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Brizape

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Variome_split_0404_dev

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[ "Methods", "and", "results" ]

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[ "Abstract" ]

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[ "5q22.2-5q23.1" ]

[ 0 ]

[ "P", "=", "0.112" ]

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[]

[]

[ "Hierarchical", "clustering", "of", "samples", "from", "colorectal", "tumors", "and", "normal", "colon", "epithelia.", "On", "the", "right,", "you", "find", "the", "chromosomal", "localization", "of", "the", "genes", "and", "the", "official", "HUGO", "symbol", "or", "prospective", "Affymetrix", "cluster", "ID.", "On", "the", "top,", "the", "binary", "tree", "of", "tissue", "samples", "based", "on", "gene", "expression", "is", "given.", "The", "tissue", "denominators", "either", "contain", "TR", "for", "tumor", "or", "E", "for", "epithelium", "and", "a", "code", "reflecting", "the", "identity", "of", "each", "patient.", "In", "the", "center,", "the", "expression", "values", "after", "normalization", "have", "been", "color-coded:", "light", "blue", "means", "high", "expression,", "black", "means", "low", "(or", "no)", "expression.", "Note", "that", "only", "a", "representative", "fraction", "of", "the", "514", "genes", "is", "visualized", "here", "(white", "bars", "replace", "some", "portions", "of", "original", "heat", "map).", "The", "right", "cluster", "contains", "only", "samples", "from", "normal", " ", "colon", "epithelia,", "the", "left", "cluster", "is", "composed", "primarily", "of", "tumors", "along", "with", "some", "interspersed", "normal", "epithelial", "samples.", "Note", "that", "misplaced", "normal", "tissue", "(E)", "samples", "often", "cluster", "along", "with", "matching", "tumor", "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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[ "Concept", "of", "discrete", "colorectal", "lesions", "and", "progression", "to", "colorectal", "cancer", "via", "independent", "pathways" ]

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[ "This", "was", "undertaken", "on", "all", "adenomas", "and", "all", "serrated", "polyps", "with", "dysplasia", "(traditional", "SA", "and", "MP).", "Most", "of", "these", "polyps", "had", "been", "immunostained", "previously", "for", "MGMT.24", "Following", "deparaffinization", "and", "rehydration", "of", "4-µm", "sections", "and", "antigen", "retrieval", "using", "ethylene", "diamine", "tetra-acetic", "acid", "and", "microwaving,", "the", "sections", "were", "subjected", "to", "peroxidase", "blockade", "(Dako", "EnVision", "bottle", "1;", "Mississauga,", "Canada)", "and", "then", "incubated", "in", "10%", "goat", "serum", "to", "minimize", "non-specific", "staining.", "They", "were", "subsequently", "incubated", "with", "the", "primary", "anti-p53", "antibody", "(DO-7,", "from", "DakoCytomation,", "Mississauga,", "Canada)", "at", "a", "dilution", "of", "1", ":", "100", "for", "60", "min", "at", "37°C.", "After", "washing,", "the", "sections", "were", "incubated", "with", "secondary", "antibody", "(EnVision", "bottle", "2)", "for", "30", "min,", "washed", "again", "and", "then", "developed", "with", "the", "chromogen", "AEC", "for", "30", "min.", "Finally,", "the", "sections", "were", "counterstained", "with", "Gill's", "haematoxylin.", "Polyps", "were", "scored", "as", "showing", "loss", "of", "expression", "of", "MGMT", "if", "there", "was", "complete", "absence", "of", "nuclear", "expression", "throughout", "one", "or", "more", "crypts.", "Polyps", "were", "scored", "as", "positive", "for", "aberrant", "p53", "expression", "V599E", ")", "was", "performed", "by", "a", "real-time", "PCR-based", "allelic", "discrimination", "method", "as", "previously", "described.29", "Briefly,", "real-time", "PCR", "was", "performed", "using", "allele-specific", "primers", "designed", "to", "amplify", "selectively", "the", "wild-type", "(T1796)", "and", "mutant", "(A1796)", "BRAF", "alleles.", "The", "primer", "sequences", "were", "as", "follows:", "V,", "5′-GTGATTTTGGTCTAGCTACtGT;", "E,", "5′-CGCGGCCGGCCGCGGCGGTGATTTTGGTCTAGCTACcGA;", "AS,", "5′-TAGCCTCAATTCTTACCATCCAC.", "PCR", "amplification", "and", "melting", "curve", "analysis", "were", "performed", "on", "a", "Rotor-gene", "3000", "(Corbett", "Research,", "NSW,", "Australia).", "Genomic", "DNA", "was", "amplified", "in", "a", "15-µl", "volume", "containing", "1", "×", "Platinum", "SYBR", "Green", "qPCR", "SuperMix-UDG", "(Invitrogen,", "Carlsbad,", "CA,", "USA),", "forward", "primer", "V", "(300", "nm),", "forward", "primer", "E", "(900", "nm)", "and", "reverse", "primer", "AS", "(300", "nm).", "The", "cycling", "conditions", "were", "as", "follows:", "50°C", "for", "2", "min,", "95°C", "for", "2", "min,", "40", "cycles", "of", "95°C", "for", "15", "s", "and", "60°C", "for", "60", "s.", "After", "amplification,", "samples", "were", "subjected", "to", "a", "temperature", "ramp", "from", "60°C", "to", "99°C,", "rising", "1°C", "each", "step.", "For", "wild-type", "samples,", "single", "peaks", "were", "observed", "at", "80°C", "while", "samples", "containing", "mutant", "alleles", "produced", "single", "peaks", "at", "85°C." ]

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[ "Peripheral", "blood", "was", "collected", "from", "the", "three", "consulting", "family", "members", "and", "the", "proband's", "father", "tumor", "unaffected", "carrier", "malignancy", "mother", "Three", " ", "first-degree", "relatives", "(mother", "and", "two", "sisters)", "of", "a", "male", "who", "died", "of", "poorly", "differentiated", "colorectal", "adenocarcinoma", "at", "age", "23", "contacted", "us", "for", "genetic", "counseling.", "A", "detailed", "family", "and", "medical", "history", "was", "obtained", "through", "interview", "with", "the", "proband", "relatives", "and", "their", "consent", "for", "release", "of", "medical", "records", "and", "use", "of", "the", "pathological", "tissue", "blocks", "still", "available." ]

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[ "The", "fraction", "of", "large", "deletions", "of", "all", "APC", "mutations", "identified", "in", "the", "Swedish", "patients", "was", "9%,", "which", "is", "higher", "than", "the", "5%", "of", "large", "deletions", "reported", "in", "[38].", "The", "relatively", "large", "number", "of", "gross", "deletions", "identified", "could", "be", "a", "result", "of", "the", "thorough", "analysis", "applied", "for", "every", "patient,", "including", "the", "use", "of", "the", "MLPA", "technique.", "It", "is", "noteworthy", "that", "no", "deletion", "of", "APC", "exon", "4", "in", "patient", "3765", "was", "detected", "using", "MLPA", "although", "it", "had", "been", "identified", "and", "confirmed", "by", "other", "methods.", "A", "still", "untested", "possibility", "is", "that", "exon", "4", "has", "been", "translocated", "to", "another", "chromosomal", "locus", "and", "thus", "generates", "the", "positive", "MLPA", "result." ]

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[ "Frequency", "of", "KRAS", "and", "BRAF", "mutation", "and", "loss", "of", "expression", "of", "O-6-methylguanine", "DNA", "methyltransferase", "(MGMT)", "by", "polyp", "type" ]

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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", "serrated", " ", "polyps", "comprise", "conventional", "HPs", "and", "the", "variant", "lesion", "which", "has", "been", "described", "as", "SSA.", "In", "this", "study,", "SSAs", "accounted", "for", "approximately", "3%", "of", "the", "overall", "series", "of", "polyps", "and", "were", "more", "age-related", "than", "HPs.", "Importantly,", "SSAs", "have", "been", "linked", "with", "the", "subset", "of", "colorectal", "cancer", "with", "BRAF", "mutation,", "DNA", "methylation,", "MSI", "and", "serrated", "architecture.14,18,37", "In", "this", "study", "there", "was", "a", "high", "frequency", "of", "BRAF", "mutation", "in", "conventional", "HPs", "(67%)", "as", "well", "as", "in", "SSAs", "(81%).", "Previous", "reports", "have", "shown", "very", "similar", "results", "for", "BRAF", "mutation", "in", "SSA,16", "but", "higher", "frequencies", "of", "KRAS", "mutation", "and", "lower", "frequencies", "of", "BRAF", "mutation", "in", "HPs.12,16,38", "As", "mentioned", "in", "Materials", "and", "methods,", "there", "had", "been", "selection", "of", "larger", "HPs", "in", "an", "earlier", "cell", "kinetic", "study", "involving", "the", "same", "material.", "Large", "HPs", "are", "more", "likely", "to", "include", "the", "subset", "described", "as", "‘microvesicular’,", "in", "which", "the", "columnar", "cells", "contain", "apical", "mucin", "droplets", "within", "small", "vesicles", "while", "goblet", "cells", "are", "rendered", "inconspicuous.25BRAF", "mutation", "occurs", "more", "frequently", "in", "the", "microvesicular", "variant", "of", "HP.16", "By", "contrast,", "KRAS", "mutation", "occurs", "much", "more", "commonly", "in", "the", "goblet", "cell", "variant", "of", "HP,", "which", "is", "usually", "small,", "located", "in", "the", "left", "colon", "or", "rectum", "and", "deviates", "minimally", "from", "normal", "colorectal", "mucosa", "in", "terms", "of", "differentiation", "and", "architecture.16,25", "The", "latter", "were", "under-represented", "in", "this", "series", "(details", "not", "shown)." ]

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[ "MLH1", "promoter", "hypermethylation", "by", "Methylation", "Sensitive", "Multiplex", "Ligation-dependent", "Probe", "Amplification", "(MS-MLPA),", "and", "BRAF", "p.Val600Glu", "mutation", "by", "direct", "sequencing", "from", "tumor", "DNA", "was", "also", "assess", "when", "MLH1", "loss", "of", "expression", "was", "detected." ]

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[ "5q22.2-5q23.1" ]

[ 0 ]

[ "The", "treatment", "of", "ovarian", "cancer", "is", "hindered", "by", "intrinsic", "or", "acquired", "resistance", "to", "platinum-based", "chemotherapy.", "The", "aim", "of", "this", "study", "is", "to", "determine", "the", "frequency", "of", "mismatch", "repair", "(MMR)", "inactivation", "in", "ovarian", "cancer", "and", "its", "association", "with", "resistance", "to", "platinum-based", "chemotherapy." ]

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[ "Sixty-two", "TAs,", "22", "TVAs/VAs,", "15", "SAs", "and", "10", "MPs", "were", "immunostained", "for", "p53.", "Weak", "expression", "of", "nuclear", "p53", "occurred", "frequently", "within", "the", "proliferative", "compartment", "in", "all", "types", "of", "polyps", "and", "was", "ignored.", "Aberrant", "p53", "expression", "was", "observed", "in", "only", "four", "mutation", "KRAS", " ", "mutation", "occurred", "in", "3/25", "(12%)", "adenomas", "with", "no", "MGMT", "loss", "<", " ", "10", "mm", ",", "KRAS", "mutation", "occurred", "in", "3/25", "(12%)", "adenomas", "with", "no", "MGMT", "loss", "but", "in", "4/8", "(50%)", "adenomas", "with", "MGMT", "loss", "(P", "<", "0.04).", "Since", "there", "were", "few", "KRAS", "mutations", "in", "this", "subset", "and", "most", "KRAS", "mutations", "(5/7)", "were", "G→A,", "it", "was", "not", "possible", "to", "demonstrate", "an", "association", "between", "MGMT", "loss", "and", "G→A", "mutation", "in", "KRAS." ]

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[ "No", "familial", "history", "of", "cancer", "was", "available", "from", "the", "control", "group.", "Patients", "diagnosed", "at", "an", "age", "over", "50", "years", "and", "not", "referred", "to", "Genetic", "Counselling", "Units", "were", "considered", "as", "sporadic", "CRC.", "Samples", "from", "sporadic", "CRC", "patients", "were", "obtained", "from", "the", "Elche", "University", "Hospital", "BioBank", "and", "the", "Castellon", "Provincial", "Hospital", "BioBank.", "Written", "consent", "to", "be", "included", "in", "the", "respective", "biobanks", "was", "obtained", "from", "each", "patient.", "CRC", "patients,", "as", "index", "subjects", "from", "families", "with", "suspicion", "of", "LS", "that", "attended", "Genetic", "Counselling", "at", "the", "Cancer", "Units", "of", "the", "Elche", "and", "La", "Fe", "Hospitals,", "were", "recruited.", "The", "study", "was", "approved", "by", "the", "Ethics", "Committee", "of", "the", "Elche", "University", "Hospital." ]

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[]

[]

[ "MLH1", "promoter", "hypermethylation", "by", "Methylation", "Sensitive", "Multiplex", "Ligation-dependent", "Probe", "Amplification", "(MS-MLPA),", "and", "BRAF", "familial", "group", " ", "and", "nine", "from", "the", "sporadic", "CRC", "group)", "was", "screened", "for", "MSI", "status", "using", "five", "mononucleotide", "markers", "(BAT26,", "BAT25,", "NR21,", "NR24", "and", "NR27)", "and", "multiplex", "PCR", "as", "previously", "described", "by", "Buhard", "et", "al", "[8]." ]

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[ "Mutation-detection", "frequency" ]

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[ "The", "mutation", "between", "the", "MSI-L", "and", "MSI-H" ]

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[ "Statistical", "analysis" ]

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[ "Conclusion" ]

[ 0 ]

[ "**", "IGNORE", "LINE", "**" ]

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[ "Pedigree", "for", "Family", "#3", "(CRC:", "Colorectal", "cancer;", "ESC:", "Oesophageal", "cancer;", "LC:", "Lung", "cancer)." ]

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[ "Background" ]

[ 0 ]