Solutions for Genomic
and Epigenomic Research
and Epigenomic Research
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| Poster Presentated at AACR 2008: |
1. Rietschel P, Wolchok JD, Krown S, Gerst S, Jungbluth AA, Busam K, Smith K, Orlow I, Panageas K, Chapman PB Phase II
study of extended-dose temozolomide in patients with melanoma. J Clin Oncol. 2008 May 10;26(14):2299-304.
2. Kim HR, Hwang KA, Kim KC, Kang I. Down-regulation of IL-7Ralpha expression in human T cells via DNA methylation
J Immunol. 2007 May 1;178(9):5473-9
3. Dejeux E, Audard V, Cavard C, Gut IG, Terris B, Tost J. Rapid identification of promoter hypermethylation in
hepatocellular carcinoma by pyrosequencing of etiologically homogeneous sample pools J Mol Diagn. 2007
Sep;9(4):510-20. Epub 2007 Aug 9
4. Pasquali L, Bedeir A, Ringquist S, Styche A, Bhargava R, Trucco G. Quantification of CpG island methylation in
progressive breast lesions from normal to invasive carcinoma Cancer Lett. 2007 Nov 8;257(1):136-44. Epub 2007 Aug 15
5. Marcos R.H. Estécio, Vazganush Gharibyan, Lanlan Shen, Ashraf E.K. Ibrahim, Ketan Doshi, Rong He, Jaroslav Jelinek,
Allen S. Yang, Pearlly S. Yan, Tim H-M. Huang, Eloiza H. Tajara, and Jean-Pierre J. Issa LINE-1 Hypomethylation in Cancer Is
Highly Variable and Inversely Correlated with Microsatellite Instability PLoS ONE. 2007; 2(5): e399. Published online 2007
May 2. doi: 10.1371/journal.pone.0000399. PMCID: 1851990
6. Liu T, Zhang X, So CK, Wang S, Wang P, Yan L, Myers R, Chen Z, Patterson AP, Yang CS, Chen X Regulation of
Cdx2 expression by promoter methylation, and effects of Cdx2 transfection on morphology and gene expression of human
esophageal epithelial. Cell Carcinogenesis, 2007 Feb; 28(2): 488-96
7. Brakensiek K, Wingen LU, Langer F, Kreipe H, Lehmann U Quantitative high-resolution CpG island mapping with
Pyrosequencing reveals disease-specific methylation patterns of the CDKN2B gene in myelodysplastic syndrome and myeloid
leukemia Clin Chem. 2007 Jan;53(1):17-23. Epub 2006 Nov 9
8 Ogino S, Kawasaki T, Kirkner GJ, Loda M, Fuchs CS. CpG island methylator phenotype-low (CIMP-low) in colorectal
cancer: possible associations with male sex and KRAS mutations. J Mol Diagn 2006;8:582-588.
9 Schernhammer ES, Giovannucci EL, Fuchs CS, Ogino S. A prospective study of dietary folate and vitamin B and colon
cancer according to MSI and KRAS mutational status. Cancer Epidemiol Biomarkers Prev 2008;17:2895-2898.
10. Ogino S, Nosho K, Kirkner GJ, Kawasaki T, Meyerhardt JA, Loda M, Giovannucci EL, Fuchs CS. CpG island methylator
phenotype, microsatellite instability, BRAF mutation and clinical outcome in colon cancer. Gut 2009;58:90-96.
11. England RPM, Pyro-QCpG:
Quantitative analysis of methylation in multiple CpG sites by Pyrosequencing(R).
Nature Method: 2005;2:1-2.
study of extended-dose temozolomide in patients with melanoma. J Clin Oncol. 2008 May 10;26(14):2299-304.
2. Kim HR, Hwang KA, Kim KC, Kang I. Down-regulation of IL-7Ralpha expression in human T cells via DNA methylation
J Immunol. 2007 May 1;178(9):5473-9
3. Dejeux E, Audard V, Cavard C, Gut IG, Terris B, Tost J. Rapid identification of promoter hypermethylation in
hepatocellular carcinoma by pyrosequencing of etiologically homogeneous sample pools J Mol Diagn. 2007
Sep;9(4):510-20. Epub 2007 Aug 9
4. Pasquali L, Bedeir A, Ringquist S, Styche A, Bhargava R, Trucco G. Quantification of CpG island methylation in
progressive breast lesions from normal to invasive carcinoma Cancer Lett. 2007 Nov 8;257(1):136-44. Epub 2007 Aug 15
5. Marcos R.H. Estécio, Vazganush Gharibyan, Lanlan Shen, Ashraf E.K. Ibrahim, Ketan Doshi, Rong He, Jaroslav Jelinek,
Allen S. Yang, Pearlly S. Yan, Tim H-M. Huang, Eloiza H. Tajara, and Jean-Pierre J. Issa LINE-1 Hypomethylation in Cancer Is
Highly Variable and Inversely Correlated with Microsatellite Instability PLoS ONE. 2007; 2(5): e399. Published online 2007
May 2. doi: 10.1371/journal.pone.0000399. PMCID: 1851990
6. Liu T, Zhang X, So CK, Wang S, Wang P, Yan L, Myers R, Chen Z, Patterson AP, Yang CS, Chen X Regulation of
Cdx2 expression by promoter methylation, and effects of Cdx2 transfection on morphology and gene expression of human
esophageal epithelial. Cell Carcinogenesis, 2007 Feb; 28(2): 488-96
7. Brakensiek K, Wingen LU, Langer F, Kreipe H, Lehmann U Quantitative high-resolution CpG island mapping with
Pyrosequencing reveals disease-specific methylation patterns of the CDKN2B gene in myelodysplastic syndrome and myeloid
leukemia Clin Chem. 2007 Jan;53(1):17-23. Epub 2006 Nov 9
8 Ogino S, Kawasaki T, Kirkner GJ, Loda M, Fuchs CS. CpG island methylator phenotype-low (CIMP-low) in colorectal
cancer: possible associations with male sex and KRAS mutations. J Mol Diagn 2006;8:582-588.
9 Schernhammer ES, Giovannucci EL, Fuchs CS, Ogino S. A prospective study of dietary folate and vitamin B and colon
cancer according to MSI and KRAS mutational status. Cancer Epidemiol Biomarkers Prev 2008;17:2895-2898.
10. Ogino S, Nosho K, Kirkner GJ, Kawasaki T, Meyerhardt JA, Loda M, Giovannucci EL, Fuchs CS. CpG island methylator
phenotype, microsatellite instability, BRAF mutation and clinical outcome in colon cancer. Gut 2009;58:90-96.
11. England RPM, Pyro-QCpG:
Quantitative analysis of methylation in multiple CpG sites by Pyrosequencing(R).
Nature Method: 2005;2:1-2.
SNP Genotyping and Allele Quantification Analysis:
1. Katsuhiko Nosho, Takako Kawasaki,Mutsuko Ohnishi, Yuko Suemoto, Gregory J. Kirkner, Dimity Zepf‡, Liying Yan,
Janina A. Longtine‡, Charles S. Fuchs, and Shuji Ogino PIK3CA Mutation in Colorectal Cancer: Relationship with Genetic and
Epigenetic Alterations Neoplasia: 2008;10(6): 534-541
2. Ogino S, Nosho K, Kirkner GJ, Shima K, Irahara N, Kure S, Chan AT, Engelman JA, Kraft P, Cantley LC, Giovannucci EL,
Fuchs CS. PIK3CA mutation is associated with poor prognosis among patients with curatively resected colon cancer. J Clin
Oncol 2009;27:1477-1484.
3. Kure S, Nosho K, Baba Y, Irahara N, Shima K, Ng K, Meyerhardt JA, Giovannucci EL, Fuchs CS, Ogino S. Vitamin D
receptor expression is associated with PIK3CA and KRAS mutations in colorectal cancer. Cancer Epidemiol Biomarkers Prev
2009: in press.
4. Ogino S, Meyerhardt JA, Irahara N, Niedzwiecki D, Hollis D, Saltz LB, Mayer RJ, Schaefer P, Whittom R, Hantel A, Benson
III AB, Goldberg RM, Bertagnolli MM, Fuchs CS. KRAS Mutation in Stage III Colon Cancer and Clinical Outcome Following
Intergroup Trial CALGB 89803. Clin Cancer Res 2009: in press.
5. Ogino S, Kawasaki T, Brahmandam M, Yan L, Cantor M, Namgyal C, Mino-Kenudson M, Lauwers GY, Loda M, Fuchs
CS Sensitive sequencing method for KRAS mutation detection by Pyrosequencing. J Mol Diagn. 2005 Aug;7(3):413-21
Janina A. Longtine‡, Charles S. Fuchs, and Shuji Ogino PIK3CA Mutation in Colorectal Cancer: Relationship with Genetic and
Epigenetic Alterations Neoplasia: 2008;10(6): 534-541
2. Ogino S, Nosho K, Kirkner GJ, Shima K, Irahara N, Kure S, Chan AT, Engelman JA, Kraft P, Cantley LC, Giovannucci EL,
Fuchs CS. PIK3CA mutation is associated with poor prognosis among patients with curatively resected colon cancer. J Clin
Oncol 2009;27:1477-1484.
3. Kure S, Nosho K, Baba Y, Irahara N, Shima K, Ng K, Meyerhardt JA, Giovannucci EL, Fuchs CS, Ogino S. Vitamin D
receptor expression is associated with PIK3CA and KRAS mutations in colorectal cancer. Cancer Epidemiol Biomarkers Prev
2009: in press.
4. Ogino S, Meyerhardt JA, Irahara N, Niedzwiecki D, Hollis D, Saltz LB, Mayer RJ, Schaefer P, Whittom R, Hantel A, Benson
III AB, Goldberg RM, Bertagnolli MM, Fuchs CS. KRAS Mutation in Stage III Colon Cancer and Clinical Outcome Following
Intergroup Trial CALGB 89803. Clin Cancer Res 2009: in press.
5. Ogino S, Kawasaki T, Brahmandam M, Yan L, Cantor M, Namgyal C, Mino-Kenudson M, Lauwers GY, Loda M, Fuchs
CS Sensitive sequencing method for KRAS mutation detection by Pyrosequencing. J Mol Diagn. 2005 Aug;7(3):413-21
Tel. - 1 508.852.4200 · Fax - 1 508.852.4202 · email - info@epigendx.com Pyrosequencing and Pyrogram are registered trademarks of Biotage. © Copyright 2006 EpigenDx. |
| DNA Methylation Analysis: |
Pyosequencing is an Effective Method for the Quantitative Analysis of Global and Gene-specific DNA Methylation
Using Low Quantities of DNA
Because DNA isolated from clinical blood serum samples are treated in different ways and the quantity is often limiting, it is
important to show that consistent methylation results can be obtained with small quantities of DNA. In this study we
quantitatively analyzed both global and gene specific methylation of DNA isolated from different sera samples. Additionally, we
analyzed DNA from cells that were sorted in 2-fold decreasing amounts to determine the limit of sensitivity of a variety of
assays. Among the genes we analyzed were the Alu and Line-1 elements for global methylation and gene specific MGMT, p16
and RASSF1 assays. We demonstrated that Pyrosequencing® methylation analysis achieves a high degree of consistency
and sensitivity when used on DNA isolated from blood serum and different assays differ in there lower limit of DNA that can be
analyzed.
To request a copy, Please contact: info@epigendx.com
Using Low Quantities of DNA
Because DNA isolated from clinical blood serum samples are treated in different ways and the quantity is often limiting, it is
important to show that consistent methylation results can be obtained with small quantities of DNA. In this study we
quantitatively analyzed both global and gene specific methylation of DNA isolated from different sera samples. Additionally, we
analyzed DNA from cells that were sorted in 2-fold decreasing amounts to determine the limit of sensitivity of a variety of
assays. Among the genes we analyzed were the Alu and Line-1 elements for global methylation and gene specific MGMT, p16
and RASSF1 assays. We demonstrated that Pyrosequencing® methylation analysis achieves a high degree of consistency
and sensitivity when used on DNA isolated from blood serum and different assays differ in there lower limit of DNA that can be
analyzed.
To request a copy, Please contact: info@epigendx.com
| Posters Presented at AMP 2008: |
- The Use of Pyrosequencing as a Valuable Tool for Detecting Epigenetic and Genetic Alterations in Ovarian
Cancer Cell Lines (TT24)
- Pyrosequencing Methylation Profile of Seven Thyroid Cancer Cell Lines (Poster number ST07)
- Pyrosequencing Methylation Profile of Five Breast Cancer Cell Lines (Poster number ST09)
Cancer Cell Lines (TT24)
- Pyrosequencing Methylation Profile of Seven Thyroid Cancer Cell Lines (Poster number ST07)
- Pyrosequencing Methylation Profile of Five Breast Cancer Cell Lines (Poster number ST09)