cells at the site of tumor initiation. The exact trajectory behind this bi-lineage phenomenon remains poorly understood. Here we used a breast cancer relevant transduction protocol including hTERT, shp16, shp53, and PIK3CA(H1047R) to immortalize FACS isolated luminal cells, and we identified a candidate multipotent progenitor. We found that the apparent luminal phenotype of these oncogene transduced progenitors was metastable giving rise to basal-like cells dependent on culture conditions.

  Study EGAS50000000505

• 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

• WXS of 147 lung cancer patients treated with immunotherapy

  We first attempted to predict MHC-binding neoantigens at high accuracy with convolutional neural networks. This prediction model outperformed previous methods in &gt; 70% of test cases. Importantly, our method remarkably increased the predictive value of neoantigen load especially in combination with known resistance parameters. We then developed a classifier that can predict resistance from point mutations that are deleterious to protein function. Notably, genes involved in the adaptive immune response, cytokine signaling,and EGFR signaling held high explanatory power. Furthermore, when integrated with our neoantigen profiling, these anti-immunogenic mutations revealed significantly higher predictive power than known resistance factors.

  Study EGAS00001003781

• CCND1-negative MCL

  A subset of CCND1-negative mantle cell lymphoma MCL (CCND1- MCL) has been recognized, and around half of them harbor CCND2 translocations. To identify other potential mechanisms driving MCL pathogenesis we investigated CCND1− MCL by by whole genome/exome sequencing. We identified a cryptic insertion of IGK and IGL enhancer regions near the CCND3 gene in three cases. Specific FISH probes detected 10 additional cryptic IGK juxtapositions to CCND3 (6 cases) and CCND2 (4 cases). In conclusion, virtually all CCND1-/SOX11+ MCL carry CCND2/CCND3 rearrangement with IG genes, including cryptic IGK/L enhancer regions not detected with currently used FISH probes.

  Study EGAS00001003060

• Whole exome sequencing on Pediatric MDS patients

  WES was performed on 126 cases (SAMD9/9Lmut: 64/67; GATA2mut 24/35, MDS wildtype 38/471) using SureSelect Human All Exon V6 enrichment (Agilent, cat# 5190-8863). The generated libraries were sequenced on the Illumina Hiseq 2500 with 150bp paired-end reads. FASTQ files were processed using SeqNext platform (JSI medical system, Germany), with gene-based alignment to a virtual panel of 300 genes consisting of genes relevant to bone marrow failure, MDS predisposition, and hematological cancers as per the Pan-Cancer studies with cohorts of &gt;10,000 cancers. The generated BAM files are submitted here.

  Study EGAS00001005432

• Genome-wide Ancestry and Demographic History of African-Descendant Maroon Communities from French Guiana and Surname.

  The transatlantic slave trade (TAST) was the largest forced migration in world history. However, the origins of the enslaved Africans and their admixture dynamics remain unclear. To investigate the demographic history of African-descendant Marron populations, we generated genome-wide SNP data (4.3 million markers) from 107 individuals from three African-descendant populations in South America, as well as 124 individuals from six west African populations to complement underrepresented African data sets. Our study sheds additional light on the demographic consequences of the TAST and illustrates how genetic data can complement historical sources.

  Study EGAS00001002535

• Multiple Tissue Monitoring in Huntington disease - RNAseq skeletal muscle

  We examined whether peripheral tissues can serve as a source of readily accessible biological signatures at the RNA and protein level in Huntington disease (HD) patients. Under the MTM-HD study we generated large, high-quality human datasets from skeletal muscle, skin and adipose tissue, as well as primary human fibroblast lines to probe molecular changes in human pre-manifest and early manifest HD patients. We document the involvement of inflammation, energy metabolism and extracellular vesicle homeostasis. This demonstrates the potential to identify biological signatures from peripheral tissues in HD suitable as biomarkers in clinical trials.

  Study EGAS00001006474

• Multiple Tissue Monitoring in Huntington disease - RNAseq fibroblasts

  We examined whether peripheral tissues can serve as a source of readily accessible biological signatures at the RNA and protein level in Huntington disease (HD) patients. Under the MTM-HD study we generated large, high-quality human datasets from skeletal muscle, skin and adipose tissue, as well as primary human fibroblast lines to probe molecular changes in human pre-manifest and early manifest HD patients. We document the involvement of inflammation, energy metabolism and extracellular vesicle homeostasis. This demonstrates the potential to identify biological signatures from peripheral tissues in HD suitable as biomarkers in clinical trials.

  Study EGAS00001006472

• Multiple Tissue Monitoring in Huntington disease - RNAseq adipose tissue

  We examined whether peripheral tissues can serve as a source of readily accessible biological signatures at the RNA and protein level in Huntington disease (HD) patients. Under the MTM-HD study we generated large, high-quality human datasets from skeletal muscle, skin and adipose tissue, as well as primary human fibroblast lines to probe molecular changes in human pre-manifest and early manifest HD patients. We document the involvement of inflammation, energy metabolism and extracellular vesicle homeostasis. This demonstrates the potential to identify biological signatures from peripheral tissues in HD suitable as biomarkers in clinical trials.

  Study EGAS00001006473

• Single-cell proteogenomics of MDS upon AZA

  To study the evolution of the clonal molecular and cellular architecture of MDS upon the treatment with AZA, we performed scDNA-seq of an amplicon panel of 53 genes recurrently mutated in myeloid malignancies, as well as typically lost or gain DNA regions, and scProt-seq of 42 cell-surface proteins to provide a simultaneous landscape of the genetic setting and immunophenotype using the Tapestri platform (MissionBio). We sequenced thousands of cells from 14 MDS patients, where paired bone marrow samples were obtained at the timepoint of diagnosis and after AZA treatment.

  Study EGAS00001007427

• Pediatric CNS tumor classification by DNA-methylation dataset

  In this study nanopore sequencing was applied to obtain sparse DNA methylation profiles from pediatric CNS tumor samples. A neural network was used to classify the tumor based on the obtained methylation profile.

  Dataset EGAD00010002599

• Extracellular RNA Profiling of Serum, Plasma, and Urine of Healthy Subjects

  This study was conducted to generate a reference dataset of extracellular RNA (exRNA) from standard human biofluids. Small RNA-seq data was obtained from plasma, serum, and urine of healthy subjects.

  Study phs003054

• Optimized Polyepitope Neoantigen DNA Vaccines Elicit Neoantigen-Specific Immune Responses in Preclinical Models and in Clinical Translation

  A patient with Lynch syndrome and a neuroendocrine tumor sequenced with exome, whole genome, and bulk RNAseq. Sequence data was used to create a personalized cancer vaccine.

  Study phs002342

• Next Generation Mendelian Genetics: Hereditary Neurological Disorders

  The NHGRI Next Generation Mendelian Genetics project uses exome resequencing to identify variants in unsolved Mendelian diseases. This dataset was obtained from exome analyses of people with hereditary neurologic disorders of unknown cause.

  Study phs000707

• Disease recurrence after pathologic response

  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. Therefore we analyzed in-depth paired baseline and recurrent tumor samples through a.o. DNA sequencing analyses.

  Dataset EGAD50000000699

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

  This dataset included human plasma EBV DNA target-capture sequencing data. The capture probes were designed to cover the entire EBV genome and selected human autosomal regions. After enrichment, the products were sequenced on the NextSeq500 System (Illumina) and aligned to the EBV genome (AJ507799.2) and the human genome (hg19) in BAM format.

  Dataset EGAD50000000580

• shallow whole genome sequencing BAM files aligned to the human reference genome GRCh38

  We profiled large B-cell lymphoma (LBCL) patient plasma samples with ultra-low-pass (shallow) whole genome sequencing. The DNA sequencing was performed on pre-capture genomic libraries, with an intended mean coverage of at least 0.1X, FASTQ files were cleaned by fastp and mapped to the reference human genome (GRCh38) with bwa.

  Dataset EGAD50000001497

• Establishment of iPS cells from Japanese healthy volunteers

  We performed whole exome sequencing of Japanese volunteers. We established iPSCs from those volunteers, and the iPSCs were deposited to Riken Bioresource Bank. The whole exome sequencing were performed using their PBMCs.

  Study JGAS000287

• Spatial transcroptomic analyses against non-metastatic and metastatic lymph node from breast cancer patients

  We performed spatial transcroptomic analyses against non-metastatic and metastatic lymph node from breast cancer patients to investigate how metastasized breast cancer cells affect gene expression in lymph nodes

  Study JGAS000616

• The RNA, ChIP and whole exome sequencing analysis of human colorectal cancer organoids and normal colon organoids treated with (+)-JQ1

  To reveal the mechanism of anti-tumor effect of (+)-JQ1, we performed RNA, ChIP and whole exome sequencing using human colorectal cancer and normal colon organoids.

  Study JGAS000378

• Whole-genome shotgun metagenomic sequencing of rectal mucus from patients suspected to have colorectal cancer

  This dataset contains whole-genome shotgun metagenomic sequencing data of 408 rectal mucus samples from patients suspected to have colorectal cancer and healthy controls. Sequencing was performed on the Illumina NovaSeq platform, producing paired-end FASTQ files. These data support microbial community profiling and biomarker discovery analyse

  Dataset EGAD50000001867

• Small intestinal neuroendocrine tumors

  The goal of this study was to gain insights into the transcriptomes, mutations and copy number variants present in small intestinal neuroendocrine tumors. The present dataset contains RNA-sequencing performed on seven such tumors.

  Study EGAS00001003358

• 20_Matched_Pair_Breast_Cancer_Genomes

  We propose to definitively characterise the somatic genetics of 20 breast cancers through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing coupled with integrated transcriptomic data.

  Study EGAS00001000170

• RNAseq of mCRC xenografts under cetuximab treatment, placebo or after treatment release

  Determine if cetuximab treatment selects any pre-existing resistant subclones or if the resistant cells, which in vivo determines residual disease, are driven by plasticity effects not linked to mutations.

  Study EGAS00001003765