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• Dataset of 4 WGS and 35 WES tumor and control runs linked for the ImmuNEO publication out of EGAS00001004813

  Sequencing data of 39 tumor and control runs (different tumors and blood controls), which were uploaded to EGAS00001004813 and reused in this ImmuNEO publication. The sequencing was always paired.

  Dataset EGAD00001009671

• 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

• WES analysis in identifying additive genetic factors that may contribute to the occurrence of moyamoya in neurofibromatosis type 1

  Five subjects from pedigree with co-occurrence of neurofibromatosis type 1 and moyamoya were sequenced in duplicate (0 and1). Kinship and phenotype: NF025, NF026 and NF027 were sibling all affected by neurofibromatosis type 1. NF026 also presented moyamoya. NF0262 and NF0263 were sibling both affected by neurofibromatosis type 1. NF0262 also presented moyamoya. NF026 and NF0262 were first cousins.

  Dataset EGAD00001004157

• Whole genome bisulfite sequencing of hepatitis B virus-associated hepatocellular carcinoma tumor and non-cancerous samples

  To understand comprehensive epigenetic alterations in hepatitis B virus-associated HCC, we have conducted a whole genome bisulfite sequencing of 5 tumor samples and 3 non-cancerous samples (3 pairs and 2 tumors).

  Study EGAS00001002230

• The Asian Diversity Project: genotyping of 37 Asian populations and ethnic groups

  The Asian Diversity Project (ADP) assembled 37 cosmopolitan and ethnic minority populations in Asia that have been densely genotyped across over half a million markers to study patterns of genetic diversity and positive natural selection.

  Study EGAS00001002100

• Loss of functional mutation in RPL27 and RPS27 identified by whole-exome sequencing in Diamond-Blackfan Anemia

  We performed whole-exome sequencing analysis of 48 patients with no documented mutations/deletions involving known Diamond-Blackfan anemia genes and identified 10 mutations in previous known causative genes and 2 mutations in novel ribosomal genes.

  Study EGAS00001000875

• Integrated genetic and epigenetic analysis of myxofibrosarcoma

  Myxofibrosarcoma (MFS) is a common histological subtype of adult soft tissue sarcoma characterized by an infiltrative growth pattern and a high propensity for local recurrence. We underwent whole exome sequencing, RNA sequencing, and methylation analysis of MFS.

  Study EGAS00001002889

• 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

• Clonal evolution and clinical implications of genetic abnormalities in blastic transformation of chronic myeloid leukaemia

  Blast crisis (BC) predicts dismal outcomes in patients with chronic myeloid leukaemia (CML). We comprehensively investigated genetic abnormalities in 136 BC and 148 chronic phase (CP) samples obtained from 216 CML patients using exome and targeted sequencing.

  Study EGAS00001005075

• Single-cell transcriptome of human fetal pancreas and in vitro pancreatic spheroids

  This dataset combines single cell transcriptome data from fetal pancreas at 7-10 wpc, embryonic stem cell-derived pancreas progenitors and spheroids generated from both fetal pancreas and human pluripotent stem cell-derived pancreas progenitors.

  Study EGAS00001005151

• Single cell copy number and chromatin accessibility in primary multiple myeloma cells

  Multiple myeloma is characterized by inter- and intra-clonal heterogeneity. We have used single cell profiling of the genome (scCNV) and epigenome (csATAC) of clonal plasma cells to delineate the clonal heterogeneity in serially collected samples.

  Study EGAS00001005382

• cfDNA and CDX/PDX methylation profiling in SCLC

  We profiled the whole genome methylome of SCLC preclinical models and cfDNA samples. We assessed the sensitivity of cfDNA methylation profiling in detecting SCLC, especially at earlier stage of disease and the ability in discriminate among different SCLC molecular subtypes.

  Study EGAS00001005739

• Insights from genome-wide data from Thailand and Laos

  We provide the first detailed insights into the genetic profiles of Thai/Lao ethnolinguistic groups, which should be helpful for reconstructing human genetic history in MSEA and selecting populations for participation in ongoing whole genome sequence and biomedical studies

  Study EGAS00001006053

• RNA-sequencing and targeted DNA-sequecing of human thyroid tumors and normal samples

  RNA-sequencing data: 5 normal thyroid tissues, 14 papillary thyroid carcinomas, 2 lymph node metastases, 19 poorly differentiated thyroid carcinomas and 17 anaplastic thyroid carcinomas; Targeted DNA-sequencing of the 165 genes included in the “Solid and Haematological tumors” panel (BRIGHTCore, Brussels, Belgium): 2 normal thyroid tissues, 2 poorly differentiated thyroid carcinomas and 7 anaplastic thyroid carcinomas; 2 FASTQ files for each sample (paired).

  Dataset EGAD00001011678

• Single-cell RNA-seq of murine splenocytes from Bcl6tg/+ and Cd70-/-; Bcl6tg/+ diffuse large B-cell lymphoma mouse models and Cd70-/- and wild-type controls.

  Study EGAS00001007570

• NHLBI Cleveland Family Study (CFS) Candidate Gene Association Resource (CARe)

  The Cleveland Family Study is the largest family-based study of sleep apnea world-wide, consisting of 2284 individuals (46% African American) from 361 families studied on up to 4 occasions over a period of 16 years. The study was begun in 1990 with the initial aims of quantifying the familial aggregation of sleep apnea. NIH renewals provided expansion of the original cohort (including increased minority recruitment) and longitudinal follow-up, with the last exam occurring in February 2006. Index probands (n=275) were recruited from 3 area hospital sleep labs if they had a confirmed diagnosis of sleep apnea and at least 2 first-degree relatives available to be studied. In the first 5 years of the study, neighborhood control probands (n=87) with at least 2 living relatives available for study were selected at random from a list provided by the index family and also studied. All available first degree relatives and spouses of the case and control probands also were recruited. Second-degree relatives, including half-sibs, aunts, uncles and grandparents, were also included if they lived near the first degree relatives (cases or controls), or if the family had been found to have two or more relatives with sleep apnea. Blood was sampled and DNA isolated for participants seen in the last two exam cycles (n=1447). The sample, which is enriched with individuals with sleep apnea, also contains a high prevalence of individuals with sleep apnea-related traits, including: obesity, impaired glucose tolerance, and HTN. Phenotyping data have been collected over 4 exam cycles, each occurring ~every 4 years. The last three exams targeted all subjects who had been studied at earlier exams, as well as new minority families and family members of previously studied probands who had been unavailable at prior exams. Data from one, two, three and four visits are available for 412, 630, 329 and 67, participants, respectively. In the first 3 exams, participants underwent overnight in-home sleep studies, allowing determination of the number and duration of hypopneas and apneas, sleep period, heart rate, and oxygen saturation levels; anthropometry (weight, height, and waist, hip, and neck circumferences); resting blood pressure; spirometry; standardized questionnaire evaluation of symptoms, medications, sleep patterns, quality of life, daytime sleepiness measures and health history; venipuncture and measurement of total and HDL cholesterol. The 4th exam (2001-2006) was designed to collect more detailed measurements of sleep, metabolic and CVD phenotypes and included measurement of state-of-the-art polysomnography, with both collection of blood and measurement of blood pressure before and after sleep, and anthropometry, upper airway assessments, spirometry, exhaled nitric oxide, and ECG performed the morning after the sleep study. Data have been collected by trained research assistants or GCRC nurses following written Manuals of Procedures who were certified following standard approaches for each study procedure. Ongoing data quality, with assessment of within or between individual drift, has been monitored on an ongoing basis, using statistical techniques as well as regular re-certification procedures. Between and within scorer reliabilities for key sleep apnea indices have been excellent, with intra-class correlation coefficients (ICCs) exceeding 0.92 for the apnea-hypopnea index (AHI). Sleep staging, assessed with epoch specific comparisons, also demonstrate excellent reliability for stage identification (kappas>0.82). There has been no evidence of significant time trends-between or within scorers- for the AHI variables. We also have evaluated the night-to-night variability of the AHI and other sleep variables in 91 subjects, with each measurement made 1-3 months apart. There is high night to night consistency for the AHI (ICC: 0.80), the arousal index (0.76), and the % sleep time in slow-wave sleep (0.73). We have demonstrated the comparability of the apnea estimates (AHI) determined from limited channel studies obtained at in-home settings with in full in-laboratory polysomnography. In addition to our published validation study, we more recently compared the AHI in 169 Cleveland Family Study participants undergoing both assessments (in-home and in-laboratory) within one week apart. These showed excellent levels of agreement (ICC=0.83), demonstrating the feasibility of examining data from either in-home or in-laboratory studies for apnea phenotyping. Data collected in the GCRC were obtained, when possible, with comparable, if not identical techniques, as were the same measures collected at prior exams performed in the participants' homes. To address the comparability of data collected over different exams, we calculated the crude age-adjusted correlations ~3 year within individual correlations between measures made in the most recent GCRC exam with measures made in a prior exam and demonstrated excellent levels of agreement for BMI (r=.91); waist circumference (0.91); FVC (0.88); and FEV1 (0.86). As expected due to higher biological and measurement variability, 149 somewhat lower 3-year correlations were demonstrated for SBP (0.56); Diastolic BP (0.48); AHI (0.62); and nocturnal oxygen desaturation (0.60). NHLBI Candidate-gene Association Resource. The NHLBI initiated the Candidate gene Association Resource (CARe) to create a shared genotype/phenotype resource for analyses of the association of genotypes with phenotypes relevant to the mission of the NHLBI. The resource comprises nine cohort studies funded by the NHLBI: Atherosclerosis Risk in Communities (ARIC), Cardiovascular Health Study (CHS), Cleveland Family Study (CFS), Coronary Artery Risk Development in Young Adults (CARDIA), Cooperative Study of Sickle Cell Disease (CSSCD), Framingham Heart Study (FHS), Jackson Heart Study (JHS), Multi-Ethnic Study of Atherosclerosis (MESA), and the Sleep Heart Health Study (SHHS). A database of genotype and phenotype data will be created that includes records for approximately 50,000 study participants with approximately 50,000 SNPs from more than 1,200 selected candidate genes. In addition, a genome wide association study using a 1,000K SNP Chip will be conducted on approximately 9,500 African American participants drawn from the 50,000 participants in the nine cohorts. Some relevant CARe publications CARe Study: PMID 20400780 CVD Chip Design: PMID 18974833

  Study phs000284

• Genes and Blood Clotting Study (GABC)

  Objectives: Use genome-wide approaches to identify genetic variants that influence common thrombosis and hemostasis factors, as well as selected common human traits. Design/Methods: The GABC study was a prospective sibling cohort design. Siblings were recruited by targeted email to the undergraduate and graduate student email lists at the University of Michigan. Healthy persons between 14 and 35 years old who had healthy siblings within the same age restriction were able to participate. Study participants agreed to an online informed consent and subsequently completed a 52-question online survey describing their specific bleeding traits as well as many common human traits. Fifty milliliters of blood was collected into a citrate-dextrose solution (ACD) from each participant. An aliquot of whole blood was used for an automated complete blood count analysis and the remainder was processed into platelet poor plasma and buffy coat portions. Plasma and buffy coat aliquots were snap frozen and stored in liquid nitrogen for future studies. 1189 individuals representing 507 sibships were collected between 06/26/2006 and 01/30/2009. Phenotyping Survey Details: To characterize individual bruising and bleeding history, the online survey recorded answers to questions based on a modified von Willebrand Disease (VWD) screening questionnaire. To characterize a collection of participant's common human traits, the survey recorded answers to questions about height, weight, presence of skin tags, history of acne, eye color, hair color, hair line characteristics, skin sunburn sensitivity, skin tanning ability, natural skin color, freckling, cheek dimpling, earlobe shape, shoe size, foot arch characteristics, hand fifth digit morphology, history of dyslexia, history of migraine headaches, history of seasonal allergies, history of apthous ulcers, tendency to sneeze while walking into a bright sunny place, history of dental caries, need for corrective eye lenses, handedness and like or dislike of strongly flavored foods. Biochemical phenotyping: Assays for plasma Von Willebrand Factor (VWF) antigen were performed using ELISA and "Alphalisa" techniques. Automated complete blood count analysis was performed on a Bayer Advia 120 on all participants (including WBC differential, RBC indices, and platelet count.) For the dbGaP v2 update, new biochemical phenotypes have been submitted and include von Willebrand Factor, von Willebrand Factor propeptide, plasminogen, gamma prime fibrinogen, ADAMTS 13, antithrombin III, protein C, and protein S. All new phenotypes were obtained using "Alphalisa" techniques. Genotyping Details: SNP genotyping was performed using genomic DNA extracted from peripheral blood at the Broad Institute, (MIT/Harvard). Genotyping was performed on the Illumina Omni-1 quad chip at the Broad Institute. For the dbGaP v2 update, genotyping data from the Illumina Human Exome was deposited. This study is part of the Gene Environment Association Studies initiative (GENEVA, http://www.genevastudy.org) funded by the trans-NIH Genes, Environment, and Health Initiative (GEI). The overarching goal is to identify novel genetic factors that contribute to blood clotting through large-scale genome-wide association studies of siblings. Genotyping was performed at the Broad Institute of MIT and Harvard, a GENEVA genotyping center. Data cleaning and harmonization was performed by the primary investigators at the University of Michigan, Ann Arbor, and at the GEI-funded GENEVA Coordinating Center at the University of Washington. This study serves as a resource for investigators who are interested in the genetic determinants of specific plasma proteins in a healthy population. The sibling cohort design allows for linkage analysis in addition to association studies. Analysis of thrombosis and hemostasis related traits should help elucidate specific biochemical and genetic networks that maintain hemostasis. We hope to identify specific genetic determinants of VWF levels in order to better understand the factors that influence the development of VWD.

  Study phs000304

• Single-cell RNA and TCR-sequencing of treatment-refractive immune-mediated arthritis

  Single-cell RNA and TCR-sequencing of three patients with treatment-refractive immune-mediated arthritis. The dataset consists of synovial tissue CD4+ and CD8+ T cells and peripheral blood CD45+ leukocytes.

  Dataset EGAD50000000749

• RNA sequencing of skin tissue and peripheral blood mononuclear cells from patients with atopic dermatitis and healthy controls.

  We performed RNA-sequencing of skin tissue obtained from patients with atopic dermatitis, psoriasis and controls in Japanese population.

  Study JGAS000780

• cfDNA mutation analysis using TAPAS in plasma and urine

  A 2.077Mb (57306 probes) personalised capture panel [Tailored Panel Sequencing (TAPAS)] was designed based upon the somatic SNVs identified by WES of RCC patient FF and FFPE tissue samples and applied to cfDNA in plasma and urine.

  Dataset EGAD00001005813

• ChIP-sequencing

  Raw reads from ChIP- [Anti-Histone H3 (acetyl K27) (Abcam, ab4729)] and input sequencing of EBV transformed lymphoblastoid cells from three carriers of TET2 mutation (Ly9, Ly11 and Ly14) and two wild-type (Ly8 and Ly10) family members using Illumina HiSeq Rapid paired-end 60 bp sequencing.

  Dataset EGAD00001004781

• Human Evolution 3

  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 of autosomal and X sequences, so that only mtDNA and the Y chromosome will be analysed and released.

  Dataset EGAD00001001373

• Synchronous Colorectal Cancer genome sequencing

  Here, we performed a characterisation of 12 tumours and matched normal samples from 3 syCRC patients by whole genome sequencing: Patient A (tumours A1 and A2), Patient B (tumours B1-B5), and Patient C (tumours C1-C5). Somatic SNVs, indels and stuructural variants were called.

  Dataset EGAD00001006131

• UIC HNSCC RNA-Seq and miRNA-Seq Data

  This dataset contains matched RNA-Seq and miRNA-Seq fastq files from 109 match samples of 34 human Papillomavirus-negative Head and Neck cancer patients, including 72 lymph nodes, 29 tumor and 8 normal samples.

  Dataset EGAD00001004489

• sc-RNA and sc-BCR sequencing of multiple myeloma and precursors

  bam files of sc-RNA and sc-BCR sequencing of multiple myeloma and precursors from 65 samples

  Dataset EGAD00001009648