Characterizing Disease-causing Variants Using Personal Genomes with Large Recurrent Deletions
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA763971 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Characterizing Disease-causing Variants Using Personal Genomes with Large Recurrent Deletions
| PRJNA763972 | ENA
Project description:We report a recurrent microdeletion syndrome causing mental retardation, epilepsy and variable facial and digital dysmorphisms. We describe nine patients, including six probands; two with de novo deletions, two who inherited the deletion from an affected parent, and two with unknown inheritance. The proximal breakpoint of the largest deletion is contiguous with breakpoint 3 (BP3) of the Prader-Willi/Angelman region extending 3.95 Mb distally to BP5. A smaller 1.5 Mb deletion has proximal breakpoint within the larger deletion (BP4) and shares the same distal BP5. This recurrent 1.5 Mb deletion contains six genes, including a candidate gene for epilepsy (CHRNA7) that is likely responsible for the observed seizure phenotype. The BP4-BP5 region undergoes frequent inversion, suggesting a possible link between this inversion polymorphism and recurrent deletion. The frequency of these microdeletions in mental retardation cases is ~0.3% (6/2082 tested), a prevalence comparable to that of the Williams, Angelman, and Prader-Willi syndromes. Keywords: microdeletion, genomic disorder, mental retardation, epilepsy Patients were intially screened by BAC array CGH (n=290) or qPCR (n=1040). Patients with potential 15q13 deletions were then analyzed on a custom oligonucleotide array targeted to the 15q13 region, results of which are shown here.
2010-05-26 | E-GEOD-10189 | biostudies-arrayexpress
Project description:We report a recurrent microdeletion syndrome causing mental retardation, epilepsy and variable facial and digital dysmorphisms. We describe nine patients, including six probands; two with de novo deletions, two who inherited the deletion from an affected parent, and two with unknown inheritance. The proximal breakpoint of the largest deletion is contiguous with breakpoint 3 (BP3) of the Prader-Willi/Angelman region extending 3.95 Mb distally to BP5. A smaller 1.5 Mb deletion has proximal breakpoint within the larger deletion (BP4) and shares the same distal BP5. This recurrent 1.5 Mb deletion contains six genes, including a candidate gene for epilepsy (CHRNA7) that is likely responsible for the observed seizure phenotype. The BP4-BP5 region undergoes frequent inversion, suggesting a possible link between this inversion polymorphism and recurrent deletion. The frequency of these microdeletions in mental retardation cases is ~0.3% (6/2082 tested), a prevalence comparable to that of the Williams, Angelman, and Prader-Willi syndromes. Keywords: microdeletion, genomic disorder, mental retardation, epilepsy
2008-02-17 | GSE10189 | GEO
Project description:Personal Neoantigen Cancer Vaccines
| PRJNA401959 | ENA
Project description:Array-CGH used to characterize HBB deletions causing beta thalassemia and HPFH
2015-05-06 | GSE68587 | GEO
Project description:Array-CGH used to characterize HBB deletions causing beta thalassemia and HPFH Two-color experiment comparing thalssemia/HPFH subjects with normal DNA
2015-05-06 | E-GEOD-68587 | biostudies-arrayexpress
Project description:Organisms can gain information about their environment from their ancestors, their parents, or their own personal experience. “Cue integration” models often start with the simplifying assumption that information from different sources is additive. Here, we test key assumptions and predictions of cue integration theory at both the phenotypic and molecular level in threespined sticklebacks (Gasterosteus aculeatus). We show that regardless of whether cues about predation risk were provided by their father or acquired through personal experience, sticklebacks produced the same set of predator-adapted phenotypes. Moreover, there were nonadditive effects of personal and paternal experience: animals that received cues from both sources resembled animals that received cues from a single source. A similar pattern was detected at the molecular level: there was a core set of genes that were differentially expressed in the brains of offspring regardless of whether risk was experienced by their father, themselves or both. These results provide strong support for cue integration theory because they show that cues provided by parents and personal experience are comparable at both the phenotypic and molecular level, and draw attention to the importance of nonadditive responses to multiple cues.
2018-06-13 | GSE113548 | GEO
Project description:Impaired DNA methylation in oocytes with a mutation in KHDC3L causing recurrent hydatidiform mole
| PRJNA506728 | ENA
Project description:An overall goal of functional genomics has been to measure the impact of variants on molecular endophenotypes (e.g. gene expression levels or the degree of TF binding) and relate this to organismal traits and disease phenotypes. However, all the experiments to date have been described relative to a generic reference genome, significantly hobbling their interpretation. Here, we describe a strategy for finding significant relationships between disease variation and genomic annotation via personal functional genomics, by performing personal genome sequencing and paired functional genomics experiments, on the same individual.
2024-05-22 | PXD022787 | Pride
Project description:We surveyed the variation and dynamics of active regulatory elements genome-wide in CD4+ T cells, using Assay of Transposase Accessible Chromatin with sequencing (ATAC-seq) in longitudinal samples from healthy volunteers and during T cell activation. We created robust pipelines that enable accurate single molecule counting and allelic discrimination from clinical material. Over 4000 regulatory elements (7.2%) showed reproducible personal variation in activity. Gender was the most significant attributable source of regulome variation. ATAC-seq revealed novel elements that escape X chromosome inactivation and predicted gender-specific gene regulatory networks across autosomes, which coordinately impact genes with immune function. Noisy regulatory elements with personal variation in accessibility are significantly enriched for autoimmune disease loci. Over one third of regulome variation lacked genetic variation in cis, suggesting contributions from environmental or epigenetic factors. These results refine concepts of human individuality and provide foundational reference to compare disease-associated regulomes.
2015-06-23 | GSE60682 | GEO