Methods and systems for predicting HIV-1 coreceptor tropism
AssigneeLaboratory Corporation of America Holdings
InventorMojgan Haddad
Life of this patent
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Abstract
The present methods for predicting coreceptor tropism may include obtaining the amino acid and/or nucleic acid sequence of at least a portion of the envelope or envelope coding region from a biological sample obtained from a subject; analyzing the amino acid sequence, nucleic acid sequence, or both of the portion of the envelope or envelope coding region using a case based reasoning analysis; and determining the coreceptor tropism. Also described are systems and computer readable media for utilizing the systems or performing the methods.
Claims19
A method for treating a patient having a human immunodeficiency virus 1 (HIV-1) infection based on the tropism of the HIV-1 present in a sample from the patient, comprising:
- (a) analyzing a biological sample obtained from a clinical patient to obtain an amino acid sequence, nucleic acid sequence, or both, of at least one portion of an envelope or envelope coding region of the viruses from the biological sample, wherein the at least one portion of the envelope or envelope coding region comprises the variable region 3 (V3) loop or coding region;
- (b) comparing the amino acid sequence, nucleic acid sequence, or both, of the at least one portion of the envelope or envelope coding region to sequence data stored in a database that comprises sequence and tropism data of a statistically significant number of viral isolates, wherein the comparing comprises a case based reasoning (CBR) analysis, and wherein the data comprises a plurality of sequences for the portion of the envelope or envelope coding region from viruses for which the tropism has been evaluated;
- (c) determining the tropism of the viruses from the biological sample based on the CBR analysis, wherein the tropism is X4 tropic, R5 tropic, or dual or mixed tropic (DM);
- and
- (d) treating the patient with an effective amount of an entry inhibitor based on the tropism determined in step (c).
Dependencies are inferred from the claim text.