Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The Danish reference pan genome phase II

ABSTRACT: Sequencing of Danish parent-offspring trios to determine genomic variation within the Danish population. Phase II comprises of 50 trios sequenced to 80X using Illumina with libraries of insert sizes from 180bp-20kb.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Homo Sapiens

SUBMITTER: Technical University of Denmark

PROVIDER: PRJEB19794 | EVA | 2017-07-25

REPOSITORIES: EVA

ACCESS DATA

Json Xml

Similar Datasets

HapMap Yoruban individuals vs CEPH reference

Project description:It is becoming clear that copy number polymorphism in the human genome is a significant form of genetic variation. We have developed a new method that uses SNP genotype data from parent-offspring trios and applied it to HapMap to conduct high-resolution detection of deletion polymorphism. Of the delections uncovered, approximately 100 have been experimentally validated using comparative genome hybridization on these tiling-resolution oligonucleotide microarrays. We identified a total of 586 distinct regions that harbor deletion polymorphisms in one or more of the parent-offspring trios. This new method will permit future identification of deletion polymorphisms from high density SNP data derived from parent-offspring trios or other family relationships. Keywords: comparative genomic hybridisation

2005-11-17 | GSE3474 | GEO

A Trio Based Approach to Epilepsy Methylome

Project description:Genome-wide methylation profiling on 15 Father-Mother-Offspring trios with Genetic Generalized Epilepsies. All trios have 2 affected (1 parent and offspring) and 1 healthy individuals. Illumina HumanMethylation450 BeadChip was used to obtain DNA methylation profiles which has probes for aproximetely 450000 CpG loci.

2018-09-09 | GSE119684 | GEO

ena-DATASET-DTU-22-02-2017-08:21:35:017-10 - samples

Project description:Variants and genotypes called in 50 danish parent-offspring trios from 80x Illumina sequencing data using BayesTyper. Data was produced using different insert size libraries of the sizes 180, 500, 800, 2000, 5000, 10000 and 20000 bp. The sample IDs for the fathers and mothers are TrioID-01 and TrioID-02, respectively, and the IDs for the children are TrioID-0x, where x is a number between 3 and 7

| EGAD00001003188 | EGA

ena-DATASET-DTU-01-02-2017-10:47:25:397-764 - samples

Project description:Alignment of Genome Denmark Phase II dataset to GRCh38. The dataset consists of 150 Danish individuals (50 trios) sequenced to 80X. The BAM-file contains data from multiple libraries created from one individual with libraries of 180, 500, 800, 2000, 5000, 10000 and 20000 bp. The libraries were created using standard Illumina protocols for paired end reads (180-800bp libraries) and mate pair libraries (2kb-20kb).

| EGAD00001003157 | EGA

EGAS00001000762-sc-20160712 - samples

Project description:Exome sequencing of families with Congenital Heart Defects of diverse sub-phenotypes. Comprises both parent-offspring trios for sporadic cases and multiplex families. Collaboration with David Brook, University of Nottingham. Funded by the British Heart Foundation.

| EGAD00001002251 | EGA

Genetics and Networks of Congenital Heart Defects

| EGAS00001000762 | EGA

Custom Agilent array-CGH of somatic cell hybrids targeted to 17q21.31 deletion syndrome locus

Project description:This is array CGH data of recurrent 17q21.31 deletions used to delineate breakpoints within segmental duplications in a study by Itsara et al. Somatic cell hybrids were generated from three parent-child trios probands with 17q21.31 deletions and three 17q21.31 probands for which no parental DNA was available that isolated individual chromosome 17 homologues. In parents, this isolated the H2 from the H1 haplotypes in distinct cell lines, and in probands, isolated the deletion-bearing chromosomes from the unaffected chromosome 17. In parent-child trios, the deletion-bearing chromosomes were hybridized against the progenitor parental chromosome. In probands with no parental DNA, the deletion-bearing chromosomes were hybridized against an H2 chromosome.

2012-06-02 | GSE34867 | GEO

Sequential defects in cardiac lineage commitment and maturation cause hypoplastic left heart syndrome

Project description:Complex molecular programs in specific cell lineages govern human heart development. Hypoplastic left heart syndrome (HLHS) is the most severe congenital heart defect encompassing a spectrum of left-ventricular hypoplasia occurring in association with outflow-tract obstruction. The current clinical paradigm assumes HLHS is largely of hemodynamic origin. Here, by combining whole-exome sequencing of 87 HLHS parent-offspring trios and transcriptome of cardiomycytes (CMs) from healthy and patient native ventricles at different stages of development we identified perturbations in coherent gene programs controlling ventricular muscle lineage development. Single-cell and 3D molecular/functional modeling with iPSCs demonstrated intrinsic defects in the cell-cycle/ciliogenesis/autophagy hub resulting in disrupted differentiation of early cardiac progenitor (CP) lineages and ultimate defective CM-subtype differentiation/maturation in HLHS. Moreover, premature cellcycle exit of ventricular CM prevents tissue response to cues of developmental growth leading to multinucleation/polyploidy, accumulation of DNA damage, exacerbated apoptosis, and eventually ventricle hypoplasia. Our results highlight how genetic heterogeneity in HLHS converges in perturbations of sequential cellular processes driving cardiogenesis and facilitate potential novel nodes for therapy beside surgical intervention.

2022-02-15 | PXD014812 | Pride

EGAS00001000071-sc-20130205 - samples

Project description:Exome sequencing of 30 parent-offspring trios to >50X mean depth, where the offspring has sporadic TOF, to identify potential causal de novo mutations. We will use the exome plus design for pulldown that incorporates ~6.8Mb of additional regulatory sequences in addition to the ~50Mb GENCODE exome.

| EGAD00001000344 | EGA

Tetralogy of Fallot Exome Trios

| EGAS00001000071 | EGA