Novel genetic and epigenetic alterations in ... - Ous-research.no
Novel genetic and epigenetic alterations in ... - Ous-research.no Novel genetic and epigenetic alterations in ... - Ous-research.no
References133. Lind GE, Thorstensen L, Løvig T, Meling GI, Hamelin R, Rognum TO, Esteller M,Lothe RA (2004) A CpG island hypermethylation profile of primary colorectalcarcinomas and colon cancer cell lines. Mol Cancer 3:28134. De Luca A, Buccino A, Gianni D, Mangino M, Giustini S, Richetta A, Divona L,Calvieri S, Mingarelli R, Dallapiccola B (2003) NF1 gene analysis based onDHPLC. Hum Mutat 21(2): 171-172135. Upadhyaya M, Kluwe L, Spurlock G, Monem B, Majounie E, Mantripragada K,Ruggieri M, Chuzhanova N, Evans DG, Ferner R, Thomas N, Guha A, Mautner V(2007) Germline and somatic NF1 gene mutation spectrum in NF1-associatedmalignant peripheral nerve sheath tumors (MPNSTs). Hum Mutat 29(1): 74-82136. Bottillo I, Ahlquist T, Brekke HR, Danielsen SA, van den Berg E, Mertens F, LotheRA, Dallapiccola B. Germline and somatic NF1 mutations in sporadic andNF1-associated malignant peripheral nerve sheath tumors. The Journal ofPathology. In Press137. Shapiro R, Weisgras JM (1970) Bisulfite-catalyzed transamination of cytosineand cytidine. Biochem Biophys Res Commun 40(4): 839-843138. Frommer M, McDonald LE, Millar DS, Collis CM, Watt F, Grigg GW, Molloy PL,Paul CL (1992) A genomic sequencing protocol that yields a positive display of5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci U S A89(5): 1827-1831139. Clark SJ, Harrison J, Paul CL, Frommer M (1994) High sensitivity mapping ofmethylated cytosines. Nucleic Acids Res 22(15): 2990-2997140. Clark SJ (2005) Studying Mammalian DNA Methylation: Bisulfite Modification. In:Esteller M (ed) DNA Methylation - Approaches, Methods, and Applications.CRC press, pp 53-63141. Herman JG, Graff JR, Myöhänen S, Nelkin BD, Baylin SB (1996) MethylationspecificPCR: a novel PCR assay for methylation status of CpG islands. ProcNatl Acad Sci U S A 93(18): 9821-9826142. Jones PA (1999) The DNA methylation paradox. Trends Genet 15(1): 34-37143. Deng G, Chen A, Hong J, Chae HS, Kim YS (1999) Methylation of CpG in asmall region of the hMLH1 promoter invariably correlates with the absence ofgene expression. Cancer Res 59(9): 2029-2033144. Herman JG (2005) Bisulfite PCR-Based Techniques for the Study of DNAMethylation. In: Esteller M (ed) DNA Methylation - Approaches, Methods, andApplications. CRC press, pp 65-7278
References145. Oefner PJ, Underhill P (1995) Comparative DNA sequencing by denaturinghigh-performance liquid chromatography (DHPLC). Am J Hum Genet57(A266):146. Xiao W, Oefner PJ (2001) Denaturing high-performance liquidchromatography: A review. Hum Mutat 17(6): 439-474147. Jones AC, Austin J, Hansen N, Hoogendoorn B, Oefner PJ, Cheadle JP, O'DonovanMC (1999) Optimal temperature selection for mutation detection bydenaturing HPLC and comparison to single-stranded conformationpolymorphism and heteroduplex analysis. Clin Chem 45(8 Pt 1): 1133-1140148. Orita M, Suzuki Y, Sekiya T, Hayashi K (1989) Rapid and sensitive detection ofpoint mutations and DNA polymorphisms using the polymerase chainreaction. Genomics 5(4): 874-879149. Sørlie T, Johnsen H, Vu P, Lind GE, Lothe RA, Børresen-Dale AL (2005) Mutationscreening of the TP53 gene by temporal temperature gradient gelelectrophoresis. Methods Mol Biol 291 207-216150. Ganguly A, Rock MJ, Prockop DJ (1993) Conformation-sensitive gelelectrophoresis for rapid detection of single-base differences in doublestrandedPCR products and DNA fragments: evidence for solvent-inducedbends in DNA heteroduplexes. Proc Natl Acad Sci U S A 90(21): 10325-10329151. Fischer SG, Lerman LS (1983) DNA fragments differing by single base-pairsubstitutions are separated in denaturing gradient gels: correspondence withmelting theory. Proc Natl Acad Sci U S A 80(6): 1579-1583152. Stanssens P, Zabeau M, Meersseman G, Remes G, Gansemans Y, Storm N, HartmerR, Honisch C, Rodi CP, Bocker S, van den BD (2004) High-throughput MALDI-TOF discovery of genomic sequence polymorphisms. Genome Res 14(1): 126-133153. De Luca A, Schirinzi A, Buccino A, Bottillo I, Sinibaldi L, Torrente I, Ciavarella A,Dottorini T, Porciello R, Giustini S, Calvieri S, Dallapiccola B (2004) Novel andrecurrent mutations in the NF1 gene in Italian patients withneurofibromatosis type 1. Hum Mutat 23(6): 629154. De Luca A, Bottillo I, Dasdia MC, Morella A, Lanari V, Bernardini L, Divona L,Giustini S, Sinibaldi L, Novelli A, Torrente I, Schirinzi A, Dallapiccola B (2007)Deletions of NF1 gene and exons detected by multiplex ligation-dependentprobe amplification. J Med Genet 44(12): 800-808155. Leitner T, Halapi E, Scarlatti G, Rossi P, Albert J, Fenyo EM, Uhlen M (1993)Analysis of heterogeneous viral populations by direct DNA sequencing.Biotechniques 15(1): 120-12779
- Page 28 and 29: IntroductionInstabilities involved
- Page 30 and 31: Introductionthere seems to be a fid
- Page 32 and 33: Introductionsevere alterations are
- Page 34 and 35: Introductionpopulation-wide screeni
- Page 36 and 37: IntroductionFigure 12. Present and
- Page 38 and 39: RESULTS IN BRIEFPaper Ia. “DNA hy
- Page 40 and 41: Results in Briefinstability, and se
- Page 42 and 43: Results in BriefUnivariate survival
- Page 44 and 45: Discussionseveral factors, and full
- Page 46 and 47: Discussionlow threshold, we increas
- Page 48 and 49: DiscussionIt may seem like unnecess
- Page 50 and 51: Discussionthan 96% DHPLC do not sta
- Page 52 and 53: DiscussionFigure 13. Mutation detec
- Page 54 and 55: DiscussionClinical impact of molecu
- Page 56 and 57: Discussionmarkers with a very high
- Page 58 and 59: Discussionchromosomes in metaphase[
- Page 60 and 61: DiscussionThese examples underline
- Page 62 and 63: Discussiongenes. One is based on mu
- Page 64 and 65: CONCLUSIONSWe have identified novel
- Page 66 and 67: Future PerspectivesMolecular risk a
- Page 68 and 69: REFERENCES1. Breasted J (1930) The
- Page 70 and 71: References29. Deng G, Chen A, Pong
- Page 72 and 73: References57. Al-Sukhni W, Aronson
- Page 74 and 75: References84. Kunkel TA (1993) Nucl
- Page 76 and 77: ReferencesLeggett B, Levine J, Kim
- Page 80 and 81: References156. Meling GI, Lothe RA,
- Page 82 and 83: ReferencesT, Song X, Day RH, Sledzi
- Page 84 and 85: References196. Honda S, Haruta M, S
- Page 86 and 87: ORIGINAL ARTICLESAPPENDIXAppendix I
- Page 89 and 90: GASTROENTEROLOGY 2007;132:1631-1639
- Page 91: Paper IbGuro E Lind, Terje Ahlquist
- Page 94 and 95: Journal of Translational Medicine 2
- Page 96 and 97: Journal of Translational Medicine 2
- Page 98 and 99: Journal of Translational Medicine 2
- Page 100 and 101: Journal of Translational Medicine 2
- Page 102 and 103: Journal of Translational Medicine 2
- Page 105: Paper IITerje Ahlquist, Guro E Lind
- Page 108 and 109: BackgroundMost cases of colorectal
- Page 110 and 111: ADAMTS1 CDKN2A CRABP1 HOXA9 MAL MGM
- Page 112 and 113: pseudogene, leading to a high rate
- Page 114 and 115: strands. Proc Natl Acad Sci U S A 1
- Page 116 and 117: concomitant absence of transcript a
- Page 119 and 120: Volume 10 Number 7 July 2008 pp. 68
- Page 121 and 122: 682 RAS Signaling in Colorectal Car
- Page 123 and 124: 684 RAS Signaling in Colorectal Car
- Page 125 and 126: 686 RAS Signaling in Colorectal Car
- Page 127: Table W2. Detailed Somatic Events o
References133. L<strong>in</strong>d GE, Thorstensen L, Løvig T, Mel<strong>in</strong>g GI, Hamel<strong>in</strong> R, Rognum TO, Esteller M,Lothe RA (2004) A CpG isl<strong>and</strong> hypermethylation profile of primary colorectalcarc<strong>in</strong>omas <strong>and</strong> colon cancer cell l<strong>in</strong>es. Mol Cancer 3:28134. De Luca A, Bucc<strong>in</strong>o A, Gianni D, Mang<strong>in</strong>o M, Giust<strong>in</strong>i S, Richetta A, Divona L,Calvieri S, M<strong>in</strong>garelli R, Dallapiccola B (2003) NF1 gene analysis based onDHPLC. Hum Mutat 21(2): 171-172135. Upadhyaya M, Kluwe L, Spurlock G, Monem B, Majounie E, Mantripragada K,Ruggieri M, Chuzha<strong>no</strong>va N, Evans DG, Ferner R, Thomas N, Guha A, Mautner V(2007) Germl<strong>in</strong>e <strong>and</strong> somatic NF1 gene mutation spectrum <strong>in</strong> NF1-associatedmalignant peripheral nerve sheath tumors (MPNSTs). Hum Mutat 29(1): 74-82136. Bottillo I, Ahlquist T, Brekke HR, Danielsen SA, van den Berg E, Mertens F, LotheRA, Dallapiccola B. Germl<strong>in</strong>e <strong>and</strong> somatic NF1 mutations <strong>in</strong> sporadic <strong>and</strong>NF1-associated malignant peripheral nerve sheath tumors. The Journal ofPathology. In Press137. Shapiro R, Weisgras JM (1970) Bisulfite-catalyzed transam<strong>in</strong>ation of cytos<strong>in</strong>e<strong>and</strong> cytid<strong>in</strong>e. Biochem Biophys Res Commun 40(4): 839-843138. Frommer M, McDonald LE, Millar DS, Collis CM, Watt F, Grigg GW, Molloy PL,Paul CL (1992) A ge<strong>no</strong>mic sequenc<strong>in</strong>g protocol that yields a positive display of5-methylcytos<strong>in</strong>e residues <strong>in</strong> <strong>in</strong>dividual DNA str<strong>and</strong>s. Proc Natl Acad Sci U S A89(5): 1827-1831139. Clark SJ, Harrison J, Paul CL, Frommer M (1994) High sensitivity mapp<strong>in</strong>g ofmethylated cytos<strong>in</strong>es. Nucleic Acids Res 22(15): 2990-2997140. Clark SJ (2005) Study<strong>in</strong>g Mammalian DNA Methylation: Bisulfite Modification. In:Esteller M (ed) DNA Methylation - Approaches, Methods, <strong>and</strong> Applications.CRC press, pp 53-63141. Herman JG, Graff JR, Myöhänen S, Nelk<strong>in</strong> BD, Bayl<strong>in</strong> SB (1996) MethylationspecificPCR: a <strong>no</strong>vel PCR assay for methylation status of CpG isl<strong>and</strong>s. ProcNatl Acad Sci U S A 93(18): 9821-9826142. Jones PA (1999) The DNA methylation paradox. Trends Genet 15(1): 34-37143. Deng G, Chen A, Hong J, Chae HS, Kim YS (1999) Methylation of CpG <strong>in</strong> asmall region of the hMLH1 promoter <strong>in</strong>variably correlates with the absence ofgene expression. Cancer Res 59(9): 2029-2033144. Herman JG (2005) Bisulfite PCR-Based Techniques for the Study of DNAMethylation. In: Esteller M (ed) DNA Methylation - Approaches, Methods, <strong>and</strong>Applications. CRC press, pp 65-7278
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