Optimization of allele-specific PCR using patient-specific HIV consensus sequences for primer design

• Published in: Journal of virological methods Vol. 164; no. 1; pp. 122 - 126
• Main Authors: Boltz, Valerie F., Maldarelli, Frank, Martinson, Neil, Morris, Lynn, McIntyre, James A., Gray, Glenda, Hopley, Mark J., Kimura, Toshio, Mayers, Douglas L., Robinson, Patrick, Mellors, John W., Coffin, John M., Palmer, Sarah E.
• Format: Journal Article
• Language: English
• Published: Kidlington Elsevier B.V 01.03.2010; Elsevier
• Subjects: Allele-specific PCR; Alleles; Biological and medical sciences; Consensus Sequence; DNA Primers - genetics; Drug resistance; Fundamental and applied biological sciences. Psychology; Genotype; HIV Infections - virology; HIV-1; HIV-1 - classification; HIV-1 - genetics; HIV-1 - isolation & purification; Human immunodeficiency virus 1; Humans; Low frequency variants; Medicin och hälsovetenskap; Microbiology; Patient-specific HIV-1 consensus sequence; Polymerase Chain Reaction - methods; Polymorphism, Genetic; RNA, Viral - genetics; Subtype consensus sequence; Techniques used in virology; Virology; HIV-1; Low frequency variants; Allele-specific PCR; Subtype consensus sequence; Patient-specific HIV-1 consensus sequence; Immunopathology; HIV-1 virus; Consensus sequence; Retroviridae; AIDS; Method; Immune deficiency; Lentivirus; Optimization; Infection; Virus; Polymerase chain reaction; Allele; Viral disease; Human immunodeficiency virus; Subtype
• ISSN: 0166-0934; 1879-0984; 1879-0984
• DOI: 10.1016/j.jviromet.2009.11.025

Allele-specific PCR based on subtype consensus sequences is a powerful technique for detecting low frequency drug resistant mutants in HIV-1 infected patients. However, this approach can be limited by genetic variation in the region complementary to the primers, leading to variability in allele detection. The goals of this study were to quantify this effect and then to improve assay performance.