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Massively parallel sequencing (MPS) technologies, such as 454-pyrosequencing, allow for the identification of variants in sequence populations at lower levels than consensus sequencing and most single-template Sanger sequencing experiments. We sought to determine if the greater depth of population sampling attainable using MPS technology would allow detection of minor variants in HIV founder virus populations very early in infection in instances where Sanger sequencing detects only a single variant. We compared single nucleotide polymorphisms (SNPs) during acute HIV-1 infection from 32 subjects using both single template Sanger and 454-pyrosequencing. Pyrosequences from a median of 2400 viral templates per subject and encompassing 40% of the HIV-1 genome, were compared to a median of five individually amplified near full-length viral genomes sequenced using Sanger technology. There was no difference in the consensus nucleotide sequences over the 3.6kb compared in 84% of the subjects infected with single founders and 33% of subjects infected with multiple founder variants: among the subjects with disagreements, mismatches were found in less than 1% of the sites evaluated (of a total of nearly 117,000 sites across all subjects). The majority of the SNPs observed only in pyrosequences were present at less than 2% of the subject's viral sequence population. These results demonstrate the utility of the Sanger approach for study of early HIV infection and provide guidance regarding the design, utility and limitations of population sequencing from variable template sources, and emphasize parameters for improving the interpretation of massively parallel sequencing data to address important questions regarding target sequence evolution.

Massively-parallel DNA sequencing using the 454/pyrosequencing platform allows in-depth probing of diverse sequence populations, such as within an HIV-1 infected individual. Analysis of this sequence data, however, remains challenging due to the shorter read lengths relative to that obtained by Sanger sequencing as well as errors introduced during DNA template amplification and during pyrosequencing. The ability to distinguish real variation from pyrosequencing errors with high sensitivity and specificity is crucial to interpreting sequence data. We introduce a new algorithm, CorQ (Correction through Quality), which utilizes the inherent base quality in a sequence-specific context to correct for homopolymer and non-homopolymer insertion and deletion (indel) errors. CorQ also takes uneven read mapping into account for correcting pyrosequencing miscall errors and it identifies and corrects carry forward errors. We tested the ability of CorQ to correctly call SNPs on a set of pyrosequences derived from ten viral genomes from an HIV-1 infected individual, as well as on six simulated pyrosequencing datasets generated using non-zero error rates to emulate errors introduced by PCR. When combined with the AmpliconNoise error correction method developed to remove ambiguities in signal intensities, we attained a 97% reduction in indel errors, a 98% reduction in carry forward errors, and >97% specificity of SNP detection. When compared to four other error correction methods, AmpliconNoise+CorQ performed at equal or higher SNP identification specificity, but the sensitivity of SNP detection was consistently higher (>98%) than other methods tested. This combined procedure will therefore permit examination of complex genetic populations with improved accuracy.

After pretreatment with phenobarbital, female B6AF1 mice showed considerably higher serum glutamic oxaloacetic transaminase (SGOT) elevations and more periportal necrosis from a single injection of cocaine than males. This sex difference was androgen dependent. Castration or treatment with flutamide made males respond like females, while testosterone made females behave like males. There was no significant sex difference in enzymes of cocaine metabolism. When the mice were induced by exposure to pine bedding, males showed higher SGOT elevations and more centrilobular necrosis after cocaine than females. In this case, the sex difference could be attributed to increased levels of cytochrome P-450 and cocaine N-demethylase in liver microsomes. BALB/cBy mice on pine bedding snowed much less liver damage from cocaine than B6AF1 mice, but they were more sensitive to norcocaine and N-hydroxy norcocaine. This difference was correlated with low levels of cocaine N-demethylase in the BALB/cBy mice. Liver microsomes from phenobarbital-induced BALB/cBy mice had less norcocaine N-hydroxylase activity than those from B6AF1 mice. These studies demonstrate that the pattern of sex and strain differences in liver damage from cocaine depends on the inducing agent and can be related to a large extent to the microsomal enzymes induced by that agent.