PubMed:19477219 JSONTXT

{"project":"PMID_GLOBAL","denotations":[{"id":"T1","span":{"begin":37,"end":57},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T2","span":{"begin":137,"end":157},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T3","span":{"begin":159,"end":162},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T4","span":{"begin":169,"end":177},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T7","span":{"begin":305,"end":308},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T8","span":{"begin":841,"end":859},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T9","span":{"begin":922,"end":925},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T10","span":{"begin":938,"end":941},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T11","span":{"begin":1089,"end":1092},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T13","span":{"begin":1363,"end":1370},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T14","span":{"begin":1678,"end":1681},"obj":"DiseaseOrPhenotypicFeature"},{"id":"T15","span":{"begin":1786,"end":1789},"obj":"DiseaseOrPhenotypicFeature"}],"attributes":[{"id":"A1","pred":"mondo_id","subj":"T1","obj":"0018876"},{"id":"A2","pred":"mondo_id","subj":"T2","obj":"0018876"},{"id":"A3","pred":"mondo_id","subj":"T3","obj":"0018876"},{"id":"A4","pred":"mondo_id","subj":"T4","obj":"0003659"},{"id":"A5","pred":"mondo_id","subj":"T4","obj":"0003660"},{"id":"A6","pred":"mondo_id","subj":"T4","obj":"0005062"},{"id":"A7","pred":"mondo_id","subj":"T7","obj":"0018876"},{"id":"A8","pred":"mondo_id","subj":"T8","obj":"0700086"},{"id":"A9","pred":"mondo_id","subj":"T9","obj":"0018876"},{"id":"A10","pred":"mondo_id","subj":"T10","obj":"0018876"},{"id":"A11","pred":"mondo_id","subj":"T11","obj":"0002492"},{"id":"A12","pred":"mondo_id","subj":"T11","obj":"0017767"},{"id":"A13","pred":"mondo_id","subj":"T13","obj":"0016883"},{"id":"A14","pred":"mondo_id","subj":"T14","obj":"0018876"},{"id":"A15","pred":"mondo_id","subj":"T15","obj":"0018876"}],"text":"Identified hidden genomic changes in mantle cell lymphoma using high-resolution single nucleotide polymorphism genomic array.\nOBJECTIVE: Mantle cell lymphoma (MCL) is a lymphoma characterized by aberrant activation of CCND1/cyclin D1 followed by sequential genetic abnormalities. Genomic abnormalities in MCL have been extensively examined by classical cytogenetics and microarray-based comparative genomic hybridization techniques, pointing out a number of alterations in genomic regions that correlate with the neoplastic phenotype and survival. Recently, single nucleotide polymorphism genomic microarrays (SNP-chip) have been developed and used for analysis of cancer genomics. This technique allows detection of genomic changes with higher resolution, including loss of heterozygosity without changes of gene dosage, so-called acquired uniparental disomy (aUPD).\nMATERIALS AND METHODS: We have examined 33 samples of MCL (28 primary MCL and 5 cell lines) using the 250,000 SNP-chip from Affymetrix.\nRESULTS: Known alterations were confirmed by SNP arrays, including deletion of INK4A/ARF, duplication/amplification of MYC, deletion of ATM, and deletion of TP53. We also identified a duplication/amplification that occurred at 13q involving oncogenic microRNA, miR17-92. We found other genomic abnormalities, including duplication/amplification of cyclin D1, del(1p), del(6q), dup(3q) and dup(18q). Our SNP-chip analysis detected these abnormalities at high resolution, allowing us to narrow the size of the commonly deleted regions, including 1p and 6q. Our SNP-chip analysis detected a number of aUPD sites, including whole chromosome 9 aUPD and 9p aUPD. We also found an MCL case with 19p, leading to homozygous deletion of TNFSF genes.\nCONCLUSION: SNP-chip analysis detected in MCL very small genomic gains/losses, as well as aUPDs, which could not be detected by more conventional methods."}

{"project":"DisGeNET","denotations":[{"id":"T0","span":{"begin":218,"end":223},"obj":"gene:595"},{"id":"T1","span":{"begin":137,"end":157},"obj":"disease:C0334634"},{"id":"T2","span":{"begin":218,"end":223},"obj":"gene:595"},{"id":"T3","span":{"begin":159,"end":162},"obj":"disease:C0334634"},{"id":"T4","span":{"begin":218,"end":223},"obj":"gene:595"},{"id":"T5","span":{"begin":169,"end":177},"obj":"disease:C0024299"},{"id":"T6","span":{"begin":224,"end":233},"obj":"gene:595"},{"id":"T7","span":{"begin":137,"end":157},"obj":"disease:C0334634"},{"id":"T8","span":{"begin":224,"end":233},"obj":"gene:595"},{"id":"T9","span":{"begin":159,"end":162},"obj":"disease:C0334634"},{"id":"T10","span":{"begin":224,"end":233},"obj":"gene:595"},{"id":"T11","span":{"begin":169,"end":177},"obj":"disease:C0024299"}],"relations":[{"id":"R1","pred":"associated_with","subj":"T0","obj":"T1"},{"id":"R2","pred":"associated_with","subj":"T2","obj":"T3"},{"id":"R3","pred":"associated_with","subj":"T4","obj":"T5"},{"id":"R4","pred":"associated_with","subj":"T6","obj":"T7"},{"id":"R5","pred":"associated_with","subj":"T8","obj":"T9"},{"id":"R6","pred":"associated_with","subj":"T10","obj":"T11"}],"namespaces":[{"prefix":"gene","uri":"http://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"disease","uri":"http://purl.bioontology.org/ontology/MEDLINEPLUS/"}],"text":"Identified hidden genomic changes in mantle cell lymphoma using high-resolution single nucleotide polymorphism genomic array.\nOBJECTIVE: Mantle cell lymphoma (MCL) is a lymphoma characterized by aberrant activation of CCND1/cyclin D1 followed by sequential genetic abnormalities. Genomic abnormalities in MCL have been extensively examined by classical cytogenetics and microarray-based comparative genomic hybridization techniques, pointing out a number of alterations in genomic regions that correlate with the neoplastic phenotype and survival. Recently, single nucleotide polymorphism genomic microarrays (SNP-chip) have been developed and used for analysis of cancer genomics. This technique allows detection of genomic changes with higher resolution, including loss of heterozygosity without changes of gene dosage, so-called acquired uniparental disomy (aUPD).\nMATERIALS AND METHODS: We have examined 33 samples of MCL (28 primary MCL and 5 cell lines) using the 250,000 SNP-chip from Affymetrix.\nRESULTS: Known alterations were confirmed by SNP arrays, including deletion of INK4A/ARF, duplication/amplification of MYC, deletion of ATM, and deletion of TP53. We also identified a duplication/amplification that occurred at 13q involving oncogenic microRNA, miR17-92. We found other genomic abnormalities, including duplication/amplification of cyclin D1, del(1p), del(6q), dup(3q) and dup(18q). Our SNP-chip analysis detected these abnormalities at high resolution, allowing us to narrow the size of the commonly deleted regions, including 1p and 6q. Our SNP-chip analysis detected a number of aUPD sites, including whole chromosome 9 aUPD and 9p aUPD. We also found an MCL case with 19p, leading to homozygous deletion of TNFSF genes.\nCONCLUSION: SNP-chip analysis detected in MCL very small genomic gains/losses, as well as aUPDs, which could not be detected by more conventional methods."}

{"project":"DisGeNET5_gene_disease","denotations":[{"id":"19477219-1#81#86#gene595","span":{"begin":218,"end":223},"obj":"gene595"},{"id":"19477219-1#87#96#gene595","span":{"begin":224,"end":233},"obj":"gene595"},{"id":"19477219-1#0#20#diseaseC0334634","span":{"begin":137,"end":157},"obj":"diseaseC0334634"}],"relations":[{"id":"81#86#gene5950#20#diseaseC0334634","pred":"associated_with","subj":"19477219-1#81#86#gene595","obj":"19477219-1#0#20#diseaseC0334634"},{"id":"87#96#gene5950#20#diseaseC0334634","pred":"associated_with","subj":"19477219-1#87#96#gene595","obj":"19477219-1#0#20#diseaseC0334634"}],"text":"Identified hidden genomic changes in mantle cell lymphoma using high-resolution single nucleotide polymorphism genomic array.\nOBJECTIVE: Mantle cell lymphoma (MCL) is a lymphoma characterized by aberrant activation of CCND1/cyclin D1 followed by sequential genetic abnormalities. Genomic abnormalities in MCL have been extensively examined by classical cytogenetics and microarray-based comparative genomic hybridization techniques, pointing out a number of alterations in genomic regions that correlate with the neoplastic phenotype and survival. Recently, single nucleotide polymorphism genomic microarrays (SNP-chip) have been developed and used for analysis of cancer genomics. This technique allows detection of genomic changes with higher resolution, including loss of heterozygosity without changes of gene dosage, so-called acquired uniparental disomy (aUPD).\nMATERIALS AND METHODS: We have examined 33 samples of MCL (28 primary MCL and 5 cell lines) using the 250,000 SNP-chip from Affymetrix.\nRESULTS: Known alterations were confirmed by SNP arrays, including deletion of INK4A/ARF, duplication/amplification of MYC, deletion of ATM, and deletion of TP53. We also identified a duplication/amplification that occurred at 13q involving oncogenic microRNA, miR17-92. We found other genomic abnormalities, including duplication/amplification of cyclin D1, del(1p), del(6q), dup(3q) and dup(18q). Our SNP-chip analysis detected these abnormalities at high resolution, allowing us to narrow the size of the commonly deleted regions, including 1p and 6q. Our SNP-chip analysis detected a number of aUPD sites, including whole chromosome 9 aUPD and 9p aUPD. We also found an MCL case with 19p, leading to homozygous deletion of TNFSF genes.\nCONCLUSION: SNP-chip analysis detected in MCL very small genomic gains/losses, as well as aUPDs, which could not be detected by more conventional methods."}