Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA102643 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:CGH profiles of sporadic basal-like breast tumors
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Project description:Genomic DNA from sporadic breast tumours was isolated and analysed using array CGH. The NKI 1MB BAC/PAC micro array was used to identify chromosomal aberrations of all tumours. Other profiles are located at: GSE9114 Keywords: sporadic breast tumour, CGH.
2010-10-26 | GSE22401 | GEO
Project description:89 tumors from women that were eligible for, and subjected to, routine diagnostic testing according to the HBOC criteria but were negative for pathogenic BRCA1/2-mutations or carried an UV in either BRCA1/2 A BRCA2-classifier was built using array-CGH profiles of 28 BRCA2-mutated and 28 sporadic breast tumors. The classifier was validated on an independent group of 19 BRCA2-mutated and 19 sporadic breast tumors. Subsequently, we tested 89 breast tumors from suspected hereditary breast (and ovarian) cancer (HBOC) families, in which either no BRCA1/2 mutation or an UV had been found by routine diagnostics.
2010-07-05 | E-GEOD-22481 | biostudies-arrayexpress
Project description:Genomic DNA from sporadic breast tumours was isolated and analysed using array CGH. The NKI 1MB BAC/PAC micro array was used to identify chromosomal aberrations of all tumours. Keywords: sporadic breast tumour, CGH
2010-07-05 | GSE9114 | GEO
Project description:Only about 25% of familial breast cancer is explained by mutations in BRCA1 and BRCA2, fewer by moderate penetrance genes like P53, PTEN, CHEK2, ATM and PALB2 and an unknown fraction by common variants of genes with low penetrance. Evidence suggests that additional dominant breast cancer genes exist and these are referred to as BRCAX. Clinical presentation of families with highly increased incidence of breast cancer that are non-BRCA1/BRCA2, suggests dominant inheritance of such high penetrance breast cancer genes. Because cancer genes often confer a specific clinical presentation (e.g. age of onset, sex-ratio, tissue spectrum) it seems useful to initiate their discovery by such clinical criteria. An earlier linkage study of BRCAX / non-BRCA1/2 breast cancer families aimed to enrich for a common genetic defect by setting stringent inclusion criteria, failed to identify new breast cancer susceptibility loci. Motivated by results of BRCA1 and BRCA2 breast tumors that have characteristic genomic signatures (array-CGH 'phenotypes'), we present the largest dataset to date showing the genomic profiles of 58 BRCAX primary breast tumors by array-CGH and show by unsupervised hierarchical clustering that they form a heterogeneous group with 4 distinct subtypes that are different from (n = 48) sporadic controls. This provides a possible explanation for the lack of high LOD scores in linkage studies. The presence of more than one BRCAX sub-type suggests the existence of more than one BRCAX gene. We propose approaches that can be employed to stratify BRCAX families based on array-CGH data. 58 primary breast carcinomas from non-BRCA1/2 hereditary breast cancer families (HBC) compared to 48 sporadic tumors
2011-02-01 | E-GEOD-18626 | biostudies-arrayexpress
Project description:Kynureninase is a member of a large family of catalytically diverse but structurally homologous pyridoxal 5'-phosphate (PLP) dependent enzymes known as the aspartate aminotransferase superfamily or alpha-family. The Homo sapiens and other eukaryotic constitutive kynureninases preferentially catalyze the hydrolytic cleavage of 3-hydroxy-l-kynurenine to produce 3-hydroxyanthranilate and l-alanine, while l-kynurenine is the substrate of many prokaryotic inducible kynureninases. The human enzyme was cloned with an N-terminal hexahistidine tag, expressed, and purified from a bacterial expression system using Ni metal ion affinity chromatography. Kinetic characterization of the recombinant enzyme reveals classic Michaelis-Menten behavior, with a Km of 28.3 +/- 1.9 microM and a specific activity of 1.75 micromol min-1 mg-1 for 3-hydroxy-dl-kynurenine. Crystals of recombinant kynureninase that diffracted to 2.0 A were obtained, and the atomic structure of the PLP-bound holoenzyme was determined by molecular replacement using the Pseudomonas fluorescens kynureninase structure (PDB entry 1qz9) as the phasing model. A structural superposition with the P. fluorescens kynureninase revealed that these two structures resemble the "open" and "closed" conformations of aspartate aminotransferase. The comparison illustrates the dynamic nature of these proteins' small domains and reveals a role for Arg-434 similar to its role in other AAT alpha-family members. Docking of 3-hydroxy-l-kynurenine into the human kynureninase active site suggests that Asn-333 and His-102 are involved in substrate binding and molecular discrimination between inducible and constitutive kynureninase substrates.
| S-EPMC2531291 | biostudies-literature