Datasets:

Brizape

/

Variome_split_0404_dev

like 0

[ "Associations", "between", "BRAF", "mutation", "and", "clinicopathological", "features", "of", "colorectal", "cancer." ]

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[ "Results" ]

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[ "20q11.22-q11.23" ]

[ 0 ]

[]

[]

[ "KRAS", "and", "BRAF", "mutations" ]

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[ "Results" ]

[ 0 ]

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[ "The", "MSI-positive", "patient", "from", "the", "familial", "CRC", "two", "Colorectal", " ", "cancer;", "ESC:", "Oesophageal", "cancer;", "LC:", "Lung", "cancer)." ]

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[ "Conclusion" ]

[ 0 ]

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[]

[]

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[ "DNA", "sequencing", "of", "hMSH2", "and", "hMLH1", "genes" ]

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[ "The", "semi-nested", "PCR", "products", "from", "samples", "without", "a", "truncating", "APC", "mutation", "were", "screened", "for", "mutations", "using", "denaturing", "high-pressure", "liquid", "chromatography", "(dHPLC)", "on", "a", "WAVE", "3500", "HT", "system", "(Transgenomic", "Inc.,", "UK).", "WAVE", "analysis", "was", "optimised", "and", "validated", "using", "specific", "mutations", "in", "cell", "line", "DNA,", "i.e.", "HCT116", "(codon", "45:", "3", "bp", "deletion)", "and", "SW48", "(codon", "33:", "C→A)", "as", "well", "as", "DNA", "derived", "from", "desmoid", "exon", "1", "fragment", "of", "the", "K-ras", "oncogene,", "spanning", "codons", "8–29", "mutation", " ", "analysis" ]

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[ "Lynch", "syndrome", "(MIM#", "120435)", "(LS)", "is", "an", "autosomal", "dominant", "inherited", "cancer", "syndrome", "characterized", "by", "early", "onset", "colorectal", "cancer", "(CRC),", "cancer", "of", "the", "endometrium", "and", "tumours", "colorectal", "cancer", " ", "(CRC),", "cancer", "of", "the", "endometrium", "and", "tumours", "of", "the", "stomach,", "pancreas,", "small", "intestine,", "ovary,", "bladder", "and", "bile", "duct", "[4].", "LS-associated", "tumours", "strong", "history", "of", "cancer", "cancer", " ", "cases", "in", "which", "a", "causative", "mutation", "is", "identified", "is", "far", "from", "ideal.", "All", "members", "from", "a", "family", "with", "a", "strong", "history", "of", "cancer", " ", "and", "no", "causative", "mutation", "detected", "are", "included", "in", "a", "surveillance", "program.", "Identification", "of", "mutations", "depends", "on", "the", "specific", "syndrome", "and", "the", "criteria", "applied", "to", "select", "patients", "for", "genetic", "analyses." ]

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[ "Results" ]

[ 0 ]

[ "The", "MTT", "colorimetric", "assay,", "which", "measures", "the", "number", "of", "viable", "cells", "capable", "of", "reducing", "the", "tetrazolium", "compound", "(Sigma-Aldrich,", "Zwijndrecht,", "The", "Netherlands)", "to", "a", "blue", "formazan", "product,", "was", "used", "to", "quantitate", "the", "chemosensitivity", "of", "the", "ovarian", "cancer", "cell", "lines", "to", "cisplatin.", "The", "assay", "was", "performed", "as", "described", "previously", "by", "us", "[38]." ]

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[ "DNA", "preparation", "for", "genetic", "testing" ]

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[ "dysplastic", "serrated", "polyps:", "MP", "and", "SA" ]

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[]

[ "Mutation", "screening", "was", "done", "in", "both", "sisters", "to", "assign", "their", "risk", "to", "develop", "HNPCC", "and", "other", "related", "cancers.", "We", "found", "the", "mutation", "in", "one", "of", "them", "and", "opportune", "recommendations", "for", "surveillance", "and", "prophylaxis", "were", "given.", "Two", "years", "after", "that,", "the", "proband's", "mother", "mother", ",", "unaffected", "during", "this", "study,", "developed", "an", "endometrial", " ", "adenocarcinoma", "sisters", " ", "to", "assign", "their", "risk", "to", "develop", "HNPCC", "and", "other", "related", "cancers", "HNPCC", "sisters", " ", "to", "assign", "their", "risk", "to", "develop", "HNPCC", "and", "other", "related", "cancers.", "We", "found", "the", "mutation", "in", "one", "of", "them", "and", "opportune", "recommendations", "for", "surveillance", "and", "prophylaxis", "were", "given.", "Two", "years", "after", "that,", "the", "proband's", "mother,", "unaffected", " ", "during", "this", "study,", "developed", "an", "endometrial", "adenocarcinoma." ]

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[ "Prior", "to", "the", "analysis", "of", "chromosomal", "expression", "domains,", "we", "aimed", "to", "check", "whether", "the", "quality", "of", "our", "complete", "array", "expression", "data", "set", "(>", "44", "k", "genes)", "allows", "to", "extract", "discrepancies", "between", "tumor", "samples", "and", "normal", "epithelial", "tissues.", "Purely", "unsupervised", "hierarchical", "clustering", "of", "tissue", "samples", "based", "on", "gene", "expression", "vectors", "can", "provide", "such", "information.", "The", "use", "of", "the", "full", "set", "of", "44", "k", "genes", "for", "clustering", "is", "not", "desirable,", "because", "of", "high", "signal-noise", "ratios", "and", "computational", "considerations.", "Therefore,", "we", "pre-selected", "potentially", "informative", "genes", "for", "hierarchical", "clustering.", "We", "selected", "only", "genes", "which", "had", "reliable", "information", "about", "genomic", "localization", "and", "for", "which", "probe", "sets", "exceeded", "a", "minimum", "expression", "threshold", "in", "at", "least", "20%", "of", "the", "experiments.", "To", "enrich", "informative", "genes", "for", "tissue", "distinction,", "we", "required", "a", "minimum", "standard", "deviation", "across", "all", "50", "samples.", "The", "pre-selection", "resulted", "in", "514", "probe", "sets.", "Note", "that", "we", "avoided", "to", "pre-select", "genes", "based", "on", "differential", "expression", "between", "tumor", "and", "normal", "tissue.", "We", "applied", "three", "rounds", "of", "normalization", "to", "genes", "and", "arrays.", "Finally,", "we", "applied", "standard", "centroid", "hierarchical", "clustering", "(Pearson", "correlation)", "to", "this", "dataset.", "Two", "large", "clusters", "were", "revealed", "(Figure", "1).", "18", "out", "of", "25", "normal", "tissues", "formed", "one", "single", "cluster.", "The", "remaining", "8", "normal", "tissues", "mainly", "clustered", "together", "with", "matching", "tumor", "samples", "from", "same", "patients.", "This", "suggests", "that", "coalescence", "between", "tumor", "and", "normal", "samples", "from", "the", "same", "patients", "could", "be", "due", "to", "patient", "-specific", "gene", "expression", "characteristics.", "As", "the", "majority", "of", "normal", "samples", "could", "be", "clearly", "separated", "from", "tumors,", "we", "concluded", "that", "our", "data", "set", "is", "well", "suited", "to", "explore", "differences", "in", "gene", "expression", "between", "normal", "and", "tumor", "cells", "of", "colorectal", "origin." ]

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