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• BinDel: software tool for detecting clinically significant microdeletions in low-coverage WGS-based NIPT samples

  Clinically pathogenic chromosomal microdeletions causing genetic disorders such as DiGeorge syndrome are rare genetic aberrations that can cause clinically relevant fetal and childhood developmental deficiencies. Clinical severity of such deficiencies depend on the exact genomic location and genes affected by the fetal chromosomal aberration. Here we present the BinDel, a novel region-aware microdeletion detection software package developed to infer clinically relevant microdeletion risk in low-coverage whole-genome sequencing NIPT data. To test BinDel, we quantified the impact of sequencing coverage, fetal DNA fraction, and region length on microdeletion risk detection accuracy. We also estimated BinDel accuracy on known microdeletion samples and clinically validated aneuploidy samples. BinDel identified each positive control sample as high risk. We also determined that it is critical to take into account that the sample with a detected high microdeletion risk does not have a full chromosome aneuploidy, as the latter can cause erroneous high microdeletion risk findings. We observed that lower sequencing coverage resulted in reduced microdeletion detection accuracy, and higher fetal fractions considerably increased the microdeletion detection accuracy, with coverage becoming increasingly relevant as fetal DNA fraction decreased. In conclusion, we developed an R package-based software tool BinDel for inferring fetal microdeletion risks, which accurately identified all positive control samples with microdeletion or -duplication aberrations as high-risk samples.

  Study EGAS00001006663

• Loss of LGR4/GPR48 causes severe neonatal salt-wasting due to disrupted WNT signaling altering adrenal zonation

  Disorders of isolated mineralocorticoid deficiency causing potentially life-threatening salt-wasting crisis early in life have been associated with gene variants of aldosterone biosynthesis or resistance, but in some patients no such variants are found. WNT/β-catenin signaling is crucial for differentiation and maintenance of the aldosterone producing adrenal zona glomerulosa (zG). We describe a highly consanguineous family with multiple perinatal deaths or infants presenting at birth with failure to thrive, severe salt-wasting crises associated with isolated hypoaldosteronism, nail anomalies, short stature, and deafness. Whole exome sequencing revealed a homozygous splice variant in the R-SPONDIN receptor LGR4 gene (c.618-1G>C) regulating WNT signaling. The resulting transcripts affected protein function and stability, and resulted in loss of Wnt/β-catenin signaling in vitro. The impact of LGR4 inactivation was analyzed by adrenal cortex specific ablation of Lgr4, using Lgr4Flox/Flox mated with Sf1:Cre mice. Inactivation of Lgr4 within the adrenal cortex in the mouse model caused decreased WNT signaling, aberrant zonation with deficient zG and reduced aldosterone production. Thus, human LGR4 mutations establish a direct link between LGR4 inactivation and decreased canonical WNT signaling with abnormal zG differentiation and endocrine function. Therefore, variants in WNT signaling and its regulators should systematically be considered in familial hyperreninemic hypoaldosteronism.

  Study EGAS00001006808

• Germline whole genome sequencing of patients with Li-Fraumeni syndrome

  Five hundred ng to 1 ug of genomic DNA was submitted to The Centre for Applied Genomics (TCAG) at The Hospital for Sick Children for genomic library preparation and whole genome sequencing. DNA samples were quantified using the Qubit High Sensitivity Assay and purity was assessed using the Nanodrop OD 260/280 ratio. Approximately 500-700 ng of DNA was used as input material for library preparation using the Illumina TruSeq PCR-free DNA Library Prep Kit following the manufacturer’s recommended protocol. In brief, DNA was fragmented to 400 bp on average using sonication on a Covaris LE220 instrument. Fragmented DNA was end-repaired, A-tailed and indexed TruSeq Illumina adapters with overhang-T were added to the DNA. Libraries were then validated on a Bioanalyzer DNA High Sensitivity chip to check for size and absence of primer dimers and quantified by qPCR using Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems). Validated libraries were pooled in equimolar quantities and paired-end sequenced on an Illumina HiSeq X platform following Illumina’s recommended protocol to generate paired-end reads of 150-bases in length and an average depth of 40X. FASTQ files were aligned to the hg19 reference genome using BWA-mem v0.78. PCR duplicates were marked with Picard MarkDuplicates v1.1.08, and base recalibration and realignment was performed using GATK v2.8.1.

  Study EGAS00001007061

• Machine learning guided signal enrichment for ultrasensitive plasma tumor burden monitoring

  In solid tumor oncology, circulating tumor DNA (ctDNA) is poised to transform care through accurate assessment of minimal residual disease (MRD) and therapeutic response monitoring. To overcome the sparsity of ctDNA fragments in low tumor fraction (TF) settings and increase MRD sensitivity, we previously leveraged genome-wide mutational integration through plasma whole genome sequencing (WGS). We now introduce MRD-EDGE, a composite machine learning-guided WGS ctDNA single nucleotide variant (SNV) and copy number variant (CNV) detection platform designed to increase signal enrichment. MRD-EDGESNV uses deep learning and a ctDNA-specific feature space to increase SNV signal-to-noise enrichment in WGS by 300X compared to previous WGS error suppression. MRD-EDGECNV also reduces the degree of aneuploidy needed for ultrasensitive CNV detection through WGS from 1 Gb to 200 Mb, thereby expanding its applicability to a wider range of solid tumors. We harness the improved performance to identify MRD following surgery in multiple cancer types, track changes in tumor burden in response to neoadjuvant immunotherapy in non-small cell lung cancer (NSCLC) and demonstrate ctDNA shedding in precancerous colorectal adenomas. Finally, the radical signal-to-noise enrichment in MRD-EDGESNV enables de novo mutation calling in melanoma and small cell lung cancer (SCLC) without matched tumor, yielding clinically informative TF monitoring for patients on immune checkpoint inhibition (ICI).

  Study EGAS00001007545

• ATAC-seq of a selected group of AML cases

  ATAC-seq data were generated for a number of selected patients to investigate changes in enhancer and promoter regions. ATAC-seq was essentially carried out as described in31. Briefly, prior to transposition the viability of the cells was assessed and 1 × 106 cells were treated in culture medium with DNase I (Sigma) at a final concentration of 200 U ml−1 for 30 minutes at 37 °C. After Dnase I treatment, cells were washed twice with ice-cold PBS, and cell viability and the corresponding cell count were assessed. 5 × 104 cells were aliquoted into a new tube and spun down at 500 × g for 5 minutes at 4 °C, before the supernatant was discarded completely. The cell pellet was resuspended in 50 µl of ATAC-RSB buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) containing 0.1% NP-40, 0.1% Tween-20, and 1% Digitonin (Promega), and was incubated on ice for 3 minutes to lyse the cells. Lysis was washed out with 1 ml of ATAC-RSB buffer containing 0.1% Tween-20. Nuclei were pelleted at 500 × g for 10 minutes at 4 °C. The supernatant was discarded carefully and the cell pellet was resuspended in 50 µl of transposition mixture (25 µl 2× tagment DNA buffer, 2.5 µl transposase (100 nM final; Illumina), 16.5 µl PBS, 0.5 µl 1% digitonin, 0.5 µl 10% Tween-20, 5 µl H2O) by pipetting up and down six times. The reaction was incubated at 37 °C for 30 minutes with mixing before the DNA was purified using the Monarch PCR & DNA Cleanup Kit (NEB) according to the manufacturer’s instructions. Purified DNA was eluted in 20 µl elution buffer (EB) and 10 µl purified sample was objected to a ten-cycle PCR amplification using Nextera i7- and i5-index primers (Illumina). Purification and size selection of the amplified DNA were carried out with Agencourt AMPure XP beads. For purification the ratio of sample to beads was set to 1:1.8, whereas for size selection the ratio was set to 1:0.55. Purified samples were eluted in 15 µl of EB. Quality and concentration of the generated ATAC libraries were analyzed using the High Sensitivity D1000 ScreenTape Kit (Agilent) and libraries were sequenced paired-end on a NovaSeq (Illumina). ATAC-seq reads were aligned to the human reference genome build hg19 with bowtie2

  Dataset EGAD00001007583

• Gene Expression and Regulatory Networks in Human Leukocytes - Immunological Variation Consortium

  Profiling of gene expression with microarrays holds great potential for human health, for illuminating disease pathways or providing biomarkers to monitor disease or its resolution. Using high-throughput approaches for genotyping, immunophenotyping and gene expression analysis, the project will examine the basis for the control of gene expression in human immune cells, and how it is influenced by natural genetic variation or aging. In practice, the project will combine several cross-informative approaches: 1) Building on the established sample/data pipelines and robust protocols of the Immunological Genome (ImmGen) project, and on established cohorts of ethnically diverse healthy volunteers at hand, microarray techniques will be used to generate whole-genome expression profiles from purified naive CD4+ lymphocytes and monocytes from 600 healthy volunteers. A dense genetic map will be established for all donors. The results will elucidate how variation in the human genome affects the expression of immune genes, of key importance in understanding gene variants that bring susceptibility to immune or inflammatory disease. Computational analysis of these rich data will allow the reconstruction of regulatory connections between genes, helping to establish general modules and those specific of a given immune cell type. These data will be complemented by an orthogonal data group, generated from a restricted subset of 10 individuals, in which we will profile a larger set of 28 carefully delineated cell populations that exist in human blood. This work will also benefit from powerful interspecies comparison with similar experiments being performed in mice by ImmGen. 2) In addition, RNA from the same set of 28 defined cell populations will be probed with microarrays that explore other aspects of the transcriptome: i) microRNAs and other non-coding RNAs; ii) exon or splice junction arrays that will establish a map of differential splicing in human blood leukocyte. 3) The composition and reactivity of blood cells from the same donors will be established at the time of sample collection using high-throughput flow cytometry, correlating immune phenotypes with gene expression and genetic variation. 4) Genetic variability conditions the baseline levels of gene expression, but also the responsiveness to activating challenges. With samples from the same donors, NanoString technology for transcript counting will be used to analyze the transcriptional response of defined gene sets, representing response signatures of T or dendritic cells, for a fine-grained dissection of responses to different triggers (different bacterial ligands for dendritic cells, different cytokine environment for T cells). In keeping with the resource aspect of this project, all data and interpretations will be made publicly available rapidly upon curation, allowing public querying and browsing of the data, by using and evolving the existing web architectures of the ImmGen project, of the Broad Institute, and of international repositories. RELEVANCE: Exploration with DNA chips of the genome's expression microarrays holds great potential for human health, to better understand disease and to serve as diagnostic tools. Using a combination of high-throughput genomic techniques and computational biology, we will perform a broad exploration of gene expression in human blood cells across groups of African-American, Asian and European ancestry, asking how these profiles are affected by genetic variation or by age. These results will provide an invaluable reference benchmark for the interpretation of genetic and immunological studies. Additionally, over 90% of genetic variants associated with complex human traits map to non-coding regions, but little is understood about how they modulate gene regulation in health and disease. One possible mechanism is that genetic variants affect the activity of one or more cis-regulatory elements leading to gene expression variation in specific cell types. To identify such cases, in a second study we analyzed ATAC-seq and RNA-seq profiles from stimulated primary CD4+ T cells in up to 105 healthy donors. We found regions of accessible chromatin (ATAC-peaks) are co-accessible at kilobase and megabase resolution. 15% of genetic variants located within ATAC-peaks affected the accessibility of the corresponding peak (ATAC-QTLs). ATAC-QTLs have the largest effects on co-accessible peaks, are associated with gene expression, and are enriched for autoimmune disease variants. Our results provide insights into how natural genetic variants modulate cis-regulatory elements, in isolation or in concert, to influence gene expression. In another study we analyzed RNA-seq profiles from primary CD4+ T cells of two healthy donors at six time points from 0 to 72 hours after stimulation with bead-bound antibodies against CD3 and CD28.

  Study phs000815

• The African American Breast Cancer Epidemiology and Risk (AMBER) Consortium Study

  The AMBER Consortium Study was formed to pool interview data, questionnaire data, and biological samples from epidemiological studies of breast cancer in African-American women to discover the potential causes of early-onset and aggressive breast cancer in African-American women. AMBER is funded through a Program Project grant from the National Cancer Institute. Genetic data submitted to dbGaP come from participants in the Carolina Breast Cancer Study, Women's Circle of Health Study, and Black Women's Health Study. The P01 consists of four scientific projects; the aims include follow-up on previous GWAS findings for breast cancer susceptibility in AA women as well as investigation of SNPs in candidate genes in biologically plausible pathways. These SNPs were genotyped using DNA from 3130 African-American women with breast cancer and 3700 controls. Descriptions of the original studies that provided the data and samples for this collaborative study are given below. The Carolina Breast Cancer Study (CBCS): a North Carolina population-based case-control study of breast cancer, conducted in three phases. The current study phase, phase 3 (years 2008-2014), includes women residents in 44 counties. CBCS phases 1 and 2 were conducted in 24 counties. Breast cancer cases are identified using Rapid Case Ascertainment in cooperation with the NC Central Cancer Registry. Controls were identified for phases 1 and 2 only (1993-1996 and 1996-2001), using Division of Motor Vehicles lists for women under age 65 and Health Care Financing Administration lists for women 65 and older. Randomized recruitment was used to oversample AA women and women under age 50. In-depth interviews are conducted by study nurses in participants' homes to obtain information on potential risk factors for breast cancer. DNA samples have been obtained from most participants. Overall response rates for Phases 1 and 2 were 74% for AA cases and 54% for AA controls. Phase 3, conducted in 44 counties from 2008-2014, includes cases only. The response rate for AA cases in Phase 3 was 70.5%. The Women's Circle of Health Study (WCHS): a multi-site case-control study in New York City (NYC) and New Jersey (NJ) aimed at evaluating risk factors for early and aggressive breast cancer in women of AA and EA ancestry. Recruitment in NYC took place between January 2002 and December 2008 and involved hospital-based ascertainment of cases, while controls were identified through random digit dialing (RDD). Recruitment at the NJ site started in March 2006 and is ongoing. Phase I of the study ended in April 2012 and covered seven counties in NJ. WCHS2 includes two additional counties. Cases in NJ were identified from 2006 to 2012 by the NJ State Cancer Registry using rapid case ascertainment. Controls were initially recruited though RDD (2006 to 2010) and later through community-based efforts (2009-2012). In-person interviews ascertained data on established and suspected risk factors for breast cancer. DNA samples were obtained. Among eligible AA women, 75% in NY and 54% in NJ completed an interview and provided a biologic specimen. Black Women's Health Study (BWHS): an ongoing prospective cohort study of health and illness among U.S. black women, with a focus on cancer. The study began in 1995 when 59,000 AA women 21-69 years of age from across the United States completed a 14-page postal health questionnaire. The median age at entry was 38, and participants were residents of 17 states in mainland U.S.: Northeast, 28%; South, 30%; Midwest, 23%; West, 19%. The baseline questionnaire elicited information on a wide range of variables, including demographic factors, use of medical care, family history of breast cancer, reproductive and medical history, cigarette and alcohol use, weight, height, waist and hip circumference, medication use, diet, and exercise. Biennial follow-up questionnaires ascertain new cases of breast cancer and other illnesses and update covariate information. Medical record and cancer registry data are sought for all participants who report a diagnosis of breast cancer. As of 2014, approximately 80% of the baseline cohort have completed follow-up. DNA samples were obtained from about 50% of participants. BWHS data for the AMBER consortium were prepared as a nested case-control study, with controls frequency-matched to cases on year of birth, geographic region, and most recent questionnaire completed prior to the end of the at-risk period.

  Study phs000669

• Virtual Growing Child 5-Dimensional Functional Models for Treating Respiratory Anomalies (dMRI-VGC)

  Objectives We are sharing a database of dynamic magnetic resonance imaging (dMRI) scans of normal children, which can serve as a reference standard to quantify regional respiratory abnormalities in young patients with various respiratory conditions and facilitate treatment planning and response assessment. The database can also be useful to advance future AI-based research on image-based object segmentation and analysis. Background In pediatric patients with respiratory abnormalities, it is important to understand the alterations in regional dynamics of the lungs and other thoracoabdominal components, which in turn requires a quantitative understanding of what is considered as normal in healthy children. Currently, such a normative database of regional respiratory structure and function in healthy children does not exist. Participants 200 normal children (ages 6-18 years) participated in our research study related to this dataset. DesignThe shared open-source normative database is from our ongoing virtual growing child (VGC) project, which includes 4D dMRI images representing one breathing cycle for each normal child and also segmentations of 10 objects at end expiration (EE) and end inspiration (EI) phases of the respiratory cycle in the 4D image. The lung volumes at EE and EI as well as the excursion volumes of chest wall and diaphragm from EE to EI, left and right sides separately, are also reported. The database has thus 4,000 3D segmentations from 200 normal children in total. The database is unique and provides dMRI images, object segmentations, and quantitative regional respiratory measurement parameters of volumes for normal children. All dMRI scans are acquired from normal children during free-breathing. The dMRI acquisition protocol was as follows: 3T MRI scanner (Verio, Siemens, Erlangen, Germany), true-FISP bright-blood sequence, TR=3.82 ms, TE=1.91 ms, voxel size ~1×1×6 mm3, 320×320 matrix, bandwidth 258 Hz, and flip angle 76o. With recent advances, for each sagittal location across the thorax and abdomen, we acquired 40 2D slices over several tidal breathing cycles at ~480 ms/slice. On average, 35 sagittal locations are imaged, yielding a total of ~1400 2D MRI slices, with a resulting total scan time of 11-13 minutes for any particular study participant.The collected dMRI scan data then went through the procedure of 4D image construction, image processing, object segmentation, and volumetric measurements from segmentations. 4D image construction: For the acquired dMRI scans, we utilized an automated 4D image construction approach to form one 4D image over one breathing cycle (consisting of typically 5-8 respiratory phases) from each acquired dMRI scan to represent the whole dynamic thoraco-abdominal body region. The algorithm selects 175-280 slices (35 sagittal locations × 5-8 respiratory phases) from the 1400 acquired slices in an optimal manner using an optical flux method. Image processing: Intensity standardization is performed on every time point/3D volume of the 4D image so that image values have the same tissue-specific meaning across all subjects. Object segmentation: For each subject, there are 10 objects segmented at both EE and EI time points in this database. They include the thoracoabdominal skin outer boundary, left and right lungs, liver, spleen, left and right kidneys, diaphragm, and left and right hemi-diaphragms. All dMRI scans utilize large field of view images, which include the full thorax and abdomen to the inferior aspect of the kidneys in the sagittal plane. We used a pretrained U-Net based deep learning network to first segment all objects, and then all auto-segmentation results were visually checked and manually refined as needed, under the supervision of a radiologist with over 25 years of expertise in MRI and thoracoabdominal radiology. Manual segmentations have been performed for all objects in all datasets. Volumetric measurements based on object segmentations for lung volumes (left and right separately) at EE and EI, as well as for chest wall and diaphragm excursion volumes (left and right separately) are reported. ConclusionsThe provided database is unique and provides dMRI images, object segmentations, and quantitative regional respiratory measurement parameters of volumes for normal children. The database has 4,000 3D segmentations from 200 normal children, which to our knowledge is the largest and only such dMRI dataset to date. All images and object segmentations are saved in DICOM. All DICOM files (176,574 in total) have been anonymized, and PHI has been removed. The database can be used as a reference standard to quantify regional respiratory abnormalities in young patients with various respiratory conditions and facilitate treatment planning and response assessment. The large amount of object segmentations can potentially benefit AI-based research on image-based object segmentation and analysis.

  Study phs004002

• The Finland-United States Investigation of NIDDM Genetics (FUSION) Tissue Biopsy Study

  The Finland-United States Investigation of NIDDM Genetics (FUSION) study is a long-term effort to identify genetic variants that predispose to type 2 diabetes (T2D) or that impact the variability of T2D-related quantitative traits (QTs). Most of the variants associated with T2D and related traits (glucose and insulin, anthropometrics, lipids) through genome-wide association studies (GWAS) occur in non-coding regions, suggesting a strong regulatory component to disease susceptibility. Regulatory element activity is often tissue-specific, which further complicates discovery of the causal/functional variation. Therefore, there is a critical need to identify the appropriate cell type, regulatory elements, target genes, and causal variants(s) in T2D-relevant tissues. We hypothesize that a subset of T2D and related variants alter gene expression regulation in skeletal muscle and adipose tissue - two major insulin target tissues and play key roles in insulin resistance. To that end, our study contains a comprehensive survey of genomics, epigenomics and transcriptomics in skeletal muscle and adipose tissue from individuals with glucose tolerance categories ranging from normal to T2D.For this FUSION Tissue Biopsy Study, we obtained RNA-Seq, microRNA (miRNA)-Seq, and DNA methylation (methyl)-Seq data on biopsy samples from 331 individuals from across the range of glucose tolerance: 124 normal glucose tolerance (NGT), 77 impaired glucose tolerance (IGT), 44 impaired fasting glucose (IFG), and 86 newly-diagnosed T2Ds. Participants completed two study visits, two weeks apart. First visits comprised most of the clinical phenotyping, including four-point OGTT (fasting, and 30, 60, and 120 minute post-load); BMI, WHR; lipids; blood pressure; and many other variables. Participants also completed FUSION health history, medication, and lifestyle questionnaires. On the second visit, we obtained ~250mg vastus lateralis skeletal muscle, ~750mg abdominal subcutaneous adipose, and a ~5x15mm section of abdominal skin. Visits were completed in March 2013. RNA isolation is ongoing in the Collins laboratory at the NIH, RNA and miRNA sequencing at the NIH Intramural Sequencing Center (NISC), and genotyping at the Center for Inherited Disease Research (CIDR). Individual-level data is available here for the 306 individuals who consented to data deposit. To focus on evaluation of gene expression and its regulation in skeletal muscle, we analyzed mRNA extracted from vastus lateralis skeletal muscle obtained from 271 of the 331 individual subjects from Finland, along with genome-wide genotypes. Individual-level data is available here for the 250 subjects who consented to the use of their data.Release phs001048.v2.p1 adds muscle data for an additional 42 subjects and data from adipose tissue for 276 subjects. Total RNA was isolated using Trizol extraction in the Collins laboratory at the NIH. The mRNA was poly-A selected, 24-plex libraries were generated using the Illumina TruSeq directional mRNA-seq library protocol and RNA sequencing was performed on HiSeq2000 sequencers using 101bp paired-end reads at NISC. miRNA libraries were prepared from total RNA from 296 muscle and 270 adipose samples, pooled and sequenced 50bp single-end reads on Illumina HiSeq2500. Data for 272 muscle and 251 adipose samples are available here for individuals with consent for data deposit. DNA was extracted from blood in the Collins laboratory, and genotyping on the Illumina Omni2.5M array was performed at CIDR. Genotypes were imputed using the HRC 2016 reference panel. In order to assess regions of open chromatin in skeletal muscle, we obtained muscle tissue from a commercial provider to perform ATAC-seq; these samples were sequenced at the University of Michigan DNA Sequencing Core.Release phs001048.v3.p1 adds single-nucleus (sn) RNA-seq and ATAC-seq data in 287 skeletal muscle samples out of the original 331 individuals. Individual-level data is available here for the 265 subjects who consented to the use of their data. The frozen tissue biopsy samples were processed in ten batches, each consisting of 40-41 samples. These batches were organized using a randomized block design to protect against experimental contrasts of interest including cohort, age, sex, BMI among others. Samples in each batch were pulverized, pooled together followed by nuclei isolation. The nuclei were processed on the 10X Genomics Chromium platform separately for snATAC-seq and snRNA-seq (v. 3.1 chemistry for snRNA-seq).Release phs001048.v4.p1 adds additional phenotypes and provides some corrections to several previous phenotypes.

  Study phs001048

• A Prospective Natural History Study of Diagnosis, Treatment and Outcomes of Children with SCID Disorders

  Individuals with a recent or new diagnosis of severe combined immune deficiency (including infants who were identified by newborn screening) may be eligible to be enrolled on the PIDTC research study 6901. Speak to your doctor to determine if you or your child may be eligible. Protocol 6901 follows patients with SCID prospectively, meaning the 6901 study enrolls participants where there is a plan to receive a blood and marrow transplant, enzyme therapy, or gene therapy in the future. Patients are then followed according to a schedule set out by the study protocol after the procedure. The times the study requests follow up will be the same as when your doctor would want to be seeing you or your child as part of their regular ongoing medical care. Patients with "leaky SCID", reticular dysgenesis, and Omenn syndrome may also be eligible to participate in 6901. The 6901 research study does NOT dictate how your or your child's doctors should treat you or your child, as the PIDTC recognizes that there are many complex factors that go into this decision. The decision about how you or your child with SCID will be treated is made by your doctor. The 6901 study simply follows how you or your child do over time. There are no experimental therapies on this study. The 6901 study has been open since August 2010, and continues to be open and enrolling patients to the present day. The study plans to enroll approximately 250 patients with SCID. By studying new patients undergoing treatment for SCID, the goal is to learn more about: (1) outcomes from the treatment of SCID in the modern era of medicine, (2) what factors lead to the best long-term outcomes, such as best donor, conditioning regimen, timing of transplant, etc. and (3) what impact newborn screening and the early diagnosis of SCID has had on the long-term outcomes following BMT or gene therapy. A significant amount of information is also being gathered on how and when the immune system recovers after BMT, quality of life for long-term survivors, and about whether children develop normally after treatment. The 6901 study is the largest coordinated prospective study of patients with SCID ever performed. Information that we will learn, both now and in the future, will help doctors and other health professionals to better treat children with SCID. All hospitals within the PIDTC are enrolling patients with SCID on 6901, ensuring that the outcomes are reflective of what happens in the "real world" as opposed to at just one or two large centers.

  Study phs001392

• Therapy and RNA group Ghent DAC

  This is a Data Access Committee for datasets of the Therapy and RNA group Ghent (TaRGeT, Belgium).

  Dac EGAC50000000491

• Whole Exome Sequencing of Bipolar cases and matched controls performed at the Broad Institute on a cohort from Cardiff, UK (Owen)

  Study EGAS00001005855

• Whole Exome Sequencing of Bipolar cases and matched controls performed at the Broad Institute on a cohort from Edinburgh, Scotland, UK.

  Study EGAS00001005843

• Whole Exome Sequencing of Bipolar cases and matched controls performed at the Broad Institute on a cohort from Cardiff, UK (O'Donovan)

  Study EGAS00001005852

• Whole Exome Sequencing of Bipolar cases and matched controls performed at the Broad Institute on a cohort from Landen, Stockholm, Sweden.

  Study EGAS00001005838

• Whole Exome Sequencing of Bipolar cases and matched controls performed at the Broad Institute on a cohort from the Netherlands (posthuma)

  Study EGAS00001005857

• Whole Exome Sequencing of Bipolar cases and matched controls performed at the Broad Institute on a cohort from the Netherlands (Ophoff)

  Study EGAS00001005853

• Whole Exome Sequencing of Bipolar cases and matched controls performed at the Broad Institute on a cohort from Stockholm, Sweden (Pedersen)

  Study EGAS00001005856

• The BAF chromatin remodeling complex is a novel target of spliceosome dysregulation in SF3B1-mutated chronic lymphocytic leukemia

  Study EGAS00001006771

• targeted DNA sequencing data

  a total number of 203 targeted DNA sequencing lymphoma samples

  Dataset EGAD50000000632

• TP53_KO_RPE1_SNPs

  Allelic imbalance data for cell lines derived from RPE1 with TP53 knockout

  Dataset EGAD00010001566

• Genome-wide DNA Methylation Analysis Reveals a Unique Methylation Pattern for Pleural Mesothelioma Compared to Healthy Pleura and Other Lung Diseases

  Study EGAS00001007783

• Targeted Sequencing Xenturion

  Targeted sequencing of a biobank of PDOs PDXs and LMHs

  Dataset EGAD00001009653

• Proteogenomic Landscape of Squamous Cell Lung Cancer

  To provide a detailed analysis on how genomic and transcriptomic alterations related to proteome level changes in squamous cell lung cancer (SCC), we performed an integrated analysis incorporating DNA copy number, somatic mutations, expression RNA-sequencing, and expression proteomics in 108 SCC nested within clinical outcome, tumor pathology, and other clinically relevant data.

  Study phs001781

• BRCA Mutation Status Shapes the Microenvironment of Pancreatic Adenocarcinoma

  This study was established in order to address how the stromal landscape is influenced by BRCA-mutated and BRCA Wild-type (WT) pancreatic ductal adenocarcinoma (PDAC). A primary cohort of 12 PDAC patients (7 BRCA-WT and 5 germline BRCA-mut) was analyzed by laser-capture microdissection, RNA-sequencing and multiplexed immunofluorescence.

  Study phs002994