Stanford University HIV Drug Resistance Database - A curated public database designed to represent, store, and analyze the divergent forms of data underlying HIV drug resistance.

Genotype-Treatment Correlations

Queries

1. Treatment Profiles
2. Mutation Profiles
3. Detailed Treatment Queries
4. Detailed Mutation Queries
5. Advanced Queries
 

Data Summaries

1. Mutation Prevalence
According to Subtype and Treatment
2. Downloadable Dataset

Mutation frequencies at each position of protease or RT according to subtype and treatment. Users can also select a reference profile (usually viruses from untreated person) for comparison. The results are graphical.
 
Users specify a particular position. The program then returns a separate table for each observed mutation at that position. The table entries show the prevalence of the mutation in untreated persons, in persons receiving the relevant drug class (PIs for protease; NRTIs and NNRTIs for RT), and in persons receiving each of the drugs of the relevant drug class. Significant differences between the prevalence of a mutation in treated and untreated persons is calculated using a chi-square test and shown in each row of each table.
 
Users specify treatment and subtype information. The query then returns a table of virus isolates meeting the selected criteria. The table contains links to Medline (Author-Yr column) and GenBank (Accession column). The sequences in the table can also be viewed as a sequence alignment, downloaded in fasta format, or viewed with the graphical Treatment Profile format. Users can specify the number of drugs of a particular class, specific drugs, and specific drug combinations. Users can also specify the manner win which the mutation data and treatment data are displayed in the table. Users can also filter their results according to a variety of criteria.
 
Users specify one or more mutations and subtype information. Users can retrieve all sequences containing the specified mutations or only those sequences exactly matching. The query then returns a table of virus isolates meeting the selected criteria. The table contains links to Medline (Author-Yr column) and GenBank (Accession column). The sequences in the table can also be viewed as a sequence alignment, downloaded in fasta format, or viewed with the graphical Treatment Profile format.
 
Retrieve pairs of sequences that one was obtained before and the other was obtained after a selected treatment
Retrieve pairs of sequences that were developing or regressing selected mutations
Retrieve sequences of isolates containing or not containing selected mutations
 
Summary tables listing the prevalence of each mutation according to subtype and drug-class experience. Users can adjust the threshold for the minimum prevalence of a mutation required for it to appear in the summary tables. Users can also choose whether or not mutations present as part of electrophoretic mixtures should be counted as a mutation or ignored.

Mutation prevalence is indicated by the superscripted number following each mutation. Each mutation is also a hyperlink to a separate web page with detailed information on each isolate containing the mutation and meeting the appropriate subtype and treatment criteria.Graphical summary of protease mutations, RT mutations and IN mutations shows the mutation prevalence according to subtype in untreated persons.

This work was based on a review of the published literature from the Stanford HIV Drug Resistance Database, and collaborative efforts of the Non-B Workgroup.