;PMID: 9726011 ;source_file_1399.mrg ;Release 0.9 of PennBioIE ;Funded by NSF ITR EIA-0205448 ;0)section:[e:0..38] = [t:0..38] ;1)sentence:[e:43..255] = [t:43..255] ;2)section:[e:259..402] = [t:259..402] ;3)section:[e:406..472] = [t:406..472] ;4)sentence:[e:476..643] = [t:476..643] ;5)sentence:[e:644..915] = [t:644..915] ;6)sentence:[e:916..974] = [t:916..974] ;7)sentence:[e:975..1084] = [t:975..1084] ;8)sentence:[e:1085..1206] = [t:1085..1206] ;9)sentence:[e:1207..1275] = [t:1207..1275] ;10)sentence:[e:1276..1416] = [t:1276..1416] ;11)sentence:[e:1417..1573] = [t:1417..1573] ;12)sentence:[e:1574..1782] = [t:1574..1782] ;13)sentence:[e:1783..1980] = [t:1783..1980] ;14)section:[e:1984..2028] = [t:1984..2028] ;section 0 Span:0..38 ;Mutat Res 1998 Jul 17;403(1-2):103-12 (SEC (FRAG (DT:[0..5] Mutat) (NNP:[6..9] Res) (CD:[11..15] 1998) (NNP:[16..19] Jul) (CD:[20..27] 17;403-LRB-) (CD:[27..28] 1) (HYPH:[28..29] -) (CD:[29..30] 2) (HYPH:[30..31] -RRB-) (CD:[31..35] :103) (HYPH:[35..36] -) (CD:[36..38] 12))) ;sentence 1 Span:43..255 ;Mutation analyses of KRAS exon 1 comparing three different techniques: ;temporal temperature gradient electrophoresis, constant denaturant capillary ; electrophoresis and allele specific polymerase chain reaction. ;[64..68]:gene-rna:"KRAS" ;[69..75]:variation-location:"exon 1" ;[229..239]:gene-protein:"polymerase" (SENT (NP-HLN (NP (NP (NN:[43..51] Mutation) (NNS:[52..60] analyses)) (PP (IN:[61..63] of) (NP (NN:[64..68] KRAS) (NN:[69..73] exon) (CD:[74..75] 1)))) (VP (VBG:[76..85] comparing) (NP (NP (CD:[86..91] three) (JJ:[92..101] different) (NNS:[102..112] techniques)) (::[112..113] :) (NP (NP (JJ:[114..122] temporal) (NML (NN:[124..135] temperature) (NN:[136..144] gradient)) (NN:[145..160] electrophoresis)) (,:[160..161] ,) (NP (NML (JJ:[162..170] constant) (NN:[171..181] denaturant)) (NN:[182..191] capillary) (NN:[193..208] electrophoresis)) (CC:[209..212] and) (NP (ADJP (NN:[213..219] allele) (JJ:[220..228] specific)) (NN:[229..239] polymerase) (NN:[240..245] chain) (NN:[246..254] reaction))))) (.:[254..255] .))) ;section 2 Span:259..402 ;Bjorheim J, Lystad S, Lindblom A, Kressner U, Westring S, Wahlberg S, ;Lindmark G, Gaudernack G, Ekstrom P, Roe J, Thilly WG, Borresen-Dale AL. (SEC (FRAG (NNP:[259..267] Bjorheim) (NNP:[268..270] J,) (NNP:[271..277] Lystad) (NNP:[278..280] S,) (NNP:[281..289] Lindblom) (NNP:[290..291] A) (,:[291..292] ,) (NNP:[293..301] Kressner) (NNP:[302..303] U) (,:[303..304] ,) (NNP:[305..313] Westring) (NNP:[314..316] S,) (NNP:[317..325] Wahlberg) (NNP:[326..328] S,) (NNP:[329..337] Lindmark) (NNP:[339..340] G) (,:[340..341] ,) (NNP:[342..352] Gaudernack) (NNP:[353..354] G) (,:[354..355] ,) (NNP:[356..363] Ekstrom) (NNP:[364..365] P) (,:[365..366] ,) (NNP:[367..370] Roe) (NNP:[371..373] J,) (NNP:[374..380] Thilly) (NNP:[381..383] WG) (,:[383..384] ,) (NNP:[385..393] Borresen) (HYPH:[393..394] -) (NNP:[394..398] Dale) (NNP:[399..401] AL) (.:[401..402] .))) ;section 3 Span:406..472 ;Department of Immunology, Norwegian Radium Hospital, Oslo, Norway. (SEC (FRAG (NNP:[406..416] Department) (IN:[417..419] of) (NNP:[420..430] Immunology) (,:[430..431] ,) (NNP:[432..441] Norwegian) (NNP:[442..448] Radium) (NNP:[449..457] Hospital) (,:[457..458] ,) (NNP:[459..463] Oslo) (,:[463..464] ,) (NNP:[465..471] Norway) (.:[471..472] .))) ;sentence 4 Span:476..643 ;Mutations in the KRAS gene is a key event in the carcinogenesis of many human ; cancers and may serve as a diagnostic marker and a target for therapeutic ;intervention. ;[493..497]:gene-rna:"KRAS" (SENT (S (NP-SBJ (NP (NNS:[476..485] Mutations)) (PP (IN:[486..488] in) (NP (DT:[489..492] the) (NN:[493..497] KRAS) (NN:[498..502] gene)))) (VP (VP (VBZ:[503..505] is) (NP-PRD (DT:[506..507] a) (JJ:[508..511] key) (NN:[512..517] event)) (PP (IN:[518..520] in) (NP (NP (DT:[521..524] the) (NN:[525..539] carcinogenesis)) (PP (IN:[540..542] of) (NP (JJ:[543..547] many) (JJ:[548..553] human) (NNS:[555..562] cancers)))))) (CC:[563..566] and) (VP (MD:[567..570] may) (VP (VB:[571..576] serve) (PP (IN:[577..579] as) (NP (NP (DT:[580..581] a) (JJ:[582..592] diagnostic) (NN:[593..599] marker)) (CC:[600..603] and) (NP (NP (DT:[604..605] a) (NN:[606..612] target)) (PP (IN:[613..616] for) (NP (JJ:[617..628] therapeutic) (NN:[630..642] intervention))))))))) (.:[642..643] .))) ;sentence 5 Span:644..915 ;In this study we have applied three different techniques for mutation ;detection of KRAS exon 1 mutations: Allele specific polymerase chain ;reaction (AS-PCR), temporal temperature gradient electrophoresis (TTGE) and ;constant denaturant capillary electrophoresis (CDCE). ;[728..732]:gene-rna:"KRAS" ;[733..739]:variation-location:"exon 1" ;[767..777]:gene-protein:"polymerase" (SENT (S (PP (IN:[644..646] In) (NP (DT:[647..651] this) (NN:[652..657] study))) (NP-SBJ (PRP:[658..660] we)) (VP (VBP:[661..665] have) (VP (VBN:[666..673] applied) (NP (NP (NP (CD:[674..679] three) (JJ:[680..689] different) (NNS:[690..700] techniques)) (PP (IN:[701..704] for) (NP (NP (NN:[706..714] mutation) (NN:[715..724] detection)) (PP (IN:[725..727] of) (NP (NML (NN:[728..732] KRAS) (NN:[733..737] exon) (CD:[738..739] 1)) (NNS:[740..749] mutations)))))) (::[749..750] :) (NP (NP (NP (ADJP (NN:[751..757] Allele) (JJ:[758..766] specific)) (NN:[767..777] polymerase) (NN:[778..783] chain) (NN:[785..793] reaction)) (NP (-LRB-:[794..795] -LRB-) (NN:[795..801] AS-PCR) (-RRB-:[801..802] -RRB-))) (,:[802..803] ,) (NP (NP (JJ:[804..812] temporal) (NML (NN:[813..824] temperature) (NN:[825..833] gradient)) (NN:[834..849] electrophoresis)) (NP (-LRB-:[850..851] -LRB-) (NN:[851..855] TTGE) (-RRB-:[855..856] -RRB-))) (CC:[857..860] and) (NP (NP (NML (JJ:[862..870] constant) (NN:[871..881] denaturant)) (NN:[882..891] capillary) (NN:[892..907] electrophoresis)) (NP (-LRB-:[908..909] -LRB-) (NN:[909..913] CDCE) (-RRB-:[913..914] -RRB-))))))) (.:[914..915] .))) ;sentence 6 Span:916..974 ;Samples from 191 sporadic colon carcinomas were analyzed. ;[933..959]:malignancy:"sporadic colon carcinomas" (SENT (S (NP-SBJ-1 (NP (NNS:[916..923] Samples)) (PP (IN:[924..928] from) (NP (CD:[929..932] 191) (JJ:[933..941] sporadic) (NN:[943..948] colon) (NNS:[949..959] carcinomas)))) (VP (VBD:[960..964] were) (VP (VBN:[965..973] analyzed) (NP-1 (-NONE-:[973..973] *)))) (.:[973..974] .))) ;sentence 7 Span:975..1084 ;AS-PCR were performed with oligonucleotides specific for know mutations in ;codon 12 and 13 of the KRAS gene. ;[1038..1047]:variation-event:"mutations" ;[1051..1059]:variation-location:"codon 12" ;[1051..1056]...[1064..1066]:variation-location:"codon"..."13" ;[1074..1078]:gene-rna:"KRAS" (SENT (S (NP-SBJ-2 (NN:[975..981] AS-PCR)) (VP (VBD:[982..986] were) (VP (VBN:[987..996] performed) (NP-2 (-NONE-:[996..996] *)) (PP-MNR (IN:[997..1001] with) (NP (NP (NNS:[1002..1018] oligonucleotides)) (ADJP (JJ:[1020..1028] specific) (PP (IN:[1029..1032] for) (NP (NP (JJ:[1033..1037] know) (NNS:[1038..1047] mutations)) (PP-LOC (IN:[1048..1050] in) (NP (NP (NP (NML-1 (NN:[1051..1056] codon)) (CD:[1057..1059] 12)) (CC:[1060..1063] and) (NP (NML-1 (-NONE-:[1063..1063] *P*)) (CD:[1064..1066] 13))) (PP (IN:[1067..1069] of) (NP (DT:[1070..1073] the) (NN:[1074..1078] KRAS) (NN:[1079..1083] gene)))))))))))) (.:[1083..1084] .))) ;sentence 8 Span:1085..1206 ;In TTGE analyses, linear ramping of the temperature were performed during ;electrophoresis in a constant denaturant gel. (SENT (S (PP (IN:[1085..1087] In) (NP (NN:[1088..1092] TTGE) (NNS:[1094..1102] analyses))) (,:[1102..1103] ,) (NP-SBJ-1 (NP (JJ:[1104..1110] linear) (NN:[1111..1118] ramping)) (PP (IN:[1119..1121] of) (NP (DT:[1122..1125] the) (NN:[1126..1137] temperature)))) (VP (VBD:[1138..1142] were) (VP (VBN:[1143..1152] performed) (NP-1 (-NONE-:[1152..1152] *)) (PP-TMP (IN:[1153..1159] during) (NP (NP (NN:[1161..1176] electrophoresis)) (PP-LOC (IN:[1177..1179] in) (NP (DT:[1180..1181] a) (NML (JJ:[1182..1190] constant) (NN:[1191..1201] denaturant)) (NN:[1202..1205] gel))))))) (.:[1205..1206] .))) ;sentence 9 Span:1207..1275 ;CDCE analyses were performed using fluorescin labeled PCR-products. (SENT (S (NP-SBJ-1 (NN:[1207..1211] CDCE) (NNS:[1212..1220] analyses)) (VP (VBD:[1221..1225] were) (VP (VBN:[1226..1235] performed) (NP-1 (-NONE-:[1235..1235] *)) (S-MNR (NP-SBJ (-NONE-:[1235..1235] *)) (VP (VBG:[1236..1241] using) (NP (ADJP (NN:[1243..1253] fluorescin) (VBN:[1254..1261] labeled)) (NN:[1262..1265] PCR) (HYPH:[1265..1266] -) (NNS:[1266..1274] products)))))) (.:[1274..1275] .))) ;sentence 10 Span:1276..1416 ;Separation was achieved under constant denaturing conditions using high ;temperature in a gel-filled capillary followed by laser detection. (SENT (S (NP-SBJ-1 (NN:[1276..1286] Separation)) (VP (VBD:[1287..1290] was) (VP (VBN:[1291..1299] achieved) (NP-1 (-NONE-:[1299..1299] *)) (PP (IN:[1300..1305] under) (NP (JJ:[1306..1314] constant) (VBG:[1316..1326] denaturing) (NNS:[1327..1337] conditions))) (S-MNR (NP-SBJ (-NONE-:[1337..1337] *)) (VP (VBG:[1338..1343] using) (NP (NP (NP (JJ:[1344..1348] high) (NN:[1349..1360] temperature)) (PP (IN:[1361..1363] in) (NP (DT:[1364..1365] a) (ADJP (NN:[1366..1369] gel) (HYPH:[1369..1370] -) (VBN:[1370..1376] filled)) (NN:[1377..1386] capillary)))) (VP (VBN:[1387..1395] followed) (NP (-NONE-:[1395..1395] *)) (PP (IN:[1397..1399] by) (NP-LGS (NN:[1400..1405] laser) (NN:[1406..1415] detection))))))))) (.:[1415..1416] .))) ;sentence 11 Span:1417..1573 ;A mutated KRAS gene was found in 42/191 (22.0%) of the samples using AS-PCR, ;in 62/191 (32.5%) using TTGE and in 66/191 (34.6%) of the samples using ;CDCE. ;[1427..1431]:gene-rna:"KRAS" (SENT (S (NP-SBJ-1 (DT:[1417..1418] A) (VBN:[1419..1426] mutated) (NN:[1427..1431] KRAS) (NN:[1432..1436] gene)) (VP (VBD:[1437..1440] was) (VP (VP (VBN:[1441..1446] found) (NP-1 (-NONE-:[1446..1446] *)) (PP-LOC=2 (IN:[1447..1449] in) (NP (NP (CD:[1450..1452] 42)) (PP (SYM:[1452..1453] /) (NP (CD:[1453..1456] 191))) (PRN (-LRB-:[1457..1458] -LRB-) (NP (CD:[1458..1462] 22.0) (NN:[1462..1463] %)) (-RRB-:[1463..1464] -RRB-)) (PP (IN:[1465..1467] of) (NP (DT:[1468..1471] the) (NNS:[1473..1480] samples))))) (S-MNR=3 (NP-SBJ (-NONE-:[1480..1480] *)) (VP (VBG:[1481..1486] using) (NP (NN:[1487..1493] AS-PCR))))) (,:[1493..1494] ,) (VP (PP-LOC=2 (IN:[1495..1497] in) (NP (NP (CD:[1498..1500] 62)) (PP (SYM:[1500..1501] /) (NP (CD:[1501..1504] 191))) (PRN (-LRB-:[1505..1506] -LRB-) (NP (CD:[1506..1510] 32.5) (NN:[1510..1511] %)) (-RRB-:[1511..1512] -RRB-)))) (S-MNR=3 (NP-SBJ (-NONE-:[1512..1512] *)) (VP (VBG:[1513..1518] using) (NP (NN:[1519..1523] TTGE))))) (CC:[1524..1527] and) (VP (PP-LOC=2 (IN:[1528..1530] in) (NP (NP (CD:[1531..1533] 66)) (PP (SYM:[1533..1534] /) (NP (CD:[1534..1537] 191))) (PRN (-LRB-:[1538..1539] -LRB-) (NP (CD:[1539..1543] 34.6) (NN:[1543..1544] %)) (-RRB-:[1544..1545] -RRB-)) (PP (IN:[1546..1548] of) (NP (DT:[1549..1552] the) (NNS:[1554..1561] samples))))) (S-MNR=3 (NP-SBJ (-NONE-:[1561..1561] *)) (VP (VBG:[1562..1567] using) (NP (NN:[1568..1572] CDCE))))))) (.:[1572..1573] .))) ;sentence 12 Span:1574..1782 ;In the TTGE and CDCE analyses the sequence of the mutant were determined by ;comparing the electrophoretic pattern to that of known mutations or by ;mixing the sample with known mutations prior to reanalysis. (SENT (S (PP (IN:[1574..1576] In) (NP (DT:[1577..1580] the) (NML (NML (NN:[1581..1585] TTGE) (NML-1 (-NONE-:[1585..1585] *P*))) (CC:[1586..1589] and) (NML (NN:[1590..1594] CDCE) (NML-1 (NNS:[1595..1603] analyses)))))) (NP-SBJ-2 (NP (DT:[1604..1607] the) (NN:[1608..1616] sequence)) (PP (IN:[1617..1619] of) (NP (DT:[1620..1623] the) (NN:[1624..1630] mutant)))) (VP (VBD:[1632..1636] were) (VP (VBN:[1637..1647] determined) (NP-2 (-NONE-:[1647..1647] *)) (PP-MNR (PP (IN:[1648..1650] by) (S-NOM (NP-SBJ (-NONE-:[1650..1650] *)) (VP (VBG:[1651..1660] comparing) (NP (DT:[1661..1664] the) (JJ:[1665..1680] electrophoretic) (NN:[1681..1688] pattern)) (PP-CLR (TO:[1689..1691] to) (NP (NP (DT:[1692..1696] that)) (PP (IN:[1697..1699] of) (NP (JJ:[1700..1705] known) (NNS:[1707..1716] mutations)))))))) (CC:[1717..1719] or) (PP (IN:[1720..1722] by) (S-NOM (NP-SBJ (-NONE-:[1722..1722] *)) (VP (VBG:[1723..1729] mixing) (NP (DT:[1730..1733] the) (NN:[1734..1740] sample)) (PP (IN:[1741..1745] with) (NP (JJ:[1746..1751] known) (NNS:[1752..1761] mutations))) (S-TMP (NP-SBJ (-NONE-:[1761..1761] *)) (ADJP-PRD (RB:[1762..1767] prior) (PP (TO:[1768..1770] to) (NP (NN:[1771..1781] reanalysis))))))))))) (.:[1781..1782] .))) ;sentence 13 Span:1783..1980 ;In a titration experiment mixing mutant and wild-type alleles prior to PCR, ;the sensitivity for mutation detection was shown to be 10(-2) for TTGE and ;under optimized conditions 10(-3) for CDCE. (SENT (S (PP (IN:[1783..1785] In) (NP (NP (DT:[1786..1787] a) (NN:[1789..1798] titration) (NN:[1799..1809] experiment)) (VP (VBG:[1810..1816] mixing) (NP (NP (JJ:[1817..1823] mutant) (NML-1 (-NONE-:[1823..1823] *P*))) (CC:[1824..1827] and) (NP (NML (JJ:[1828..1832] wild) (HYPH:[1832..1833] -) (NN:[1833..1837] type)) (NML-1 (NNS:[1838..1845] alleles)))) (S-TMP (NP-SBJ (-NONE-:[1845..1845] *)) (ADJP-PRD (RB:[1846..1851] prior) (PP (TO:[1852..1854] to) (NP (NN:[1855..1858] PCR)))))))) (,:[1858..1859] ,) (NP-SBJ-2 (NP (DT:[1860..1863] the) (NN:[1865..1876] sensitivity)) (PP (IN:[1877..1880] for) (NP (NN:[1881..1889] mutation) (NN:[1890..1899] detection)))) (VP (VBD:[1900..1903] was) (VP (VBN:[1904..1909] shown) (S (NP-SBJ-2 (-NONE-:[1909..1909] *)) (VP (TO:[1910..1912] to) (VP (VP (VB:[1913..1915] be) (NP-PRD=3 (CD:[1916..1922] 10-LRB--2-RRB-)) (PP=4 (IN:[1923..1926] for) (NP (NN:[1927..1931] TTGE)))) (CC:[1932..1935] and) (VP (PP (IN:[1936..1941] under) (NP (VBN:[1943..1952] optimized) (NNS:[1953..1963] conditions))) (NP-PRD=3 (CD:[1964..1970] 10-LRB--3-RRB-)) (PP=4 (IN:[1971..1974] for) (NP (NN:[1975..1979] CDCE))))))))) (.:[1979..1980] .))) ;section 14 Span:1984..2028 ;PMID: 9726011 [PubMed - indexed for MEDLINE] (SEC (FRAG (NNP:[1984..1988] PMID) (::[1988..1989] :) (CD:[1990..1997] 9726011) (IN:[1998..1999] -LSB-) (NNP:[1999..2005] PubMed) (HYPH:[2006..2007] -) (JJ:[2008..2015] indexed) (IN:[2016..2019] for) (NNP:[2020..2028] MEDLINE-RSB-)))