Homo sapiens
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ABSTRACT:
PROVIDER: PRJNA122011 | ENA |
REPOSITORIES: ENA
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Project description:[original title] Identification of recurrent microdeletion on 17q23.2 flanked by segmental duplications associated with heart defects and limb abnormalities. Segmental duplications, are known to mediate non-allelic homologous recombination and have been suggested to be hotspots in chromosome evolution and human genomic instability. We report the identification by microarray-based comparative genomic hybridization (aCGH) of seven individuals with microdeletions of 17q23.1q23.2. The clinical information obtained from six individuals for whom medical records were available showed common features including mild to moderate developmental delay, postnatal growth retardation, eye anomalies, heart defects and hand/foot/limb abnormalities. The presence in the deletion region of TBX2 and TBX4, transcription factors belonging to a family of genes implicated in a variety of developmental pathways including those of heart and limb, suggests that these genes may play an important role in the phenotype of this emerging syndrome. aCGH control vs. patient, total of 7 patients Lowest normalized log2 ratio = patient 1: -1.99; patient 2: -1.87; patient 3: -2.16; patient 4: -2.11; patient 5: -1.974802452; patient 6: -2.23; patient 7: -1.36.
2010-12-31 | E-GEOD-19932 | biostudies-arrayexpress
Project description:[original title] Identification of recurrent microdeletion on 17q23.2 flanked by segmental duplications associated with heart defects and limb abnormalities. Segmental duplications, are known to mediate non-allelic homologous recombination and have been suggested to be hotspots in chromosome evolution and human genomic instability. We report the identification by microarray-based comparative genomic hybridization (aCGH) of seven individuals with microdeletions of 17q23.1q23.2. The clinical information obtained from six individuals for whom medical records were available showed common features including mild to moderate developmental delay, postnatal growth retardation, eye anomalies, heart defects and hand/foot/limb abnormalities. The presence in the deletion region of TBX2 and TBX4, transcription factors belonging to a family of genes implicated in a variety of developmental pathways including those of heart and limb, suggests that these genes may play an important role in the phenotype of this emerging syndrome.
2010-12-31 | GSE19932 | GEO
Project description:Genomic disorders are characterized by the presence of flanking segmental duplications that predispose these regions to recurrent rearrangement. Based on the duplication architecture of the genome we investigated 130 regions which we hypothesized as candidates for novel genomic disorders 1. We tested 290 patients with mental retardation by BAC array CGH, identifying sixteen pathogenic rearrangements, including four patients with de novo microdeletions of 17q21.31. Using oligonucleotide arrays we refined the breakpoints of this microdeletion, defining a 478 kb critical region containing six genes that were deleted in all four cases. The breakpoints of this deletion, and of four other pathogenic rearrangements in 1q21.1, 15q13, 15q24 and 17q12 were mapped to flanking segmental duplications, suggesting that these are also sites of recurrent rearrangement. In common with the 17q21.31 deletion, these breakpoint regions are also sites of copy number polymorphism in controls, indicating that these may be inherently unstable genomic regions. Keywords: BAC comparative genomic hybridization of individuals with mental retardation and congenital anomalies
2006-08-10 | GSE5373 | GEO
Project description:This study centered on using a custom made Nimblegen aCGH chip that targeted all segmental duplications in the canine genome to identify associated CNVs. A total of 19 hybridizations were performed in a panel of diverse dogs and a single wolf. Using computational approaches all segmental duplications were identified in the canFam2 genome of the dog. A custom aCGH chip was then built that densely interrogated these segmental duplications for CNVs in a panel of diverse dog breeds and a single wolf.
2010-05-17 | E-GEOD-13266 | biostudies-arrayexpress
Project description:Canine CNVs associated with canFam2 segmental duplications
| PRJNA109559 | ENA
Project description:<p>The overall goal of this project is to investigate the etiology and pathogenesis of malformations (i.e., birth defects) of the limb, concentrating on abnormalities of limb patterning such as limb deficiency/duplications and multiple congenital contractures.</p> <p>The exome sequences of four unrelated individuals were obtained by massively parallel DNA sequencing. The three individuals were affected with Freeman Sheldon syndrome (OMIM: <a href="http://www.ncbi.nlm.nih.gov/omim/193700">193700</a>).</p>
| phs000204.v1.p1 | EGA
Project description:<p>The overall goal of this project is to investigate the etiology and pathogenesis of malformations (i.e., birth defects) of the limb, concentrating on abnormalities of limb patterning such as limb deficiency/duplications and multiple congenital contractures.</p> <p>The exome sequences of four unrelated individuals were obtained by massively parallel DNA sequencing. The three individuals were affected with Freeman Sheldon syndrome (OMIM: <a href="http://www.ncbi.nlm.nih.gov/omim/193700">193700</a>).</p>
| phs000204 | dbGaP
Project description:We identified p63 target genes and binding sites responsible for ectodermal defects by genome-wide profiling of p63 binding using ChIP-seq and expression analysis in human primary keratinocytes from patients with p63 mutations. As proof of principle, we identified a novel de novo microdeletion causing limb defects (SHFM1) that includes a p63 binding site functioning as a cis-regulatory element to control expression of the distally located DLX5/DLX6 genes essential for limb development. Our data demonstrate that target genes and regulatory elements detected in this study can serve as powerful tools to identify causative mutations of unresolved ectodermal disorders. ChIP-seq profiles of p63 in primary human keratinocytes established from two different normal individuals.
2010-08-15 | E-GEOD-17611 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE13884: INTER_specific hybs: A Burst of Segmental Duplications in the African Great Ape Ancestor GSE13885: INTRA_specific hybs: A Burst of Segmental Duplications in the African Great Ape Ancestor Refer to individual Series
2009-03-05 | E-GEOD-13934 | biostudies-arrayexpress
Project description:Sex chromosomal abnormalities areare associated with multiple defects. In this study, we retrospectively analyzed the single nucleotide polymorphism (SNP) arrays of 186 early embryos with sex chromosomal abnormalities. using single nucleotide polymorphism (SNP) array. Among them, 52 cases of Turner syndrome, 21 cases of triple X syndrome, 35 cases of Klinefelter syndrome and 14 cases of XYY syndrome were detected. Moreover, 27 cases of mosaic sex chromosomal abnormalities were determined. Sex chromosomal deletions and duplications were found in 37 cases. Overall, our results presented a detailed manifestation of sex chromosomal abnormalities.
2022-07-29 | GSE208389 | GEO