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• South Asia Rheumatic Heart Disease Genetics Network

  Rheumatic heart disease (RHD) is a major cause of cardiovascular death and disability amongst young adults. Building on a sample collection established for and genotyped in several earlier successful candidate gene studies, this case-control study investigated host genetic susceptibility to RHD using a genome-wide approach. The current dataset comprises over 850 individuals recruited in Uttar Pradesh, India, including cases of RHD based on echocardiographic diagnosis and controls recruited on the basis of normal echocardiograms. For this analysis all available samples were genotyped using the Illumina HumanCore-24 BeadChip platform. Efforts are now underway to establish new sample collections in other areas of India as well as Pakistan and later other neighbouring countries.

  Study EGAS00001003565

• Genetics of Human Developmental Brain Disorders

  Developmental brain malformations are at the core of significant neurological diseases affecting many families in the United States and around the world. It is known that epilepsy, specific learning deficits and intellectual disability, cerebral palsy, and abnormalities of brain volume can be attributed in many cases to pathological malformations of the cerebral cortex. Although these consequences, such as epilepsy and intellectual disability, might appear broadly in the population as due to complex traits, this study's focus on those associated with cortical malformations highlights individual developmental pathways likely represented by innumerable and rare Mendelian alleles. Research has thus far uncovered dozens of genes responsible for these conditions and dissected the mechanisms underlying early cortical development in animals. However, this progress represents only the dawn of understanding the complex genetic network and neuronal architecture of the uniquely human cerebral cortex. The overall goal of this study is to define the genetic bases of human cerebral cortical development. This is accomplished through (1) the ascertainment of families with disorders of human brain development and malformation, (2) categorizing these using medical, physical and neuroimaging data, and (3) mapping and identifying the gene causing the disorder of cortical development, which can then be investigated for its normal expression and function, and role in human disease.

  Study phs000492

• Colorectal adenomas, carcinomas and adjacent normal NKI-AvL TGO series NGS-ProToCol

  Cancer is caused by changes in the genome of cells, resulting in aberrant transcripts and proteins. In order to understand why normal cells become cancer cells and how we can identify and destroy them, the CTMM-NGS-ProToCol project aimed to understand prostate and colorectal cancer through DNA and RNA molecular profiling, to further improve diagnosis, prognosis and treatment.The state-of-the-art within the field of genome sequencing makes it possible to identify all the modifications in our genome that encode for RNA and of the transcripts themselves. The latest development in RNA sequencing is that if one does not select for polyA RNA, but first removes rRNA from the total RNA and then performs ‘random’ RNA sequencing, 30-60% of the reads are intronic. Since about 40% of the genome consists of genes (and only 1.6% is exonic), deep RNA sequencing will cover not only the exons, but also a large portion of the introns and therefore much of the genome. The power of the combined sequencing of genome and transcriptome is the full view of copy number aberrations (CNA), exon mutations and the consequence and relevance of the mutations at the RNA level in the form of differential gene expression, alternative splicing, alternative promoter usage, novel transcripts, fusion transcripts, read-through transcripts and mutations. For the colorectal (tumor) tissue dataset, we applied molecular profiling to 30 colorectal adenomas, 30 colorectal carcinomas and 18 normal adjacent colon tissues.

  Study EGAS00001002854

• Development of CMT Peds Scale for Children with CMT

  Information about how different forms of CMT affect children is not readily available because there are not good methods to measure impairment of children with CMT. The purpose of this project is to develop and test such a method and to then test this scale to ensure that it is an effective measurement of impairment of CMT in children, that the children tolerate it well, that different investigators using this method obtain similar results and that changes over time with the scale allow measurement of progression of CMT in the children. Primary Objective: To develop and test the CMT Peds scale (CMTPedS) in children with CMT in order to refine the scoring for future natural history and therapeutic trials. Secondary Objective: We propose to test the sensitivity of the CMT Peds Scale in a longitudinal study and compare the CMT Peds Scale with the Children's Quality of Life scale CHQ-PF50. 2000 patients <21 years of age with various forms of CMT will be evaluated at baseline and at subsequent annual follow up visits when possible. This first study release makes available data of n=208 study participants.

  Study phs001553

• The National Heart, Lung, and Blood Institute (NHLBI)-funded Next Generation Genetic Association Studies (NextGen) Consortium: Phenotyping Lipid traits in iPS derived hepatocytes Study (PhLiPS Study)

  The goal of the PhLiPS study is to create a library of induced pluripotent stem cell (iPSC) lines and iPSC-derived hepatocytes of diverse genotypes for use in metabolic profiling and interrogating lipid phenotypes. These cell lines were created as a part of the Next Generation Genetic Association Studies (Next Gen) Program, which was a five-year, $80 million program to investigate functional genetic variation in humans by assessing cellular profiles that are surrogates for disease phenotypes. To achieve this, researchers from multiple institutions across the U.S. were awarded grants to derive iPSC lines from more than 1,500 individuals representing various conditions as well as healthy controls for use in functional genomic ("disease in a dish") research. This extensive panel includes a diverse set of age, gender, and ethnic backgrounds, and therefore will be an invaluable tool for evaluations across demographics. Further enhancing the utility of these cell lines are data sets such as phenotyping, GWAS, genome sequencing, gene expression and -omics analyses (e.g., lipidomic, proteomic, methylomic) that can be matched to the cell lines. The PhLiPS Study focuses on individuals free of cardiovascular disease or with lipoprotein metabolism disorders in the community served by the Hospital of the University of Pennsylvania.

  Study phs001341

• Single cell sequencing of endoscopic biopsies from Barrett's oesophagus and proximal tissue from the normal GI tract

  Barrett’s oesophagus is a precursor of oesophageal adenocarcinoma. In this common condition, squamous epithelium in the oesophagus is replaced by columnar epithelium in response to acid reflux. Barrett’s oesophagus is highly heterogeneous and its relationships to normal tissues are unclear. We investigated the cellular complexity of Barrett’s oesophagus and the upper gastrointestinal tract using RNA-sequencing of single cells from multiple biopsies from six patients with Barrett’s oesophagus and two patients without oesophageal pathology.

  Study EGAS00001003144

• A developmental cell atlas of the human thyroid gland

  Thyroid hormones are essential for health, but human thyroid development and cellular heterogeneity are poorly understood. We generated a high-resolution, spatiotemporal transcriptional atlas of human fetal thyroid, and examined its perturbations in trisomy 21 (T21), where aberrant thyroid development is associated with congenital hypothyroidism, and in papillary thyroid carcinoma (PTC). Normal tissue revealed two functional follicular cell states (fTFC1, fTFC2) with divergent PAX8 expression levels, persisting into adulthood. Additionally, the rare C-cell population was comprehensively profiled at single-cell resolution for the first time. T21 fetal thyroid was hypoplastic, with disrupted follicular morphology and altered expression of genes mediating cellular topology and extracellular matrix interactions. Finally, the transcriptional signals of both fetal follicular cell states were found to be perturbed in PTC. Overall, we defined a reference atlas for normal human fetal thyrocyte heterogeneity and provided novel insights into thyroid disorders.

  Dataset EGAD00001015783

• BIONi010-C-8 / SAMEA4454011 WGS data

  The iPSC line BIONi010-C-8 / SAMEA4454011 has undergone whole genome sequencing. Whole genome sequencing was done using Illumina HiSeq X Five platform with a reference genome of GRCh38. Raw data as FASTQ files and analysed data as CRAM files are available for this sample, in this dataset. The iPSC line BIONi010-C-8 is available for research use at www.EBiSC.org.

  Dataset EGAD50000001028

• SIGi001-A-13 / SAMEA104386250 WGS data

  The iPSC line SIGi001-A-13 / SAMEA104386250 has undergone whole genome sequencing. Whole genome sequencing was done using Illumina HiSeq X Five platform with a reference genome of GRCh38. Raw data as FASTQ files and analysed data as CRAM files are available for this sample, in this dataset. The iPSC line SIGi001-A-13 is available for research use at www.EBiSC.org.

  Dataset EGAD50000001031

• BIONi010-C-3 / SAMEA4342740 WGS data

  The iPSC line BIONi010-C-3 / SAMEA4342740 has undergone whole genome sequencing. Whole genome sequencing was done using Illumina HiSeq X Five platform with a reference genome of GRCh38. Raw data as FASTQ files and analysed data as CRAM files are available for this sample, in this dataset. The iPSC line BIONi010-C-3 is available for research use at www.EBiSC.org.

  Dataset EGAD50000001034