Rhee2006: HIV Drug Resistance Mutations

In pbreheny/hdrm: High-Dimensional Regression Modeling

HIV Drug Resistance Mutations

Description

Although there are many drugs that have been approved for treating the Human Immunodeficiency Virus (HIV), one of the hallmarks of the virus is its ability to rapidly mutate and gain resistance to these drugs. In this study, isolates of HIV were extracted from infected individuals and sequenced. These isolates were also tested for their resistance to various drugs used in HIV therapy. The scientific goal of the project is to determine which mutations are associated with drug resistance, thereby helping to develop new antiretroviral drugs and to optimize the use of existing drugs.

The full study examined many drugs and is available at the Stanford HIV Drug Resistance Database. This data set contains the results for one specific drug, Nelfinavir, a protease inhibitor, and the presence of mutations in the protease gene, which potentially confer resistance to the drug.

Format

• y: Outcome of the drug susceptibility assay. Higher numbers indicate greater resistance to the drug.

• X: 1/0 indicators for presence/absence of a mutation at a given position. Column names indicate the position and mutation. For example, the protease gene is 99 amino acids long; for any isolates with a 1 in column P13.V, this indicates that at position 13 in the amino acid sequence, the isolate has the amino acid (V)aline instead of the usual amino acid found at position 13.

Dimensions

• n = 842

• p = 361

References

The data come from the Stanford HIV Drug Resistance Database and were originally described in:

Rhee S-Y, Taylor J, Wadhera G, Ben-Hur A, Brutlag DL, and Shafer RW (2006). Genotypic predictors of human immunodeficiency virus type 1 drug resistance. Proceedings of the National Academy of Sciences, 103: 17355-17360.

pbreheny/hdrm documentation built on Jan. 17, 2024, 8:53 p.m.