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amia_tokenized_split_0404_dev

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[ "Lynch", "syndrome", "is", "characterized", "by", "mutations", "in", "one", "of", "four", "mismatch", "repair", "genes,", "MLH1,", "MSH2,", "MSH6,", "or", "PMS2.", "Clinical", "mutation", "analysis", "of", "these", "genes", "includes", "sequencing", "of", "exonic", "regions", "and", "deletion/duplication", "analysis.", "However,", "detection", "of", "deletions", "and", "duplications", "in", "PMS2", "has", "previously", "been", "confined", "to", "Exons", "1-11", "due", "to", "gene", "conversion", "between", "PMS2", "and", "the", "pseudogene", "PMS2CL", "in", "the", "remaining", "3'", "exons", "(Exons", "12-15).", "We", "have", "recently", "described", "an", "MLPA-based", "method", "that", "permits", "detection", "of", "deletions", "of", "PMS2", "Exons", "12-15;", "however,", "the", "frequency", "of", "such", "deletions", "has", "not", "yet", "been", "determined.", "To", "address", "this", "question,", "we", "tested", "for", "3'", " ", "deletions", "in", "58", "samples", "that", "were", "reported", "to", "be", "negative", "for", "PMS2", "mutations", "using", "previously", "available", "methods.", "All", "samples", "were", "from", "individuals", "whose", "tumors", "exhibited", "loss", "of", "PMS2", "immunohistochemical", "staining", "without", "concomitant", "loss", "of", "MLH1", "immunostaining.", "We", "identified", "seven", "samples", "in", "this", "cohort", "with", "deletions", "in", "the", "3'", "region", "of", "PMS2,", "including", "three", "previously", "reported", "samples", "with", "deletions", "of", "Exons", "13-15", "(two", "samples)", "and", "Exons", "14-15.", "Also", "detected", "were", "deletions", "deletion", "/duplication", "analysis.", "However,", "detection", "of", "deletions", " ", "and", "duplications", "in", "PMS2", " ", "has", "previously", "been", "confined", "to", "Exons", "1-11", "due", "to", "gene", "conversion", "between", "PMS2", "and", "the", "pseudogene", "PMS2CL", "in", "the", "remaining", "3'", "exons", "(Exons", "12-15).", "We", "have", "recently", "described", "an", "MLPA-based", "method", "that", "permits", "detection", "of", "deletions", "of", "PMS2", "Exons", "12-15;", "however,", "the", "frequency", "of", "such", "deletions", "has", "not", "yet", "been", "determined.", "To", "address", "this", "question,", "we", "tested", "for", "3'", "deletions", "in", "58", "samples", "that", "were", "reported", "to", "be", "negative", "for", "PMS2", "mutations", "using", "previously", "available", "methods.", "All", "samples", "were", "from", "individuals", "whose", "tumors", "exhibited", "loss", "of", "PMS2", "immunohistochemical", "staining", "without", "concomitant", "loss", "of", "MLH1", "immunostaining.", "We", "identified", "seven", "samples", "in", "this", "cohort", "with", "deletions", "in", "the", "3'", "region", "of", "PMS2,", "including", "three", "previously", "reported", "samples", "with", "deletions", "of", "Exons", "13-15", "(two", "samples)", "and", "Exons", "14-15", "duplication", " ", "analysis.", "However,", "detection", "of", "deletions", "and", "duplications", " ", "in", "PMS2", "has", "previously", "been", "confined", "to", "Exons", "1-11", "due", "to", "gene", "conversion", "between", "PMS2", "and", "the", "pseudogene", "PMS2CL", "in", "the", "remaining", "3'", "exons", "(Exons", "12-15).", "We", "have", "recently", "described", "an", "MLPA-based", "method", "that", "permits", "detection", "of", "deletions", "of", "PMS2", "Exons", "12-15;", "however,", "the", "frequency", "of", "such", "deletions", "has", "not", "yet", "been", "determined.", "To", "address", "this", "question,", "we", "tested", "for", "3'", "deletions", "in", "58", "samples", "that", "were", "reported", "to", "be", "negative", "for", "PMS2", "mutations", "using", "previously", "available", "methods.", "All", "samples", "were", "from", "individuals", "whose", "tumors", "exhibited", "loss", "of", "PMS2", "immunohistochemical", "staining", "without", "concomitant", "loss", "of", "MLH1", "immunostaining.", "We", "identified", "seven", "samples", "in", "this", "cohort", "with", "deletions", "in", "the", "3'", "region", "of", "PMS2,", "including", "three", "previously", "reported", "samples", "with", "deletions", "of", "Exons", "13-15", "(two", "samples)", "and", "Exons", "14-15.", "Also", "detected", "were", "deletions", "of", "Exons", "12-15,", "Exon", "13", "3'", "exons", "PMS2CL", " ", "in", "the", "remaining", "3'", "exons", "(Exons", "12-15).", "We", "have", "recently", "described", "an", "MLPA-based", "method", "that", "permits", "detection", "of", "deletions", "of", "PMS2", "Exons", "12-15;", "however,", "the", "frequency", "of", "such", "deletions", "has", "not", "yet", "been", "determined.", "To", "address", "this", "question,", "we", "tested", "for", "3'", "deletions", "in", "58", "samples", "that", "were", "reported", "to", "be", "negative", "for", "PMS2", "mutations", "using", "previously", "available", "methods.", "All", "samples", "were", "from", "individuals", "whose", "tumors", "exhibited", "loss", "of", "PMS2", "immunohistochemical", "staining", "without", "concomitant", "loss", "of", "MLH1", "immunostaining.", "We", "identified", "seven", "samples", "in", "this", "cohort", "with", "deletions", "in", "the", "3'", "region", "of", "PMS2,", "including", "three", "previously", "reported", "samples", "with", "deletions", "of", "Exons", "13-15", "(two", "samples)", "and", "Exons", "14-15.", "Also", "detected", "were", "deletions", "of", "Exons", "12-15", "PMS2", " ", "and", "the", "pseudogene", "PMS2CL", "in", "the", "remaining", "3'", "exons", "(Exons", "12-15).", "We", "have", "recently", "described", "an", "MLPA-based", "method", "that", "permits", "detection", "of", "deletions", "of", "PMS2", "Exons", "12-15;", "however,", "the", "frequency", "of", "such", "deletions", "has", "not", "yet", "been", "determined.", "To", "address", "this", "question,", "we", "tested", "for", "3'", "deletions", "in", "58", "samples", "that", "were", "reported", "to", "be", "negative", "for", "PMS2", "mutations", "using", "previously", "available", "methods.", "All", "samples", "were", "from", "individuals", "whose", "tumors", "exhibited", "loss", "of", "PMS2", "immunohistochemical", "staining", "without", "concomitant", "loss", "of", "MLH1", "immunostaining.", "We", "identified", "seven", "samples", "in", "this", "cohort", "with", "deletions", "in", "the", "3'", "region", "of", "PMS2,", "including", "three", "previously", "reported", "samples", "with", "deletions", "of", "Exons", "13-15", "(two", "samples)", "and", "Exons", "14-15.", "Also", "detected", "were", "deletions", "of", "Exons", "12-15,", "Exon", "13,", "and", "Exon", "14", "(two", "samples).", "Breakpoint", "analysis", "of", "the", "intragenic", "deletions", "mutations", "deletions", " ", "has", "not", "yet", "been", "determined.", "To", "address", "this", "question,", "we", "tested", "for", "3'", "deletions", "in", "58", "samples", "that", "were", "reported", "to", "be", "negative", "for", "PMS2", "deletions", " ", "in", "58", "samples", "that", "were", "reported", "to", "be", "negative", "for", "PMS2", "mutations", "using", "previously", "available", "methods.", "All", "samples", "were", "from", "individuals", "whose", "tumors", "exhibited", "loss", "of", "PMS2", "immunohistochemical", "staining", "without", "concomitant", "loss", "of", "MLH1", "PMS2", " ", "immunohistochemical", "staining", "without", "concomitant", "loss", "of", "MLH1", "immunostaining.", "We", "identified", "seven", "samples", "in", "this", "cohort", "with", "deletions", " ", "in", "the", "3'", "region", "of", "PMS2,", "including", "three", "previously", "reported", "samples", "with", "deletions", "PMS2", ",", "including", "three", "previously", "reported", "samples", "with", "deletions", "of", "Exons", "13-15", "(two", "samples)", "and", "Exons", "14-15.", "Also", "detected", "were", "deletions", "of", "Exons", "12-15,", "Exon", "13,", "and", "Exon", "14", "deletions", " ", "involving", "3'", 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"compatible", "with", "the", "cytometry", "results.", "There", "was", "one", "discordant", "case", "i.e.", "pAb", "240", "antibody", "being", "positive", "on", "cytometry", "and", "entirely", "negative", "on", "immunohistochemistry.", "This", "small", "series", "allowed", "us", "to", "show", "that", "81", "percent", "of", "tumor", "samples", "stained", "with", "monoclonal", "antibody", "pAb", "240,", "considered", "to", "be", "specific", "to", "mutated", "pAb", "240", "pAb", "240", "p53", ")", "flow", "cytometry.", "Two", "different", "types", "of", "preparations", "were", "compared", "in", "order", "to", "verify", "the", "conservation", "of", "the", "antigen.", "Nuclear", "suspensions", "prepared", "from", "frozen", "tumor", "fragments", "were", "shown", "to", "produce", "results", "equivalent", "to", "those", "of", "whole", "cell", "preparations", "originating", "from", "fresh", "surgical", "specimens.", "The", "p53", "protein", "was", "detected", "in", "9", "of", "the", "16", "cancers", "with", "pAb", "421", "and", "240", "monoclonal", "antibodies", "(8", "of", "which", "were", "also", "positive", "for", "pAb", "1801", "antibody).", "Four", "additional", "tumors", "were", "considered", "positive", "for", "pAb", "240", "antibody", "alone.", "Overall,", "13/16", "cancer", "specimens", "were", "shown", "to", "present", "immunoreactivity", "for", "pAb", "240", "antibody.", "Topography", "of", "staining", "was", "investigated", "by", "immunohistochemistry", "with", "peroxidase", "methods.", "Eight", "cases", "were", "informative,", "6", "of", "which", "presented", "nuclear", "staining", "compatible", "with", "the", "cytometry", "results.", "There", "was", "one", "discordant", "case", "i.e.", "pAb", "240", "1801", "pAb", "421", ",", "1801,", "240).", "Specific", "immunofluorescent", "staining", "was", "quantified", "by", "dual", "parameter", "(DNA/p53)", "flow", "cytometry.", "Two", "different", "types", "of", "preparations", "were", "compared", "in", "order", 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"was", "detected", "in", "9", "of", "the", "16", "cancers", "with", "pAb", "421", " ", "and", "240", "monoclonal", "antibodies", "(8", "of", "which", "were", "also", "positive", "for", "pAb", "1801", "p53", " ", "gene", "have", "been", "shown", "to", "be", "frequent,", "the", "protein", "was", "present", "in", "only", "approximately", "50", "percent", "of", "specimens", "examined.", "However", "only", "one", "monoclonal", "antibody", "recognizing", "an", "epitope", "present", "on", "wild-type", "p53", "had", "been", "used.", "We", "studied", "the", "p53", "expression", "in", "a", "series", "of", "16", "colorectal", "carcinoma", "specimens", "using", "3", "different", "monoclonal", "antibodies", "(pAb", "421,", "1801,", "240).", "Specific", "immunofluorescent", "staining", "was", "quantified", "by", "dual", "parameter", "(DNA/p53)", "flow", "cytometry.", "Two", "different", "types", "of", "preparations", "were", "compared", "in", "order", "to", "verify", "the", "conservation", "of", 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"profiles", "of", "56", "additional", "colorectal", "cancer", "cell", "lines.", "Combining", "these", "data", "shows", "that", "focal", "recombination", "events", "disrupt", "the", "genomic", "integrity", "of", "KIAA0146", " ", "and", "neighboring", "cFS", "genes", "in", "12.3%", "of", "colorectal", "cancer", "cell", "lines.", "Moreover,", "data", "analysis", "revealed", "evidence", "that", "KIAA0146", "is", "a", "translocation", "partner", "of", "the", "immunoglobulin", "heavy", "chain", "gene", "in", "recurrent", "t(8;14)(q11;q32)", "translocations", " ", "in", "a", "subset", "of", "patients", "with", "B-cell", "precursor", "acute", "lymphoblastic", "leukemia.", "Our", "data", "molecularly", "describe", "a", "region", "of", "enhanced", "chromosomal", "instability", "KIAA0146", "common", "fragile", "sites", " ", "(cFSs).", "CFSs", "represent", "parts", "of", "the", "normal", "chromosome", "structure", "that", "are", "prone", "to", "breakage", "under", "replication", "stress.", "In", "this", "study,", "we", "identified", "the", "genomic", "location", "of", "FRA8I,", "spanning", "530", "kb", "at", "8q11.21", "and", "assessed", "the", "composition", "of", "the", "fragile", "DNA", "sequence.", "FRA8I", "encompasses", "KIAA0146,", "a", "large", "protein-coding", "gene", "with", "yet", "unknown", "function,", "as", "well", "as", "CEBPD", "and", "part", "of", "PRKDC,", "two", "genes", "encoding", "proteins", "involved", "in", "tumorigenesis", "in", "a", "variety", "of", "cancers.", "We", "show", "that", "FRA8I", "is", "unstable", "in", "lymphocytes", "and", "epithelial", "cells,", "displaying", "similar", "expression", "rates.", "We", "examined", "copy", "number", "alteration", "patterns", "within", "FRA8I", "centromeric", " ", "portion", "of", "chromosome", "8", "is", "particularly", "sensitive", "to", "breakage.", "Genomic", "alterations", "frequently", "occur", "in", "the", "early", "stages", "of", "tumorigenesis", "at", "specific", "genomic", "regions", "known", "as", "common", "fragile", "sites", "(cFSs).", "CFSs", "represent", "parts", "of", "the", "normal", "chromosome", "structure", "that", "are", "prone", "to", "breakage", "under", "replication", "stress.", "In", "this", "study,", "we", "identified", "the", "genomic", "location", "of", "FRA8I,", "spanning", "530", "kb", "at", "8q11.21", "and", "assessed", "the", "composition", "of", "the", "fragile", "DNA", "sequence.", "FRA8I", "encompasses", "KIAA0146,", "a", "large", "protein-coding", "gene", "with", "yet", "unknown", "function,", "as", "well", "as", "CEBPD", "and", "part", "of", "PRKDC,", "two", "genes", "encoding", "proteins", "involved", "in", "tumorigenesis", "in", "a", "variety", "of", "cancers.", "We", "show", "that", "FRA8I", "is", "unstable", "in", "lymphocytes", "and", "epithelial", "cells,", "displaying", "similar", "expression", "rates.", "We", "examined", "copy", "number", "alteration", "patterns", "within", "FRA8I", "in", "a", "panel", "of", "25", "colorectal", "cancer", 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