Table 6.

Reproducibility of HIV-1 Protease and Reverse Transcriptase Sequencing

Reference	Comparison	Main Findings
(Demeter et al., 1998)	Dideoxynucleotide cycle sequencing of cultured cell pellets in 11 laboratories	99.7% nucleotide concordance. The homogeneity of cultured virus and the fact that RNA extraction and reverse transcription were not required probably contributed to the high concordance.
(Gunthard et al., 1998b)	Comparison of dideoxynucleotide and GeneChip sequencing of PCR-amplified DNA	98.8% nucleotide concordance.
(Schuurman, et al., 1999b)	Dideoxy terminator and GeneChip sequencing of mixtures of plasmid clones in 23 laboratories. Mutations at three positions were studied.	20/23 laboratories reliably detected 100% wildtype and 100% mutant codons. Most laboratories detected the mutants present as 50% mixtures. Laboratories were inconsistent at detecting mutations present as 25% mixtures.
(Schuurman, et al., 1999a)	Dideoxynucleotide and GeneChip sequencing of plasma samples seeded with different proportions of plasmid clones.	Detailed results pending. The number of correctly identified results did not vary among the three most widely used methods (ABI Kit, homebrew assay with ABI sequencer, VGI kit and sequencer).
(Vahey et al., 1999)	Comparison of dideoxynucleotide and GeneChip sequencing	GeneChip sequencing inaccurately tested non-subtype B sequences.
(Shafer et al., 2000c)	Dideoxynucleotide sequencing of replicate plasma samples in the same laboratory	99.4% amino acid concordance. Most discordances were partial and were caused by the distribution of genetic variants within the plasma samples.
(Hanna et al., 2000b)	Comparison of dideoxynucleotide and GeneChip sequencing of cultured virus stock supernatant.	97.4% concordance. Dideoxyterminator sequencing was more sensitive at detecting drug-resistance mutations.
(Wilson et al., 2000)	Comparison of dideoxynucleotide and GeneChip sequencing and Line Probe Assay	96.6% concordance between dideoxynucleotide and GeneChip sequencing.
(Shafer et al., 2001)	Comparison of dideoxynucleotide sequencing of 46 plasma samples in two laboratories	99.1% concordance. 90% of discordances were partial defined as one laboratory detecting a mixture and the second laboratory detecting just one of the components of the mixture.