Gingeras TR, Winters M, Dutta D, Shen N, Drenkow J, Merigan T, Mamtora G; Conference on Retroviruses and Opportunistic Infections.
Program Abstr 4th Conf Retrovir Oppor Infect Conf Retrovir Oppor Infect 4th 1997 Wash DC. 1997 Jan 22-26; 4th: 182 (abstract no. 638).
Affymetrix, Santa Clara, CA.
Objective: To compare the population-based sequencing of HIV-1 quasispecies present in plasma samples using both high density oligonucleotide arrays and conventional dideoxynucleotide sequencing with sequences obtained from multiple clones isolated from several of the pre- and post-treatment plasma samples. Methods: A total of 23 pairs of pre- and post-ddl treated plasma samples were sequenced using population based sequencing. Eighty-two clones from 12 patient samples were also sequenced with polymorphic nucleotide positions (mixtures) present in each of the samples identified. Results: A total of 40,851 nucleotides were analyzed using both sequencing methods with a concordance of 99% (range 98-100%). Sequence analysis of 82 clones indicated that 389 (37%) of the 1041 nucleotide positions were polymorphic. Both dideoxynucleotide and array-based sequencing concurred on the predominant base for 366 (94%) of the polymorphic positions. At 15 (65%) of the discordant 23 nucleotide positions, the second most prevalent nucleotide was preferred by the array-based method. Drug resistance conferring mutations were detected (10% sensitivity) only in post-treatment clone samples. Conclusions: Both sequencing methods were highly concordant with both methods identifying the predominant nucleotide of a mixture at 94% of the polymorphic positions. Population based sequencing using high density oligonucleotide arrays provides accurate representation of predominant virus genotypes in mixed samples.
Publication Types:
Keywords:
- Base Sequence
- Endopeptidases
- Genotype
- HIV Protease
- HIV-1
- Humans
- Mutation
- genetics
- reverse transcriptase, Human immunodeficiency virus 1
Other ID:
UI: 102223583
From Meeting Abstracts