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1266026-05-Discussion-p01
[]
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2386495-03-Methods-p01
[ "Age,", "age", "at", "diagnosis;", "DL,", "duodenal", "mutation", " ", "in", "APC", "or", "MUTYH" ]
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Age, age at diagnosis; DL, duodenal mutation in APC or MUTYH
[ 2, 2632, 16, 2632, 2019, 3574, 31, 5268, 16, 17752, 3979, 1922, 9187, 2014, 2446, 1012, 1023, 3 ]
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[ -100, 0, 0, 0, 0, 0, 0, 0, 0, 3, 5, 0, 0, 0, 0, 0, 0, -100 ]
1557864-01-Abstract-p01
[ "MSI", "was", "detected", "in", "three", "of", "the", "eight", "cell", "lines", "i.e.", "A2780", "(no", "MLH1", "mRNA", "expression", "due", "to", "promoter", "methylation),", "SKOV3", "(no", "MLH1", " ", "mRNA", "expression)", "and", "2774", "(no", "altered", "expression", "of", "MMR", "genes).", "Overall,", "there", "was", "no", "association", "between", "cisplatin", "response", "and", "MMR", "status", "in", "these", "eight", "cell", "lines." ]
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MSI was detected in three of the eight cell lines i.e. A2780 (no MLH1 mRNA expression due to promoter methylation), SKOV3 (no MLH1 mRNA expression) and 2774 (no altered expression of MMR genes). Overall, there was no association between cisplatin response and MMR status in these eight cell lines.
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2275286-04-Results-p02
[ "The", "mutation", "between", "the", "MSI-L", "and", "MSI-H" ]
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The mutation between the MSI-L and MSI-H
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1334229-02-Background-p01
[ "Genetic", "instability", "is", "seen", "in", "most", "types", "of", "cancer", "[10].", "Two", "distinct", "types", "of", "genetic", "instability", "appear", "to", "occur", "in", "colorectal", "cancer", "[11]:", "chromosomal", "and", "microsatellite", "instability.", "Chromosomal", "instability", "results", "in", "gains", "or", "losses", "of", "entire", "chromosomes", "or", "parts", "of", "them,", "and", "gives", "rise", "to", "aneuploid", "tumours", "and", "occurs", "in", "the", "majority", "of", "cancers.", "A", "smaller", "proportion", "of", "colorectal", "cancers", "displays", "microsatellite", "instability,", "represented", "by", "diploid", "cells", "acquiring", "high", "mutation", "rates,", "and", "was", "found", "to", "be", "associated", "with", "defective", "mismatch", "repair", "[12].", "These", "tumours", "are", "less", "likely", "to", "harbour", "mutations", "in", "genes", "associated", "with", "chromosomally", "instable", "and", "generally", "aneuploid", "tumours,", "such", "as", "APC,", "K-ras", "and", "TP53", "[13-21],", "suggesting", "that", "these", "tumours", "form", "a", "distinct", "group.", "Moreover,", "microsatellite", "instable", "tumours", "are", "found", "predominantly", "in", "the", "proximal", "colon", "[22,23],", "are", "more", "likely", "to", "occur", "in", "patients", "with", "a", "positive", "family", "history", "of", "colorectal", "cancer", "[22,23],", "are", "often", "less", "differentiated", "than", "microsatellite", "stable", "tumours", "colorectal", "colorectal", "cancer", " ", "has", "been", "proposed,", "which", "describes", "the", "sequential", "accumulation", "of", "specific", "genetic", "alterations", "in", "various", "pathways,", "involving", "tumour", "suppressor", "genes", "(e.g.", "APC,", "SMAD4,", "TP53)", "and", "oncogenes", "(e.g.", "CTNNB1,", "K-ras)", "[3,4].", "Important", "molecular", "pathways", "that", "upon", "activation", "affect", "the", "early", "and", "intermediate", "stages", "of", "colorectal", "carcinogenesis", "are", "the", "Wnt", "and", "Ras", "signalling", "pathways,", "whereas", "TP53", "inactivation", "is", "considered", "a", "late", "event." ]
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Genetic instability is seen in most types of cancer [10]. Two distinct types of genetic instability appear to occur in colorectal cancer [11]: chromosomal and microsatellite instability. Chromosomal instability results in gains or losses of entire chromosomes or parts of them, and gives rise to aneuploid tumours and occurs in the majority of cancers. A smaller proportion of colorectal cancers displays microsatellite instability, represented by diploid cells acquiring high mutation rates, and was found to be associated with defective mismatch repair [12]. These tumours are less likely to harbour mutations in genes associated with chromosomally instable and generally aneuploid tumours, such as APC, K-ras and TP53 [13-21], suggesting that these tumours form a distinct group. Moreover, microsatellite instable tumours are found predominantly in the proximal colon [22,23], are more likely to occur in patients with a positive family history of colorectal cancer [22,23], are often less differentiated than microsatellite stable tumours colorectal colorectal cancer has been proposed, which describes the sequential accumulation of specific genetic alterations in various pathways, involving tumour suppressor genes (e.g. APC, SMAD4, TP53) and oncogenes (e.g. CTNNB1, K-ras) [3,4]. Important molecular pathways that upon activation affect the early and intermediate stages of colorectal carcinogenesis are the Wnt and Ras signalling pathways, whereas TP53 inactivation is considered a late event.
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1334229-03-Methods-p02
[ "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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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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1601966-02-Background-p01
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In tumors different genetic mechanisms are known to affect gene expression in wider chromosomal regions. Chromosomal aberrations, like homozygous and heterozygous deletions or amplifications, alter the DNA copy number of large genomic regions or even whole chromosome arms, leading to inactivation of tumor suppressor genes [7,8] or to activation of oncogenes. Another genetic phenomenon that is assumed to have drastic effects on gene expression in cancer cells is the aberrant alteration of chromatin structure. Methylation of genomic DNA, histone acetylation, and histone methylation are assumed to have a large impact on the accessibility of DNA for transcription initiation [9]. Such epigenetic mechanisms can affect large genomic regions by possibly either silencing or activating large arrays of genes. However, the regulatory mechanisms governing chromatin assembly and disassembly are only beginning to emerge. So far, due to methodological limitations it has not been possible to study the role of such phenomena for gene expression in cancer cells on a genome-wide scale. Nevertheless, evidence from single-gene focused studies suggests that chromatin regulation does play an important role in tumorigenesis [10,11].
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3034663-03-Methods-p01
[ "Families", "carrying", "the", "p.Lys618Ala", "variant" ]
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Families carrying the p.Lys618Ala variant
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1334229-04-Results-p01
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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 tumours Tumours from 464 of 656 patients, which did not harbour a truncating APC mutation or lacked hMLH1 expression, were analysed for mutations in exon 3 of the CTNNB1 gene. Table 1 describes the tumour and patient characteristics of seven colorectal tumours tumour and patient characteristics of seven colorectal tumours that harboured a mutation in CTNNB1 exon 3. In five colorectal cancers, a CTNNB1 mutation that would lead to loss of one of the Ser/Thr phosphorylation sites and subsequent stabilisation of the protein, occurred at codons 37 and 45, all were C→T transitions, leading to Ser→Phe amino acid changes and occurred in the proximal colon. All bar one also had an activating mutation in the K-ras gene. Three of these five tumours showed hMLH1 deficiency. Two colorectal cancer patients harboured a 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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1360090-03-Results-p01
[ "a", "Data", "was", "unavailable", "for", "MSI", "status", "in", "40", "cases,", "methylation", "status", "in", "83", "cases,", "KRAS", "mutation", "in", "26", "cases", "and", "TP53", "colorectal", "cancer", "." ]
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a Data was unavailable for MSI status in 40 cases, methylation status in 83 cases, KRAS mutation in 26 cases and TP53 colorectal cancer .
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1601966-03-Results-p10
[ "Not", "unexpected,", "we", "found", "loss", "of", "expression", "in", "region", "5q22.2-5q23.1", "(see", "Figures", "27,", "28,", "29).", "This", "interval", "harbors", "two", "known", "TSGs", "in", "colon", "cancer,", "the", "adenomatous", "polyposis", "coli", "gene", "(APC)", "gene", "and", "the", "mutated", "in", "colorectal", "cancer", "(MCC).", "We", "were", "not", "able", "to", "obtain", "expression", "values", "for", "APC.", "APC", "is", "located", "at", "the", "border", "of", "a", "region", "at", "5q22.2-5q22.3", "that", "harbors", "several", "drastically", "down-regulated", "genes.", "Central", "in", "this", "region", "is", "the", "MCC", "gene.", "The", "distal", "border", "is", "the", "CDO1", "gene.", "We", "assume", "that", "deletion", "or", "epigenetic", "silencing", "of", "this", "region", "is", "a", "frequent", "mechanism", "contributing", "to", "colorectal", "tumorigenesis.", "It", "is", "possible", "that", "also", "APC", "or", "MCC", "show", "reduced", "expression,", "that", "genes", "in", "this", "region", "other", "than", "APC", "and", "MCC", "are", "piggy-back", "genes,", "and", "that", "their", "misregulation", "is", "not", "of", "functional", "significance", "for", "tumorigenesis." ]
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Not unexpected, we found loss of expression in region 5q22.2-5q23.1 (see Figures 27, 28, 29). This interval harbors two known TSGs in colon cancer, the adenomatous polyposis coli gene (APC) gene and the mutated in colorectal cancer (MCC). We were not able to obtain expression values for APC. APC is located at the border of a region at 5q22.2-5q22.3 that harbors several drastically down-regulated genes. Central in this region is the MCC gene. The distal border is the CDO1 gene. We assume that deletion or epigenetic silencing of this region is a frequent mechanism contributing to colorectal tumorigenesis. It is possible that also APC or MCC show reduced expression, that genes in this region other than APC and MCC are piggy-back genes, and that their misregulation is not of functional significance for tumorigenesis.
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1601966-03-Results-p04
[ "The", "region", "20q11.22-q11.23", "was", "among", "the", "most", "frequently", "up-regulated", "regions", "(see", "Figures", "12,", "13,", "14).", "Amplifications", "of", "regions", "on", "chromosome", "20q", "have", "been", "identified", "independently", "by", "several", "groups", "in", "CRCs", "[19,21,23,24].", "The", "interval", "comprises", "the", "known", "tumor", "gene", "SRC", "(located", "between", "MANBAL", "and", "BLCAP", "in", "Figures", "12,", "13,", "14)", "for", "which", "no", "informative", "expression", "measures", "were", "obtained.", "We", "note", "that", "it", "is", "possible", "that", "the", "SRC", "gene", "is", "the", "primary", "target", "of", "up-regulation", "in", "our", "CRC", "patients", "tumor", "tumor", "-versus-normal", "expression.", "Genes", "are", "given", "in", "chromosomal", "order", "on", "the", "horizontal", "axis.", "Patient", "codes", "are", "given", "on", "the", "vertical", "axis.", "The", "legend", "depicts", "which", "colors", "code", "for", "which", "expression", "changes", "on", "a", "loge", "scale", "(green:", "down", "in", "tumor;", "red:", "up", "in", "tumor).", "View", "in", "conjunction", "with", "Figures", "7", "and", "8." ]
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The region 20q11.22-q11.23 was among the most frequently up-regulated regions (see Figures 12, 13, 14). Amplifications of regions on chromosome 20q have been identified independently by several groups in CRCs [19,21,23,24]. The interval comprises the known tumor gene SRC (located between MANBAL and BLCAP in Figures 12, 13, 14) for which no informative expression measures were obtained. We note that it is possible that the SRC gene is the primary target of up-regulation in our CRC patients tumor tumor -versus-normal expression. Genes are given in chromosomal order on the horizontal axis. Patient codes are given on the vertical axis. The legend depicts which colors code for which expression changes on a loge scale (green: down in tumor; red: up in tumor). View in conjunction with Figures 7 and 8.
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2386495-05-Discussion-p02
[ "The", "fraction", "of", "large", "deletions", "high", "age", "at", "diagnosis", ",", "and", "a", "low", "frequency", "of", "extracolonic", "manifestations.", "Whether", "these", "patients", "really", "are", "affected", "by", "APC-associated", "FAP", "can", "(of", "course)", "be", "called", "into", "question.", "However,", "among", "attenuated", "cases", "of", "FAP", "in", "these", "study", "we", "have", "found", "very", "subtle", "mutations", "such", "as", "the", "mosaic", "case", "as", "well", "as", "the", "c.70C", ">", "T", "mutation", "and", "splice-site", "mutations.", "Considering", "these", "facts,", "at", "least", "some", "of", "the", "cases", "could", "be", "caused", "by", "mutations", "in", "APC", "resulting", "in", "only", "partially", "inactivation", "of", "the", "gene", "function.", "Since", "the", "main", "purpose", "of", "this", "study", "was", "to", "achieve", "as", "high", "mutation-detection", "rate", "as", "possible", "in", "families", "with", "colorectal", "polyposis", "syndromes,", "using", "a", "range", "of", "different", "molecular", "genetic", "techniques,", "we", "have", "not", "yet", "performed", "any", "further", "analyses", "of", "the", "relatively", "few", "mutation", "negative", "cases", "to", "determine", "if", "they", "belong", "to", "non-polyposis", "CRC", "syndromes." ]
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The fraction of large deletions high age at diagnosis , and a low frequency of extracolonic manifestations. Whether these patients really are affected by APC-associated FAP can (of course) be called into question. However, among attenuated cases of FAP in these study we have found very subtle mutations such as the mosaic case as well as the c.70C > T mutation and splice-site mutations. Considering these facts, at least some of the cases could be caused by mutations in APC resulting in only partially inactivation of the gene function. Since the main purpose of this study was to achieve as high mutation-detection rate as possible in families with colorectal polyposis syndromes, using a range of different molecular genetic techniques, we have not yet performed any further analyses of the relatively few mutation negative cases to determine if they belong to non-polyposis CRC syndromes.
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1601966-03-Results-p10
[ "Down-regulation", "of", "mRNA", "expression", "in", "human", "chromosomal", "region", "18q21.2-18q23", "–", "the", "BCL2", "region", "(patient", "counts", "with", "coordinate", "down-regulation).", "Grayscale", "cross-comparison", "plot", "of", "down-regulation", "patterns", "across", "patients", "(analogous", "to", "Figures", "8,", "11,", "14).", "View", "this", "plot", "in", "conjunction", "with", "Figures", "24", "and", "25.", "Note,", "that", "many", "more", "patients", "show", "down-regulation", "as", "indicated", "by", "dark", "spots", "in", "this", "plot", "than", "up-regulation", "as", "indicated", "by", "dark", "spots", "in", "Figure", "25.", "This", "region", "has", "been", "reported", "in", "other", "studies", "to", "be", "frequently", "deleted", "in", "colon", "cancer", "(see", "Table", "4).", "Note", "the", "expression", "down-regulation", "of", "BCL2.", "SMAD4", "(Hs.298320)", "and", "TCF4", "are", "only", "weakly", "down-regulated.", "The", "DCC", "gene", "is", "also", "located", "in", "this", "region", "between", "LOC51320", "and", "MBD2", "but", "no", "informative", "expression", "measures", "were", "obtained." ]
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Down-regulation of mRNA expression in human chromosomal region 18q21.2-18q23 – the BCL2 region (patient counts with coordinate down-regulation). Grayscale cross-comparison plot of down-regulation patterns across patients (analogous to Figures 8, 11, 14). View this plot in conjunction with Figures 24 and 25. Note, that many more patients show down-regulation as indicated by dark spots in this plot than up-regulation as indicated by dark spots in Figure 25. This region has been reported in other studies to be frequently deleted in colon cancer (see Table 4). Note the expression down-regulation of BCL2. SMAD4 (Hs.298320) and TCF4 are only weakly down-regulated. The DCC gene is also located in this region between LOC51320 and MBD2 but no informative expression measures were obtained.
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1601966-03-Results-p08
[ "4p15.31-4p15.2" ]
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4p15.31-4p15.2
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2386495-01-Abstract-p01
[ "Methods" ]
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Methods
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1334229-03-Methods-p02
[ "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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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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1619718-01-Abstract-p01
[ "Conclusions" ]
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Conclusions
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1266026-05-Discussion-p01
[ "An", "epigenetic", "mechanism", "may", "help", "explain", "why", "sporadic", "MSI+", "cancers", "colorectal", "germline", "mutations", " ", "(APC", "and", "MMR", "loci)", "in", "both", "common", "colorectal", "familial", "cancer", "familial", " ", "cancer", "syndromes", "(", "FAP", " ", "and", "HNPCC)", "appear", "to", "advance", "progression", "by", "more", "than", "a", "single", "mutation", "relative", "to", "their", "sporadic", "counterparts." ]
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An epigenetic mechanism may help explain why sporadic MSI+ cancers colorectal germline mutations (APC and MMR loci) in both common colorectal familial cancer familial cancer syndromes ( FAP and HNPCC) appear to advance progression by more than a single mutation relative to their sporadic counterparts.
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1373649-03-Methods-p01
[ "As", "screening", "method", "for", "HNPCC", "we", "searched", "for", "MSI", "in", "the", "proband's", "primary", "tumor", "and", "metastasis", "tissue", "blocks.", "The", "absence", "of", "proband's", "non-tumor", "DNA", "for", "MSI", "testing", "was", "overcome", "studying", "the", "alleles", "carried", "by", "his", "progenitors.", "Once", "the", "MSI", "was", "established,", "a", "second", "blood", "sample", "was", "obtained", "from", "the", "proband's", "mother", "(obligate", "carrier", "but", "at", "the", "moment", "of", "the", "study", "still", "unaffected", "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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As screening method for HNPCC we searched for MSI in the proband's primary tumor and metastasis tissue blocks. The absence of proband's non-tumor DNA for MSI testing was overcome studying the alleles carried by his progenitors. Once the MSI was established, a second blood sample was obtained from the proband's mother (obligate carrier but at the moment of the study still unaffected 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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2275286-04-Results-p02
[ "Details", "of", "the", "8", "patients", "in", "MSS", "group", "identified", "to", "have", "MMR", "gene", "germline", "mutation" ]
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Details of the 8 patients in MSS group identified to have MMR gene germline mutation
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1557864-02-Background-p01
[ "Ovarian", "cancer", "is", "the", "leading", "cause", "of", "death", "from", "gynecological", "cancer", "in", "the", "Western", "world", "[1].", "The", "treatment", "of", "ovarian", "adenocarcinoma", "has", "improved", "over", "the", "last", "20", "years", "owing", "to", "the", "combined", "treatment", "of", "cytoreductive", "surgery", "and", "chemotherapy", "[2].", "Although", "the", "response", "of", "the", "primary", "tumor", "to", "taxane", "and", "platinum-based", "chemotherapy", "is", "high,", "about", "20%", "of", "patients", "never", "achieve", "a", "clinical", "response", "and", "the", "majority", "of", "the", "patients", "will", "relapse", "and", "eventually", "die", "of", "drug-resistant", " ", "disease", "[3]." ]
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Ovarian cancer is the leading cause of death from gynecological cancer in the Western world [1]. The treatment of ovarian adenocarcinoma has improved over the last 20 years owing to the combined treatment of cytoreductive surgery and chemotherapy [2]. Although the response of the primary tumor to taxane and platinum-based chemotherapy is high, about 20% of patients never achieve a clinical response and the majority of the patients will relapse and eventually die of drug-resistant disease [3].
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1601966-03-Results-p04
[ "20q11.22-q11.23" ]
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20q11.22-q11.23
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2275286-04-Results-p02
[ "*Amsterdam", "criteria", "II" ]
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*Amsterdam criteria II
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2275286-02-Background-p01
[ "MSI", "is", "an", "important", "phenotype", "of", "MMR", "gene", "mutation.", "In", "1997,", "the", "National", "Cancer", "Institute", "(NCI)", "recommended", "screening", "MSI", "CRCs", "using", "the", "Bethesda", "guidelines", "[5].", "After", "compiling", "evidence", "from", "years", "of", "global", "studies", "and", "follow", "up,", "NCI", "revised", "the", "Bethesda", "guidelines", "in", "2004,", "which", "is", "called", "the", "revised", "Bethesda", "standard", "[6].", "NCI", "recommended", "screening", "of", "HNPCC", "based", "on", "detection", "of", "MSI", "in", "the", "tumor", "and", "loss", "of", "expression", "of", "a", "MMR", "gene", "using", "immunohistochemistry", "(IHC)", "staining", "[6].", "However,", "until", "now,", "there", "has", "been", "no", "research", "about", "the", "applicability", "of", "the", "NCI", "recommendations", "to", "the", "Chinese", "population", "with", "colorectal", "cancers.", "The", "aim", "of", "this", "study", "is", "to", "detect", "and", "study", "MSI", "carrier", "and", "mismatch", "repair", "(MMR)", "gene", "germline", "mutation", "carriers", "HNPCC", " ", "is", "an", "autosomal", "dominant", "syndrome,", "which", "accounts", "for", "about", "1–5%", "of", "colorectal", "cancer", "[1].", "HNPCC", " ", "patients", "are", "characterized", "by", "earlier", "symptoms,", "more", "mucinous", "carcinoma,", "more", "synchronous", "and", "metachronous", "colorectal", "tumors", "and", "more", "extra-colonic", "tumors,", "but", "have", "better", "survival", "[1,2].", "It", "is", "believed", "that", "HNPCC", "is", "secondary", "to", "a", "germline", "mutation", "resulting", "in", "a", "defective", "MMR", "gene.", "A", "defective", "MMR", "gene", "results", "in", "increased", "DNA", "replication", "errors", "and", "MSI,", "which", "causes", "the", "occurrence", "of", "tumors", "in", "different", "organs,", "especially", "in", "the", "colorectum.", "Identification", "of", "HPNCC", "families", "is", "important", "because", "the", "diagnosis,", "treatment", "and", "follow", "up", "of", "these", "individuals", "should", "be", "different", "from", "those", "with", "sporadic", "colorectal", "cancer", "[2].", "However,", "the", "clinical", "diagnosis", "of", "HNPCC", "patients", "is", "very", "difficult", "for", "lack", "of", "specific", "clinical", "phenotype.", "Though", "Amsterdam", "criteria", "I", "and", "II", "were", "established", "for", "HNPCC", "diagnosis[3,4],", "many", "HNPCC", "families", "still", "do", "not", "meet", "the", "criteria." ]
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MSI is an important phenotype of MMR gene mutation. In 1997, the National Cancer Institute (NCI) recommended screening MSI CRCs using the Bethesda guidelines [5]. After compiling evidence from years of global studies and follow up, NCI revised the Bethesda guidelines in 2004, which is called the revised Bethesda standard [6]. NCI recommended screening of HNPCC based on detection of MSI in the tumor and loss of expression of a MMR gene using immunohistochemistry (IHC) staining [6]. However, until now, there has been no research about the applicability of the NCI recommendations to the Chinese population with colorectal cancers. The aim of this study is to detect and study MSI carrier and mismatch repair (MMR) gene germline mutation carriers HNPCC is an autosomal dominant syndrome, which accounts for about 1–5% of colorectal cancer [1]. HNPCC patients are characterized by earlier symptoms, more mucinous carcinoma, more synchronous and metachronous colorectal tumors and more extra-colonic tumors, but have better survival [1,2]. It is believed that HNPCC is secondary to a germline mutation resulting in a defective MMR gene. A defective MMR gene results in increased DNA replication errors and MSI, which causes the occurrence of tumors in different organs, especially in the colorectum. Identification of HPNCC families is important because the diagnosis, treatment and follow up of these individuals should be different from those with sporadic colorectal cancer [2]. However, the clinical diagnosis of HNPCC patients is very difficult for lack of specific clinical phenotype. Though Amsterdam criteria I and II were established for HNPCC diagnosis[3,4], many HNPCC families still do not meet the criteria.
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1619718-05-Discussion-p03
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ACF, Aberrant crypt foci (hyperplastic or dysplastic); HP, hyperplastic polyp; SSA, sessile serrated adenoma; SA SSA , sessile serrated adenoma; SA, serrated adenoma; TA, tubular serrated adenoma; TA lesions serrated mutation BRAF polyps dysplasia polyps serrated polyps with dysplasia evolve through at least two independent histogenetic pathways. Group A polyps are likely to be initiated by BRAF mutation and are serrated lesions at the outset. Group B polyps may begin as conventional adenomas and then become serrated and villous following mutation of KRAS. There may be instances in which KRAS mutation can initiate lesions which are serrated at the outset and become dysplastic. While this suggestion remains speculative, it may apply to the Group A serrated polyps that show a distinct likeness to the goblet cell variant of HP in which columnar cells are eosinophilic and lack mucin-filled microvesicles and KRAS mutation is frequent (Figure 1E,F).16,25 The literature refers to the concept of ‘traditional’ SA.43 Based on the current findings, it is likely that several mechanisms can account for adenomatous lesions with glandular serration and that ‘traditional’ SA is not a single entity.
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3034663-03-Methods-p01
[ "Families", "carrying", "the", "p.Lys618Ala", "variant" ]
[ 0, 0, 0, 0, 0 ]
Families carrying the p.Lys618Ala variant
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3034663-03-Methods-p01
[ "Genotyping", "of", "the", "MLH1", "p.Lys618Ala", "variant" ]
[ 0, 0, 0, 0, 0, 0 ]
Genotyping of the MLH1 p.Lys618Ala variant
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1619718-04-Results-p01
[ "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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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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1334229-05-Discussion-p02
[ "The", "method", "for", "mutation", "analysis", "of", "the", "APC", "mutation", "cluster", "region", "and", "exon", "1", "of", "K-ras", "is", "based", "on", "nested", "amplification", "and", "direct", "sequencing", "of", "purified", "PCR", "fragments,", "a", "highly", "sensitive", "method.", "Since", "no", "screening", "step", "was", "performed", "prior", "to", "the", "sequencing", "of", "the", "gene", "fragments,", "it", "is", "unlikely", "that", "mutations", "would", "have", "escaped", "detection.", "The", "reproducibility", "of", "the", "applied", "assays", "was", "good,", "with", "a", "reproducibility", "of", "85%", "and", "88%", "for", "APC", "and", "K-ras,", "respectively.", "Arguably,", "this", "indicates", "the", "extent", "of", "heterogeneity", "present", "in", "the", "tumour", "samples." ]
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The method for mutation analysis of the APC mutation cluster region and exon 1 of K-ras is based on nested amplification and direct sequencing of purified PCR fragments, a highly sensitive method. Since no screening step was performed prior to the sequencing of the gene fragments, it is unlikely that mutations would have escaped detection. The reproducibility of the applied assays was good, with a reproducibility of 85% and 88% for APC and K-ras, respectively. Arguably, this indicates the extent of heterogeneity present in the tumour samples.
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2386495-06-Conclusion-p01
[ "**", "IGNORE", "LINE", "**" ]
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** IGNORE LINE **
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1334229-03-Methods-p02
[ "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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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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1334229-02-Background-p01
[ "Activation", "of", "the", "Wnt", "pathway", "plays", "a", "central", "role", "in", "the", "aetiology", "of", "most", "colorectal", "cancers", "and", "is", "often", "the", "result", "of", "mutations", "in", "the", "N-terminal", "domain", "of", "the", "APC", "gene,", "that", "lead", "to", "partial", "or", "complete", "loss", "of", "this", "region", "and", "thereby", "to", "loss", "of", "the", "β-catenin", "regulating", "function", "[5,6].", "Conversely,", "in", "tumours", "lacking", "these", "APC", "mutations", "[7],", "activating", "missense", "mutations", "at", "one", "of", "the", "phosphorylation", "sites", "at", "codons", "31,", "33,", "37", "and", "45", "of", "exon", "3", "of", "the", "CTNNB1", "gene", "(encoding", "the", "β-catenin", "protein)", "can", "render", "it", "stable", "as", "it", "can", "no", "longer", "be", "tagged", "for", "cellular", "degradation.", "Activation", "of", "the", "Ras", "pathway", "in", "cancer", "is", "marked", "by", "the", "loss", "of", "the", "intrinsic", "GTPase", "activity", "of", "the", "Ras", "protein,", "which", "can", "be", "ascribed", "to", "missense", "mutations", "in", "codons", "12", "and", "13", "of", "exon", "1,", "which", "are", "responsible", "for", "90%", "activating", "mutations", "in", "the", "of", "the", "K-ras", "gene", "[8]." ]
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Activation of the Wnt pathway plays a central role in the aetiology of most colorectal cancers and is often the result of mutations in the N-terminal domain of the APC gene, that lead to partial or complete loss of this region and thereby to loss of the β-catenin regulating function [5,6]. Conversely, in tumours lacking these APC mutations [7], activating missense mutations at one of the phosphorylation sites at codons 31, 33, 37 and 45 of exon 3 of the CTNNB1 gene (encoding the β-catenin protein) can render it stable as it can no longer be tagged for cellular degradation. Activation of the Ras pathway in cancer is marked by the loss of the intrinsic GTPase activity of the Ras protein, which can be ascribed to missense mutations in codons 12 and 13 of exon 1, which are responsible for 90% activating mutations in the of the K-ras gene [8].
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3034663-03-Methods-p01
[ "Concomitant", "deleterious", "variants", "were", "detected", "in", "two", "of", "the", "families:", "one", "in", "the", "MLH1", "gene", "(c.676C>T;", "p.Arg226X)", "and", "the", "other", "in", "the", "MSH6", "gene", "(c.3013C>T;", "p.Arg1005X).", "Seventeen", "affected", "and", "unaffected", "46.7%", "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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Concomitant deleterious variants were detected in two of the families: one in the MLH1 gene (c.676C>T; p.Arg226X) and the other in the MSH6 gene (c.3013C>T; p.Arg1005X). Seventeen affected and unaffected 46.7% 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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1619718-01-Abstract-p01
[ "To", "establish", "and", "explain", "the", "pattern", "of", "molecular", "signatures", "across", "colorectal", "polyps." ]
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To establish and explain the pattern of molecular signatures across colorectal polyps.
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2275286-01-Abstract-p01
[ "Results" ]
[ 0 ]
Results
[ 2, 2274, 3 ]
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1619718-03-Materials-and-methods-p02
[ "p53", "immunohistochemistry", "and", "scoring" ]
[ 0, 0, 0, 0 ]
p53 immunohistochemistry and scoring
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[ 1, 1, 1, 1, 1, 1 ]
[ -100, 0, 0, 0, 0, -100 ]
1619718-02-Introduction-p01
[ "In", "recent", "years,", "the", "fundamental", "division", "of", "colorectal", "polyps", "into", "precancerous", "adenomas", " ", "and", "innocent", "HPs", "has", "begun", "to", "erode", "and", "the", "concept", "of", "an", "alternative", "serrated", "pathway", "has", "gained", "support.", "This", "revision", "began", "with", "the", "description", "of", "an", "intermediate", "lesion", "described", "as", "serrated", "adenoma", " ", "(SA).10", "Initially,", "however,", "SA", "was", "not", "conceived", "as", "an", "intermediate", "category", "of", "polyp", "but", "essentially", "as", "an", "adenoma", "with", "a", "superimposed", "serrated", "architecture", "that", "conferred", "only", "a", "superficial", "likeness", "to", "a", "HP.10", "Additionally,", "the", "mixed", "polyp", "(MP)", "was", "perceived", "as", "a", "chance", "collision", "between", "a", "HP", "and", "an", "adenoma,", "giving", "a", "combined", "polyp.", "These", "preliminary", "interpretations", "did", "not", "represent", "a", "major", "departure", "from", "the", "traditional", "classification", "of", "colorectal", "polyps", "but", "preserved", "the", "fundamental", "distinction", "of", "neoplastic", "adenomas", "versus", "non-neoplastic", "HPs." ]
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In recent years, the fundamental division of colorectal polyps into precancerous adenomas and innocent HPs has begun to erode and the concept of an alternative serrated pathway has gained support. This revision began with the description of an intermediate lesion described as serrated adenoma (SA).10 Initially, however, SA was not conceived as an intermediate category of polyp but essentially as an adenoma with a superimposed serrated architecture that conferred only a superficial likeness to a HP.10 Additionally, the mixed polyp (MP) was perceived as a chance collision between a HP and an adenoma, giving a combined polyp. These preliminary interpretations did not represent a major departure from the traditional classification of colorectal polyps but preserved the fundamental distinction of neoplastic adenomas versus non-neoplastic HPs.
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2275286-04-Results-p02
[ "Details", "of", "the", "8", "patients", "in", "MSS", "group", "identified", "to", "have", "MMR", "MSS", "CRCs", " ", "are", "summarized", "in", "Table", "6.", "Six", "CRCs", "with", "mutations", "were", "MSI-H", "and", "two", "patients", "with", "mutations", "were", "MSI-L." ]
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Details of the 8 patients in MSS group identified to have MMR MSS CRCs are summarized in Table 6. Six CRCs with mutations were MSI-H and two patients with mutations were MSI-L.
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1334229-03-Methods-p02
[ "APC", "mutation", "analysis" ]
[ 0, 0, 0 ]
APC mutation analysis
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[ 0, 0, 0, 0, 0 ]
[ 1, 1, 1, 1, 1 ]
[ -100, 0, 0, 0, -100 ]
1334229-03-Methods-p02
[ "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", "tumours", "from", "patients", "(codon", "41:", "A→G", "and", "codon", "45:", "C→T)", "as", "positive", "controls", "APC", "mutation", "K-ras", " ", "mutation", "analysis" ]
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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 tumours from patients (codon 41: A→G and codon 45: C→T) as positive controls APC mutation K-ras mutation analysis
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1334229-01-Abstract-p01
[ "In", "a", "group", "of", "656", "unselected", "sporadic", "colorectal", "cancer", "patients,", "aberrations", "in", "the", "APC,", "K-ras", ",", "CTNNB1", "genes,", "and", "expression", "of", "hMLH1", "were", "investigated.", "Additionally,", "tumours", "were", "divided", "in", "groups", "based", "on", "molecular", "features", "and", "compared", "with", "respect", "to", "patient's", "age", "at", "diagnosis,", "sex,", "family", "history", "of", "colorectal", "cancer,", "tumour", "sub-localisation,", "Dukes'", "stage", "and", "differentiation." ]
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In a group of 656 unselected sporadic colorectal cancer patients, aberrations in the APC, K-ras , CTNNB1 genes, and expression of hMLH1 were investigated. Additionally, tumours were divided in groups based on molecular features and compared with respect to patient's age at diagnosis, sex, family history of colorectal cancer, tumour sub-localisation, Dukes' stage and differentiation.
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2386495-04-Results-p01
[ "Mutation", "spectrum", "of", "the", "APC", "gene.", "(A)", "The", "spectrum", "of", "APC", "mutations", "identified", "among", "families", "from", "the", "Swedish", "Polyposis", "Registry", "showing", "the", "distribution", "between", "previously", "reported", "and", "novel", "mutations", "in", "our", "patients.", "(B)", "A", "schematic", "representation", "of", "the", "APC", "coding", "region,", "shown", "in", "the", "same", "scale", "as", "in", "(A).", "The", "arrow", "with", "an", "asterisk", "indicates", "codon", "24", "and", "the", "second", "arrow", "points", "at", "codon", "184.", "(C)", "Distribution", "of", "six", "large", "deletions", "found", "in", "seven", "unrelated", "patients", "of", "the", "Swedish", "Polyposis", "Registry.", "Novel", "deletions", "are", "marked", "with", "an", "asterisk.", "Patient", "numbers", "are", "shown", "to", "the", "left.", "Scale", "as", "in", "(A)." ]
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Mutation spectrum of the APC gene. (A) The spectrum of APC mutations identified among families from the Swedish Polyposis Registry showing the distribution between previously reported and novel mutations in our patients. (B) A schematic representation of the APC coding region, shown in the same scale as in (A). The arrow with an asterisk indicates codon 24 and the second arrow points at codon 184. (C) Distribution of six large deletions found in seven unrelated patients of the Swedish Polyposis Registry. Novel deletions are marked with an asterisk. Patient numbers are shown to the left. Scale as in (A).
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2386495-04-Results-p01
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Large deletions of the APC CRC mutations in the region from codon 1250 to 1464 Probands with mutations in the region from codon 1250 to 1464 of the APC gene which predicts a severe phenotype [36] had a median age at diagnosis of 21.8 (range, 11–49) years compared with 34.4 (range, 14–57) years among those with mutations outside this region range, 14–57 34.4 range, 11–49 ) years compared with 34.4 (range, 14–57) years among those with mutations outside this region (P < 0.017). Available data on colorectal polyp number shows that, in spite of higher age at diagnosis, dense polyposis (> 1000) only occurred in 30% of the probands compared with 75% in those with mutations between codon 1250 and 1464. In the former group 29% (7 out of 24) had CRC at diagnosis compared with 25% (2 out of 8) in the latter group. The mean age at CRC was 46.6 (range 28–57) and 37.5 (range 26–49) years, respectively. The total morbidity in CRC among probands was 34% (11 out of 32). Of all probands diagnosed after 1996, four out of nine (44%) had cancer at diagnosis. The median age in this group was 47.5 (range 45–51) years and none had, despite high age at diagnosis of CRC, dense colorectal polyposis at diagnosis indicating a less-severe phenotype. A compilation of clinical status of all patients analyzed in this study is shown in Additional file 1.
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3034663-05-Discussion-p01
[ "Classification", "of", "the", "MLH1", "p.Lys618Ala", "variant", "according", "to", "the", "InSiGHT", "database", "(accessed", "on", "07/2010)." ]
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Classification of the MLH1 p.Lys618Ala variant according to the InSiGHT database (accessed on 07/2010).
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1360090-03-Results-p01
[ "Associations", "between", "BRAF", "mutation", "and", "molecular", "features", "of", "colorectal", "cancer." ]
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Associations between BRAF mutation and molecular features of colorectal cancer.
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1601966-03-Results-p02
[ "Whole-chromosome", "plots", "of", "running", "average", "of", "fractions", "of", "samples", "showing", "up-/down-regulation", "in", "tumor", "versus", "normal", "normal", " ", "samples", "(Chromosomes", "1,", "2,", "3,", "4).", "For", "each", "chromosome", "you", "see", "a", "separate", "figure.", "Gray", "dots", "denote", "the", "number", "of", "patients", "with", "up-", "or", "down-regulation", "for", "a", "single", "gene.", "Orange/green", "lines", "represent", "a", "running", "average", "of", "these", "values.", "The", "plots", "are", "made", "to", "be", "easily", "comparable", "with", "whole-genome", "CGH", "plots", "(like", "e.g.", "those", "in", "Knösel", "et", "al.", "[21])", "Further", "details", "of", "plot", "construction", "are", "described", "in", "the", "methods", "section." ]
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Whole-chromosome plots of running average of fractions of samples showing up-/down-regulation in tumor versus normal normal samples (Chromosomes 1, 2, 3, 4). For each chromosome you see a separate figure. Gray dots denote the number of patients with up- or down-regulation for a single gene. Orange/green lines represent a running average of these values. The plots are made to be easily comparable with whole-genome CGH plots (like e.g. those in Knösel et al. [21]) Further details of plot construction are described in the methods section.
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1619718-02-Introduction-p02
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This paper explores the possibility that the early evolution of colorectal cancer is not limited to two essentially independent pathways, but often combines components of these pathways. Indeed, the successful ‘fusion’ of the hyperproliferation and crypt fission that characterize adenomas21 with the inhibition of apoptosis that has been linked with serrated polyps22,23 may generate lesions with enhanced aggressiveness. Specifically, it is suggested that methylation of the DNA repair gene O-6-methylguanine DNA methyltransferase (MGMT), mutation of KRAS and inactivation BRAF and extensive DNA methylation.12 This viewpoint was consolidated through the formal recognition of two largely independent pathways of colorectal tumorigenesis: (i) the traditional adenoma– carcinoma DNA methylation .12 This viewpoint was consolidated through the formal recognition of two largely independent pathways of colorectal tumorigenesis: (i) the traditional adenoma colorectal tumorigenesis : (i) the traditional adenoma–carcinoma sequence associated with chomosomally unstable CRCs,13 and (ii) the ‘serrated pathway’ culminating in CRCs with DNA microsatellite instability (MSI), mutation of BRAF and extensive DNA methylation.12,14–20
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1557864-02-Background-p01
[ "Inactivation", "of", "MMR", "leads", "to", "the", "occurrence", "of", "unrepaired", "deletions", "in", "mono-", "and", "dinucleotide", "repeats", "resulting", "in", "variable", "lengths", "of", "these", "repeats.", "This", "is", "called", "microsatellite", "instability", "(MSI)", "and", "MSI", "is", "therefore", "used", "as", "a", "marker", "for", "MMR", "deficiency.", "MSI", "can", "be", "caused", "by", "genetic", "or", "epigenetic", "inactivation", "of", "several", "genes", "involved", "in", "MMR.", "Mouse", "knockout", "models", "have", "demonstrated", "that", "MSH2-/-,", "MSH3-/-,", "MLH1-/-", "and", "PMS2-/-", "leads", "to", "a", "high", "frequency", "of", "MSI", "while", "MSH6-/-", "and", "PMS1-/-", "cause", "a", "low", "frequency", "(reviewed", "by", "Wei", "et", "al.", "[10]).", "However,", "in", "hereditary", "nonpolyposis", "colon", "cancer", "(HNPCC)", "families", "ovarian", "ovarian", " ", "adenocarcinoma", "has", "improved", "over", "the", "last", "20", "years", "owing", "to", "the", "combined", "treatment", "of", "cytoreductive", "surgery", "and", "chemotherapy", "[2].", "Although", "the", "response", "of", "the", "primary", "tumor", "to", "taxane", "and", "platinum-based", "chemotherapy", "is", "high,", "about", "20%", "of", "patients", "never", "achieve", "a", "clinical", "response", "and", "the", "majority", "of", "the", "patients", " ", "will", "relapse", "and", "eventually", "die", "of", "drug-resistant", "disease", "[3]." ]
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Inactivation of MMR leads to the occurrence of unrepaired deletions in mono- and dinucleotide repeats resulting in variable lengths of these repeats. This is called microsatellite instability (MSI) and MSI is therefore used as a marker for MMR deficiency. MSI can be caused by genetic or epigenetic inactivation of several genes involved in MMR. Mouse knockout models have demonstrated that MSH2-/-, MSH3-/-, MLH1-/- and PMS2-/- leads to a high frequency of MSI while MSH6-/- and PMS1-/- cause a low frequency (reviewed by Wei et al. [10]). However, in hereditary nonpolyposis colon cancer (HNPCC) families ovarian ovarian adenocarcinoma has improved over the last 20 years owing to the combined treatment of cytoreductive surgery and chemotherapy [2]. Although the response of the primary tumor to taxane and platinum-based chemotherapy is high, about 20% of patients never achieve a clinical response and the majority of the patients will relapse and eventually die of drug-resistant disease [3].
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2386495-06-Conclusion-p01
[ "Conclusion" ]
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1334229-04-Results-p02
[ "When", "comparing", "tumours", "with", "a", "missense", "(but", "not", "a", "truncating)", "mutation", "in", "APC", "to", "tumours", "with", "a", "truncating", "mutation", "in", "APC,", "missense", "mutations", "occurred", "relatively", "more", "frequently", "in", "the", "colon", "(P", "=", "0.002),", "less", "often", "also", "harboured", "an", "activating", "K-ras", "mutation", "(P", "=", "0.004),", "and", "more", "often", "also", "lacked", "hMLH1", "hMLH1", " ", "expression,", "and", "these", "results", "are", "presented", "in", "table", "4.", "Patients", "harbouring", "hMLH1", " ", "deficient", "tumours", "were", "slightly", "older", "when", "diagnosed", "with", "colorectal", "cancer", "(69.3", "yr", "(68.0–70.5)", "versus", "67.8", "(67.4–68.3),", "P", "=", "0.03),", "were", "relatively", "less", "frequently", "men", "(40%", "versus", "58%,", "P", "=", "0.02).", "Tumours", "without", "hMLH1", "expression", "occurred", "relatively", "more", "frequently", "in", "the", "proximal", "colon", "(P", "<", "0.001)", "and", "relatively", "more", "frequently", "showed", "poor", "differentiation", "or", "are", "undifferentiated", "(P", "<", "0.001)." ]
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When comparing tumours with a missense (but not a truncating) mutation in APC to tumours with a truncating mutation in APC, missense mutations occurred relatively more frequently in the colon (P = 0.002), less often also harboured an activating K-ras mutation (P = 0.004), and more often also lacked hMLH1 hMLH1 expression, and these results are presented in table 4. Patients harbouring hMLH1 deficient tumours were slightly older when diagnosed with colorectal cancer (69.3 yr (68.0–70.5) versus 67.8 (67.4–68.3), P = 0.03), were relatively less frequently men (40% versus 58%, P = 0.02). Tumours without hMLH1 expression occurred relatively more frequently in the proximal colon (P < 0.001) and relatively more frequently showed poor differentiation or are undifferentiated (P < 0.001).
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1619718-05-Discussion-p03
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The preceding findings indicate that serrated polyps with dysplasia evolve through at least two independent histogenetic pathways. Group A polyps are likely to be initiated by BRAF mutation and are serrated lesions at the outset. Group B polyps may begin as conventional adenomas and then become serrated and villous following mutation of KRAS. There may be instances in which KRAS mutation can initiate lesions which are serrated at the outset and become dysplastic. While this suggestion remains speculative, it may apply to the Group A serrated polyps that show a distinct likeness to the goblet cell variant of HP in which columnar cells are eosinophilic and lack mucin-filled microvesicles and KRAS mutation is frequent (Figure 1E,F).16,25 The literature refers to the concept of ‘traditional’ SA.43 Based on the current findings, it is likely that several mechanisms can account for adenomatous lesions with glandular serration and that ‘traditional’ SA is not a single entity.
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2386495-01-Abstract-p01
[ "Methods" ]
[ 0 ]
Methods
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2275286-04-Results-p02
[ "*Amsterdam", "criteria", "II" ]
[ 0, 0, 0 ]
*Amsterdam criteria II
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[ 0, 0, 0, 0, 0, 0 ]
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1360090-03-Results-p01
[ "Associations", "between", "BRAF", "mutation", "and", "clinicopathological", "features", "of", "colorectal", "cancer." ]
[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]
Associations between BRAF mutation and clinicopathological features of colorectal cancer.
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3034663-04-Results-p01
[ "There", "were", "no", "significant", "associations", "in", "the", "case-control", "and", "case-case", "studies", "(80%", "detection", "power,", "OR", "=", "3.0;", "two-sided", "test,", "alpha", "level", "=", "5%)", "(Table", "2)", "and", "no", "statistically", "significant", "associations", "when", "the", "OR", "was", "adjusted", "for", "age", "and", "sex." ]
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There were no significant associations in the case-control and case-case studies (80% detection power, OR = 3.0; two-sided test, alpha level = 5%) (Table 2) and no statistically significant associations when the OR was adjusted for age and sex.
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3034663-03-Methods-p01
[ "Three", "characterized", "LS", "families", "that", "fulfilled", "the", "Amsterdam", "II", "Criteria", "and", "that", "consisted", "of", "members", "with", "the", "p.Lys618Ala", "variant", "were", "included", "to", "assess", "co-occurrence", "and", "co-segregation.", "Two", "families", "attended", "the", "Genetic", "Counselling", "in", "Cancer", "Units", "of", "the", "Elche", "and", "La", "Fe", "Hospitals", "and", "one", "family", "was", "a", "member", "of", "the", "EPICOLON", "cohort", "[7]." ]
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Three characterized LS families that fulfilled the Amsterdam II Criteria and that consisted of members with the p.Lys618Ala variant were included to assess co-occurrence and co-segregation. Two families attended the Genetic Counselling in Cancer Units of the Elche and La Fe Hospitals and one family was a member of the EPICOLON cohort [7].
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1557864-01-Abstract-p01
[ "Results" ]
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Results
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2386495-02-Background-p02
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In the present study patients included in the Swedish Polyposis Registry were subjected to a thorough clinical characterization and mutational screening of the APC gene including screening for large deletions and detection of low-frequency alleles caused by germline mosaicism. Sixty-one mutations Sixty-one APC gene including screening for large deletions and detection of low-frequency alleles caused by germline mosaicism. Sixty-one mutations, including 27 not described previously, are reported. Among the characterized mutations are elusive changes such as a case of mosaicism, splicing defects, and a mutation in APC exon 1 which is the most 5' APC APC exon 1 which is the most 5' APC mutation hitherto reported. The detection of reduced APC expression in one family splicing defects , and a mutation in APC exon 1 which is the most 5' APC mutation hitherto reported. The detection of reduced APC patients included in the Swedish Polyposis Registry were subjected to a thorough clinical characterization and mutational screening of the APC gene including screening for large deletions and detection of low-frequency alleles caused by germline mosaicism. Sixty-one mutations, including 27 not described previously, are reported. Among the characterized mutations are elusive changes such as a case of mosaicism, splicing defects, and a mutation in APC exon 1 which is the most 5' APC mutation hitherto reported. The detection of reduced APC expression in one Swedish Polyposis Registry were subjected to a thorough clinical characterization and mutational screening of the APC gene including screening for large deletions and detection of low-frequency alleles caused by germline mosaicism. Sixty-one mutations, including 27 not described previously, are reported. Among the characterized mutations are elusive changes such as a case of mosaicism , splicing defects, and a mutation in APC exon 1 which is the most 5' APC mutation hitherto reported. The detection of reduced APC expression in one family is also described. A combination of mutation screening techniques was used to achieve as high a mutation-detection frequency as possible.
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1266026-05-Discussion-p02
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Multistage models are mechanistically different from tumor progression models and more consistent with a hypothesis that mutations acquired early during progression help determine extent of invasion (Figure 3). Mutations sequentially accumulate before transformation in both models, but the adenoma-cancer sequence suggests most cancer mutations start to accumulate after the age of 50 years in adenomas [7]. Such tumor progression imposes purpose to early mutations because each additional mutation confers incremental changes to a non-invasive adenoma phenotype. Therefore, tumor progression models would likely differ between MSI+ and MSI- cancers because their biology and types of mutations are quite different [7,8].
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2386495-01-Abstract-p01
[ "Sixty-one", "different", "APC", "mutations", "in", "81", "of", "the", "96", "families", "were", "identified", "and", "27", "of", "those", "are", "novel.", "We", "have", "previously", "shown", "that", "6", "of", "the", "96", "patients", "27", " ", "of", "those", "are", "novel.", "We", "have", "previously", "shown", "that", "6", "of", "the", "96", "patients", "carried", "biallelic", "MUTYH", "mutations.", "The", "9", "mutation-negative", "cases", "families" ]
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Sixty-one different APC mutations in 81 of the 96 families were identified and 27 of those are novel. We have previously shown that 6 of the 96 patients 27 of those are novel. We have previously shown that 6 of the 96 patients carried biallelic MUTYH mutations. The 9 mutation-negative cases families
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1601966-03-Results-p05
[ "12q14.2-12q22" ]
[ 0 ]
12q14.2-12q22
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2275286-04-Results-p02
[ "The", "mutation", "between", "the", "MSI-L", "and", "MSI-H" ]
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The mutation between the MSI-L and MSI-H
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1619718-02-Introduction-p01
[ "**", "IGNORE", "LINE", "**" ]
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** IGNORE LINE **
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1373649-03-Methods-p01
[ "**", "IGNORE", "LINE", "**" ]
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** IGNORE LINE **
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3034663-04-Results-p01
[ "Results", "of", "genotyping", "for", "the", "p.Lys618Ala", "variant", "using", "the", "iPLEX", "Sequenom", "(A)", "and", "sequencing", "(B)", "methods." ]
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Results of genotyping for the p.Lys618Ala variant using the iPLEX Sequenom (A) and sequencing (B) methods.
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1334229-03-Methods-p01
[ "Incident", "cancer", "cases", "are", "identified", "by", "monitoring", "of", "the", "entire", "cohort", "for", "cancer", "occurrence", "through", "annual", "record", "linkage", "to", "the", "Netherlands", "Cancer", "Registry,", "i.e.", "nine", "regional", "cancer", "registries", "throughout", "the", "Netherlands,", "and", "to", "PALGA,", "a", "nationwide", "network", "and", "registry", "of", "histo-", "and", "cytopathology", "[30].", "Together,", "the", "NCR", "and", "PALGA", "provide", "a", "near", "100%", "coverage", "of", "the", "municipalities", "included", "in", "the", "NLCS.", "The", "first", "2.3", "years", "of", "follow", "up", "were", "excluded", "because", "of", "possible", "pre-clinical", "disease", "affecting", "exposure", "status", "and", "because", "of", "incomplete", "nationwide", "coverage", "of", "PALGA", "in", "some", "of", "the", "municipalities", "included", "in", "the", "NLCS", "in", "that", "period.", "From", "1989", "until", "1994,", "929", "incident", "cases", "with", "histologically", "confirmed", "colorectal", "cancer", "were", "identified", "within", "the", "cohort,", "of", "whom", "819", "could", "also", "be", "linked", "to", "a", "PALGA", "report", "of", "the", "lesion." ]
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Incident cancer cases are identified by monitoring of the entire cohort for cancer occurrence through annual record linkage to the Netherlands Cancer Registry, i.e. nine regional cancer registries throughout the Netherlands, and to PALGA, a nationwide network and registry of histo- and cytopathology [30]. Together, the NCR and PALGA provide a near 100% coverage of the municipalities included in the NLCS. The first 2.3 years of follow up were excluded because of possible pre-clinical disease affecting exposure status and because of incomplete nationwide coverage of PALGA in some of the municipalities included in the NLCS in that period. From 1989 until 1994, 929 incident cases with histologically confirmed colorectal cancer were identified within the cohort, of whom 819 could also be linked to a PALGA report of the lesion.
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1334229-02-Background-p01
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Genetic instability is seen in most types of cancer [10]. Two distinct types of genetic instability appear to occur in colorectal cancer [11]: chromosomal and microsatellite instability. Chromosomal instability results in gains or losses of entire chromosomes or parts of them, and gives rise to aneuploid tumours and occurs in the majority of cancers. A smaller proportion of colorectal cancers displays microsatellite instability, represented by diploid cells acquiring high mutation rates, and was found to be associated with defective mismatch repair [12]. These tumours are less likely to harbour mutations in genes associated with chromosomally instable and generally aneuploid tumours, such as APC, K-ras and TP53 [13-21], suggesting that these tumours form a distinct group. Moreover, microsatellite instable tumours are found predominantly in the proximal colon [22,23], are more likely to occur in patients with a positive family history of colorectal cancer [22,23], are often less differentiated than microsatellite stable tumours [22], and occur more frequently in women [24] and at older age [25]. Moreover, in tumours colorectal cancer has been proposed, which describes the sequential accumulation of specific genetic alterations in various pathways, involving tumour suppressor genes (e.g. APC, SMAD4, TP53) and oncogenes (e.g. CTNNB1, K-ras) [3,4]. Important molecular pathways that upon activation affect the early and intermediate stages of colorectal carcinogenesis are the Wnt and Ras signalling pathways, whereas TP53 inactivation is considered a late event.
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1266026-03-Methods-p01
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** IGNORE LINE **
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1334229-03-Methods-p02
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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 tumours from patients (codon 41: A→G and codon 45: C→T) as positive controls. All of these mutations were repeatedly confirmed by sequencing. WAVE analysis was carried out at two different temperatures (57.7 en 60°C). Samples showing an aberrant elution profile were re-amplified and re-screened. When an aberrant elution profile was confirmed, direct sequencing was performed. All samples without hMLH1 expression codon 45: C→T ) as positive controls. All of these mutations were repeatedly confirmed by sequencing. WAVE analysis was carried out at two different temperatures (57.7 en 60°C). Samples showing an aberrant elution profile were re-amplified and re-screened. When an aberrant elution profile was confirmed, direct sequencing was performed. All samples hMLH1 APC mutation analysis
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2275286-04-Results-p02
[ "P", "=", "0.112" ]
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P = 0.112
[ 2, 58, 33, 20, 18, 11147, 3 ]
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[ -100, 0, 0, 0, 0, 0, -100 ]
1334229-04-Results-p02
[ "Next,", "we", "compared", "the", "patient", "and", "tumour", "characteristics", "of", "tumours", "harbouring", "a", "truncating", "APC", "and/or", "an", "activating", "K-ras", "mutation", "to", "those", "of", "tumours", "without", "hMLH1", "expression,", "and", "these", "results", "are", "presented", "in", "table", "4.", "Patients", "harbouring", "hMLH1", "deficient", "tumours", "were", "slightly", "older", "when", "diagnosed", "with", "colorectal", "cancer", "(69.3", "yr", "(68.0–70.5)", "versus", "67.8", " ", "(67.4–68.3),", "P", "=", "0.03),", "were", "relatively", "less", "frequently", "men", "(40%", "versus", "58%,", "P", "=", "0.02).", "Tumours", "without", "hMLH1", "expression", "occurred", "relatively", "more", "frequently", "in", "the", "proximal", "colon", "(P", "<", "0.001)", "and", "relatively", "more", "frequently", "showed", "poor", "differentiation", "or", "are", "undifferentiated", "(P", "<", "0.001)." ]
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Next, we compared the patient and tumour characteristics of tumours harbouring a truncating APC and/or an activating K-ras mutation to those of tumours without hMLH1 expression, and these results are presented in table 4. Patients harbouring hMLH1 deficient tumours were slightly older when diagnosed with colorectal cancer (69.3 yr (68.0–70.5) versus 67.8 (67.4–68.3), P = 0.03), were relatively less frequently men (40% versus 58%, P = 0.02). Tumours without hMLH1 expression occurred relatively more frequently in the proximal colon (P < 0.001) and relatively more frequently showed poor differentiation or are undifferentiated (P < 0.001).
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3034663-03-Methods-p01
[ "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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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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2386495-01-Abstract-p01
[ "**", "IGNORE", "LINE", "**" ]
[ 0, 0, 0, 0 ]
** IGNORE LINE **
[ 2, 14, 14, 27354, 2823, 14, 14, 3 ]
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[ -100, 0, 0, 0, 0, 0, 0, -100 ]
1373649-03-Methods-p02
[ "After", "establishing", "the", "familial", "mutation", "in", "the", "proband's", "mother,", "located", "in", "the", "exon", "12", "of", "hMSH2", "hMSH2", " ", "and", "hMLH1", "genes" ]
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After establishing the familial mutation in the proband's mother, located in the exon 12 of hMSH2 hMSH2 and hMLH1 genes
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1601966-03-Results-p11
[ "14q24.3" ]
[ 0 ]
14q24.3
[ 2, 2607, 23470, 1006, 18, 23, 3 ]
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[ 1, 1, 1, 1, 1, 1, 1 ]
[ -100, 0, 0, 0, 0, 0, -100 ]
2275286-04-Results-p02
[ "The", "MSI", "state,", "mutation", "sites,", "and", "consequential", "changes", "in", "amino-acid", "sequences", "of", "MMR", "genes", "are", "summarized", "in", "Table", "4.", "In", "34", "MSI", "CRCs", "and", "one", "MSS", "CRC", "with", "MLH1", "negative", "staining,", "8", "had", "MMR", "gene", "germline", "mutations,", "accounting", "for", "22.9%", "of", "MSI", "colorectal", "cancers", "and", "5.5%", "of", "all", "colorectal", "cancers.", "Three", "patients", "had", "MSH6", "germline", "mutations", "and", "5", "had", "MSH2", "germline", "mutations;", "the", "clinical", "features", "of", "these", "patients", "are", "summarized", "in", "Table", "5.", "None", "of", "the", "patients", "had", "MLH1", "gene", "mutations.", "Seven", "patients", "in", "the", "MSI", "group", "had", "A/T", "heterozygosis", "in", "MSH6", "codon", "380", "of", "exon", "5,", "but", "it", "did", "not", "cause", "changes", "in", "the", "amino", "acid", "sequence.", "The", "germline", "mutations", "of", "the", "MSI-L", "and", "MSI-H", "CRCs", "are", "summarized", "in", "Table", "6.", "Six", "CRCs", "with", "mutations", "were", "MSI-H", "and", "two", "patients", "with", "mutations", "were", "MSI-L." ]
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The MSI state, mutation sites, and consequential changes in amino-acid sequences of MMR genes are summarized in Table 4. In 34 MSI CRCs and one MSS CRC with MLH1 negative staining, 8 had MMR gene germline mutations, accounting for 22.9% of MSI colorectal cancers and 5.5% of all colorectal cancers. Three patients had MSH6 germline mutations and 5 had MSH2 germline mutations; the clinical features of these patients are summarized in Table 5. None of the patients had MLH1 gene mutations. Seven patients in the MSI group had A/T heterozygosis in MSH6 codon 380 of exon 5, but it did not cause changes in the amino acid sequence. The germline mutations of the MSI-L and MSI-H CRCs are summarized in Table 6. Six CRCs with mutations were MSI-H and two patients with mutations were MSI-L.
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1334229-01-Abstract-p01
[ "Results" ]
[ 0 ]
Results
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1334229-01-Abstract-p01
[ "In", "a", "group", "of", "656", "unselected", "sporadic", "colorectal", "cancer", "patients,", "aberrations", "in", "the", "APC,", "K-ras,", "CTNNB1", "genes,", "and", "expression", "of", "hMLH1", "were", "investigated.", "Additionally,", "tumours", "were", "divided", "in", "groups", "based", "on", "molecular", "features", "and", "compared", "with", "respect", "to", "patient's", "age", "at", "diagnosis,", "sex,", "family", "history", "of", "colorectal", "cancer,", "tumour", "sub-localisation,", "Dukes'", "stage", "and", "differentiation." ]
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In a group of 656 unselected sporadic colorectal cancer patients, aberrations in the APC, K-ras, CTNNB1 genes, and expression of hMLH1 were investigated. Additionally, tumours were divided in groups based on molecular features and compared with respect to patient's age at diagnosis, sex, family history of colorectal cancer, tumour sub-localisation, Dukes' stage and differentiation.
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1334229-03-Methods-p02
[ "CTNNB1", "mutation", "analysis" ]
[ 0, 0, 0 ]
CTNNB1 mutation analysis
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2386495-03-Methods-p01
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Patient C896, with only five adenomas, was included because of a family history of FAP FAP FAP ). Sixty-one of these families are now extinct but 135 families with at least one living disease-affected member remain. Presently, 315 disease-affected living patients are included in the registry. The geographical catchment area comprises the whole of Sweden. Details of how patients have been eligible for accession into the registry are given in [30]. In this study we have analyzed 96 families included in the registry for mutations in the APC gene. Twenty-four of the remaining 39 families have been analyzed for APC gene mutations at other genetic laboratories and 15 families remain to be tested. We have previously reported six of these patients who carried bi-allelic MUTYH mutations [31]. Probands were defined as those diagnosed on the basis of the occurrence of symptoms and irrespective of other cases in the family and call-up patients, as those identified as subjects at risk on the basis of studies of pedigrees and found to have FAP. De novo mutations were defined in those individuals where none of the parents carried the mutation or where the parents had a negative colonoscopy after the age of 50 or died of a non-FAP related cause after the age of 75. All patients have given their consent and the local ethics committees have approved the study. The clinical features of index patients of each of the families families families families families families are now extinct but 135 families with at least one living disease-affected member remain. Presently, 315 disease-affected living patients are included in the registry. The geographical catchment area comprises the whole of Sweden. Details of how patients have been eligible for accession into the registry are given in [30]. In this study we have analyzed 96 families included in the registry for mutations in the APC gene. Twenty-four of the remaining 39 families have been analyzed for APC gene mutations at other genetic laboratories and 15 families remain to be tested. We have previously reported six of these patients who carried bi-allelic MUTYH mutations [31]. Probands were defined as those diagnosed on the basis of the occurrence of symptoms and irrespective of other cases in the family and call-up patients, as those identified as subjects at risk on the basis of studies of pedigrees and found to have FAP. De novo mutations were defined in those individuals where none of the parents carried the mutation or where the parents had a negative colonoscopy after the age of 50 or died of a non-FAP related cause after the age of 75. All patients have given their consent and the local ethics committees have approved the study. The clinical features of index patients of each of the families analyzed are listed in Additional file 1 and Table 1.
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1373649-02-Background-p01
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This autosomal dominantly inherited disorder is caused by germline mutations in genes coding proteins responsible for the repair of DNA replication errors, which are referred to as DNA mismatch repair (MMR) genes [5]. DNA mismatch repair machinery plays a critical role in genomic stability, including correction of mispaired bases associated with DNA replication and recombination. Germline mutations in one allele of any of these genes followed by the somatic loss or inactivation of the wild-type allele leads to a defective mismatch repair mechanism. The current "gold standard" for assessing tumor DNA MMR activity is molecular microsatellite instability (MSI) testing. In most cases, it involves extracting DNA from both tumor and normal tissue. The DNA is subjected to polymerase chain reaction (PCR) amplification of five or more different chromosomal loci that compare "microsatellites", running the PCR products through a gel to separate DNA fragments by size, comparing the tumor-normal pairs, and scoring for differences between the two. Instability at two or more out of five markers defines a tumor as MSI-H and prompts further analysis, as sequencing of DNA MMR genes. A number of them have been associated with HNPCC, including hMSH2, hMLH1, hPMS1, hPMS2, hMSH3 , and hMSH6 . Most of the HNPCC families in which mutations have been identified involved hMSH2 and hMLH1 genes [6].
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3034663-04-Results-p01
[ "There", "were", "no", "significant", "associations", "in", "the", "case-control", "and", "case-case", "studies", "(80%", "detection", "power,", "OR", "=", "3.0;", "two-sided", "test,", "alpha", "level", "=", "5%)", "(Table", "2)", "and", "no", "statistically", "significant", "associations", "when", "the", "OR", "was", "adjusted", "for", "age", "and", "sex." ]
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There were no significant associations in the case-control and case-case studies (80% detection power, OR = 3.0; two-sided test, alpha level = 5%) (Table 2) and no statistically significant associations when the OR was adjusted for age and sex.
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1619718-03-Materials-and-methods-p01
[ "Tissues" ]
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1619718-05-Discussion-p01
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In previous studies of KRAS in colorectal adenomas, mutation has been associated negatively with flat and depressed TAs and positively with polypoid appearance, increasing size, dysplasia, villous change and synchronous colorectal cancer .6,33–35 In by far the largest study, which included 738 adenomas obtained from 639 participants in a dietary intervention trial, multivariate analysis showed that the independent predictors of KRAS mutation were age of subject, presence of villous architecture and high-grade dysplasia, but not size of adenoma.6 It is well known that adenoma size, dysplasia and villous architecture are interrelated and account has to be taken of this in assessing results. In this study KRAS mutation occurred with the same frequency in small (18%) and large (17%) adenomas but was significantly more frequent in adenomas that included a villous architecture (50%). A previous study showed a very high frequency of KRAS mutation (93%) in flat synchronous adenomas , second on non-dysplastic serrated polyps and will then conclude with the concept that features of these two types of polyp can co-occur or become ‘fused’ in subtypes of advanced polyps with mixed cytomorphology (hyperplastic and dysplastic) and a serrated and/or villous architecture.
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1619718-04-Results-p03
[ "Aberrant", "expression", "of", "p53", "and", "correlation", "with", "MGMT", "loss" ]
[ 0, 0, 0, 0, 0, 0, 0, 0, 0 ]
Aberrant expression of p53 and correlation with MGMT loss
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1619718-03-Materials-and-methods-p02
[ "p53", "immunohistochemistry", "and", "scoring" ]
[ 0, 0, 0, 0 ]
p53 immunohistochemistry and scoring
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1266026-04-Results-p01
[ "Duke's", "stage", "and", "age", "at", "clinical", "presentation", "(Figure", "1B)", "were", "documented", "for", "884", "of", "the", "895", "MSI-", "sporadic", "cancers", "(Table", "1).", "Average", "ages", "were", "68.6", "years", "for", "stage", "A,", "69.0", "years", "for", "stage", "B,", "65.2", "years", "for", "stage", "C,", "and", "65.4", "years", "for", "stage", "D.", "The", "most", "likely", "numbers", "of", "oncogenic", "mutations", "were", "seven", "for", "stage", "A", "cancers,", "eight", "for", "stage", "B", "cancers,", "and", "six", "for", "stage", "C", "or", "D", "cancers", "(Table", "1)." ]
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Duke's stage and age at clinical presentation (Figure 1B) were documented for 884 of the 895 MSI- sporadic cancers (Table 1). Average ages were 68.6 years for stage A, 69.0 years for stage B, 65.2 years for stage C, and 65.4 years for stage D. The most likely numbers of oncogenic mutations were seven for stage A cancers, eight for stage B cancers, and six for stage C or D cancers (Table 1).
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3034663-05-Discussion-p01
[ "LS", "is", "the", "most", "common", "hereditary", "CRC-predisposing", "syndrome", "and", "accounts", "for", "3%", "of", "unselected", "CRC", "cases.", "A", "significant", "proportion", "of", "DNA", "variations", "found", "in", "patients", "suspected", "of", "having", "LS", "are", "UVs", "(32%,", "18%", "and", "38%", "for", "MLH1,", "MSH2", "and", "MSH6,", "respectively)", "[6].", "The", "pathogenicity", "of", "the", "MLH1", "p.Lys618Ala", "variant", "remains", "controversial", "because", "of", "conflicting", "data", "[InSiGHT,", "http://www.insight-group.org]", "(Figure", "5)." ]
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LS is the most common hereditary CRC-predisposing syndrome and accounts for 3% of unselected CRC cases. A significant proportion of DNA variations found in patients suspected of having LS are UVs (32%, 18% and 38% for MLH1, MSH2 and MSH6, respectively) [6]. The pathogenicity of the MLH1 p.Lys618Ala variant remains controversial because of conflicting data [InSiGHT, http://www.insight-group.org] (Figure 5).
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1557864-01-Abstract-p01
[ "MSI", "was", "detected", "in", "three", "of", "the", "eight", "cell", "lines", "i.e.", "A2780", "(no", "MLH1", "mRNA", "expression", "due", "to", "promoter", "methylation),", "SKOV3", "(no", "MLH1", "mRNA", "expression)", "and", "2774", "(no", "altered", "expression", "of", "MMR", "genes).", "Overall,", "there", "was", "no", "association", "between", "cisplatin", "response", "and", "MMR", "status", "in", "these", "eight", " ", "cell", "lines." ]
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MSI was detected in three of the eight cell lines i.e. A2780 (no MLH1 mRNA expression due to promoter methylation), SKOV3 (no MLH1 mRNA expression) and 2774 (no altered expression of MMR genes). Overall, there was no association between cisplatin response and MMR status in these eight cell lines.
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1266026-03-Methods-p01
[ "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", "adenocarcinoma", ",", "ICD-0-2", "codes", "8000–8500),", "and", "stage", "(localized,", "regional,", "or", "distant).", "These", "cancers", "were", "not", "characterized", "with", "respect", "to", "HNPCC", "or", "MSI." ]
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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 adenocarcinoma , ICD-0-2 codes 8000–8500), and stage (localized, regional, or distant). These cancers were not characterized with respect to HNPCC or MSI.
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3034663-04-Results-p01
[ "Results", "of", "case-control", "and", "case-case", "analyses.", "Odds", "ratios", "(ORs)", "and", "95%", "confidence", "intervals", "(95%", "CIs)", "for", "the", "p.Lys618Ala", "variant" ]
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Results of case-control and case-case analyses. Odds ratios (ORs) and 95% confidence intervals (95% CIs) for the p.Lys618Ala variant
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2275286-01-Abstract-p01
[ "Our", "data", "may", "imply", "that", "the", "characteristics", "of", "HNPCC", "in", "the", "Chinese", "population", "are", "probably", "different", "from", "those", "of", "Western", "countries.", "Application", "of", "NCI", "recommended", "criteria", "may", "not", "be", "effective", "enough", "to", "identify", "Chinese", "HNPCC", "families.", "Further", "studies", "are", "necessary", "to", "echo", "or", "refute", "our", "results", "so", "as", "to", "make", "the", "NCI", "recommendation", "more", "universally", "applicable." ]
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Our data may imply that the characteristics of HNPCC in the Chinese population are probably different from those of Western countries. Application of NCI recommended criteria may not be effective enough to identify Chinese HNPCC families. Further studies are necessary to echo or refute our results so as to make the NCI recommendation more universally applicable.
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2386495-05-Discussion-p03
[ "Splice-site", "affecting", "mutations" ]
[ 0, 0, 0 ]
Splice-site affecting mutations
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1334229-01-Abstract-p01
[ "Methods" ]
[ 0 ]
Methods
[ 2, 2860, 3 ]
[ 0, 0, 0 ]
[ 1, 1, 1 ]
[ -100, 0, -100 ]
1266026-01-Abstract-p01
[ "Results" ]
[ 0 ]
Results
[ 2, 2274, 3 ]
[ 0, 0, 0 ]
[ 1, 1, 1 ]
[ -100, 0, -100 ]
1619718-04-Results-p01
[ "Frequency", "of", "KRAS", "and", "BRAF", "mutation", "and", "loss", "of", "expression", "of", "O-6-methylguanine", "DNA", "methyltransferase", "(MGMT)", "by", "polyp", "type" ]
[ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ]
Frequency of KRAS and BRAF mutation and loss of expression of O-6-methylguanine DNA methyltransferase (MGMT) by polyp type
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2386495-02-Background-p02
[]
[]
[ 2, 3 ]
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1334229-05-Discussion-p01
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Mutations in exon 3 of the CTNNB1 gene leading to loss of one of the phosphorylation sites were rare. Strikingly, all five of these mutations occurred in the proximal colon and three of these also had absent hMLH1 expression. This may indicate that these proximal colon tumours, which often also show mismatch repair deficiency, are more likely to harbour CTNNB1 mutations. This was also found in a study of microsatellite instable colorectal tumours [26]. The WAVE screening technique has not been used previously for formalin-fixed, paraffin-embedded tissue, and therefore it seems plausible that samples harbouring a CTNNB1 mutation have escaped detection. However, all 58 hMLH1 APC , CTNNB1 and K-ras genes as well as expression of the hMLH1 protein in tumour tissue of 656 sporadic colorectal cancer cases were investigated. The occurrence of mutations in the CTNNB1 gene, which codes for β-catenin, was rare: only five of 464 tumours analysed were found to have a mutation at one of the phosphorylation sites in exon 3. Truncating mutations in APC and activating mutations in K-ras appeared to occur at similar frequencies. Although tumours harbouring both mutations were relatively rare, mutations in APC and K-ras seemed to occur co-dependently. Nine percent of all tumours (58/656) lacked hMLH1 expression, and in these tumours almost no APC or K-ras mutations was detected. Patients harbouring a tumour with absent hMLH1 expression were older, more often women, more often had proximal colon tumours that showed poorer differentiation when compared to patients who harboured a tumour with an APC and/or K-ras mutation.
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1619718-01-Abstract-p01
[ "Conclusions" ]
[ 0 ]
Conclusions
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