Application of random amplified polymorphic DNA PCR for genomic analysis of HIV-1-infected individuals

• Published in: Mutation research Vol. 406; no. 1; pp. 25 - 31
• Main Authors: Aikhionbare, Felix O, Newman, Cheryl, Womack, Chad, Roth, William, Shah, Ketan, Bond, Vincent C
• Format: Journal Article
• Language: English
• Published: Amsterdam Elsevier B.V 01.11.1998; Elsevier
• Subjects: Base Sequence; Biological and medical sciences; CCR5 gene; DNA - blood; DNA Fingerprinting - methods; Genetic Carrier Screening; Genotype; HIV Infections - genetics; HIV Infections - immunology; HIV-1; Homozygote; Human viral diseases; Humans; Infectious diseases; Leukocytes, Mononuclear - immunology; Medical sciences; Molecular Sequence Data; Polymorphism; Polymorphism, Genetic; Random Amplified Polymorphic DNA Technique; RAPD-PCR; Receptors, CCR5 - genetics; Viral diseases; Viral diseases of the lymphoid tissue and the blood. Aids; HIV-1; RAPD-PCR; CCR5 gene; Polymorphism; Human; Immunopathology; Genetic marker; HIV-1 virus; Retroviridae; AIDS; Immune deficiency; Lentivirus; Random amplified polymorphic DNA marker; Virus; Infection; Viral disease; Human immunodeficiency virus
• ISSN: 1383-5726; 0027-5107; 1873-1341
• DOI: 10.1016/S1383-5726(98)00007-7

Random amplified polymorphic DNA polymerase chain reaction (RAPD-PCR) is a DNA fingerprinting technique used to detect genomic polymorphisms. We employed sixteen different RAPD-PCR 10-mer primers to amplify DNA from the peripheral blood mononuclear cells (PBMC) of 80 HIV-1-infected individuals. These individuals were previously identified as either heterozygotes (+/Δ32) and homozygotes (+/+) for the CCR5 locus by PCR with gene specific primers. Four of the sixteen randomly selected RAPD primers produced distinguishable banding profiles between CCR5 (+/Δ32) heterozygotes and CCR5 (+/+) homozygotes. Direct sequencing of some RAPD-PCR products obtained with one of the four RAPD primers that were tested yielded clearly readable, but limited sequences, which were similar to portions of the previously published sequences for (+/+) homozygotes (98% similarity) and (+/Δ32) heterozygotes (87% similarity) of the CCR5 alleles. Thus, the RAPD-PCR technique may be useful for the identification of human molecular markers that may correlate with susceptibility to HIV-1-infection, or differences in disease progression among HIV-1-infected individuals.