Genome Research cityscape

Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
QUICK SEARCH:   [advanced]


     

This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Right arrow Citation Map
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Paulson, T. G.
Right arrow Articles by Reid, B. J.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Paulson, T. G.
Right arrow Articles by Reid, B. J.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us   Add to Digg   Add to Reddit   Add to Technorati  
What's this?

Vol. 9, Issue 5, 482-491, May 1999

METHODS
Loss of Heterozygosity Analysis Using Whole Genome Amplification, Cell Sorting, and Fluorescence-Based PCR

Thomas G. Paulson,1,2,4 Patricia C. Galipeau,1,4 and Brian J. Reid1,2,3,5

1 Programs in Cancer Biology and GI Oncology, Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98104 USA; 2 Division of Gastroenterology, Department of Medicine, 3 Department of Genetics, University of Washington, Seattle, Washington 98195 USA

Loss of heterozygosity (LOH) is a common genetic lesion found in many human neoplasms. Extending investigation of LOH to large-scale clinical and public health science studies has proven difficult because of the small size and cellular and genetic heterogeneity of human neoplasms, in addition to the challenges associated with increasing throughput. Our approach to LOH analysis was developed using clinical biopsy samples from patients with Barrett's esophagus (BE) and uses flow cytometric cell sorting to increase sample purity, whole genome amplification to increase sample amount, and automated fluorescent genotyping to increase sample throughput. This approach allows LOH assessment at 20 loci in DNA extracted from 1000 flow-purified cells while maintaining accurate and reproducible allele ratios compared with the standard method of using genomic DNA. This method of analysis should allow accurate, reproducible determination of allele ratios in a variety of human tumors and premalignant conditions.

4   These authors contributed equally to this work.
5   Corresponding author.

9:482-491 ©1999 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/99 $5.00
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us   Add to Digg Digg   Add to Reddit Reddit   Add to Technorati Technorati    What's this?


This article has been cited by other articles:


Home page
 J. Mol. Diagn.Home page
C. M. Heaphy, W. C. Hines, K. S. Butler, C. M. Haaland, G. Heywood, E. G. Fischer, M. Bisoffi, and J. K. Griffith
Assessment of the Frequency of Allelic Imbalance in Human Tissue Using a Multiplex Polymerase Chain Reaction System
J. Mol. Diagn., April 1, 2007; 9(2): 266 - 271.
[Abstract] [Full Text] [PDF]

Home page
 BloodHome page
J. A. Pollard, T. A. Alonzo, R. B. Gerbing, W. G. Woods, B. J. Lange, D. A. Sweetser, J. P. Radich, I. D. Bernstein, and S. Meshinchi
FLT3 internal tandem duplication in CD34+/CD33- precursors predicts poor outcome in acute myeloid leukemia
Blood, October 15, 2006; 108(8): 2764 - 2769.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Epidemiol. Biomarkers Prev.Home page
D. L. Chao, C. C. Maley, X. Wu, D. C. Farrow, P. C. Galipeau, C. A. Sanchez, T. G. Paulson, P. S. Rabinovitch, B. J. Reid, M. R. Spitz, et al.
Mutagen Sensitivity and Neoplastic Progression in Patients with Barrett's Esophagus: A Prospective Analysis.
Cancer Epidemiol. Biomarkers Prev., October 1, 2006; 15(10): 1935 - 1940.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Epidemiol. Biomarkers Prev.Home page
J. C. Finley, B. J. Reid, R. D. Odze, C. A. Sanchez, P. Galipeau, X. Li, S. G. Self, K. A. Gollahon, P. L. Blount, and P. S. Rabinovitch
Chromosomal Instability in Barrett's Esophagus Is Related to Telomere Shortening.
Cancer Epidemiol. Biomarkers Prev., August 1, 2006; 15(8): 1451 - 1457.
[Abstract] [Full Text] [PDF]

Home page
 Clin. Cancer Res.Home page
T. G. Paulson, L. Xu, C. Sanchez, P. L. Blount, K. Ayub, R. D. Odze, and B. J. Reid
Neosquamous Epithelium Does Not Typically Arise from Barrett's Epithelium
Clin. Cancer Res., March 15, 2006; 12(6): 1701 - 1706.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Epidemiol. Biomarkers Prev.Home page
V. J. Wongsurawat, J. C. Finley, P. C. Galipeau, C. A. Sanchez, C. C. Maley, X. Li, P. L. Blount, R. D. Odze, P. S. Rabinovitch, and B. J. Reid
Genetic Mechanisms of TP53 Loss of Heterozygosity in Barrett's Esophagus: Implications for Biomarker Validation.
Cancer Epidemiol. Biomarkers Prev., March 1, 2006; 15(3): 509 - 516.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
D. M. Crooks, G. Pacheco-Rodriguez, R. M. DeCastro, J. P. McCoy Jr., J.-a. Wang, F. Kumaki, T. Darling, and J. Moss
Molecular and genetic analysis of disseminated neoplastic cells in lymphangioleiomyomatosis
PNAS, December 14, 2004; 101(50): 17462 - 17467.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
C. C. Maley, P. C. Galipeau, X. Li, C. A. Sanchez, T. G. Paulson, P. L. Blount, and B. J. Reid
The Combination of Genetic Instability and Clonal Expansion Predicts Progression to Esophageal Adenocarcinoma
Cancer Res., October 15, 2004; 64(20): 7629 - 7633.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
C. C. Maley, P. C. Galipeau, X. Li, C. A. Sanchez, T. G. Paulson, and B. J. Reid
Selectively Advantageous Mutations and Hitchhikers in Neoplasms: p16 Lesions Are Selected in Barrett's Esophagus
Cancer Res., May 15, 2004; 64(10): 3414 - 3427.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Epidemiol. Biomarkers Prev.Home page
R. E. Ellsworth, D. L. Ellsworth, S. M. Lubert, J. Hooke, R. I. Somiari, and C. D. Shriver
High-Throughput Loss of Heterozygosity Mapping in 26 Commonly Deleted Regions in Breast Cancer
Cancer Epidemiol. Biomarkers Prev., September 1, 2003; 12(9): 915 - 919.
[Abstract] [Full Text] [PDF]

Home page
 JNCI J Natl Cancer InstHome page
R. E. Rudolph, T. L. Vaughan, A. R. Kristal, P. L. Blount, D. S. Levine, P. C. Galipeau, L. J. Prevo, C. A. Sanchez, P. S. Rabinovitch, and B. J. Reid
Serum Selenium Levels in Relation to Markers of Neoplastic Progression Among Persons With Barrett's Esophagus
J Natl Cancer Inst, May 21, 2003; 95(10): 750 - 757.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Epidemiol. Biomarkers Prev.Home page
T. L. Vaughan, A. R. Kristal, P. L. Blount, D. S. Levine, P. C. Galipeau, L. J. Prevo, C. A. Sanchez, P. S. Rabinovitch, and B. J. Reid
Nonsteroidal Anti-inflammatory Drug Use, Body Mass Index, and Anthropometry in Relation to Genetic and Flow Cytometric Abnormalities in Barrett's Esophagus
Cancer Epidemiol. Biomarkers Prev., August 1, 2002; 11(8): 745 - 752.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
F. B. Dean, S. Hosono, L. Fang, X. Wu, A. F. Faruqi, P. Bray-Ward, Z. Sun, Q. Zong, Y. Du, J. Du, et al.
Comprehensive human genome amplification using multiple displacement amplification
PNAS, April 16, 2002; 99(8): 5261 - 5266.
[Abstract] [Full Text] [PDF]

Home page
 Am. J. Pathol.Home page
E. L. Schubert, L. Hsu, L. A. Cousens, J. Glogovac, S. Self, B. J. Reid, P. S. Rabinovitch, and P. L. Porter
Single Nucleotide Polymorphism Array Analysis of Flow-Sorted Epithelial Cells from Frozen Versus Fixed Tissues for Whole Genome Analysis of Allelic Loss in Breast Cancer
Am. J. Pathol., January 1, 2002; 160(1): 73 - 79.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
D. J. Wong, T. G. Paulson, L. J. Prevo, P. C. Galipeau, G. Longton, P. L. Blount, and B. J. Reid
p16INK4a Lesions Are Common, Early Abnormalities that Undergo Clonal Expansion in Barrett's Metaplastic Epithelium
Cancer Res., November 1, 2001; 61(22): 8284 - 8289.
[Abstract] [Full Text] [PDF]

Home page
 BloodHome page
D. A. Sweetser, C.-S. Chen, A. A. Blomberg, D. A. Flowers, P. C. Galipeau, M. T. Barrett, N. A. Heerema, J. Buckley, W. G. Woods, I. D. Bernstein, et al.
Loss of heterozygosity in childhood de novo acute myelogenous leukemia
Blood, August 15, 2001; 98(4): 1188 - 1194.
[Abstract] [Full Text] [PDF]

Home page
 RadiologyHome page
P. C. Stomper, C. C. Stewart, and D. L. Stoler
Stereotactic Core Biopsy Breast and Blood Cell By-products: A Source of Material for Molecular Genetics Research-Initial Experience
Radiology, March 1, 2001; 218(3): 881 - 885.
[Abstract] [Full Text]

Home page
 BloodHome page
S. Meshinchi, W. G. Woods, D. L. Stirewalt, D. A. Sweetser, J. D. Buckley, T. K. Tjoa, I. D. Bernstein, and J. P. Radich
Prevalence and prognostic significance of Flt3 internal tandem duplication in pediatric acute myeloid leukemia
Blood, January 1, 2001; 97(1): 89 - 94.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
R. Mei, P. C. Galipeau, C. Prass, A. Berno, G. Ghandour, N. Patil, R. K. Wolff, M. S. Chee, B. J. Reid, and D. J. Lockhart
Genome-wide Detection of Allelic Imbalance Using Human SNPs and High-density DNA Arrays
Genome Res., August 1, 2000; 10(8): 1126 - 1137.
[Abstract] [Full Text]

Home page
 Genome Res.Home page
I. L. Medintz, C.-C. R. Lee, W. W. Wong, K. Pirkola, D. Sidransky, and R. A. Mathies
Loss of Heterozygosity Assay for Molecular Detection of Cancer Using Energy-transfer Primers and Capillary Array Electrophoresis
Genome Res., August 1, 2000; 10(8): 1211 - 1218.
[Abstract] [Full Text]

Home page
 JNCI J Natl Cancer InstHome page
P. C. Galipeau, L. J. Prevo, C. A. Sanchez, G. M. Longton, and B. J. Reid
Clonal Expansion and Loss of Heterozygosity at Chromosomes 9p and 17p in Premalignant Esophageal (Barrett's) Tissue
J Natl Cancer Inst, December 15, 1999; 91(24): 2087 - 2095.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
L. J. Prevo, C. A. Sanchez, P. C. Galipeau, and B. J. Reid
p53-Mutant Clones and Field Effects in Barrett's Esophagus
Cancer Res., October 1, 1999; 59(19): 4784 - 4787.
[Abstract] [Full Text] [PDF]


Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
Genes Dev. Learn. Mem.
Protein Science RNA Genome Res.