Genotypic resistance testing in HIV by arrayed primer extension.

Analytical and Bioanalytical Chemistry
Michaela SchannéJörg D Hoheisel

Abstract

The analysis of mutations that are associated with the occurrence of drug resistance is important for monitoring the antiretroviral therapy of patients infected with human immunodeficiency virus (HIV). Here, we describe the establishment and successful application of Arrayed Primer Extension (APEX) for genotypic resistance testing in HIV as a rapid and economical alternative to standard sequencing. The assay is based on an array of oligonucleotide primers that are immobilised via their 5'-ends. Upon hybridisation of template DNA, a primer extension reaction is performed in the presence of the four dideoxynucleotides, each labelled with a distinct fluorophore. The inserted label immediately indicates the sequence at the respective position. Any mutation changes the colour pattern. We designed a microarray for the analysis of 26 and 33 codons in the HIV protease and reverse transcriptase, respectively, which are of special interest with respect to drug resistance. The enormous genome variability of HIV represents a big challenge for genotypic resistance tests, which include a hybridisation step, both in terms of specificity and probe numbers. The use of degenerated oligonucleotides resulted in a significant reduction in the numbe...Continue Reading

References

Dec 1, 1977·Proceedings of the National Academy of Sciences of the United States of America·F SangerA R Coulson
Nov 25, 1988·Science·B D PrestonL A Loeb
Nov 25, 1988·Science·J D RobertsT A Kunkel
Jun 11, 1996·Proceedings of the National Academy of Sciences of the United States of America·L MoutouhD D Richman
Dec 2, 2000·Transfusion·C F de OliveiraM P Busch
Mar 20, 2001·Annals of Internal Medicine·M C WeinsteinK A Freedberg
Mar 27, 2001·Nucleic Acids Research·F DiehlJ D Hoheisel
Sep 6, 2001·Proceedings of the National Academy of Sciences of the United States of America·K FellenbergM Vingron
Apr 5, 2002·Clinical Microbiology Reviews·Robert W Shafer
Apr 18, 2002·Proceedings of the National Academy of Sciences of the United States of America·Neeme TõnissonAndres Metspalu
Jun 29, 2002·Journal of Clinical Microbiology·V ChizhikovK Chumakov
Feb 14, 2004·Journal of Clinical Virology : the Official Publication of the Pan American Society for Clinical Virology·Rami Kantor, David Katzenstein
Feb 27, 2004·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Scott A WegnerUNKNOWN RV-125 Centers for Education and Research on Therapeutics Study Team
May 1, 1995·Clinical and Diagnostic Virology·R T D'Aquila
Apr 20, 2006·Journal of Medical Virology·Francine E McCutchan
Aug 22, 2006·The Journal of Infectious Diseases·Andrew R Zolopa

❮ Previous
Next ❯

Citations

Jan 17, 2015·Clinica Chimica Acta; International Journal of Clinical Chemistry·Nutjaree JeenduangChamras Promptmas

❮ Previous
Next ❯

Methods Mentioned

BETA
PCR
genotyping
chip

Software Mentioned

GenePix
APEX
Rega HIV - 1 Subtyping Tool

Related Concepts

Related Feeds

Antimicrobial Resistance (ASM)

Antimicrobial resistance poses a significant threat to the continued successful use of antimicrobial agents for the treatment of bacterial infections.

Antimicrobial Resistance

Antimicrobial resistance poses a significant threat to the continued successful use of antimicrobial agents for the treatment of bacterial infections.

Related Papers

Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America
Omobosola AkinseteKeith Henry
Clinical Chemistry and Laboratory Medicine : CCLM
Neeme TõnissonAndres Metspalu
© 2021 Meta ULC. All rights reserved