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amia_tokenized_split_0404_dev

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"a", "BRAF", "result,", "whereas", "38/201", "(19%)", "were", "positive.", "By", "IHC", "45/216", "(20%)", "were", "positive.", "Of", "the", "7", "discordant", "cases,", "real-time", "PCR", "confirmed", "the", "IHC", "result", "in", "6.", "In", "the", "51", "CRCs", "from", "the", "ACCFR,", "IHC", "was", "concordant", "with", "allele-specific", "PCR", "in", "50", "cases.", "BRAFV600E", "and", "MSI", "IHC", "on", "1403", "CRCs", "demonstrated", "the", "following", "phenotypes:", "BRAF/MSS", "(1029", "cases,", "73%),", "BRAF/MSS", "(98,", "7%),", "BRAF/MSI", "(183,", "13%),", "and", "BRAF/", "MSI", "V600E", " ", "IHC", "with", "multiplex", "polymerase", "chain", "reaction", "(PCR)", "and", "matrix-assisted", "laser", "desorption/ionization-time", "of", "flight", "mass", "spectrometry", "in", "216", "consecutive", "CRCs", "from", "2011.", "Discordant", "cases", "were", "resolved", "with", "real-time", "PCR.", "BRAFV600E", "IHC", "was", "performed", "on", "51", "CRCs", "from", "the", "Australasian", "Colorectal", "Cancer", "Family", "Registry", "(ACCFR),", "which", "were", "fully", "characterized", "for", "BRAF", "mutation", "by", "allele-specific", "PCR,", "MMR", "status", "(MMR", "IHC", "and", "MSI),", "MLH1", "promoter", "methylation,", "and", "germline", "MLH1", "mutation.", "We", "then", "assessed", "MMR", "and", "BRAFV600E", "IHC", "on", "1403", "consecutive", "CRCs.", "By", "matrix-assisted", "laser", "desorption/ionization-time", "of", "flight", "mass", "spectrometry", "15", "cases", "did", "not", "yield", "a", "BRAF", "result,", "whereas", "38/201", "(19%)", "were", "positive.", "By", "IHC", "45/216", "(20%)", "were", "positive.", "Of", "the", "7", "discordant", "cases,", "real-time", "PCR", "confirmed", "the", "IHC", "result", "in", "6.", "In", "the", "51", "CRCs", "from", "the", "ACCFR,", "IHC", "was", "concordant", "with", "allele-specific", "PCR", "in", "50", "cases.", "BRAFV600E", "and", "MSI", "IHC", "on", "1403", "CRCs", "demonstrated", "the", "following", "phenotypes:", "BRAF/MSS", "(1029", "cases,", "73%),", "BRAF/MSS", "(98,", "7%),", "BRAF/MSI", "(183,", "13%),", "and", "BRAF/MSI", "(93,", "7%).", "All", "11/1403", "cancers", "associated", "with", "proven", "LS", "were", "BRAF/", "MSI", "V600E", " ", "IHC", "was", "performed", "on", "51", "CRCs", "from", "the", "Australasian", "Colorectal", "Cancer", "Family", "Registry", "(ACCFR),", "which", "were", "fully", "characterized", "for", "BRAF", "mutation", "by", "allele-specific", "PCR,", "MMR", "status", "(MMR", "IHC", "and", "MSI),", "MLH1", "promoter", "methylation,", "and", "germline", "MLH1", "mutation.", "We", "then", "assessed", "MMR", "and", "BRAFV600E", "IHC", "on", "1403", "consecutive", "CRCs.", "By", "matrix-assisted", "laser", "desorption/ionization-time", "of", "flight", "mass", "spectrometry", "15", "cases", "did", "not", "yield", "a", "BRAF", "result,", "whereas", "38/201", "(19%)", "were", "positive.", "By", "IHC", "45/216", "(20%)", "were", "positive.", "Of", "the", "7", "discordant", "cases,", "real-time", "PCR", "confirmed", "the", "IHC", "result", "in", "6.", "In", "the", "51", "CRCs", "from", "the", "ACCFR,", "IHC", "was", "concordant", "with", "allele-specific", "PCR", "in", "50", "cases.", "BRAFV600E", "and", "MSI", "IHC", "on", "1403", "CRCs", "demonstrated", "the", "following", "phenotypes:", "BRAF/MSS", "(1029", "cases,", "73%),", "BRAF/MSS", "(98,", "7%),", "BRAF/MSI", "(183,", "13%),", "and", "BRAF/MSI", "(93,", "7%).", "All", "11/1403", "cancers", "associated", "with", "proven", "LS", "were", "BRAF/MSI.", "We", "conclude", "that", "BRAF", "BRAF", "/MSI", "(93,", "7%).", "All", "11/1403", "cancers", "associated", "with", "proven", "LS", "were", "BRAF/MSI.", "We", "conclude", "that", "BRAF", "IHC", "is", "highly", "concordant", "with", "2", "commonly", "used", "PCR-based", "BRAFV600E", "assays;", "it", "performed", "well", "in", "identifying", "MLH1", "BRAF", " ", "mutation", "by", "allele-specific", "PCR,", "MMR", "status", "(MMR", "IHC", "and", "MSI),", "MLH1", " ", "promoter", " ", "methylation,", "and", "germline", "MLH1", "methylation", ",", "and", "germline", "MLH1", "mutation", "BRAF", "V600E", "IHC", "was", "performed", "on", "51", "CRCs", "from", "the", "Australasian", "Colorectal", "Cancer", "Family", "Registry", "(ACCFR),", "which", "were", "fully", "characterized", "for", "BRAF", "mutation", " ", "by", "allele-specific", "PCR,", "MMR", "status", "(MMR", "IHC", "and", "MSI),", "MLH1", "promoter", "methylation,", "and", "germline", "MLH1", "mutation.", "We", "then", "assessed", "MMR", "and", "BRAFV600E", "IHC", "on", "1403", "consecutive", "CRCs.", "By", "matrix-assisted", "laser", "desorption/ionization-time", "of", "flight", "mass", "spectrometry", "15", "cases", "did", "not", "yield", "a", "BRAF", "result,", "whereas", "38/201", "(19%)", "were", "positive.", "By", "IHC", "45/216", "(20%)", "were", "positive.", "Of", "the", "7", "discordant", "cases,", "real-time", "PCR", "confirmed", "the", "IHC", "result", "in", "6.", "In", "the", "51", "CRCs", "from", "the", "ACCFR,", "IHC", "was", "concordant", "with", "allele-specific", "PCR", "in", "50", "cases.", "BRAFV600E", "and", "MSI", "IHC", "on", "1403", "CRCs", "demonstrated", "the", "following", "phenotypes:", "BRAF/MSS", "(1029", "cases,", "73%),", "BRAF/MSS", "(98,", "7%),", "BRAF/MSI", "(183,", "13%),", "and", "BRAF/MSI", "(93,", "7%).", "All", "11/1403", "cancers", "associated", "with", "proven", "LS", "were", "BRAF", "BRAF", "MSI", ")", "colorectal", "carcinomas", "(CRCs)", "virtually", "excludes", "Lynch", "syndrome", "(LS).", "In", "microsatellite-stable", "(MSS)", "CRCs", "it", "predicts", "poor", "prognosis.", "We", "propose", "a", "universal", "CRC", "LS", "screening", "algorithm", "using", "concurrent", "reflex", "immunohistochemistry", "(IHC)", "for", "BRAFV600E", "and", "mismatch-repair", "(MMR)", "proteins.", "We", "compared", "BRAFV600E", "IHC", "with", "multiplex", "polymerase", "chain", "reaction", "(PCR)", "and", "matrix-assisted", "laser", "desorption/ionization-time", "of", "flight", "mass", "spectrometry", "in", "216", "consecutive", "CRCs", "from", "2011.", "Discordant", "cases", "were", "resolved", "with", "real-time", "PCR.", "BRAFV600E", "IHC", "was", "performed", "on", "51", "CRCs", "from", "the", "Australasian", "Colorectal", "Cancer", "Family", "Registry", "(ACCFR),", "which", "were", "fully", "characterized", "for", "BRAF", "mutation", "by", "allele-specific", "PCR,", "MMR", "status", "(MMR", "IHC", "and", "MSI),", "MLH1", "promoter", "methylation,", "and", "germline", "MLH1", "mutation.", "We", "then", "assessed", "MMR", "and", "BRAFV600E", "IHC", "on", "1403", "consecutive", "CRCs.", "By", "matrix-assisted", "laser", "desorption/ionization-time", "of", "flight", "mass", "spectrometry", "15", "cases", "did", "not", "yield", "a", "BRAF", "result,", "whereas", "38/201", "(19%)", "were", "positive.", "By", "IHC", "45/216", "(20%)", "were", "positive.", "Of", "the", "7", "discordant", "cases,", "real-time", "PCR", "confirmed", "the", "IHC", "result", "in", "6.", "In", "the", "51", "CRCs", "from", "the", "ACCFR,", "IHC", "was", "concordant", "with", "allele-specific", "PCR", "in", "50", "cases.", "BRAFV600E", "and", "MSI", "IHC", "on", "1403", "CRCs", "demonstrated", "the", "following", "phenotypes:", "BRAF/MSS", "(1029", "cases,", "73%),", "BRAF/MSS", "(98,", "7%),", "BRAF/MSI", "(183,", "13%),", "and", "BRAF/MSI", "(93,", "7%).", "All", "11/1403", "cancers", "associated", "with", "proven", "LS", "were", "BRAF/MSI.", "We", "conclude", "that", "BRAF", "IHC", "is", "highly", "concordant", "with", "2", "commonly", "used", "PCR-based", "BRAF", "BRAF", "/MSS", "(1029", "cases,", "73%),", "BRAF/MSS", "(98,", "7%),", "BRAF/MSI", "(183,", "13%),", "and", "BRAF/MSI", "(93,", "7%).", "All", "11/1403", "cancers", "associated", "with", "proven", "LS", "were", "BRAF/MSI.", "We", "conclude", "that", "BRAF", "IHC", "is", "highly", "concordant", "with", "2", "commonly", "used", "PCR-based", "BRAF", "V600E", "BRAF", "MSI", "),", "MLH1", "promoter", "methylation,", "and", "germline", "MLH1", "mutation.", "We", "then", "assessed", "MMR", "and", "BRAFV600E", "IHC", "on", "1403", "consecutive", "CRCs.", "By", "matrix-assisted", "laser", "desorption/ionization-time", "of", "flight", "mass", "spectrometry", "15", "cases", "did", "not", "yield", "a", "BRAF", "result,", "whereas", "38/201", "(19%)", "were", "positive.", "By", "IHC", "45/216", "(20%)", "were", "positive.", "Of", "the", "7", "discordant", "cases,", "real-time", "PCR", "confirmed", "the", "IHC", "result", "in", "6.", "In", "the", "51", "CRCs", "from", "the", "ACCFR,", "IHC", "was", "concordant", "with", "allele-specific", "PCR", "in", "50", "cases.", "BRAFV600E", "and", "MSI", "IHC", "on", "1403", "CRCs", "demonstrated", "the", "following", "phenotypes:", "BRAF/MSS", "(1029", "cases,", "73%),", "BRAF/MSS", "(98,", "7%),", "BRAF", "/MSI", "(183,", "13%),", "and", "BRAF/MSI", "(93,", 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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", "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", "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", "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", "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", "of", "Exons", "12-15,", "Exon", "13,", "and", "Exon", "14", "(two", "samples).", "Breakpoint", "analysis", "of", "the", "intragenic", "deletions", "suggests", "they", "occurred", "through", "Alu-mediated", "recombination.", "Our", "results", "indicate", "that", "∼12%", "of", "samples", "suspected", "of", "harboring", "a", "PMS2", "mutation", "based", "on", "immunohistochemical", "staining,", "for", "which", "mutations", "mutation", "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", "of", "Exons", "12-15,", "Exon", "13,", "and", "Exon", "14", "(two", "samples).", "Breakpoint", "analysis", "of", "the", "intragenic", "deletions", "suggests", "they", "occurred", "through", "Alu-mediated", "recombination.", "Our", "results", "indicate", "that", "∼12%", "of", "samples", "suspected", "of", "harboring", "a", "PMS2", "mutation", "based", "on", "immunohistochemical", "staining,", "for", "which", "mutations", "have", "not", "yet", "been", "identified,", "would", "benefit", "from", "testing", "using", "the", "new", "methodology." ]

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