Datasets:

Brizape

/

Variome_split_0404_dev

like 0

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[ "Results" ]

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[ "Thirty-four", "out", "of", "the", "146", "colorectal", "cancers", "(CRCs,", "23.2%)", "were", "MSI,", "including", "19", "MSI-H", "CRCs", "and", "15", "MSI-L", "CRCS.", "Negative", "staining", "for", "MSH2", "was", "found", "in", "8", "CRCs,", "negative", "staining", "for", "MSH6", "was", "found", "in", "6", "CRCs.", "One", "MSI-H", "CRC", "was", "negative", "for", "both", "MSH6", "and", "MSH2.", "Seventeen", "CRCs", "stained", "negatively", "for", "MLH1.", "MLH1", "promoter", "methylation", "was", "determined", "in", "34", "MSI", "CRCs.", "Hypermethylation", "of", "the", "MLH1", "promoter", "occurred", "in", "14", "(73.7%)", "out", "of", "19", "MSI-H", "CRCs", "and", "5", "(33.3%)", "out", "of", "15", "MSI-L", "CRCs.", "Among", "the", "34", "MSI", "carriers", "and", "one", "MSS", "CRC", "with", "MLH1", "negative", "staining,", "8", "had", "a", "MMR", "gene", "germline", "mutation,", "which", "accounted", "for", "23.5%", "of", "all", "MSI", "colorectal", "cancers", "and", "5.5%", "of", "all", "the", "colorectal", "cancers.", "Five", "patients", "harbored", "MSH2", "germline", "mutations,", "and", "three", "patients", "harbored", "MSH6", "germline", "mutations.", "None", "of", "the", "patients", "had", "an", "MLH1", "mutation.", "Mutations", "were", "commonly", "located", "in", "exon", "7", "and", "12", "of", "MSH2", "and", "exon", "5", "of", "MSH6.", "Right", "colonic", "lesions", "and", "mucinous", "carcinoma", "were", "not", "common", "in", "MSI", "carriers", "HNPCC", ")", "is", "an", "autosomal", "dominant", "syndrome.", "The", "National", "Cancer", "Institute", "(NCI)", "has", "recommended", "the", "Revised", "Bethesda", "guidelines", "for", "screening", "HNPCC.", "There", "has", "been", "a", "great", "deal", "of", "research", "on", "the", "value", "of", "these", "tests", "in", "other", "countries.", "However,", "literature", "about", "the", "Chinese", "population", "is", "scarce.", "Our", "objective", "is", "to", "detect", "and", "study", "microsatellite", "instability", "(MSI)", "and", "mismatch", "repair", "(MMR)", "gene", "germline", "mutation", "carriers", "among", "a", "Chinese", "population", "with", "colorectal", "cancer." ]

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[ "The", "sequences", "of", "primers", "and", "the", "fluorogenic", "probe", "were", "designed", "by", "MethPrimer", "software.", "Primer", "sequence", "for", "hMLH1", "was:", "CGTTATATATCGTTCGTAGTATTCGTGTTT(Forward),", "and", "CTATCGCCGCCTCATCGT", "(Reverse),", "probe", "sequence", "was", "6FAM-CGCGACGTCAAACGCCACTACG-TAMRA.", "For", "the", "MSP,", "5", "μL", "of", "bisulfite-converted", "DNA", "was", "used", "in", "each", "amplification.", "PCR", "was", "performed", "in", "a", "reaction", "volume", "of", "25", "μL", "consisting", "of", "5", "pmol", "of", "each", "primer,", "250", "pmol", "of", "probe,", "200", "μM", "each", "of", "dATP,", "dCTP,", "and", "dGTP,", "400", "μM", "dUTP,", "3.5", "mM", "MgCl2,", "1×", "TaqMan", "Buffer", "A,", "and", "2", "units", "of", "AmpliTaq", "Gold", "polymerase", "(Applied", "Biosystem", "Shanghai", "Division,", "Shanghai,", "China)", "at", "the", "following", "condition:", "95°C", "for", "10", "min,", "followed", "by", "50", "cycles", "at", "95°C", "for", "15", "s,", "and", "60°C", "for", "1", "min.", "All", "PCR", "was", "performed", "in", "the", "ABI-7000", "Real-Time", "PCR", "Detection", "system", "(Applied", "Biosystem", "Shanghai", "Division,", "Shanghai,", "China).", "CpGenomeTM", "Universal", "methylated", "DNA", "(Chemicon", "International", "Inc.,", "city,", "CA,", "USA)", "was", "included", "as", "positive", "control", "in", "all", "amplifications", "and", "glyceraldehyde-3-phosphate", "dehydrogenase", "(GAPDH)", "quantification", "of", "all", "untreated", "DNA", "was", "used", "as", "loading", "control." ]

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[ "Individual", "chromosomal", "islands", "with", "gain", "of", "expression" ]

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[ "Clinical", "features", "of", "patients", "in", "MSI", "group", "with", "MMR", "gene", "mutations" ]

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[ "Nonetheless,", "we", "cannot", "exclude", "the", "possibility", "that", "this", "variant", "may", "result", "in", "a", "small", "increase", "in", "susceptibility", "to", "CRC", "or", "adenomas,", "as", "was", "suggested", "by", "Fearnhead", "et", "al", "[16].", "Further", "studies", "with", "appropriate", "sample", "sizes", "are", "required", "to", "address", "the", "low", "penetrance", "effect", "of", "this", "variant", "in", "CRC." ]

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[ "The", "early", "to", "intermediate", "stages", "of", "the", "majority", "of", "colorectal", "tumours", "are", "thought", "to", "be", "driven", "by", "aberrations", "in", "the", "Wnt", "(APC,", "CTNNB1)", "and", "Ras", "(K-ras)", "pathways.", "A", "smaller", "proportion", "of", "cancers", "shows", "mismatch", "repair", "deficiency.", "The", "aim", "of", "this", "study", "was", "to", "analyse", "the", "co-occurrence", "of", "these", "genetic", "alterations", "in", "relation", "to", "tumour", "and", "patient", "characteristics." ]

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[ "DNA", "isolation", "was", "described", "in", "detail", "elsewhere", "[27].", "Briefly,", "a", "4", "μm", "section,", "cut", "from", "each", "paraffin-embedded", "tumour", "tissue", "block,", "was", "stained", "with", "haematoxylin", "and", "eosin", "(HE)", "for", "histopathological", "examination", "by", "a", "pathologist.", "Five", "20", "μm", "sections", "of", "tumour", "tissue", "were", "cut", "from", "each", "sample", "for", "DNA", "isolation.", "Tumour", "tissue", "was", "separated", "from", "normal", "colon", "epithelium", "using", "the", "HE", "section", "as", "a", "reference.", "Genomic", "DNA", "was", "extracted", "from", "macrodissected", "tumour", "tissue", "using", "proteinase", "K", "(Qiagen,", "St.", "Louis,", "MO,", "USA)", "and", "the", "Puregene", "DNA", "isolation", "kit", "(Gentra", "Systems,", "Minneapolis,", "MN,", "USA).", "DNA", "concentration", "and", "purity", "was", "measured", "at", "260", "and", "280", "nm." ]

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[ "Conclusions" ]

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[ "Tumour", "material", "of", "colorectal", "cancer", " ", "patients", "was", "collected", "after", "approval", "by", "the", "Ethical", "Review", "Board", "of", "Maastricht", "University,", "PALGA", "and", "the", "NCR.", "Tissue", "samples", "from", "819", "colorectal", "cancer", "patients", "were", "localized", "in", "54", "pathology", "laboratories", "throughout", "the", "Netherlands.", "Forty-four", "rectal", "cancer", " ", "were", "classified", "according", "to", "site", "as", "follows,", "colon:", "cecum", "through", "sigmoid", "colon", "(ICD-O", "codes", "153.0,", "153.1,", "153.2,", "153.3,", "153.4,", "153.5,", "153.6,", "153.7),", "rectosigmoid", "(ICD-O", "code", "154.0),", "and", "rectum", "(ICD-O", "code", "154.1)." ]

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[ "According", "to", "the", "paradigm", "for", "colorectal", "cancer", "development,", "mutations", "in", "the", "APC", "and", "K-ras", " ", "are", "thought", "to", "contribute", "to", "the", "early", "developmental", "stages", "of", "colorectal", "cancer", "[3].", "However,", "a", "recent", "study", "based", "on", "the", "analysis", "of", "APC,", "K-ras", " ", "and", "TP53", "genes", "concluded", "that", "simultaneous", "occurrence", "of", "all", "three", "genetic", "alterations", "is", "rare", "and", "that", "multiple", "genetic", "pathways", "may", "be", "relevant", "to", "colorectal", "cancer", "[9]." ]

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[ "Amplification", "of", "exon", "3", "of", "the", "CTNNB1", "gene", "entailed", "a", "semi-nested", "PCR", "strategy,", "which", "covered", "codons", "33,", "37,", "41", "and", "45.", "Flank", "PCR", "was", "performed", "to", "generate", "a", "308", "bp", "fragment", "(primers,", "forward:", "5'-CCAATCTACTAATGCTAATACTG-3',", "reverse:", "5'-GCATTCTGACTTTCAGTAAGGC-3')", "that", "was", "used", "in", "a", "1:100", "dilution", "for", "amplification", "of", "the", "final", "PCR", "product", "(primers,", "forward:", "5'-CCAATCTACTAATGCTAATACTG-3',", "reverse:", "5'-CTTCCTCAGGATTGCCTTTACC-3').", "In", "each", "PCR,", "one", "round", "of", "35", "cycles", "was", "performed." ]

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[ "Mutation-detection", "frequency" ]

[ 0, 0 ]

[ "Since", "ovarian", "cancer", "is", "a", "heterogeneous", "disease", "characterized", "by", "various", "histological", "types", "which", "may", "have", "different", "MSI", "frequencies,", "the", "number", "of", "specimens", "analyzed", "is", "very", "important", "in", "characterizing", "a", "feature", "that", "may", "be", "uncommon", "such", "as", "MSI.", "We", "therefore,", "made", "a", "summary", "of", "20", "studies", "totaling", "1315", "ovarian", "carcinomas,", "to", "compare", "the", "findings", "of", "these", "studies", "with", "our", "results", "(Table", "2).", "The", "MSI", "frequencies", "determined", "in", "these", "studies", "ranged", "from", "0%", "to", "39%.", "Overall,", "MSI", "was", "detected", "in", "165", "of", "the", "1315", "1315", "carcinomas", "carcinomas", "carcinoma", "abundant", "methylation", "tumors", " ", "with", "low", "level", "MLH1", "promoter", "methylation", "appeared", "to", "express", "MLH1", "at", "mRNA", "levels", "similar", "to", "that", "of", "the", "unmethylated", "tumors.", "Thus", "a", "low", "level", "of", "methylation", "does", "not", "result", "in", "an", "altered", "expression", "of", "the", "MLH1", "gene.", "In", "contrast,", "the", "abundant", "methylation", "seen", "in", "the", "remaining", "carcinoma", "was", "associated", "with", "the", "lowest", "MLH1", "mRNA", "expression", "level", "of", "all", "50", "ovarian", "carcinomas", "tested.", "However,", "none", "of", "the", "ovarian", "carcinomas", "showed", "MSI", "for", "BAT25,", "BAT26", "and", "for", "BAT40", "or", "D2S123", "which", "suggests", "a", "frequency", "of", "MMR", "low", "level", "MLH1", "promoter", "methylation", "tumors", "75", " ", "ovarian", "carcinomas", "to", "determine", "the", "frequency", "of", "MMR", "inactivation", "in", "ovarian", "cancer", "in", "vivo.", "Seven", "of", "the", "75", "ovarian", "carcinomas", "showed", "MLH1", "promoter", "methylation.", "We", "confirmed", "whether", "the", "observed", "MLH1", "promoter", "methylation", "results", "in", "the", "inactivation", "of", "the", "gene", "by", "determining", "the", "MLH1", "mRNA", "expression", "with", "quantitative", "RT-PCR.", "The", "six", "tumors", "with", "low", "level", "MLH1", "promoter", "methylation", "appeared", "to", "express", "MLH1", " ", "at", "mRNA", "levels", "similar", "to", "that", "of", "the", "unmethylated", "tumors.", "Thus", "a", "low", "level", "of", "methylation", "does", "not", "result", "in", "an", "altered", "expression", "of", "the", "MLH1", " ", "gene.", "In", "contrast,", "the", "abundant", "methylation", "seen", "in", "the", "remaining", "carcinoma", "was", "associated", "with", "the", "lowest", "MLH1", "mRNA", "expression", "level", "of", "all", "50", "ovarian", "carcinomas", "tested.", "However,", "none", "of", "the", "ovarian", "carcinomas", "showed", "MSI", "for", "BAT25,", "BAT26", "and", "for", "BAT40", "or", "D2S123", "which", "suggests", "a", "frequency", "of", "MMR", "inactivation", "of", "0%.", "The", "low", "MLH1", "mRNA", "expression", "seen", "in", "the", "abundant", "methylated", "carcinoma", "might", "be", "sufficient", "enough", "for", "a", "functional", "MMR", "which", "results", "in", "the", "observed", "absence", "of", "MSI." ]

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[ "Serrated", "polyps", "with", "dysplasia,", "i.e.", "MPs", "and", "SAs,", "together", "comprised", "only", "2%", "of", "the", "overall", "consecutive", "series", "of", "1250", "polyps.", "While", "mutation", "of", "KRAS", "and", "BRAF", "was", "associated", "with", "conventional", "adenoma", "and", "SSA,", "respectively", "(see", "above),", "BRAF", "and", "KRAS", "mutation", "occurred", "with", "similar", "frequency", "in", "both", "MPs", "(40%", "and", "50%,", "respectively)", "and", "SAs", "(33%", "and", "27%,", "respectively).", "In", "the", "literature,", "the", "frequency", "of", "BRAF", "and", "KRAS", "mutation", "in", "MP", "or", "SA", "has", "ranged", "from", "36", "to", "100%", "and", "from", "0%", "to", "60%,", "respectively.12,16,39–42", "These", "findings", "indicate", "that", "this", "subset", "of", "colorectal", "polyps", "is", "likely", "to", "be", "heterogeneous", "in", "terms", "of", "its", "molecular", "origins.", "These", "polyps", "were", "therefore", "reclassified", "according", "to", "their", "resemblance", "to", "HP", "or", "SSA", "(Group", "A)", "(Figure", "1A,B,E,F)", "or", "to", "conventional", "adenoma", "adenoma", "rectum", "Non-dysplastic", " ", "serrated", " ", "polyps", ":", "HP", " ", "and", "SSA" ]

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[ "Patients", "without", "any", "detected", "mutation", "in", "APC", "or", "MUTYH" ]

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[ "We", "genotyped", "the", "p.Lys618Ala", "variant", "in", "MLH1", "in", "1034", "individuals", "(373", "sporadic", "CRC", "patients,", "250", "index", "subjects", "from", "families", "suspected", "of", "having", "LS", "[revised", "Bethesda", "Guidelines]", "and", "411", "controls).", "The", "controls", "were", "selected", "from", "the", "same", "hospitals,", "had", "no", "personal", "histories", "of", "cancer", "and", "had", "diagnoses", "unrelated", "to", "the", "variables", "of", "interest.", "They", "were", "matched", "for", "age,", "gender", "and", "race/ethnicity", "with", "the", "sporadic", "CRC", "patients." ]

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[ "Of", "656", "tumours", "for", "which", "the", "other", "molecular", "alterations,", "i.e.", "mutations", "in", "the", "APC", " ", "and", "K-ras", "genes", "and", "hMLH1", "expression,", "were", "all", "successfully", "and", "completely", "analysed,", "103", "colorectal", "tumours", "did", "not", "harbour", "a", "truncating", "or", "missense", "APC", "mutation,", "an", "activating", "K-ras", "mutation", "or", "showed", "lack", "of", "hMLH1", "expression,", "as", "depicted", "in", "figure", "1.", "Truncating", "as", "well", "as", "missense", "APC", "mutations", "and", "activating", "K-ras", "mutations", "were", "relatively", "common.", "Truncating", "APC", "mutations", "alone", "and", "activating", "K-ras", "mutations", "in", "codons", "12", "and", "13", "only,", "occurred", "at", "similar", "frequencies", "(20%", "(130/656)", "and", "18%", "(121/656),", "respectively).", "A", "combination", "of", "a", "truncating", "mutation", "in", "APC", "and", "an", "activating", "mutation", "in", "K-ras", "occurred", "less", "often", "than", "the", "sole", "occurrences", "of", "mutations", "in", "both", "genes.", "However,", "as", "shown", "in", "table", "2,", "the", "simultaneous", "occurrence", "of", "mutations", "in", "both", "genes", "occurred", "more", "frequently", "than", "expected", "on", "the", "basis", "of", "chance", "alone.", "A", "χ2", "test", "for", "the", "occurrence", "of", "a", "truncating", "APC", "mutation", "and", "an", "activating", "K-ras", "mutation", "truncating", "APC", "mutation", "mutation", " ", "in", "the", "CTNNB1", "gene,", "that", "did", "not", "occur", "at", "the", "Ser/Thr", "phosphorylation", "sites,", "but", "would", "result", "in", "an", "amino", "acid", "alteration", "at", "codons", "22", "and", "29,", "the", "effects", "of", "which", "are", "unknown.", "Because", "of", "the", "very", "low", "frequency", "of", "tumours", "harbouring", "a", "CTNNB1", "mutation,", "these", "mutations", "were", "not", "included", "in", "further", "analyses.", "In", "addition,", "mutation", "analysis", "of", "remaining", "samples", "was", "abandoned,", "since", "this", "was", "deemed", "irrelevant", "as", "these", "harboured", "truncating", "APC", "mutations", "and", "are", "considered", "to", "be", "unlikely", "to", "also", "have", "CTNNB1", "mutations", "[7]." ]

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[ "Mutation", "frequencies", "for", "both", "KRAS", "(P", "<", "0.0001)", "and", "BRAF", "(P", "<", "0.0001)", "are", "distributed", "differently", "across", "the", "seven", "classes", "of", "polyp", "(see", "Results", "for", "individual", "comparisons).", "Distribution", "of", "MGMT", "loss", "differs", "across", "the", "seven", "classes", "of", "polyp", "(P", "<", "0.001)." ]

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[ "Numbers", "of", "oncogenic", "alterations", "(genetic", "mutations", "or", "epigenetic", "alterations)", "required", "for", "transformation", "were", "estimated", "from", "ages", "at", "cancer", "using", "a", "Bayesian", "approach", "as", "previously", "described", "[11].", "This", "method", "requires", "the", "use", "of", "a", "life", "table", "from", "census", "data:", "for", "the", "Finnish", "data", "set", "we", "used", "a", "Finnish", "life", "table", "from", "the", "World", "Health", "Organization", "website", ",", "for", "the", "SEER", "dataset", "we", "used", "a", "United", "States", "life", "table", "as", "described", "previously", "[11].", "The", "model", "assumes", "the", "first", "visible", "clonal", "expansion", "occurs", "at", "the", "time", "of", "transformation", "and", "ignores", "the", "interval", "after", "transformation.", "The", "analysis", "ignores", "temporal", "trends,", "which", "may", "influence", "our", "mutation", "estimates." ]

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[]

[]

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