Clinical Chemistry Link to Randox Laboratories Web Site
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
QUICK SEARCH:   [advanced]


     

Clinical Chemistry 52: 202-211, 2006. First published December 29, 2005; 10.1373/clinchem.2005.062042
This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Supplemental Data
Right arrow All Versions of this Article:
clinchem.2005.062042v1
52/2/202    most recent
Right arrow Submit an electronic Letter to
the Editor about this paper
Right arrow Alert me when this article is cited
Right arrow Alert me when eLetters are posted
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 ISI Web of Science
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 ISI Web of Science (5)
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Milani, L.
Right arrow Articles by Syvänen, A.-C.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Milani, L.
Right arrow Articles by Syvänen, A.-C.
Related Collections
Right arrow Molecular Diagnostics and Genetics
(Clinical Chemistry. 2006;52:202-211.)
© 2006 American Association for Clinical Chemistry, Inc.

Molecular Diagnostics and Genetics

Detection of Alternatively Spliced Transcripts in Leukemia Cell Lines by Minisequencing on Microarrays

Lili Milani2, Mona Fredriksson2 and Ann-Christine Syvänena

1 Molecular Medicine, Department of Medical Sciences, Uppsala University, Uppsala, Sweden.

aAddress correspondence to this author at: Molecular Medicine, Department of Medical Sciences, Uppsala University, Uppsala Academic Hospital, Entrance 70, 3rd Floor, Research Department 2, 751 85 Uppsala, Sweden. Fax 46-18-553601; e-mail Ann-Christine.Syvanen{at}medsci.uu.se.

Background: Recent genome-wide expression studies suggest that ~80% of the 25 000 human genes undergo alternative splicing. Alternative splicing may be associated with human diseases, particularly with cancer, but the molecular disease mechanisms are poorly understood. Convenient, novel methods for multiplexed detection of alternatively spliced transcripts are needed.

Methods: We devised a new approach for detecting splice variants based on a tag-microarray minisequencing system, originally developed for genotyping single-nucleotide polymorphisms. We established the system for multiplexed detection of 61 alternatively spliced transcripts in a panel of 19 cancer-related genes and used it to dissect the splicing patterns in cancer and endothelial cells.

Results: Our microarray system detected 82% of the splice variants screened for, including both simple and complex splice variants, in at least 1 of the leukemia cell types analyzed. The intraassay CV values for our method ranged from 0.01 to 0.34 (mean, 0.13) for 5 replicate measurements. Our system allowed semiquantitative comparison of the splicing patterns between the cell lines. Similar, but not identical, patterns of alternative splicing were observed among the leukemia cell lines. Size analysis of the PCR products subjected to the tag-array minisequencing system and real-time PCR with exon-junction probes verified the results from the microarray system.

Conclusions: The microarray-based method is a robust and easily accessible tool for parallel detection of alternatively spliced transcripts of multiple genes. It can be used for studying alternative splicing in cancer progression and for following up drug treatment, and it may be a useful tool in clinical diagnostics for cancer and other disorders.




The following articles in journals at HighWire Press have cited this article:


Home page
 Cancer Res.Home page
R. Klinck, A. Bramard, L. Inkel, G. Dufresne-Martin, J. Gervais-Bird, R. Madden, E. R. Paquet, C. Koh, J. P. Venables, P. Prinos, et al.
Multiple Alternative Splicing Markers for Ovarian Cancer
Cancer Res., February 1, 2008; 68(3): 657 - 663.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
C. Ben-Dov, B. Hartmann, J. Lundgren, and J. Valcarcel
Genome-wide Analysis of Alternative Pre-mRNA Splicing
J. Biol. Chem., January 18, 2008; 283(3): 1229 - 1233.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
L. Milani, M. Gupta, M. Andersen, S. Dhar, M. Fryknas, A. Isaksson, R. Larsson, and A.-C. Syvanen
Allelic imbalance in gene expression as a guide to cis-acting regulatory single nucleotide polymorphisms in cancer cells
Nucleic Acids Res., March 12, 2007; 35(5): e34 - e34.
[Abstract] [Full Text] [PDF]


HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
Copyright © 2006 by the American Association for Clinical Chemistry.