The DOI matches its Crossref record; 34 of the 34 references it cites were found in a registry or an index.
Genome-wide DNA copy number analysis in pancreatic cancer using high-density single nucleotide polymorphism arrays
Open accessAbstract
To identify genomic abnormalities characteristic of pancreatic ductal adenocarcinoma (PDAC) in vivo, a panel of 27 microdissected PDAC specimens were analysed using high-density microarrays representing approximately 116 000 single nucleotide polymorphism (SNP) loci. We detected frequent gains of 1q, 2, 3, 5, 7p, 8q, 11, 14q and 17q (> or =78% of cases), and losses of 1p, 3p, 6, 9p, 13q, 14q, 17p and 18q (> or =44%). Although the results were comparable with those from array CGH, regions of those genetic changes were defined more accurately by SNP arrays. Integrating the Ensembl public data, we have generated 'gene' copy number indices that facilitate the search for novel candidates involved in pancreatic carcinogenesis. Copy numbers in a subset of the genes were validated using quantitative real-time PCR. The SKAP2/SCAP2 gene (7p15.2), which belongs to the src family kinases, was most frequently (63%) amplified in our sample set and its recurrent overexpression (67%) was confirmed by reverse transcription-PCR. Furthermore, fluorescence in situ hybridization and in situ RNA hybridization analyses for this gene have demonstrated a significant correlation between DNA copy number and mRNA expression level in an independent sample set (P<0.001). These findings indicate that the dysregulation of SKAP2/SCAP2, which is mostly caused by its increased gene copy number, is likely to be associated with the development of PDAC.
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“In this “pseudo-bulk” summary, previously described hallmark genomic events characteristic of PDAC lesions1–6 were readily observed, albeit in some cases only in a subset of genomic subclones for each line.”
From Occult polyclonality of preclinical pancreatic cancer models drives in vitro evolution (2022) · cites this paper as [3]
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Citations
Cites
Spencer, P. M., Cameron, J. L., & Lin, L. (2000) · Cited by 7,202
Global variation in copy number in the human genome
Redon, R., Ishikawa, S., Fitch, K. R., Feuk, L., Perry, G. H., Andrews, T. D., Fiegler, H., Shapero, M. H., Carson, A. R., Chen, W., et al. (2006) · Nature · doi:10.1038/nature05329 · Cited by 4,377 · cited 2×
“Taking structural variation in the human genome into account, our software integrated the public data of CNVs (http://projects. tcag.ca/variation/) into our analysis (Iafrate et al., 2004; Redon et al., 2006).”
BackgroundMethodJemal, A., Murray, T., Ward, E., Samuels, A., Tiwari, R. C., Ghafoor, A., Feuer, E. J., & Thun, M. J. (2005) · CA: A Cancer Journal for Clinicians · doi:10.3322/canjclin.55.1.10 · Cited by 4,186 · cited 2×
“Essentially, no conventional treatment has made a significant impact on the course of the disease, so that the prognosis for patients still remains dismal with a median survival of approximately 6 months from diagnosis and an overall 5-year survival of less than 5% (Jemal et al., 2005).”
BackgroundDetection of large-scale variation in the human genome
Iafrate, A. J., Feuk, L., Rivera, M. N., Listewnik, M. L., Donahoe, P. K., Qi, Y., Scherer, S. W., & Lee, C. (2004) · Nature Genetics · doi:10.1038/ng1416 · Cited by 2,892 · cited 1×
“Taking structural variation in the human genome into account, our software integrated the public data of CNVs (http://projects. tcag.ca/variation/) into our analysis (Iafrate et al., 2004; Redon et al., 2006).”
MethodLi, D., Xie, K., Wolff, R. A., & Abbruzzese, J. L. (2004) · The Lancet · doi:10.1016/s0140-6736(04)15841-8 · Cited by 1,731 · cited 2×
“Thus, recurrent genetic changes that were previously characterized in PDAC were commonly observed in our analysis (Bardeesy and DePinho, 2002; Li et al., 2004).”
BackgroundResultGenomic and transcriptional aberrations linked to breast cancer pathophysiologies
Chin, K., DeVries, S., Fridlyand, J., Spellman, P. T., Roydasgupta, R., Kuo, W.-L., Lapuk, A. V., Neve, R. M., Qian, Z., Ryder, T., et al. (2006) · Cancer Cell · doi:10.1016/j.ccr.2006.10.009 · Cited by 1,309
Pancreatic cancer biology and genetics
Bardeesy, N. M., & DePinho, R. A. (2002) · Nature reviews. Cancer · doi:10.1038/nrc949 · Cited by 1,176
The role of focal-adhesion kinase in cancer — a new therapeutic opportunity
McLean, G. W., Carragher, N. O., Avizienyte, E., EVANS, J., Brunton, V. G., & Frame, M. C. (2005) · Nature reviews. Cancer · doi:10.1038/nrc1647 · Cited by 1,049 · cited 1×
“However, based on the ability of SCAP2 to interact with RAFTK, it is likely to modulate the spreading and motility of PDAC cells (McLean et al., 2005).”
BackgroundNannya, Y., Sanada, M., Nakazaki, K., Hosoya, N., Wang, L., Hangaishi, A., Kurokawa, M., Chiba, S., Bailey, D. K., Kennedy, G. C., et al. (2005) · Cancer Research · doi:10.1158/0008-5472.can-05-0465 · Cited by 632 · cited 1×
“0) software (http://www.genome.umin.jp/) (Nannya et al., 2005).”
Zhao, X. J., Li, C., Paez, J. G., Chin, K., Janne, P. A., Chen, T.-H., Girard, L., Minna, J. D., Christiani, D. C., Leo, C., et al. (2004) · Cancer Research · doi:10.1158/0008-5472.can-03-3308 · Cited by 543 · cited 4×
“…arrays has allowed genome-wide, high-resolution analysis of both DNA copy number (DCN) alterations and loss of heterozygosity (LOH) events in cancer cells (Lindblad-Toh et al., 2000; Bignell et al., 2004; Huang et al., 2004; Janne et al., 2004; Zhao et al., 2004, 2005; Midorikawa et al., 2006).”
BackgroundMethodInfluentialHigh-Resolution Analysis of DNA Copy Number Using Oligonucleotide MicroarraysPreprint
Bignell, G. R., Huang, J. H., Greshock, J. D., Watt, S., Butler, A. P., West, S., Grigorova, M., Jones, K. W., Wei, W., Stratton, M. R., et al. (2004) · Genome Research · doi:10.1101/gr.2012304 · Cited by 396 · cited 2×
“…arrays has allowed genome-wide, high-resolution analysis of both DNA copy number (DCN) alterations and loss of heterozygosity (LOH) events in cancer cells (Lindblad-Toh et al., 2000; Bignell et al., 2004; Huang et al., 2004; Janne et al., 2004; Zhao et al., 2004, 2005; Midorikawa et al., 2006).”
BackgroundZhao, X., Weir, B. A., LaFramboise, T., Lin, M. G., Beroukhim, R., Garraway, L. A., Beheshti, J., Lee, J. C., Naoki, K., Richards, W. G., et al. (2005) · Cancer Research · doi:10.1158/0008-5472.can-04-4603 · Cited by 337 · cited 3×
“…arrays has allowed genome-wide, high-resolution analysis of both DNA copy number (DCN) alterations and loss of heterozygosity (LOH) events in cancer cells (Lindblad-Toh et al., 2000; Bignell et al., 2004; Huang et al., 2004; Janne et al., 2004; Zhao et al., 2004, 2005; Midorikawa et al., 2006).”
BackgroundMethodWhole genome DNA copy number changes identified by high density oligonucleotide arrays
Huang, J., Wei, W., Zhang, J., Liu, G., Bignell, G. R., Stratton, M. R., Futreal, P. A., Wooster, R., Jones, K. W., & Shapero, M. H. (2004) · Human Genomics · doi:10.1186/1479-7364-1-4-287 · Cited by 279 · cited 4×
“…arrays has allowed genome-wide, high-resolution analysis of both DNA copy number (DCN) alterations and loss of heterozygosity (LOH) events in cancer cells (Lindblad-Toh et al., 2000; Bignell et al., 2004; Huang et al., 2004; Janne et al., 2004; Zhao et al., 2004, 2005; Midorikawa et al., 2006).”
BackgroundInfluentialLindblad‐Toh, K., Tanenbaum, D. M., Daly, M. J., Winchester, E., Lui, W., Villapakkam, A. C., Stanton, S. E., Larsson, C., Hudson, T. J., Johnson, B. E., et al. (2000) · Nature Biotechnology · doi:10.1038/79269 · Cited by 274 · cited 4×
“…arrays has allowed genome-wide, high-resolution analysis of both DNA copy number (DCN) alterations and loss of heterozygosity (LOH) events in cancer cells (Lindblad-Toh et al., 2000; Bignell et al., 2004; Huang et al., 2004; Janne et al., 2004; Zhao et al., 2004, 2005; Midorikawa et al., 2006).”
BackgroundInfluentialRaghavan, M., Lillington, D. M., Skoulakis, S., Debernardi, S., Chaplin, T., Foot, N. J., Lister, T. A., & Young, B. D. (2005) · Cancer Research · doi:10.1158/0008-5472.375.65.2 · Cited by 268 · cited 2×
“Analysing matched normal DNA in parallel with tumour DNA, SNP arrays can be a powerful tool for the genome-wide detection of LOH/UPD regions because we could completely exclude consanguinity as a cause of homozygosity (Fitzgibbon et al., 2005; Raghavan et al., 2005; Andersen et al., 2007).”
BackgroundSelf-citationYamamoto, G., Nannya, Y., Kato, M., Sanada, M., Levine, R. L., Kawamata, N., Hangaishi, A., Kurokawa, M., Chiba, S., Gilliland, D. G., et al. (2007) · The American Journal of Human Genetics · doi:10.1086/518809 · Cited by 242 · cited 1×
“However, the use of microdissected tumour samples is thought to be advantageous for more accurate determination of LOH regions in case constitutive DNA is not available (Yamamoto et al., 2007).”
BackgroundFitzgibbon, J., Smith, L., Raghavan, M., Smith, M. L., Debernardi, S., Skoulakis, S., Lillington, D. M., Lister, T. A., & Young, B. D. (2005) · Cancer Research · doi:10.1158/0008-5472.can-05-2017 · Cited by 241 · cited 3×
“Analysing matched normal DNA in parallel with tumour DNA, SNP arrays can be a powerful tool for the genome-wide detection of LOH/UPD regions because we could completely exclude consanguinity as a cause of homozygosity (Fitzgibbon et al., 2005; Raghavan et al., 2005; Andersen et al., 2007).”
BackgroundSelf-citationTranscriptome analysis of microdissected pancreatic intraepithelial neoplastic lesions
Buchholz, M., Braun, M., Heidenblut, A., Kestler, H. A., Klöppel, G., Schmiegel, W., Hahn, S. A., Lüttges, J., Gress, T. M., & Krebshilfe, F. T. G. P. C. N. O. T. D. (2005) · Oncogene · doi:10.1038/sj.onc.1208804 · Cited by 190 · cited 2×
“SCAP2 was first identified as a cancer-related gene by Buchholz et al., showing that this gene is overexpressed in pancreatic intraepithelial neoplasia (PanIN) lesions (Buchholz et al., 2005).”
BackgroundConsistent chromosome abnormalities in adenocarcinoma of the pancreas.
Griffin, C. A., Hruban, R. H., Morsberger, L. A., Ellingham, T. J., Long, P. P., Jaffee, E. M., Hauda, K. M., Bohlander, S. K., & Yeo, C. J. (1995) · PubMed · Cited by 126
Janne, P. A., Li, C., Zhao, X., Girard, L., Chen, T.-H., Minna, J. D., Christiani, D. C., Johnson, B. E., & Meyerson, M. M. (2004) · Oncogene · doi:10.1038/sj.onc.1207329 · Cited by 116 · cited 2×
“…arrays has allowed genome-wide, high-resolution analysis of both DNA copy number (DCN) alterations and loss of heterozygosity (LOH) events in cancer cells (Lindblad-Toh et al., 2000; Bignell et al., 2004; Huang et al., 2004; Janne et al., 2004; Zhao et al., 2004, 2005; Midorikawa et al., 2006).”
BackgroundMolecular karyotyping of human hepatocellular carcinoma using single-nucleotide polymorphism arrays
Midorikawa, Y., Yamamoto, S., Ishikawa, S., Kamimura, N., Igarashi, H., Sugimura, H., Makuuchi, M., & Aburatani, H. (2006) · Oncogene · doi:10.1038/sj.onc.1209537 · Cited by 105 · cited 2×
“…arrays has allowed genome-wide, high-resolution analysis of both DNA copy number (DCN) alterations and loss of heterozygosity (LOH) events in cancer cells (Lindblad-Toh et al., 2000; Bignell et al., 2004; Huang et al., 2004; Janne et al., 2004; Zhao et al., 2004, 2005; Midorikawa et al., 2006).”
BackgroundFrequent occurrence of uniparental disomy in colorectal cancer
Andersen, C. L., Wiuf, C., Kruhøffer, M., Korsgaard, M., Laurberg, S., & Orntoft, T. F. (2006) · Carcinogenesis · doi:10.1093/carcin/bgl086 · Cited by 105 · cited 4×
“Analysing matched normal DNA in parallel with tumour DNA, SNP arrays can be a powerful tool for the genome-wide detection of LOH/UPD regions because we could completely exclude consanguinity as a cause of homozygosity (Fitzgibbon et al., 2005; Raghavan et al., 2005; Andersen et al., 2007).”
BackgroundInfluentialGenetic aberrations in prostate cancer by microarray analysis
Saramäki, O. R., Porkka, K. P., Vessella, R. L., & Visakorpi, T. (2006) · International Journal of Cancer · doi:10.1002/ijc.21976 · Cited by 93 · cited 1×
“High-level amplification of SCAP2 was not frequent in our sample set, but it is known that even a low-level copy number change can have a significant effect on gene expression in cancer (Chin et al., 2006; Saramaki et al., 2006).”
BackgroundCalhoun, E. S., Hucl, T., Gallmeier, E., West, K. M., Arking, D. E., Maitra, A., Iacobuzio–Donahue, C. A., Chakravarti, A., Hruban, R. H., & Kern, S. E. (2006) · Cancer Research · doi:10.1158/0008-5472.can-06-0721 · Cited by 86 · cited 2×
“These results were consistent with the previous reports (Iacobuzio-Donahue et al., 2004; Calhoun et al., 2006).”
MethodResultHarada, T., Okita, K., Shiraishi, K., Kusano, N., Kondoh, S., & Sasaki, K. (2002) · PubMed · Cited by 81
Self-citationIacobuzio–Donahue, C. A., van der Heijden, M. S., Baumgartner, M. R., Troup, W. J., Romm, J., Doheny, K. F., Pugh, E., Yeo, C. J., Goggins, M., Hruban, R. H., et al. (2004) · Cancer Research · doi:10.1158/0008-5472.can-03-2756 · Cited by 65 · cited 1×
“These results were consistent with the previous reports (Iacobuzio-Donahue et al., 2004; Calhoun et al., 2006).”
ResultPancreatic adenocarcinoma—Genetic portrait from chromosomes to microarrays
Karhu, R., Mahlamäki, E., & Kallioniemi, A. H. (2006) · Genes Chromosomes and Cancer · doi:10.1002/gcc.20337 · Cited by 53 · cited 1×
“Chromosome arm 7p has long been suspected to include critical oncogenes in PDAC (Griffin et al., 1995; Harada et al., 2002a; Karhu et al., 2006).”
BackgroundConsistent chromosome abnormalities in adenocarcinoma of the pancreas
Griffin, C. A., Hruban, R. H., Morsberger, L. A., Ellingham, T. J., Long, P. P., Jaffee, E. M., Houda, K. M., Bohlander, S. K., & Yeo, C. J. (1995) · Cancer Genetics and Cytogenetics · doi:10.1016/0165-4608(96)85235-6 · Cited by 53 · cited 1×
“Chromosome arm 7p has long been suspected to include critical oncogenes in PDAC (Griffin et al., 1995; Harada et al., 2002a; Karhu et al., 2006).”
BackgroundLips, E., de Graaf, E., Tollenaar, R., van Eijk, R., Oosting, J., Szuhai, K., Karsten, T. M., Nanya, Y., Ogawa, S., van de Velde, C., et al. (2007) · The Journal of Pathology · doi:10.1002/path.2180 · Cited by 47 · cited 1×
“Genomic alterations can contribute to the dysregulation of expression levels of oncogenes and tumour suppressor genes in cancer cells, the accumulation of which is correlated with tumour progression (Ried et al., 1999; Bardeesy and DePinho, 2002; Li et al., 2004; Lips et al., 2007).”
BackgroundHarada, T., Baril, P., Gangeswaran, R., Kelly, G. P., Chelala, C., Bhakta, V., Caulee, K., Mahon, P. C., & Lemoine, N. R. (2007) · British Journal of Cancer · doi:10.1038/sj.bjc.6603563 · Cited by 43 · cited 8×
“87, respectively, corresponding to ±2 standard deviation (see Harada et al., 2007 for more details).”
BackgroundMethodInfluentialSelf-citationTakahashi, T., Yamashita, H., Nagano, Y., Nakamura, T., Ohmori, H., Avraham, H. K., Avraham, S., Yasuda, M., & Matsumoto, M. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m213217200 · Cited by 40 · cited 1×
“SCAP2 was originally described as a substrate for the src family kinases able to regulate the phosphorylation of the presynaptic protein a-Synuclein; a process considered to be crucial in the pathogenesis of several neurodegenerative diseases including Parkinson’s disease (Takahashi et al., 2003).”
BackgroundLoss of heterozygosity at 11q23.1 and survival in breast cancer: Results of a large European study
Laake, K., Launonen, V., Niederacher, D., Gudlaugsdottir, S., Seitz, S., Rio, P. G., Champ�me, M.-H., Bièche, I., Birnbaum, D., White, G. R. M., et al. (1999) · Genes Chromosomes and Cancer · doi:10.1002/(sici)1098-2264(199907)25:3 · Cited by 38
α-Synuclein Stimulates Differentiation of Osteosarcoma Cells
Fujita, M., Sugama, S., Nakai, M., Takenouchi, T., Wei, J., Urano, T., Inoue, S., & Hashimoto, M. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m606175200 · Cited by 37 · cited 1×
“Interestingly, a recent study has demonstrated that overexpression of a-Synuclein in osteosarcoma cells results in a prolonged G1 phase of the cell cycle and initiates tumour differentiation (Fujita et al., 2006).”
BackgroundHarada, T., Okita, K., Shiraishi, K., Kusano, N., Furuya, T., Oga, A., Kawauchi, S., Kondoh, S., & Sasaki, K. (2002) · Oncology · doi:10.1159/000059573 · Cited by 31 · cited 4×
“Tissue microdissection enables us to collect purified populations of cancer cells by trimming out dense stromal components (Harada et al., 2002a, 2007; Figure 4 (A) The minimal common region (7p15.”
BackgroundMethodResultInfluentialSelf-citation
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Initiative, A. P. C. G., Waddell, N., Pajic, M., Patch, A.-M., Chang, D. K., Kassahn, K. S., Bailey, P., Johns, A. L., Miller, D., Nones, K., et al. (2015) · Nature · doi:10.1038/nature14169 · Cited by 2,642
“the tumour and normal; (3) not validated—PCR yields smears or multiple bands, this potentially indicates non-specific primer pair; (4) not tested—no PCR band was observed in tumour and normal.”
BackgroundPan-cancer patterns of somatic copy number alteration
Zack, T. I., Schumacher, S. E., Carter, S. L., Cherniack, A. D., Saksena, G., Tabak, B., Lawrence, M. S., Zhang, C., Wala, J. A., Mermel, C. H., et al. (2013) · Nature Genetics · doi:10.1038/ng.2760 · Cited by 1,893
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Campbell, P. J., Yachida, S., Mudie, L. J., Stephens, P. J., Pleasance, E. D., Stebbings, L. A., Morsberger, L. A., Latimer, C., McLaren, S., Lin, M.-L., et al. (2010) · Nature · doi:10.1038/nature09460 · Cited by 1,317
Delineating copy number and clonal substructure in human tumors from single-cell transcriptomes
Gao, R., Bai, S., Henderson, Y. C., Lin, Y., Schalck, A. P., Yan, Y., Kumar, T., Hu, M. S., Sei, E., Davis, A., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-020-00795-2 · Cited by 924
Pancreatic cancer evolution and heterogeneity: integrating omics and clinical data
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Metadata
- Authors
- Harada, T., Chelala, C., Bhakta, V, Chaplin, T., Caulee, K., Baril, P., Young, B. D., & Lemoine, N. R.
- Affiliations
- University of London (GB)
- Corresponding author
- Lemoine, N R
- Venue
- Oncogene
- Published
- 2007-10-22
- Volume
- 27
- Issue
- 13
- Pages
- 1951-1960
- ISSN
- 0950-9232 (ISSN-L)
- 1476-5594
- PMC
- PMC2492386
- OpenAlex
- W1997162169
- Cited by
- 159
- References
- 34
- Citations by year
- 2026: 3 · 2025: 3 · 2024: 5 · 2023: 9 · 2022: 9 · 2021: 9 · 2020: 5 · 2019: 5 · 2018: 7 · 2017: 4 · 2016: 10 · 2015: 7 · 2014: 8 · 2013: 8 · 2012: 10
- FWCI
- 6.56
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Oncogene (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- HAL (submittedVersion)
- Funders
- Cancer Research UK (A6438, A6789, A6253)
- Topics
- Health Sciences › Medicine › Oncology › Pancreatic and Hepatic Oncology Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Keywords
- pancreatic ductal adenocarcinoma, DNA copy number alterations, single nucleotide polymorphism array, gene amplification, gene expression, pancreatic carcinogenesis, chromosomal gains and losses
- MeSH terms
- Adenocarcinoma, Adult, Aged, Chromosome Aberrations, Chromosomes, Human, DNA, Neoplasm, Female, Humans, Male, Middle Aged, Nucleic Acid Hybridization, Pancreatic Neoplasms, RNA, Neoplasm, In Situ Hybridization, Fluorescence, Gene Dosage, Loss of Heterozygosity, Reverse Transcriptase Polymerase Chain Reaction, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide, Carcinoma, Pancreatic Ductal, Microdissection, Intracellular Signaling Peptides and Proteins
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