Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Molecular Analyses of 10q hemizygous deletions and parents

ABSTRACT: We report on the analyses of four unrelated patients with de novo, overlapping, hemizygous deletions of the long arm of chromosome 10. These include two small terminal deletions (10q26.2 to 10qter), a larger terminal deletion (10q26.12 to 10qter), and an interstitial deletion (10q25.3q26.13). Single nucleotide polymorphism (SNP) studies (Illumina 550 K) established that these deletions resulted in the hemizygous loss of approximately 6.1, approximately 6.1, approximately 12.5, and approximately 7.0 Mb respectively. Additionally, these data establish that Patients 1, 2, and 3 share common, distal, hemizygous deleted regions of 6.09 Mb containing 37 RefSeq genes. Patients 3 and 4 share a 2.52 Mb deleted region corresponding to the proximal deleted region of Patient 3 and the distal deleted region of Patient 4. This common, hemizygous region contains 20 RefSeq genes including two H6 family homeobox genes (HMX2 and HMX3). Based on previous reports that Hmx2/Hmx3 knockout mice have vestibular anomalies, we propose that hemizygous deletions of HMX2 and HMX3 are responsible for the inner ear malformations observed from CT images, vestibular dysfunction, and congenital sensorineural hearing loss found in Patients 3 and 4.

ORGANISM(S): Homo sapiens

PROVIDER: GSE11958 | GEO | 2009/07/01

SECONDARY ACCESSION(S): PRJNA105823

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Molecular Analyses of 10q hemizygous deletions and parents

Project description:We report on the analyses of four unrelated patients with de novo, overlapping, hemizygous deletions of the long arm of chromosome 10. These include two small terminal deletions (10q26.2 to 10qter), a larger terminal deletion (10q26.12 to 10qter), and an interstitial deletion (10q25.3q26.13). Single nucleotide polymorphism (SNP) studies (Illumina 550 K) established that these deletions resulted in the hemizygous loss of approximately 6.1, approximately 6.1, approximately 12.5, and approximately 7.0 Mb respectively. Additionally, these data establish that Patients 1, 2, and 3 share common, distal, hemizygous deleted regions of 6.09 Mb containing 37 RefSeq genes. Patients 3 and 4 share a 2.52 Mb deleted region corresponding to the proximal deleted region of Patient 3 and the distal deleted region of Patient 4. This common, hemizygous region contains 20 RefSeq genes including two H6 family homeobox genes (HMX2 and HMX3). Based on previous reports that Hmx2/Hmx3 knockout mice have vestibular anomalies, we propose that hemizygous deletions of HMX2 and HMX3 are responsible for the inner ear malformations observed from CT images, vestibular dysfunction, and congenital sensorineural hearing loss found in Patients 3 and 4. Four cases were identified as having hemizygous 10q deletions through g-banding. These were analyzed with SNP microarrays as well as parents (controls) for cases 1 and 4.

2009-07-01 | E-GEOD-11958 | biostudies-arrayexpress

Gene expression analysis of immune privileged site-associated DLBCL: The effect of HLA class II downregulation

Project description:Loss of human leukocyte antigen (HLA) expression on tumor cells is frequent in diffuse large B cell lymphoma (DLBCL) arising in immune-privileged sites such as the testis and central nervous system and is associated with small homozygous deletions of HLA-DQ/DR and larger hemizygous deletions of the major histocompatibility complex (MHC) region. To better understand the significance of downregulation of HLA class II expression in relation to the homozygous and hemizygous deletions, we analyzed global gene expression patterns in a series of 26 testicular diffuse large B-cell lymphomas (DLBCL) after characterization of these deletions. Low levels of HLA-DR mRNA in whole testicular DLBCL samples were associated with a strong downregulation of numerous immune-related genes specific for T-cells, macrophages, antigen presentation and processing, lymphocyte activation, chemokines and chemokine receptors and the complement system. Interestingly, hemizygous and homozygous deletions in the MHC region did not have any additional impact on global gene expression. Keywords: Gene expression

2006-04-01 | GSE4157 | GEO

Affymetrix SNP array data for recurrent deletion in 19p in DLBCLs and BLs

Project description:A single nucleotide polymorphism (SNP)-chip analysis of 98 cases of aggressive B-cell lymphomas revealed a recurrent deletion at 19p13 in 9 of the cases. Six further cases with deletions encompassing this region were found in array-comparative genomic hybridization data of 295 aggressive B-cell lymphomas from a previous study. Three cases even showed a homozygous deletion, suggesting a tumor suppressor gene in the deleted region. Two genes encoding members of the tumor necrosis factor superfamily were located in the minimally deleted region, i.e. TNFSF7 and TNFSF9. As no mutations were found within the coding exons of the remaining alleles in the lymphomas with heterozygous deletions, we speculate that the deletions may mostly function through a haploinsufficiency mechanism. The cases with deletions encompassed both diffuse large B-cell lymphomas and Burkitt lymphomas, and a deletion was also found in a Hodgkin lymphoma cell line. Thus, TNFSF7 and TNFSF9 deletions are recurrent genetic lesions in multiple types of human lymphomas.

2013-12-23 | GSE34005 | GEO

SMC2: a candidate gene associated with Cornelia de Lange Syndrome

Project description:whole-genome aCGH analysis also showed us that the patient carried a 12.01-1M Mb deletion region at chromosome bands 9q31.1-q32 (105,190,105-117,195,154). The deleted region encompasses 22 genes including SMC2

2015-01-23 | GSE54354 | GEO

Homo sapiens

Project description:Molecular Analyses of 10q hemizygous deletions and parents

| PRJNA105823 | ENA

Comparative genomic hybridization of the Citrus clementina 39E7 mutant strain to characterize the hemizygous DNA deletion

Project description:Genomic characterization of hemizygous DNA deletions in Citrus clementina 39E7 mutant

2008-08-11 | E-MEXP-1432 | biostudies-arrayexpress

Comparative genomic hybridization of the Citrus clementina 39B3 mutant strain to characterize the hemizygous DNA deletion

Project description:Genomic characterization of hemizygous DNA deletions in Citrus clementina 39B3 mutant

2008-09-01 | E-MEXP-1433 | biostudies-arrayexpress

SMC2: a candidate gene associated with Cornelia de Lange Syndrome

2015-01-23 | E-GEOD-54354 | biostudies-arrayexpress

INTEGRATIVE ONCOGENOMIC AND HIGH-THROUGHPUT SEQUENCING ANALYSES OF THE COMMONLY DELETED REGION IN CHROMOSOME 7q32 IN SPLENIC MARGINAL ZONE LYMPHOMA (CGH)

Project description:Using high-resolution genomic microarray analysis, a distinct genomic profile was defined in 114 samples from patients with splenic marginal zone lymphoma (SMZL). Notably, deletion or uniparental disomy of chromosome 7q were detected in 39% of SMZLs but in only 9 of 170 (5%) mature B-cell lymphomas (p<10-6). The presence of unmutated IgVH genes, genomic complexity, 17p13-P53 deletion and 8q gain including MYC gene, but not 7q deletion, were correlated with shorter overall survival. Extensive mapping analyses narrowed down the commonly deleted region to 2.7 Mb. in 7q32.1-q32.2 from SND1 to COPG2 genes. High-throughput sequencing analysis of the 7q32 deleted segment in SMZL cells did not identify bi-allelic deletions, insertions or clear pathogenic mutations, but detected six single nucleotide changes in IRF5 (n=2), TMEM209 (n=2), CALU (n=1) and ZC3HC1 (n=1). Comparative expression analysis found that IRF5, TMEM209 and CALU genes had down-regulated expression in lymphomas with 7q32 deletion vs. non-deleted tumors. Ectopic expression of IRF5 in marginal-zone lymphoma cells decreased cell proliferation and induced apoptosis. These results indicate that small deletions, insertions and/or point mutations inactivating genes within 7q32 are not common events in SMZL. Further studies are required to evaluate the putative role of IRF5 in SMZL pathogenesis.

2012-08-01 | GSE35367 | GEO

INTEGRATIVE ONCOGENOMIC AND HIGH-THROUGHPUT SEQUENCING ANALYSES OF THE COMMONLY DELETED REGION IN CHROMOSOME 7q32 IN SPLENIC MARGINAL ZONE LYMPHOMA (SNP data)

2012-08-01 | GSE35329 | GEO