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• Influence of culture media on airway differentiation at the Air-Liquid Interface

  Single-cell dataset of human airways after in vitro regeneration at the Air-Liquid Interface. Samples from 2 donors were used for the establishment of Human Bronchial Epithelial Cell cultures (HBECs) and were analyzed during proliferation, at the onset of differentiation (ALI0) and after full differentiation (ALI28), in 4 distinct culture media. Single-cell RNAseq was performed with 10x Genomics 3’ v2 RNA-seq using hashtag antibodies for multiplexing, and sequenced on a NextSeq 500. Samples from 3 additional donors were used for the establishment of Human Nasal Epithelial Cell cultures (HNECs) and were analyzed during proliferation in three distinct culture media. Single-cell RNAseq was performed with 10x Genomics 3’ v3 RNA-seq without multiplexing, and sequenced on a NextSeq 2000.

  Dataset EGAD00001011362

• NHLBI TOPMed - NHGRI CCDG: Malmo Preventive Project (MPP)

  The Malmö Preventive Project (MPP) was a community-based disease prevention program including 33,346 inhabitants from the city of Malmö in Southern Sweden. Complete birth cohorts between 1921-1949 were invited, and the participation rate was 71%. Participants underwent screening between 1974 to 1992 for cardiovascular risk factors, alcohol abuse, and breast cancer. Between 2002-2006, surviving participants were invited to a reexamination which included blood sampling from which DNA has been extracted. Subjects with prevalent or incident AF were identified from national registers as previously described, and cases with DNA were then matched in a 1:1 fashion to controls with DNA from the same cohort by sex, age (±1 year), and date of baseline exam (±1 year). Also, controls required a follow-up exceeding that of the corresponding AF case.

  Study phs001544

• Novel Factors for Unexplained Phenotypes of Subclinical Carotid Atherosclerosis

  The overall goal for this study was to determine the genetic factors associated with extreme phenotypes of subclinical atherosclerosis (protective and deleterious). Study participants were selected from the Northern Manhattan Study (NOMAS), a population based cohort study investigating stroke and stroke risk factors in Northern Manhattan. Cases and controls were individuals at the extreme ends of the distribution for carotid intima-media thickness and carotid plaque, with cases defined as individuals with subclinical atherosclerosis that could not be explained by traditional vascular risk factors (USAth) and controls defined as individuals with unexplained protection against atherosclerosis (UPAth).

  Study phs001560

• Gut 16S rRNA/FINRISK 2002

  Gut microbiome 16S rRNA raw data for N=7174 FINRISK 2002 participants. FINRISK fecal samples were mailed to the Knight laboratory at the University of California (San Diego, CA), for microbiota sequencing using the standard Earth Microbiome Project protocols (https://earthmicrobiome.org/protocols-and-standards/). DNA was extracted using a magnetic bead-based DNA extraction protocol. Amplicon sequence data for the V4 region of the 16S rRNA gene was generated using 515F (Parada) and 806R (Apprill) primers. For a total of 25μl reaction volume, 13 µl PCR-grade water was combined with 10 µl PCR master mix (Platinum Hot Start PCR Master Mix, 2x, ThermoFisher), 0.5 µl forward primer (10 µM), 0.5 µl reverse primer (10 µM), and 1 µl template DNA. Amplification was performed in triplicate reactions, and triplicate PCR reactions were pooled afterwards. Expected products were visualized on agarose gels (300–350 bp) and quantified with Quant-iT PicoGreen dsDNA kit (Invitrogen). Equal amounts (240 ng) of amplicon were combined for each sample and cleaned (MoBio UltraClean PCR Clean-Up Kit). Cleaned amplicon pools were sequenced with 515F and 806R primers.

  Dataset EGAD50000000287

• Whole-genome sequence data for The interface of malignant and immunologic clonal dynamics in high-grade serous ovarian cancer

  Each tumor sample was cut into three pieces, yielding two end-pieces for cryovials and a middle portion placed in 10% buffered formalin. End pieces were homogenized manually and with a paddle blender (Stomacher). All paraffin-embedded blocks, including formalin-fixed tumor samples and molecular-fixed fallopian tubes, were sectioned and stained with hematoxylin and eosin prior to expert histopathological review to confirm the presence of high grade serous carcinoma. Homogenized end pieces were then flash frozen and later used for WGS. For all tumor and matched normal (peripheral blood) samples, DNA was extracted with the Qiagen AllPrep DNA/RNA kit (tumor samples from patients 25,26,28-32) or the Qiagen Blood and Tissue Extraction Kit (tumor samples from patients 1-4,7,9-17, and all blood samples). For all tumor and normal samples, DNA extraction was followed by library construction and sequencing using Illumina HiSeq2500 whole genome shotgun v4 chemistry with paired-end 125bp reads.

  Dataset EGAD00001003984

• SCLC study MGH - WES dataset

  For whole-exome sequencing 1 µg of DNA from fresh-frozen tumors was fragmented by sonication technology (for DNA from fresh-frozen tumors: Bioruptor, diagenode, Liѐge, Belgium; for DNA from FFPE material: Covaris). The fragments were end-repaired and adaptor-ligated, including incorporation of sample index barcodes. After size selection, libraries were subjected to an enrichment process with Sure select XT (Agilent). The final libraries were sequenced with a paired-end 2×75 bp protocol for an average coverage of 100-120x

  Dataset EGAD00001003970

• Human genomic and phenotypic synthetic data for the study of rare diseases

  The purpose of this dataset is to facilitate development of technical implementations for rare disease data integration, analysis, discovery, and federated access. This synthetic dataset includes clinical and genomic data from 6 rare disease cases. It consists of 18 whole genomes (6 index cases with their parents) which have genetic background based on public human data sequenced in the context of the Illumina Platinum initiative (Eberle, MA et al. (2017)) and made available by the HapMap project (https://www.genome.gov/10001688/international-hapmap-project). In each of the cases, real causative variants correlating with the phenotypic data provided were spiked-in. The cases included in this synthetic dataset correspond to the following type of disorders: CASE 1- Congenital myasthenic syndrome (Autosomal Dominant -de novo variant) CASE 2- Macular dystrophy (Autosomal Dominant) CASE 3- Muscular dystrophy (Autosomal Recessive-compound heterozygous variants) CASE 4- Mitochondrial disorder (Autosomal Recessive-consanguineous case - homozygous variant) CASE 5- Breast cancer (Autosomal Dominant) CASE 6- Similar as case 1 for patient matchmaking tests: Congenital myasthenic syndrome (Autosomal Dominant-de novo variant) For each case you will be able to download the following data: clinical information (phenopackets per individual and pedigree per family), raw genomic data (FASTQ and BAMs) and processed genomic data (vcfs). When using the data, the following should be acknowledged: the RD-Connect GPAP (https://platform.rd-connect.eu/), EC H2020 project EJP-RD (grant # 825575), EC H2020 project B1MG (grant # 951724) and Generalitat de Catalunya VEIS project (grant # 001-P-001647).

  Study EGAS00001005702

• Single-Cell RNA-Seq Profiling of Peripheral Immune Responses to Severe Infection in Uganda

  We conducted a prospective observational study (RESERVE-U-2-TOR) of adults admitted to Tororo General Hospital in eastern Uganda with severe, undifferentiated infection (i.e., suspected sepsis). Peripheral blood mononuclear cells (PBMCs) were isolated from freshly collected heparinized whole-blood samples (4 - 5 mL) using a standard density-gradient protocol (STEMCELL Technologies). PBMCs were aliquoted, cryopreserved in CryoStor CS10 (STEMCELL Technologies), stored overnight at -80°C, and transferred to liquid nitrogen for longer-term storage. Upon thawing, viability was assessed using the Nexcelom Cellaca Cell Counter, and cells were diluted to optimal concentrations for loading onto the Chromium Controller (10X Genomics). Each sample targeted the capture of ~10,000 GEMs (gel bead-in-emulsions). Single-cell RNA libraries were prepared using the Chromium Single Cell 3' Reagent Kit v3.1 following the manufacturer's standard protocol. Libraries were quality-assessed using an Agilent TapeStation and quantified using both Qubit 2.0 Fluorometer (Invitrogen) and qPCR (Applied Biosystems). Sequencing was performed on the NovaSeq X Plus platform (Illumina) using a 28×91 read configuration per 10X guidelines, targeting ~50,000 reads per cell. Data from this study available through dbGaP include raw single-cell RNA-seq data generated from PBMC samples collected from a subset of RESERVE-U-2-TOR participants at study enrollment (N=8).

  Study phs004100

• germline_2 SNP6.0

  Over 1.87 million SNP and CNV loci are screened by Affymetrix SNP 6.0 array

  Dataset EGAD00010001813

• leukemia_2 SNP6.0

  Over 1.87 million SNP and CNV loci are screened by Affymetrix SNP 6.0 array

  Dataset EGAD00010001814

• VCF file, post sample QC

  This VCF contains the full sequence data post QC. This consists of 41,911 individuals. All polymorphic sites are present in this VCF.

  Dataset EGAD00001000623

• Bulk RNA-seq osteosarcoma

  We profiled 23 patient osteosarcoma tumor samples by bulk RNA-seq. The raw fastqs are provided.

  Dataset EGAD00001011371

• E5103 Correlative Studies

  ECOG-ACRIN E5103 (E5103) was a phase III adjuvant breast cancer trial that randomized 4994 patients with node-positive or high-risk node-negative breast cancer to intravenous doxorubicin and cyclophosphamide every 2 or 3 weeks (at the discretion of treating physician), for four cycles of adriamycin and cyclophosphamide (AC) followed by 12 weeks of weekly paclitaxel (80 mg/m2) alone (Arm A), or to the same chemotherapy with either concurrent bevacizumab (Arm B), or concurrent plus sequential bevacizumab (Arm C). To develop predictive genetic biomarkers for chemotherapy efficacy and toxicities, we have successfully performed genome-wide genotyping and whole exome sequencing in the germline (blood) DNA of 3215 and 672 patients, respectively, from the E5103 trial to investigate the association of genetic variants with chemotherapy efficacy and toxicities. Case and control studies were performed with genome-wide analyses (GWAS) and whole exome analyses (WES) across all arms of E5103 to identify genotypes at single-nucleotide polymorphisms (SNPs) and deleterious gene mutations that were associated with paclitaxel-induced peripheral neuropathy (TIPN). Through GWAS, we have identified a SNP, rs3125923, and through WES, Cytochrome P450 oxidoreductase (POR), that was significantly associated with grade 3-4 TIPN.

  Study phs003201

• Genome Wide Association Studies in ECOG 2997 Trial

  The ECOG 2997 trial was a randomized controlled trial for patients with previously untreated CLL comparing fludarabine monotherapy to the combination of fludarabine and cyclophosphamide. The initial clinical findings of this study were published in the Journal of Clinical Oncology in 2007 (JCO 25:793-8). Additional laboratory studies have also published (JCO 25:799-804).

  Study phs000621

• Spatiotemporal Analysis of the Human Cerebellum

  We sought to characterize neural progenitors within spatially demarcated regions of the human cerebellum at a molecular level during neurogenesis. We used laser-capture microdissection to enrich for cells within the ventricular zone and subventricular zone regions of the rhombic lip, external granule cell layer and Purkinje cell layer, then performed RNA-sequencing on the enriched samples.

  Study phs001908

• Vulnerabilities of Midbrain Dopaminergic Neurons to Parkinson's Disease Revealed by Single-Cell Genomics

  We developed a novel protocol for the enrichment of midbrain DA neurons from frozen tissue. We subsequently performed single-nuclei RNA-sequencing on enriched samples from postmortem midbrain tissue from human, macaque, tree shrew, rat, and mouse. We identified vulnerable and resistant populations from these data and associated genetic enrichments and differential expression changes.

  Study phs002879

• An epidemiological study examining the relationship among food, health, and genome

  We conducted a cohort-based study to investigate the association between the genetic background and diet/lifestyle in 962 healthy Japanese. We analyzed the Ebetsu cohort and some participants living in Tokyo. The SNP array (Japonica Array v2) was used for genotyping. Shotgun metagenomic sequencing of fecal microbiome and metabolome of feces and blood were analyzed.

  Study JGAS000678

• Target sequencing of 11 hereditary breast cancer genes in Japanese

  We performed a case control association study for variants in coding regions of 11 hereditary breast cancer genes in 7,051 female unselected breast cancer patients, 11,241 female controls, 53 male patients, and 12,490 male controls of Japanese ancestry. The 11 genes were ATM, BRCA1, BRCA2, CDH1, CHEK2, NBN, NF1, PALB2, PTEN, STK11, and TP53.

  Study JGAS000140

• Multiregion exome sequencing of ovarian immature teratomas

  Tumor tissue from each of the indicated ovarian and disseminated GCT components was selectively punched from formalin-fixed, paraffin-embedded blocks. Genomic DNA was extracted from these tumor and matched normal tissue samples, with a total of 500 ng of genomic DNA used as input for capture employing the xGen Exome Research Panel.

  Study EGAS50000000291

• Enhanced resolution profiling in twins reveals differential methylation signatures of Type 2 Diabetes with links to its complications

  We profiled DNA methylation in blood samples from participants of European ancestry from 7 twin cohorts using a methylation sequencing platform targeting regulatory genomic regions encompassing 2,048,698 CpG sites. The results help to improve our understanding of T2D disease pathogenesis and progression and may provide biomarkers for its complications.

  Study EGAS50000000197

• Heterogeneity and evolution of DNA mutation rates in microsatellite-stable colorectal cancer

  A mutation accumulation experiment in colorectal cancer (CRC) derived tumoroids, aimed at measuring the spontaneous rates of accumulation of new single-nucleotide sequence variations in seven microsatellite stable CRCs and one microsatellite unstable CRC. Mutations accumulated over six+six months were identified via whole genome sequencing of clonal tumoroids. 150x WGS for 7 samples.

  Study EGAS50000000425

• SC_DDD-G-5

  Post-QC (pre-imputation) genotype data for N=2,166, a subset of trios described in EGAD00010001602. These data form N=722 complete trios in which the proband has a neurodevelopmental phenotype (Niemi et al. Nature 2018). Includes HPO phenotype terms for patients. Samples were genotyped on the Illumina HumanOmniExpress BeadChip

  Dataset EGAD00010001606

• Biomarker analysis and treatment dynamics following preoperative ipilimumab plus nivolumab in locally advanced urothelial cancer from the phase 1B NABUCCO study

  In the current analysis of the full NABUCCO trial population (cohorts 1 and 2), we aimed to explore both potential biomarkers for response to combination ICB, as well as treatment dynamics to gain a better understanding of the effects of ICB on the urothelial cancer tumor microenvironment (TME).

  Study EGAS50000001781

• Chromatin_accessability_in_cytokine_induced_immune_cell_states

  We isolated T cells and monocotyes from healthy platelet donors and cultured them in resting and stimulated conditions with addition of a range of cytokines. We performed K27Ac ChM sequencing to assess the chromatin activity in different cytokines treated cells. These cellular profiles were used to map risk variants to the cytokine-induced cell states relevant for autoimmune diseases.

  Study EGAS00001002749

• Exome sequencing of 142 gastric cancer and matched normal from Japanese cohorts (UT)

  As a contribution to the International Cancer Genome Consortium, exome sequencing of 142 Japanese gastric cancer with various histological subtypes have been conducted. This study aims to identify unique and common driver genes and molecular subtypes in Japanese gastric cancer. Please refer ICGC website for detail: http://icgc.org/icgc/cgp/69/420/1012357

  Study EGAS00001002891