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• Chun Lab DAC

  Data Access Committee (DAC) for datasets produced by the Chun Lab @ Sanford Burnham Prebys Medical Discovery Institute in La Jolla, California.

  Dac EGAC50000000011

• Patient-derived organoids model treatment response of metastatic gastrointestinal cancers (targeted and whole-genome sequencing)

  Patient-derived organoids (PDOs) have recently emerged as robust pre-clinical models, however, their potential to predict patient clinical outcomes remain unclear. We report a living biobank of PDOs from metastatic, heavily-pretreated colorectal and gastroesophageal cancer patients recruited in phase I/II clinical trials. Phenotypic and genotypic profiling of PDOs showed a high-degree of similarity to the original patient tumor. Molecular profiling of tumor organoids was matched to drug screening results, suggesting PDOs could complement existing approaches in defining cancer vulnerabilities and improving treatment responses. We compared ex vivo organoid responses to anticancer agents, and PDO-based orthotopic mouse tumor xenograft models to the response of the patient in clinical trials. Our data suggest that PDOs can recapitulate patient responses in the clinic, and have the potential to be implemented in personalized medicine programs.

  Study EGAS00001002784

• Circular RNA characterization in functionally distinct brain regions

  Circular RNAs (circRNAs) represent a class of endogenous, non-coding RNAs that are formed when exons back splice to each other and that are both highly conserved and pervasively expressed in the mammalian brain. The goal of this study was thus to systematically identify and characterize circRNA expression and as well as to evaluate the predicted impact on regulatory networks in five functionally distinct cortical regions of healthy aged human brain - cerebellum (BC), inferior parietal lobe (IPL), middle temporal gyrus (MTG), occipital cortex (OC) and superior frontal gyrus (SGF).

  Study EGAS00001003128

• Walter and Eliza Hall Institute - University of Melbourne

  Data Access Committee for Gocuk, Lancaster et al. 2024: nanopore sequencing data of patients with choroideremia and X-linked retinitis pigmentosa, to determine X inactivation skew.

  Dac EGAC50000000301

• HIV exome pilot, exome data hs37d5

  exome sequence data for 57 HIV elite long term non-progressors and rapid progressors. Complete dataset of improved BAMs mapped to hs37d5 and including phenotype information.

  Dataset EGAD00001003345

• Illumina HiSeq X Ten

  Three files of patients 10, 11 and 13 with WGS done on Illumina HiSeq X Ten. For research purpose and authorised user only.

  Dataset EGAD00001003439

• ATAC-Seq of human stimulated and cultured CD4+ Treg cells

  This dataset includes whole genome sequence data for ATAC-seq (42 samples) of human stimulated and cultured CD4+ Treg cells.

  Dataset EGAD00001004829

• Exome sequencing from a child with neurofibromatosis and relapsed refractory acute lymphoblastic leukaemia

  Dataset contains 5 exome BAM files from a child with neurofibromatosis and relapsed refractory acute lymphoblastic leukaemia. The samples are CD19 positive and CD19 negative bone marrow mononuclear cells at both diagnosis and relapse as well as mesenchymal stem cells as the germline control. Libraries were prepared using the SureSelect Clinical Research Exome v2 kit (Agilent Technologies, Santa Clara, CA, USA) and run on the Illumina NextSeq 500 platform.

  Dataset EGAD00001008702

• Variation and transmission of the human gut microbiota across generations - shotgun data

  Although composition and functional potential of the human gut microbiota evolve over lifespan, kinship has been identified as a key covariate of microbial community diversification. To date, sharing of microbiota features within families has however mostly been assessed between parents and their direct offspring. Here, we investigate potential transmission and persistence of familial microbiome patterns and microbial genotypes in a family cohort (N=102) spanning three to five generations over the same female bloodline. We observe microbiome community composition to be associated with kinship, with seven (low-abundant) genera displaying familial distribution patterns. While kinship and current cohabitation emerged as closely entangled variables, our explorative analyses of microbial genotype distribution and transmission estimates point at the latter as a key covariate of strain dissemination. Highest potential transmission rates are estimated between sisters and mother-daughter pairs, decreasing with increasing daughter’s age, and being higher among cohabiting pairs than those living apart. Although rare, we do detect potential transmission events spanning three and four generations, primarily involving species of the genera Alistipes and Bacteroides. Overall, while our analyses confirm the existence of family-bound microbiome community profiles, transmission or co-acquisition of bacterial strains appears to be strongly linked to cohabitation.

  Study EGAS00001005649

• Variation and transmission of the human gut microbiota across generations - 16S data

  Although composition and functional potential of the human gut microbiota evolve over lifespan, kinship has been identified as a key covariate of microbial community diversification. To date, sharing of microbiota features within families has however mostly been assessed between parents and their direct offspring. Here, we investigate potential transmission and persistence of familial microbiome patterns and microbial genotypes in a family cohort (N=102) spanning three to five generations over the same female bloodline. We observe microbiome community composition to be associated with kinship, with seven (low-abundant) genera displaying familial distribution patterns. While kinship and current cohabitation emerged as closely entangled variables, our explorative analyses of microbial genotype distribution and transmission estimates point at the latter as a key covariate of strain dissemination. Highest potential transmission rates are estimated between sisters and mother-daughter pairs, decreasing with increasing daughter’s age, and being higher among cohabiting pairs than those living apart. Although rare, we do detect potential transmission events spanning three and four generations, primarily involving species of the genera Alistipes and Bacteroides. Overall, while our analyses confirm the existence of family-bound microbiome community profiles, transmission or co-acquisition of bacterial strains appears to be strongly linked to cohabitation.

  Study EGAS00001005651

• RSV infection of primary bronchial epithelial cells in asthma

  Primary bronchial epithelial cells derived from healthy donors and asthma patients were differentiated in Air-Liquid-Interface condition and infected with the respiratory syncytial virus. Single-cell RNA sequencing analysis of these cultures was used to study the transcriptomic response of the cells to RSV.

  Study EGAS00001007450

• RNA-seq from Glioblastoma treated with Indisulam

  The dataset includes RNA-sequencing results from four patient-derived glioblastoma cell lines treated with DMSO (vehicle control) or the splicing modulating-drug indisulam (at 6 and 16 hours), resulting in 12 RNA-seq samples. Paired-end sequencing produced 24 FASTQ.gz files. The RNA libraries were prepared using PolyA selection and ERCC spike-ins and sequenced on a NovaSeq platform. This dataset supports the analysis of drug-induced transcriptomic changes and the prediction of subsequent non-canonical tumor-specific antigens (ncTSAs) using the NovumRNA pipeline.

  Dataset EGAD50000000957

• Chondrosarcoma Validation Study

  Agilent whole exome hybridisation capture was performed on genomic DNA derived from Chondrosarcoma cancer and matched normal DNA from the same patients. Next Generation sequencing performed on the resulting exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes. Now we aim to re find and validate the findings of those exome libraries using bespoke pulldown methods and sequencing the products.

  Dataset EGAD00001000392

• Combining dasatinib and IFN-α in CML – immunomodulatory effects linked to treatment response and adverse events

  We pooled 100,000 cells from the 12 scRNA+TCRab-seq samples from peripheral blood from three time points (n=4, samples at 0, 3, and 12 months) to understand the landscape of immune subsets in CML during the course of dasatinib+IFN-α treatment

  Study EGAS00001005049

• Genomic Landscape of Pediatric Germ Cell Tumors

  Germ cell tumors (GCTs) are cancers of the testis, ovary and extragonadal sites that occur in infants, children, adolescents, and adults. Post-pubertal (type II) malignant GCTs may present as a seminoma, non-seminoma or with mixed histologies. In contrast, pre-pubertal (type I) GCTs are limited to (benign) teratomas and (malignant) yolk sac tumors (YST). Epidemiologic and molecular data have shown that pre- and post-pubertal GCTs arise by distinct mechanisms. Dedicated studies of the genomic landscape of type I and II GCTs in children and adolescents are lacking. Here we present an integrated genomic analysis of extracranial GCTs across the age spectrum from 0-24 years.

  Study phs002009

• A study of resistance to novel coronavirus infection in health care workers

  There have been cases of what appear to be nosocomial infections among healthcare workers at several hospitals. The infected healthcare workers were assumed to have contracted the disease through close contact with infected patients. However, we confirmed at each medical institution that there were many healthcare workers who had apparently had closer contact with infected patients than with infected patients, but had not contracted the disease. Thus, the purpose of this study was to clarify the internal factors that make individuals less susceptible to novel coronavirus infection and their stress tolerance, and to establish a system that contributes to the appropriate allocation of healthcare workers and the creation of a system that can more safely deal with this disease in the future.

  Study JGAS000562

• Dataset of 5 RNAseq from 3 non-muscle-invasive bladder cancer patients

  RNAseq (FASTQ files) of 5 tumor from 3 non-muscle-invasive bladder cancer patients. For patient UC2, RNA from 3 different synchronous tumors was extracted. Relating to the other datasets from the project : no RNA was available from patient UC4. NB : patients aliases are the following : ROXY : UC1, OMAD : UC2, MAKI : UC3, HAPE : UC4

  Dataset EGAD50000002009

• cfMeDIP data for 30 CPC-GENE samples

  We analyzed the cell free DNA methylomes using 30 plasma samples from patients with localized prostate cancer in the CPC-GENE project. Methylation was profiled using the methylated DNA immunoprecipitation coupled to next generation sequencing (MeDIP) technology.

  Dataset EGAD00001007972

• cfMeDIP data for 14 Barrier samples

  We analyzed the cell free DNA methylomes using 14 plasma samples from patients with mCRPC in the Barrier cohort. Methylation was profiled using the methylated DNA immunoprecipitation coupled to next generation sequencing (MeDIP) technology.

  Dataset EGAD00001008712

• scRNAseq of distal colon biopsies from patients with ulcerative colitis and healthy controls

  scRNAseq dataset of colonic epithelium from distal colon biopsies from 4 patients with ulcerative colitis and 4 healthy individuals. Includes 11 samples split into three conditions: healthy, healthy margin and ulcerated. Dataset includes raw Fastq files and processed csv count matrices. Fastq files are divided into 4 lanes and into index (I1) and read (R1, R2) files. Count matrices contain comma-separated values with cell barcodes as column names and gene names as row names. Cell Ranger (v3.0.1) software from 10x Genomics was used to process the output and align the reads. The refdata-cellranger-GRCh38-3.0.0 reference was downloaded from the 10x Genomics website. First, cellranger mkfastq function was used to demultiplex raw base call files into FASTQ files. Then, the FASTQ files were aligned and filtered with cellranger count function.

  Dataset EGAD00001010167

• Long-read single-cell RNA sequencing uncovers cell-type specific transcript regulation in COVID-19

  SARS-CoV-2 infection leads to extensive host transcriptomic changes, but the role of alternative splicing in shaping the immune response remains underexplored. Here, we present the first application of long-read single-cell RNA sequencing on nasopharyngeal swabs from COVID-19 patients and healthy controls to resolve transcript-level changes across cell types. Leveraging the strengths of long-read sequencing, we characterize alterations in both gene and isoform expression within cell populations of the upper respiratory tract—the primary site of SARS-CoV-2 entry. This approach provides new insights into how transcriptional regulation and splicing shape host immune responses to viral infection.

  Study EGAS50000001290

• RNA sequencing of undifferentiated sarcomas

  Undifferentiated sarcomas (USARCs) of adults are diverse, rare, and aggressive soft tissue cancers. Recent sequencing efforts have confirmed that USARCs exhibit one of the highest burdens of structural aberrations across human cancer. Here, we sought to unravel the molecular basis of the structural complexity in USARCs by integrating DNA sequencing, ploidy analysis, gene expression, and methylation profiling. We identified whole genome duplication as a prevalent and pernicious force in USARC tumorigenesis. Using mathematical deconvolution strategies to unravel the complex copy-number profiles and mutational timing models we infer distinct evolutionary pathways of these rare cancers. In addition, 15% of tumors exhibited raised mutational burdens that correlated with gene expression signatures of immune infiltration, and good prognosis.

  Study EGAS00001003291

• Human_Evolution_3B

  The mtDNA and Y chromosome of up to 15 Australian Aborigines, concentrating on individuals with indigenous lineages will be sequenced using the standard whole-genome sequencing followed by filtering out autosomal and X sequences, so that only mtDNA and the Y chromosome would be analysed and released.

  Dataset EGAD00001001374

• The Genomic Landscape of Endocrine Resistant Advanced Breast Cancers: Paired Pre- and Post-endocrine Therapy Samples.

  The genomic evolution of breast cancers exposed to systemic therapy and its effects on clinical outcome have not been broadly characterized. We integrated the genomic sequencing of 1918 breast cancers, including 1501 hormone receptor-positive tumors, with detailed clinical information and treatment outcomes. Functional mutations in ERBB2 and loss-of-function mutations in NF1 were more than twice as common in post-endocrine therapy tumors compared to treatment-naive tumors. Additional alterations in the MAPK pathway (EGFR, KRAS among others) and in estrogen receptor transcriptional regulators (MYC, CTCF, FOXA1 and TBX3) were also more common compared to hormonal therapy-naive tumors. To determine whether candidate genomic lesions in the MAPK pathway and estrogen receptor transcriptional regulators were present prior to therapy or whether such lesions arose under the selective pressure of therapy, we performed whole-exome sequencing in select patients who had adequate samples acquired prior to and after progression on endocrine therapy. In total, 95 specimens corresponding to 30 treatment-naive primary tumors, 35 post-treatment tumors, and 30 normal samples were sequenced from 30 patients with endocrine-resistant metastatic breast cancer.

  Study phs001674

• Other NS tumors

  The dataset represents a total of 18 DNA samples from 6 male and 3 female pediatric patients affected with central or peripheral nervous system tumors not classified as embryonal central nervous system tumors, nor gliomas, glioneuronal, or neuronal tumors. One tumor tissue sample and one peripheral blood sample from each patient were subject to whole genome sequencing (WGS) and were sequenced 2x150 bp paired-end on an Illumina HiSeqX v2.5 instrument. The FASTQ files generated were aligned to the human reference genome sequence GRCh38/hg38 using bwa-mem, with the ALT-aware option turned on. Sorting of reads and marking of PCR duplicates was performed with GATK. Base quality score recalibration and joint realignment of reads around insertions and deletions (indels) were conducted using GATK tools. The dataset consists of 18 files in the CRAM format (lossless compression) with a total file size of ~3,4 TB. Additional genomic and molecular data (FASTQ, BAM, IDAT, and VCF files) and limited clinical data can be requested by ethically approved projects conducting research in the field of pediatric cancer.

  Dataset EGAD50000000299

• Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud university medical center

  Dac EGAC00001003193

• Cyr61-MAC DAC

  DAC for access to dataset on Cyr61-MAC and HUVEC

  Dac EGAC50000000355

• Immunophenotype data for a subset of NSCLC cases in OAK

  The investigators would like to correlate NGS data from OAK to immunophenotype designation performed manually based on a panCK/CD8 immunohistochemistry stain for a subset of squamous cell carcinomas.

  Dataset EGAD50000001253

• RNA-sequencing

  RNA-sequencing for a cohort of B-ALL samples : 5 Down Syndrome (DS), 16 Hyperdiploid (HeH), 6 iAMP21, 9 other. RNA-sequencing for B-cell progenitors from 3 healthy. It also contains RNA-sequencing datasets of Patient-Derived Xenografts (X) developed from the B-ALL samples : 4 Down Syndrome (DS), 4 Hyperdiploid (HeH), 1 iAMP21, 3 other.

  Dataset EGAD00001005426

• Single-cell atlas of multiple myeloma and precursor diseases

  Single cell profiling of small cohorts of myeloma precursor disease patient samples including monoclonal gammopathy of unknown significance and smoldering multiple myeloma have shown diverse evolutionary patterns and immune changes that occur early in the disease process. Using scRNAseq and scBCRseq in a large cohort of fifty-three patients with myeloma precursor disease in comparison with myeloma and normal donors we describe the early genomic drivers of malignant transformation and describe their divergent clonal expansion in hyperdiploid compared to non-hyperdiploid samples. We describe intra-patient heterogeneity with potential therapeutic implications as well as the distinct evolution patterns (linear/branching) from myeloma precursor disease to myeloma. Finally, we describe the unique adaptations of the microenvironment as a response to distinct genomic changes in myeloma cells. These results further our knowledge to characterize myeloma precursor disease evolution, inform individual patient progression risk stratification and identify potential biomarkers that could be clinically exploited.

  Study EGAS00001006694

• Roma Sequencing Study

  Present day Roma genome were shaped by the extensive inbreeding and admixture during their Diaspora. Here, we shed light on the Roma demographic history by analyzing the whole genome sequence of 46 Roma individuals pertaining to four migrant groups in six European countries. The strong reduction in effective population size (~44%), that occurred around 2kya, was not masked by the subsequent high admixture in Middle Eastern and European countries.

  Study EGAS00001004287

• 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.

  Study EGAS00001006139

• Investigating Genetics in Suspected Congenital Syndromes

  We employed forward and reverse genetics to identify individuals with heterozygous JAK1 variants associated with autoimmune and inflammatory diseases. We first recruited six unrelated probands and seven affected family members presenting with a range of autoimmune and inflammatory conditions. Whole exome sequencing revealed 4 different variants spanning all domains of the JAK1 protein: FERM domain (chr1: 64873438-G>A; c.415C>T; p.E139K), SH2 domain (chr1: 64855641-G>A; c.1516C>T; p.R506C), pseudokinase domain (chr1: 64845529-C>T; c.2099G>A; p.S700N, and kinase domain (chr1: 64838479-C>T; c.2953G>A; p.V985I). We then performed a systematic review of electronic health records of the BioME BioBank database and identified 43 additional individuals with at least one of these JAK1 variants. Comparing variant-positive and variant-negative individuals, our study revealed increased occurrences of autoimmunity, atopy, colitis, and dermatitis in patients harboring these JAK1 gain-of-function variants. We have deposited in dbGaP the whole exome sequencing files of the 43 patients identified in the BioME biobank, as well as their phenotype information.

  Study phs003453

• Detection and genomic analysis of BRAF fusions in Juvenile Pilocytic Astrocytoma through the combination and integration of multi-omic data

  Juvenile Pilocytic Astrocytoma (JPAs) are highly vascular tumors and show pervasive immune infiltration, which can lead to low tumor cell purity in clinical samples. In some instances, this results in gene fusions that are difficult to detect with conventional omics approaches including RNA-Seq. To this effect, we applied RNA-Seq as well as linked-read whole-genome sequencing and in situ Hi-C as new approaches to detect and characterize low-frequency gene fusions at the genomic, transcriptomic and spatial level. Overall, we demonstrate the power of integrating multi-omic datasets to identify low frequency fusions and characterize the JPA genome at high resolution.

  Study EGAS00001006388

• RNA sequencing from patient-derived intestinal organoids

  RNA from the duodenal organoids was isolated using an RNeasy Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions. RNA purity and concentration were measured using a NanoDrop One spectrophotometer (NanoDrop Technologies, Wilmington, Delaware, USA). Preparation of the RNA library and transcriptome sequencing was conducted by Novogene Co., LTD (Cambridge, UK). Messenger RNA was purified from total RNA using polyA selection and subjected to library construction. Sequencing was performed on an Illumina platform, and 150 bp paired-end reads were generated.

  Study EGAS50000000338

• Genomic Profile of Multiple Localised Spiradenoma and Spiradenocarcinoma

  Multiple spiradenomas and spiradenocarcinoma from a single donor were subjected to exome sequencing. Tumor samples were microdissected from formalin-fixed, paraffin-embedded tissue, and genomic DNA was extracted. The DNA samples were subjected to library generation using the xGen ssDNA & Low-Input DNA Library Preparation Kit, followed by exome capture using the xGen Exome Research Panel v2. The libraries were sequenced on DNBSEQ G400RS. Reads were aligned to GRCh37 with BWA.

  Study EGAS50000000554

• Clonal origin of lineage switch leukemia following CAR-T cell and blinatumomab therapy

  Children with ALL treated with anti-CD19 therapy occasionally develop a phenotypically distinct AML. However, the precise clonal origin of such class switch leukemias remains unresolved. Here, we reconstructed the evolution of leukemia in a child with primary ALL, two ALL relapses and AML after treatment with anti-CD19 CAR-T and blinatumomab through whole-genome sequencing. The phylogeny revealed that the AML was a monoclonal outgrowth descending from the initial ALL and harbored biallelic loss of CDKN2A, PAX5 and TP53. However, none of the ALL or AML relapses directly descended from one another, suggesting the presence of a reservoir of persistent clones. Our findings suggest anti-CD19 treatment selects pre-existing clones, with many key genetic alterations underpinning the lineage switch detectable prior to treatment.

  Dataset EGAD00001009161

• Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution

  We have used next generation sequencing to sequence genomes (>43-fold coverage) and transcriptomes of an oestrogen-receptor-alpha-positive metastatic lobular breast cancer at depth. We found 32 somatic non-synonymous coding mutations present in the metastasis, and measured the frequency of these somatic mutations in DNA from the primary tumour of the same patient.

  Study EGAS00000000054

• Complex Landscapes of Somatic Rearrangements in Human Breast Cancer Genomes

  We have used massively parallel paired end sequencing strategies to reconstruct the genomic landscape of 24 breast cancer genomes, through the identification and characterization of 2166 somatically acquired genomic rearrangements. These studies have revealed considerable complexity in the patterns of structural variation, identified novel fusion genes and unveiled new insights into the complex structure of amplicons.

  Study EGAS00000000062

• ER___HER2___PR__breast_Cancer_genome_sequencing

  Agilent whole exome hybridisation capture will be performed on genomic DNA derived from X triple negative breast cancers and matched normal DNA from the same patients. Three lanes of Illumina GA sequencing will be performed on the resulting X exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes.

  Study EGAS00001000197

• TMD_AMLK_Exome_Study

  Agilent whole exome hybridisation capture will be performed on genomic DNA derived from 20 Primary Acute Megakaryocytic Leukemia samples and matched normal DNA from the same patients. Three lanes of Illumina GA sequencing will be performed on the resulting 100 exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes

  Study EGAS00001000027

• Breast_Cancer_Exome_Sequencing

  Agilent whole exome hybridisation capture will be performed on genomic DNA derived from 100 breast cancers of all subtypes and matched normal DNA from the same patients. Three lanes of Illumina GA sequencing will be performed on the resulting 200 exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes.

  Study EGAS00001000211

• SCAT_osteosarcoma_sequencing

  Agilent whole exome hybridisation capture will be performed on genomic DNA derived from 50 osteosarcoma cancers and matched normal DNA from the same patients. Three lanes of Illumina GA sequencing will be performed on the resulting 100 exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes

  Study EGAS00001000196

• Illumina BeadArray SNP arrays

  SNP measurement. Illumina BeadArray SNP arrays for the study "Molecular characteristics in Burkitt lymphoma over age groups"

  Dataset EGAD00010002137

• Premalignant SOX2 in ovarian cancer patients

  Whole Genome Sequencing data set for the study "Premalignant SOX2 in ovarian cancer patients"

  Dataset EGAD00001002734

• Follicular T cell lymphoma

  Paired-end RNA-seq of follicular T cell lymphoma for the discovery of fusion transcripts

  Dataset EGAD00001006379

• WGS of 11 MPNSTs, 7 ANNUBPs and 7 blood and normal tissue controls

  Whole-genome sequencing (WGS) of 11 MPNSTs, 7 ANNUBPs and 7 controls (6 blood and 1 normal tissue) sequenced for Magallon-Lorenz, 2026. Sequenced at BGI with DNBseq technology (2x150bp) following standard protocols. Raw fastq files provided.

  Dataset EGAD50000002492

• H3Africa ACEGID Omni 2.5M and 5M Genotype

  SNP Genotyping for Lassa Fever cases and population controls from Nigeria and Sierra Leone using Illumina Omni 2.5M and 5M

  Dataset EGAD00010002509

• Integrated genomic, transcriptional and epigenomic analyses in germinal center-cell lymphomas link the mutation landscape with differential DNA methylation in Burkitt lymphoma

  Biologically and clinically diverse B-cell neoplasms, including Burkitt, follicular and diffuse large B-cell lymphoma, show features of germinal center (GC) B-cells. Here we present a comprehensive analysis of the epigenetic landscape of GC-B-cell lymphomas using whole genome bisulfite sequencing paired with genome and transcriptome sequencing from 29 primary tumor samples and four normal GC-B-cell samples. All lymphomas studied showed extensive genome-wide methylation losses as well as intragenic regions where DNA methylation levels were strongly correlated with expression of associated genes. Pathway analysis revealed that these intragenic regions were enriched in signaling networks differentially activated in Burkitt and follicular lymphomas and affected regulatory mechanisms deregulated by recurrent mutations in a large fraction of Burkitt lymphomas (including the ID3/TCF3 complex, the SWI/SNF remodeling complex and the inhibitory GI signaling pathway). Taken together, these results provide a global picture of Burkitt lymphoma pathomechanism and demonstrate a tight connection between epigenetic regulation and other levels of regulatory control in these tumors.

  Study EGAS00001001067

• Whole-exome sequencing of human pancreatic cancers and characterization of genomic instability caused by MLH1 haploinsufficiency and complete deficiency

  Whole-exome sequencing (Exome-Seq) has been successfully applied in several recent studies. We here performed Exome-Seq of 15 pancreatic tumor-normal pairs. We captured 162,073 exons of 16,954 genes and sequenced the targeted regions to a mean coverage of 56 folds. This study identified a total of 1,517 somatic mutations and validated 934 of them by transcriptome sequencing. We detected recurrent mutations in 56 genes. Among them, 41 have not been described. The mutation rates varied widely among tumors. The diversity of mutation rates was significantly correlated with the distinct MLH1 copy-number status. Exome-Seq revealed intensive genomic instability in a tumor with MLH1 homozygous deletion, indicated by a dramatically elevated mutation rate of somatic substitutions, small insertions/deletions (indels), as well as indels presented at microsatellites. Notably, we detected MLH1 allelic loss in 4 tumors. MLH1 expression was decreased by nearly half in these cases. While they were negative in the conventional microsatellite instability assay, they showed a 10.5-fold increase in the mutation rate of somatic indels, e.g. truncating indels in TP53 and TGFBR2, indicating MLH1 haploinsufficiency in correction of DNA indel errors. We further analyzed the exomes of 15 renal cell carcinomas (RCCs) and confirmed MLH1 haploinsufficiency. We observed a significant increase in the mutation rate of somatic indels in affected cases and identified recurrent truncating indels in several cancer genes such as VHL, PBRM1 and JARID1C. Together, our data suggest that MLH1 hemizygous deletion, through increasing the mutation rate of somatic indels, could drive the development and progression of sporadic cancers.

  Study EGAS00001000149