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Detailed genomic mapping and expression analyses of 12p amplifications in pancreatic carcinomas reveal a 3.5-Mb target region for amplification.

Heidenblad, Markus LU ; Jonson, Tord LU ; Mahlamäki, Eija H; Gorunova, Ludmila LU ; Karhu, Ritva; Johansson, Bertil LU and Höglund, Mattias LU (2002) In Genes, Chromosomes and Cancer 34(2). p.211-223
Abstract
Previous cytogenetic and comparative genomic hybridization (CGH) analyses have shown that the gain of chromosome arm 12p is frequent in pancreatic carcinomas. We investigated 15 pancreatic carcinoma cell lines using CGH, fluorescence in situ hybridization (FISH), and semiquantitative polymerase chain reaction (PCR) to characterize 12p amplifications in detail. The CGH analysis revealed gains of 12p in four of the cell lines and local amplification within 12p11-12 in six cell lines. By FISH analysis, using precisely mapped YAC clones, the commonly amplified region was found to be approximately 5 Mb. The amplified segment extended from YAC 753f12, covering the KRAS2 locus, to YAC 891f1, close to the centromere. A semiquantitative PCR... (More)
Previous cytogenetic and comparative genomic hybridization (CGH) analyses have shown that the gain of chromosome arm 12p is frequent in pancreatic carcinomas. We investigated 15 pancreatic carcinoma cell lines using CGH, fluorescence in situ hybridization (FISH), and semiquantitative polymerase chain reaction (PCR) to characterize 12p amplifications in detail. The CGH analysis revealed gains of 12p in four of the cell lines and local amplification within 12p11-12 in six cell lines. By FISH analysis, using precisely mapped YAC clones, the commonly amplified region was found to be approximately 5 Mb. The amplified segment extended from YAC 753f12, covering the KRAS2 locus, to YAC 891f1, close to the centromere. A semiquantitative PCR methodology was used to estimate genomic copy numbers of 14 precisely mapped expressed sequence tags (ESTs) and sequence-tagged sites, located within this interval. The level of amplification ranged from two- to 12-fold. The produced gene copy profiles revealed a 3.5-Mb segment with various local amplifications. This region includes KRAS2 and ranges from D12S1617 to sts-N38796. Two of the cell lines (primary and metastatic tumor from the same patient) showed amplification peaks within the distal region of this segment, two had peaks within the proximal region, one showed subpeaks in both regions, and one displayed amplification of the entire region. Chromosome segment-specific cDNA array analysis of 29 expressed sequences within the whole interval between D12S1617 and sts-N38796 indicated overexpression of four ESTs, two corresponding to DEC2 and PPFIBP1, and two to ESTs with unknown function. Expression analysis of these and of KRAS2 showed specific overexpression in the six cell lines with local 12p amplifications. These findings indicate two target regions within the 3.5-Mb segment in 12p11-12, one proximal including PPFIBP1, and one distal including KRAS2. (Less)
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keywords
Neoplasm : genetics, DNA, Gene Amplification : genetics, Gene Expression Profiling : methods, Gene Expression Regulation, Neoplastic : genetics, Structural, Genes, Human, In Situ Hybridization, Fluorescence : methods, Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis : methods, Pancreatic Neoplasms : genetics, Proto-Oncogene Proteins : biosynthesis, Proto-Oncogene Proteins : genetics, Support, Non-U.S. Gov't, DNA Mutational Analysis : methods, Comparative Study, Pair 12 : genetics, Chromosomes, Chromosome Mapping : methods, Carcinoma : genetics
in
Genes, Chromosomes and Cancer
volume
34
issue
2
pages
211 - 223
publisher
John Wiley & Sons
external identifiers
  • pmid:11979555
  • wos:000175101800008
  • scopus:0036262452
ISSN
1045-2257
DOI
10.1002/gcc.10063
language
English
LU publication?
yes
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31f8643e-575a-46f1-8426-0e9f343cf270 (old id 108399)
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http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11979555&dopt=Abstract
date added to LUP
2007-07-06 15:39:42
date last changed
2017-01-01 04:26:49
@article{31f8643e-575a-46f1-8426-0e9f343cf270,
  abstract     = {Previous cytogenetic and comparative genomic hybridization (CGH) analyses have shown that the gain of chromosome arm 12p is frequent in pancreatic carcinomas. We investigated 15 pancreatic carcinoma cell lines using CGH, fluorescence in situ hybridization (FISH), and semiquantitative polymerase chain reaction (PCR) to characterize 12p amplifications in detail. The CGH analysis revealed gains of 12p in four of the cell lines and local amplification within 12p11-12 in six cell lines. By FISH analysis, using precisely mapped YAC clones, the commonly amplified region was found to be approximately 5 Mb. The amplified segment extended from YAC 753f12, covering the KRAS2 locus, to YAC 891f1, close to the centromere. A semiquantitative PCR methodology was used to estimate genomic copy numbers of 14 precisely mapped expressed sequence tags (ESTs) and sequence-tagged sites, located within this interval. The level of amplification ranged from two- to 12-fold. The produced gene copy profiles revealed a 3.5-Mb segment with various local amplifications. This region includes KRAS2 and ranges from D12S1617 to sts-N38796. Two of the cell lines (primary and metastatic tumor from the same patient) showed amplification peaks within the distal region of this segment, two had peaks within the proximal region, one showed subpeaks in both regions, and one displayed amplification of the entire region. Chromosome segment-specific cDNA array analysis of 29 expressed sequences within the whole interval between D12S1617 and sts-N38796 indicated overexpression of four ESTs, two corresponding to DEC2 and PPFIBP1, and two to ESTs with unknown function. Expression analysis of these and of KRAS2 showed specific overexpression in the six cell lines with local 12p amplifications. These findings indicate two target regions within the 3.5-Mb segment in 12p11-12, one proximal including PPFIBP1, and one distal including KRAS2.},
  author       = {Heidenblad, Markus and Jonson, Tord and Mahlamäki, Eija H and Gorunova, Ludmila and Karhu, Ritva and Johansson, Bertil and Höglund, Mattias},
  issn         = {1045-2257},
  keyword      = {Neoplasm : genetics,DNA,Gene Amplification : genetics,Gene Expression Profiling : methods,Gene Expression Regulation,Neoplastic : genetics,Structural,Genes,Human,In Situ Hybridization,Fluorescence : methods,Nucleic Acid Hybridization,Oligonucleotide Array Sequence Analysis : methods,Pancreatic Neoplasms : genetics,Proto-Oncogene Proteins : biosynthesis,Proto-Oncogene Proteins : genetics,Support,Non-U.S. Gov't,DNA Mutational Analysis : methods,Comparative Study,Pair 12 : genetics,Chromosomes,Chromosome Mapping : methods,Carcinoma : genetics},
  language     = {eng},
  number       = {2},
  pages        = {211--223},
  publisher    = {John Wiley & Sons},
  series       = {Genes, Chromosomes and Cancer},
  title        = {Detailed genomic mapping and expression analyses of 12p amplifications in pancreatic carcinomas reveal a 3.5-Mb target region for amplification.},
  url          = {http://dx.doi.org/10.1002/gcc.10063},
  volume       = {34},
  year         = {2002},
}