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• Indonesian Microbiome Ecology and Evolution v1 (raw data)

  This dataset comprises 124 human faecal samples collected across Indonesia between 2015 and 2021, together with 6 controls. It was collected to study patterns of human microbiome variation across Indonesia’s diverse geography and lifestyles, and to generate the Indonesian Microbiome Ecology and Evolution (IndoMEE) metagenome-assembled genome (MAG) reference database. The dataset consists of 250 bp paired-end metagenomic reads from 124 faecal samples acquired from 116 individuals, at ca. 10.6 Gb / sample, together with 2 positive controls (ZymoBIOMICS Microbial Community DNA Standard by Zymo Research Cat# D6305), and 4 negative controls (for sampling: Blank, for extraction: Buffer EB by Qiagen Cat# 19086, for library prep: Nuclease Free Water by Ambion-Invitrogen Cat# AM9937). Library preparation was carried out using Illumina's TruSeq DNA Nano DNA kit, and sequencing was performed on the Illumina NovaSeq 6000 platform.

  Dataset EGAD50000001399

• Genome-wide genotyping data and exome sequencing of 100 European-descent and 100 African-descent Belgians used in the EGAS00001001895 study

  We recruited 100 healthy, male donors of self-reported European descent (EUB) and 100 of self-reported African descent (AFB) (Ghent, Belgium). For each participant, peripheral blood mononuclear cells (PBMCs) were isolated from whole blood on Ficoll-Paque density gradients. Monocytes were then positively selected with magnetic CD14 microbeads and exposed for 6 hours to different ligands activating TLR4 (LPS), TLR1/2 (Pam3CSK4), TLR7/8 (R848) and to a human seasonal influenza A virus (IAV). High-quality RNA was obtained from unstimulated and stimulated monocytes for 970 of the 1000 samples (200 x 5 conditions), and was sequenced on an Illumina HiSeq2000. On average, 34 million 101-bp single-end reads were obtained per sample.

  Dataset EGAD00001002714

• Multi-Modal Single-Cell, Spatial, and Genomic Analyses of Human Non-Small Cell Lung Cancer Brain Metastases

  We performed single nuclei RNA-sequencing (snRNA-seq) with matched T cell receptor sequencing (TCR-seq), and pool matched low pass whole genome sequencing (WGS) of 12 treatment-naive non-small cell lung cancer (NSCLC) primary tumors (PTs) and 31 treatment-naive NSCLC brain metastases (BMs). In total, we recovered 277,206 cell transcriptomes in 43 samples. Single-nuclei suspension from frozen NSCLC metastases were generated using methods published in Slyper et al. (Nature Medicine, 2020, PMID:32405060) with modifications. The tissue was first cut in 20 µm sections using a cryostat and stored on dry ice until the next step. Then the tissue was put on wet ice and washed once with 5 ml PBS to remove OCT. After this step nuclei were extracted by vigorous pipetting in salt-tris buffer with Tween-20 (TST) followed by a high-volume wash in salt-tris buffer (ST). Nuclei were counted and 10,000-14,000 and were loaded using a Chromium controller (10X genomics) and Chromium Single Cell 5' Reagents (V1.1 and V2). Complementary DNA libraries were generated according to manufacturer's instructions, with the modification of one additional cycle of amplification. Matched single nuclei T cell receptor (snTCR) sequencing libraries were prepared from amplified cDNA libraries using either Chromium Single Cell V(D)J Enrichment Kit for human T cells Reagent Kit, v1.1, or single cell human TCR amplification kit. Final snTCR sequencing libraries were prepared using Single Index Kit T Set A for V1.1 libraries or Library construction kit and Dual Index Kit TT set A for V2 libraries. Sequencing libraries were quantified using Tapestation D5000 reagents and a 2200 TapeStation and pooled for sequencing. Pool matched low pass whole-genome sequencing (lp-WGS) was performed in addition to snRNA-seq to improve the identification of the malignant and non-malignant cell compartments. Nuclei from snRNA-seq sample preparations were collected by centrifugation (500g, 5 min), snap frozen after removing excess ST buffer, and stored at -200C until further processing. If insufficient nuclei (0C for 9 minutes. Adapters were not diluted, and the optional PCR (5 cycles) and cleanup were performed. After library cleanup with AMPure beads (Beckman Coulter, Brea, CA), libraries were quantified with Tapestation D5000 HS tapes (Agilent) and stored at -200C until sequencing.Using multiplexed immunofluorescence in an independent cohort of treatment-naïve pairs of primary tumors and brain metastases from the same patients with NSCLC, we validated genomic and tumor-microenvironmental findings and identified a cancer cell population characterized by neural features that strongly enriched in brain metastases. This comprehensive analysis provides insights into human NSCLC brain metastasis biology and serves as an important resource for additional discovery.

  Study phs003865

• An Isogenic Cell Line Panel for Sequence-based Screening of Targeted Anti-cancer Drugs

  We describe the creation and characterization of an isogenic cell line panel representing common cancer pathways, with multiple features optimized for high-throughput screening. More than 1,800 cell lines from three normal human cells were generated using CRISPR-technologies. Surprisingly, we discovered most of these lines did not result in complete gene inactivation, despite integration of sgRNA at the desired genomic site. However, a subset of the lines harbored true, biallelic disruptions of the targeted tumor suppressor gene, yielding a final panel of 100 well-characterize lines covering 19 pathways frequently subject to loss of function in cancers. This panel included genetic markers optimized for sequence-based ratiometric assays for drug-based screening assays. To illustrate the potential utility of this panel, we developed a multiplexed high-throughput screen that identified Wee1 inhibitor MK-1775 as a selective growth inhibitor of cells with inactivation of TP53. These cell lines and screening approach should prove useful for researchers studying a variety of cellular and biochemical phenomena

  Study EGAS00001005974

• FASTQ files of total RNA-Seq data from the POPS SGA (Small for Gestational Age) samples

  All the samples were obtained from the Pregnancy Outcome Prediction–a prospective cohort study of nulliparous women attending the Rosie Hospital, Cambridge (UK) for their dating ultrasound scan between January 14, 2008, and July 31, 2012. Ethical approval for the study was given by the Cambridgeshire 2 Research Ethics Committee (reference number 07/H0308/163) and all participants provided written informed consent. Cases of preeclampsia (PET) were defined on the basis of the 2013 ACOG criteria and cases of small for gestational age (SGA)infants were confined to severe SGA, i.e. a customized birth weight <5th percentile. Chorionic villi from the corresponding placentas (free from decidua, visible infarction, calcification, hematoma, or damage) were collected and processed within 30 minutes of separation from the uterus. After repeated washes in chilled phosphate buffered saline, the samples were placed in RNA later (Applied Biosystems) and stored at -80°C. Total placental RNA was extracted using mirVana Isolation Kit (Ambion). For each placenta, approximately 5 mg of tissue were homogenized in the Lysis/Binding solution for 20 sec at 6 m/s using a bead beater (FastPrep24) and Lysing Matrix D Tubes (MP Biomedicals). The samples were then spun at 13,000 rpm for 5 min at 4°C and the supernatants recovered. Afterwards, the manufacturer's instructions were followed. Immediately after the RNA extraction, placental RNA samples were DNase-treated using DNA-free DNA Removal Kit (Ambion), aliquoted, and stored in -80°C. Quantity and quality of the RNA samples were assessed using the Agilent 2100 Bioanalyzer, the Agilent RNA 6000 Nano Kit (Agilent Technologies), and Qubit fluorometer. Libraries were prepared starting with 300-500 ng of good quality total RNA (RIN ≥7.5) using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human/Mouse/Rat (Illumina), according to the manufacturer's instructions. The kit contains 96 uniquely indexed adapter combinations in order to allow pooling of multiple samples prior to sequencing. After determining their size (with the Agilent 2100 Bioanalyzer and the Agilent High Sensitivity DNA Kit by Agilent Technologies) and concentration (by qPCR with the KAPA Illumina ABI Prism Library Quantification Kit, Kapa Biosystems), libraries have been pooled and sequenced (single-end, 125 bp) using a Single End V4 Cluster Kit and an Illumina HiSeq2500 or HiSeq4000 instrument.

  Dataset EGAD00001003507

• Multicenter AIDS Cohort Study (MACS)

  The Multicenter AIDS Cohort Study (MACS) - now part of the MACS-WIHS Combined Cohort Study (MWCCS) investigates the epidemiology of human immunodeficiency virus (HIV) infection among men who have sex with men. Over 7,000 participants volunteered for semiannual interview, physical examination, and laboratory testing across the 325 years of the study, in four metropolitan areas of Los Angeles, Chicago, Baltimore/Washington (DC) and Pittsburgh. The study aimed to identify risk factors for occurrence and clinical expression of the HIV infection, and to establish a repository of biologic specimens for future study. Study visits included detailed questions covering HIV-related symptoms and utilization of health services, demographic and psychosocial characteristics, a quality of life survey, a physical examination, a detailed form on medications used as prophylaxis and/or treatment, a neuropsychological screening and examination, blood samples to do measure hematologic variables including enumeration of T-cell subsets and HIV viral load and evaluate genetic risk factors via genome wide association studies using data generated using the Infinium Multi-Ethnic Global BeadChip genotyping array in all participants. Men who have sex with men, with and without HIV infection were enrolled in the MACS. MACS data continues to be available through the merged MWCCS cohort.

  Study phs002226

• Whole genome sequencing to detect spontaneous acquired mutations in mismatch repair-deficient human colon organoids

  Individual outgrowing organoids surviving the medium-based selection were manually picked and propagated as clonal lines for a couple of passages to avoid unexpected mutation accumulation before being harvested for WGS/WES. 1 µg of DNA was used for WGS/WES by Agilent SureSelect V7 kit, with 8Gb per sample (50X average mapped) data throughput, sequencing on NovaSeq 150PE

  Study EGAS50000000114

• DNA sequencing for human normal endometrial glands

  To elucidate the timing and mechanism of the clonal expansion of somatic mutations in cancer-associated genes in the normal endometrium, we conducted whole-exome and whole-genome sequencing for 56 endometrial glands and matched blood samples from 4 women. By collecting endometrial glands from different parts of the endometrium, we showed that multiple glands with the same somatic mutations occupied substantial areas of the endometrium.

  Study EGAS00001005822

• PCA Atlas Chromium scRNA-seq and demultiplexing support (FASTQs, BAMs, capture-level VCFs and mapping tables)

  This dataset contains Chromium single-cell RNA-seq data and demultiplexing support for the PCA Atlas study EGAS00001008332. Included data objects: - 16 Chromium scRNA-seq FASTQ runs (EGAR accessions) for captures PCa1–PCa16. - 16 aligned BAM analyses (one Cell Ranger possorted_genome_bam.bam per capture). - 16 capture-level genotype VCF analyses derived from the Axiom UK Biobank array, used as demultiplexing panels. - demux_map.csv (EGAZ00001945520): donor–capture–sample mapping for genotype-based demultiplexing. - chromium.csv (EGAZ00001945537): run-level mapping linking captures, EGA samples, runs (EGAR), experiments (EGAX) and BAM analyses. Together these objects provide a complete view of the Chromium scRNA-seq data and the genotype-based demultiplexing support needed to reproduce donor assignment and downstream analyses.See also https://zenodo.org/records/17372603

  Dataset EGAD00001015795

• Genomic Analysis of Prostate Tumor Heterogeneity in Metastasis

  To investigate the molecular changes, mutations, and signaling pathways that characterize the initial steps of prostate cancer metastasis to the lymph nodes, we analyzed 19 discrete lymph node (LN) metastases, 97 primary tumor foci, 39 benign lymph nodes, and 10 normal adjacent prostate tissue samples from 43 patients enrolled in a clinical trial (NCT01808222) of extended lymphadenectomy and metastasis excision guided by [18F]-fluciclovine PET imaging for high risk, newly diagnosed prostate cancer conducted at Emory University. These patients fell within high or very high-risk groups (T3a, Gleason score 8-10, or PSA greater than 20 ng/ml). Of these patients, 16 had LN metastases at least 4 mm in diameter, and 20 patients had no metastases. For metastatic patients, we performed RNA and Whole Exome Sequencing (WES) on three primary tumor foci, one benign LN, and all LN metastases greater than 4mm in diameter. For non-metastatic patients, we sequenced two primary tumor foci and one benign LN. In total, RNAseq was performed on 165 tissue samples from 43 patients, and WES was performed on 137 samples from 35 patients.

  Study phs003404

• Longitudinal profiling of circulating tumour DNA for tracking tumour dynamics in pancreatic cancer

  The utility of circulating tumour DNA (ctDNA) for longitudinal tumour monitoring in pancreatic ductal adenocarcinoma (PDAC) has not been explored beyond mutations in the KRAS proto-oncogene. We aim to characterise and track patient-specific somatic ctDNA variants, to assess longitudinal changes in disease burden and explore the landscape of actionable alterations.

  Study EGAS00001005981

• Long-read sequencing for cell-free DNA analysis (mouse)

  In this study, we compared the two long-read sequencing platforms, namely the single-molecule real-time sequencing by Pacific Biosciences and nanopore sequencing by Oxford Nanopore Technologies, for the analysis of cell-free DNA from plasma. Artificial mixtures of sonicated human and mouse DNA at different sizes were sequenced with the two platforms.

  Study EGAS00001006329

• Identify disease-related genes

  Raw data (idat file) analyzed by Illumina SNP array for patients in the 1st cohort and the 2nd cohort (51 diseases).

  Study JGAS000703

• Sensitive gene analysis of hereditary cardiovascular disease

  This research aims to identify disease sensitive genes and their gene variants by genome analysis for hereditary cardiovascular diseases.

  Study JGAS000295

• WGS files for double minute brain tumor paper.

  Whole Genome Sequencing files accompanying the paper titled "Structure and evolution of double minutes in diagnosis and relapse brain tumors". Please read the paper for more details.

  Dataset EGAD00001004337

• Epigenomics of Neurocognitive Function in Breast Cancer

  This study harnessed the data and biospecimens from the Exercise Program in Cancer and Cognition (EPICC) study (parent study) that collected data on cognitive function, demographics, other symptoms and biospecimens at two time points (T1: enrollment, T2: six months later) within the context of a six-month randomized controlled trial of a moderate intensity aerobic exercise intervention. This study collected genome wide DNA methylation data from T1 and T2 and conducted epigenome-wide association-based analyses to find genes and biological pathways explaining variability in cognitive function and explaining how exercise mitigates cognitive decline. Our initial findings identified cg10331779 near CTNND2 (p-value=9.65×10-9) associated with processing speed and cg25906741 in MLIP (p-value=2.01×10-8) associated with subjectively measured cognitive function. Additionally, differentially methylated regions were identified near SLC6A11, PRKG1/CSTF2T, and FAM3B for processing speed and near PI4KB and SGCE/PEG10 for mental flexibility.

  Study phs003959

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

  Dac EGAC00001001501

• Distinct evolutionary trajectories of primary high grade serous ovarian cancers revealed through spatial mutational profiling

  High-grade serous ovarian cancer (HGSC) is characterized by poor outcome, often attributed to emergence of treatment-resistant sub-clones. We sought to measure the degree of genomic diversity within primary, untreated HGSC to examine the natural state of tumor evolution prior to therapy. We performed exome sequencing, copy number analysis, targeted amplicon deep sequencing and gene expression profiling on thirty-one spatially and temporally separated HGSC tumor specimens (six patients) including ovarian masses, distant metastases, and fallopian tube lesions. We found widespread intra-tumoral variation in mutation, copy number, and gene expression profiles, with key driver alterations in genes present in only a subset of samples (e.g. PIK3CA, CTNNB1, NF1). On average, only 51.5% of mutations were present in every sample of a given case (range: 10.2% to 91.4%), with TP53 as the only somatic mutation consistently present in all samples. Complex segmental aneuploidies, such as whole genome doubling, were present in a subset of samples from the same individual, with divergent copy number changes segregating independently of point mutation acquisition. Reconstruction of evolutionary histories showed one patient with mixed HGSC and endometrioid histology with common etiologic origin in the fallopian tube and subsequent selection of different driver mutations in the histologically distinct samples. In this patient, we observed mixed cell populations in the early fallopian tube lesion, indicating diversity arises at early stages of tumorigenesis. Our results reveal that HGSC exhibit highly individual evolutionary trajectories and diverse genomic tapestries prior to therapy, exposing an essential biological characteristic to inform future design of personalized therapeutic solutions and investigation of drug resistance mechanisms.

  Study EGAS00001000547

• Proteogenomic Analysis of CALGB40601 (ALLIANCE) a Neoadjuvant Phase III HER2-Positive Breast Cancer Trial

  80 frozen core needle biopsies from 54 HER2+ breast cancer patients from the CALGB 40601 trial (NCT00770809) were processed for proteogenomic analysis to identify genes, proteins, and phosphosites associated with pathological complete response to neodjuvant anti-HER2 therapies. The final set included 22 patients treated with trastuzumab plus lapatinib in combination with pacletaxel (THL arm), 24 patients treated with trastuzumab in combination with pacletaxel (TH arm), and 8 patients treated lapatinib in combination with pacletaxel (TL arm). Principal findings of this study included identifying negative cases misdiagnosed as HER2+ that did not respond to targeted therapy and observing higher levels of two biomarker candidates in non-pCR tumors. Mass spec-based proteomics and phosphoproteomics data generated from 75 biopsies (all 54 patients) will be made available via the Proteomic Data Commons. Whole exome- (67 biopsies from 49 patients) and RNA-sequencing (52 biopsies from 39 patients) data for the subset profiled with proteogenomics will be made available through dbGaP, but genomic and transcriptomic profiling data for the whole cohort has previously been deposited (phs001570).

  Study phs003576

• Sampling of multi-centric lower grade glioma influences management and provides insight into gliomagenesis

  Rare multicentric lower-grade gliomas (LGG) represent a unique opportunity to study the heterogeneity between distinct tumor foci in a single patient, and to infer their origins and parallel patterns of evolution. In this study, we integrate clinical features, histology and immunohistochemistry for 4 patients with multicentric LGG, arising both synchronously and metachronously. For 3 patients we analyze the phylogeny of the lesions using exome sequencing, including one case with a total of 8 samples from the two lesions. We show that each tumor in multicentric LGG cases may arise independently or may diverge very early in their development, presenting as genetically and histologically distinct tumors suggesting that comprehensive sampling of these lesions can significantly alter diagnosis and management.

  Study EGAS00001002495

• TCRab sequencing of RCC patients

  TCRab sequencing was performed on viable frozen tumor dissociated cells from three RCC patients. The raw data is available as fastq files.

  Dataset EGAD00001011046

• MCO colorectal cancer genomics at UNSW

  This dataset contains DNA sequencing data from 95 colorectal cancer and matched-normal samples. The dataset contains targeted deep sequencing of selected regulatory elements in 95 cancer and matched-normal samples, and data for one sample that was additionally whole-genome sequenced (cancer and matched-normal).

  Study EGAS00001003450

• Single cell RNA sequencing and Whole Genome Sequencing on different cells from the same sample for a triple negative patient derived xenograft and ovarian cancer cell lines.

  Measuring gene expression of genomically defined tumour clones at single cell resolution would associate functional consequences to somatic alterations, as a prelude to elucidating pathways driving cell population growth, resistance and relapse. In the absence of scalable methods to simultaneously assay DNA and RNA from the same single cell, independent sampling of cell populations for parallel measurement of single cell DNA and single cell RNA must be computationally mapped for genome-transcriptome association. Here we present clonealign, a robust statistical framework to assign gene expression states to cancer clones using single-cell RNA-seq and DNA-seq independently sampled from an heterogeneous cancer cell population. We apply clonealign to triple-negative breast cancer patient derived xenografts and high-grade serous ovarian cancer cell lines and discover clone-specific dysregulated biological pathways not visible using either DNA-Seq or RNA-Seq alone.

  Study EGAS00001003387

• Sequencing data of the ampulla and fimbriae of the fallopian tube in pre-menopausal women

  A total of 10 pre-menopausal patients were recruited for this study. Sequencing of both the fimbriae and ampullary region of the fallopian tubes was performed using 10x Genomics single-cell RNA-seq and ATAC-seq. For one patient, data were sequenced across 4 lanes, while the remaining patients' data were sequenced in 2 lanes each, resulting in a total of 44 sequencing datasets for each platform.

  Dataset EGAD50000000889

• Whole-genome sequencing of cell-free DNA from pancreatic and breast cancer cohorts for fragmentomic and tumor fraction analysis

  This project provides whole-genome sequencing data from cell-free DNA collected from patients with pancreatic ductal adenocarcinoma and breast cancer, alongside healthy and benign controls. The study aims to identify novel liquid biopsy biomarkers by exploring the relationship between per-base quality scores and fragmentomic signals like end-motifs and fragment length. Furthermore, the data supports the development of Bayesian deep learning frameworks for the uncertainty-aware estimation of tumor fraction and ploidy in low-concentration clinical samples.

  Study EGAS50000001620

• WTCCC case-control study for Hypertension - Combined Controls

  WTCCC genome-wide case-control association study for Hypertension (HT) using six disease collections together with the 1958 British Birth Cohort and the UK National Blood Service collections as controls.

  Study EGAS00000000010

• Sequencing data for the Genomic Autopsy Study

  The .cram files of the Trio or Quad sequencing data used for generation of the genomic autopsy study. This contains a mix of genome sequencing and exome sequencing data for probands and their parents. A subset of families (n=32) did not provide consent to publicly sharing their data.

  Dataset EGAD00001009737

• Spatially resolved transcriptomics reveals profound subclonal heterogeneity and T cell dysfunction in extramedullary myeloma

  Investigating the spatial architecture and microenvironment of EMD lesions in Multiple Myeloma patients using spatial whole transcriptome sequencing (10X Visium), tomography for spatially resolved transcriptomics (TOMO-seq), and single-cell RNA sequencing (scRNAseq)

  Study EGAS50000000227

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

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

  Study EGAS00001003075

• Phenotype and Genotype determination of 400 individuals from Northern Germany

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

  Dataset EGAD00001001315

• Molecular analysis of diffuse cerebellar gliomas

  Among diffuse gliomas, oligodendrogliomas show relatively better prognosis, respond well to radiotherapy and chemotherapy, and seldom progress to very aggressive tumors. To elucidate the genetic and epigenetic background for such behavior and tumor evolution during tumor relapse, we comparatively analyzed 12 pairs of primary and recurrent oligodendrogliomas with 1p/19q-codeletion. Initial treatment for these patients was mostly chemotherapy alone. Temozolomide was used for 3, and procarbazine, nimustine and vincristine (PAV chemotherapy) were used for 7 patients. World Health Organization histological grade at recurrence was mostly stable; it was increased in 2, the same in 9, and decreased in 1 cases. Whole-exome sequencing demonstrated that the rate of shared mutation between the primary and recurrent tumors was relatively low, ranging from 3.2-57.9% (average, 33.3%), indicating a branched evolutionary pattern. The trunk alterations that existed throughout the course were restricted to IDH1 mutation, 1p/19q-codeletion, and TERT promoter mutation, and mutation of the known candidate tumor suppressor genes CIC and FUBP1 were not consistently observed between primary and recurrent tumors. Multiple sampling from different regions within a tumor showed marked intratumoral heterogeneity. Notably, in general, the number of mutations was not significantly different after recurrence, remaining under 100, and no hypermutator phenotype was observed. FUBP1 mutation, loss of chr. 9p21, and TCF12 mutation were among a few recurrent de novo alterations that were found at recurrence, indicating that these events were clonally selected at recurrence but were not enough to enhance malignancy. Genome-wide methylation status, measured by Illumina 450 K arrays, was stable between recurrence and the primary tumor. In summary, although oligodendroglioma displays marked mutational heterogeneity, histological malignant transformation accompanying events such as considerable increase in mutation number and epigenetic profile change were not observed at recurrence, indicating that noticeable temporal and spatial genetic heterogeneity in oligodendrogliomas does not result in rapid tumor progression.

  Study JGAS000106

• The MD Anderson Colorectal Cancer Case Control Study

  Colorectal cancer (CRC) is the second leading cause of cancer-related deaths in the US. Driven by common disease common variants hypothesis, genome-wide association studies only identified a number of common susceptibility loci that explained a small portion of CRC heritability. We conducted a case-control study using whole exome sequencing to identify rare genetic variants with intermediate effect size that predispose individuals to colorectal cancer.

  Study phs002691

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

  Dac EGAC00001000110

• BiSeqS

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

  Dataset EGAD00001003323

• Developing somatic copy number and mutation calling tools for a bespoke sequencing platform

  We previously developed a linked-read sequencing platform (DigiPico) for analysing whole cancer genomes from picogram quantities of tumour DNA. The aim of this study was to develop and evaluate the specialised computational approaches required to obtain clinically useful results from the raw data. To this end, we performed matched DigiPico, bulk tumour and germline WGS on samples from four patients.

  Study EGAS00001007195

• Raw scTCR-seq data for “Characterization of intestinal immune responses in generalized human and murine lipodystrophy”

  Raw 10X 5' v3 scTCR-seq data (TCR) for PBMC of 3 helthy donors and two AGLCD patient timepoints as well as of LPMC of 3 Crohns disease patients and one timepoint of the AGLCD patient.

  Dataset EGAD50000002191

• Raw scRNA-seq data for “Characterization of intestinal immune responses in generalized human and murine lipodystrophy”

  Raw 10X 5' v3 scRNA-seq data (GEX) for PBMC of 3 helthy donors and two AGLCD patient timepoints as well as of LPMC of 3 Crohns disease patients and one timepoint of the AGLCD patient.

  Dataset EGAD50000002190

• Transcriptome (RNA-seq) data for the validation of the glioblastoma progression study (GBMatch).

  37 transcriptomes derived from fresh-frozen glioblastoma tumor samples. These transcriptomes have been produced for validation purposes and match the corresponding RRBS and WGS profiles in that DNA and RNA was extracted from the same tumor samples.

  Dataset EGAD00001004076

• Genomic (WGS) data for the validation of the glioblastoma progression study (GBMatch).

  43 low-coverage genomes derived from fresh-frozen glioblastoma tumor samples. These genomes have been produced for validation purposes and match the corresponding RRBS and RNA-seq profiles in that DNA and RNA was extracted from the same tumor samples.

  Dataset EGAD00001004077

• Mapping of runs back to samples for snRNASeq data

  Mapping of runs back to samples for PDN, PDO and TIS snRNASeq data. 4 sets of matched PDN, PDO and TIS samples (12 unique samples total) underwent pooled snRNASeq (Parse Biosciences). 2 sublibraries were created from this and sequenced at separate times

  Dataset EGAD00001015609

• Gene Expression Signatures in CATHGEN

  Case control cohort: The details have been previously published: American Heart Journal. 2010;160:371-379 e372. Briefly, a nested case:control cohort of CATHGEN participants who had experienced death or MI (n = 250) after their index catheterization and age-, sex-, and race-matched controls (n = 250) who were free of death/MI > 2 years after cardiac catheterization was identified as part of the MURDOCK Horizon 1 Cardiovascular Disease Study.21 Sufficient RNA for microarray analysis was available in 447 members of this cohort. Observational cohort: 224 sequential CATHGEN samples were selected for whole blood RNA analysis, of which, 191 had sufficient RNA for microarray analysis.

  Study phs000551

• Precision Diagnosis of Neurodevelopmental Disorders in Middle Eastern Populations

  We constructed de novo genome assemblies for six family trios from diverse Middle Eastern ancestries (Sudan, Jordan, Syria, Qatar, and Afghanistan), involving probands with various unresolved neurodevelopmental conditions. We generated high-quality, nearly complete genome assemblies for trios, revealing extended novel sequence impacting known genes, novel HLA/KIR alleles, and strong signals of inbreeding, with runs of homozygosity covering large parts of individual chromosomes. We also identified potential disease variants underlying the unresolved symptoms. Also, the assemblies uncovered unique variation relative to existing references, showing enhanced mapping and variant calling of Middle Eastern genomes. The dataset available through dbGaP includes raw short (Illumina) and long (PacBio) sequencing reads and assembled haplotypes.

  Study phs003917

• Genomic profiling of IBC

  We collected matched pretreatment blood and tumor samples from 19 patients with primary TN-IBC enrolled in a phase II clinical trial (NCT02876107). Patients were treated with neoadjuvant chemotherapy (NAC) or the anti-EGFR antibody panitumumab (PmAb) plus NAC (PmAb/NAC). We conducted whole-exome sequencing, RNA sequencing, and CIBERSORT analyses for these TN-IBC samples and compare the genetic and molecular profiles with similarly analyzed stage III TN-non-IBC patient samples. We also compared the genetic and molecular characteristics of TN-IBC in patients who had a pathologic complete response (pCR) to NAC or PmAb/NAC treatment, a suitable surrogate endpoint for IBC, with those who did not have pCR (non-pCR).

  Study EGAS00001007520

• Joslin Study on the Genetics of Type 2 Diabetes

  Between 1993 and 2003, families were recruited in the Joslin Study on the Genetics of Type 2 Diabetes for the presence of an autosomal dominant mode of inheritance of diabetes. Recruiting and screening of families occurred through probands who were receiving medical care at the Joslin Clinic (Boston, MA). Screening of families included 1) a proband and at least one sibling with type 2 diabetes, 2) diabetes occurring in at least three generations, 3) diabetes inherited on one side of the prospective family. Probands had to have a diabetes diagnosis between the age range from 10 to 60 years. Demographic data, clinical data, and family history were collected from participating family members, along with blood and urine samples. This study includes genetic and phenotypic data from one family examined in Simeone, Wilkerson, et. al. (NPJ Genomic Medicine 2022, PMID: 35869090). Genotype data for 14 family members and whole genome sequencing data for 6 individuals were generated with the goal of identifying a potential genetic cause of disease in this family. To de-identify this family and protect confidentiality, information on sex in phenotype data and variants identified in X, Y, and MT chromosomes have been removed in compliance with IRB guidelines.

  Study phs002959

• Whole Exome Sequencing PPGL

  Whole exome sequencing (WES) libraries were prepared with the SureSelectXT Human All Exon V6+COSMIC target enrichment system (Agilent, 5190-9307) by following kit manufacturer`s instructions. 200 ng of genomic DNA from FFPE tumoral samples and 1 µg from FF or germline samples were used as starting material. SureSelectXT HS (Agilent, G9704A) and SureSelectXT2 (Agilent, G9621A) reagent kits were alternatively used for FFPE derived and good quality samples, respectively. DNAs were fragmented on a Covaris S2 sharing instrument based on initial sample’s integrity. Fragmented DNA samples were processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to Illumina's adapters. Adapter-ligated libraries were PCR amplified with Illumina PE primers and subsequently hybridized to SureSelect Oligo Capture Library Mix. Biotinylated hybrids were captured and the enriched fraction eluted. Libraries were completed by limited-cycle PCR with Illumina TruSeq primers and KAPA HiFi HotStart DNA pol (Roche KK2501). Sample-specific libraries were combined into equimolarly balanced pools and applied to Illumina flow cells for cluster generation. Sequencing was performed on either the Illumina HiSeq2500 or NovaSeq6000 in a paired-end 100bp reads mode to a median target coverage of ~200x and ~100x for tumors and germline, respectively.

  Study EGAS00001006043

• UK10K_RARE_FIND

  In the UK10K project we propose a series of complementary genetic approaches to find new low frequency/rare variants contributing to disease phenotypes. These will be based on obtaining the genome wide sequence of 4000 samples from the TwinsUK and ALSPAC cohorts (at 6x sequence coverage), and the exome sequence (protein coding regions and related conserved sequence) of 6000 samples selected for extreme phenotypes. Our studies will focus primarily on cardiovascular-related quantitative traits, obesity and related metabolic traits, neurodevelopmental disorders and a limited number of extreme clinical phenotypes that will provide proof-of-concept for future familial trait sequencing. We will analyse directly quantitative traits in the cohorts and the selected traits in the extreme samples, and also use imputation down to 0.1% allele frequency to extend the analyses to further sample sets with genome wide genotype data. In each case we will investigate indels and larger structural variants as well as SNPs, and use statistical methods that combine rare variants in a locus or pathway as well as single-variant approaches. The Raymond samples will be part of the “rare disease” group, and will undergo exome sequencing. For further information with regard to this cohort please contact Lucy Raymond (flr24@cam.ac.uk).

  Study EGAS00001000128

• UK10K_RARE_CILIOPATHIES

  In the UK10K project we propose a series of complementary genetic approaches to find new low frequency/rare variants contributing to disease phenotypes. These will be based on obtaining the genome wide sequence of 4000 samples from the TwinsUK and ALSPAC cohorts (at 6x sequence coverage), and the exome sequence (protein coding regions and related conserved sequence) of 6000 samples selected for extreme phenotypes. Our studies will focus primarily on cardiovascular-related quantitative traits, obesity and related metabolic traits, neurodevelopmental disorders and a limited number of extreme clinical phenotypes that will provide proof-of-concept for future familial trait sequencing. We will analyse directly quantitative traits in the cohorts and the selected traits in the extreme samples, and also use imputation down to 0.1% allele frequency to extend the analyses to further sample sets with genome wide genotype data. In each case we will investigate indels and larger structural variants as well as SNPs, and use statistical methods that combine rare variants in a locus or pathway as well as single-variant approaches. The Ciliopathies samples will be part of the rare disease group, and will undergo exome sequencing. For further information with regard to this cohort please contact Phil Beales (p.beales@ich.ucl.ac.uk).

  Study EGAS00001000126

• Diverse Cellular Composition in Alveolar Rhabdomyosarcoma Revealed by Single Cell RNA Sequencing

  Using single cell RNAseq data to characterize tumor composition and cellular states for Alveolar Rhabdomyosarcoma. We find that that ARMS tumors harbor phenotypically and transcriptionally distinct malignant subpopulations within an immune-influenced microenvironment.

  Study EGAS50000001564

• Sensitive urothelial cancer detection via high volume urine DNA analysis

  We developed a high volume (100 mL) urine DNA collection kit and laboratory platform (UroScout) analyzing 25 commonly mutated UC genes and 8 copy number-altered loci for urine tumor DNA (utDNA) alterations. To assess accuracy of UC detection, we analyzed 498 urine samples from diagnostic and surveillance timepoints from 193 UC patients and 88 cancer-negative patients evaluated for UC.

  Dataset EGAD50000000891

• Whole Exome Sequences from Eivissan and Menorcan Individuals

  30 and 21 whole exome sequences for Eivissan and Menorcan healthy unrelated volunteers, respectively. The exomes were captured with the Agilent SureSelect Human All Exon V6 capture kit and pair-end sequenced in Illumina platforms. For each individual, a pair of ".fastq" files can be found containing the raw reads.

  Dataset EGAD50000000620