Table 1.

Characteristics of Conventional Genotypic, Phenotypic, and Ultrasensitive Drug Resistance Assays

Assay	Advantages	Disadvantages	Currently in Clinical Use
Conventional genotypic (Sanger DNA sequencing)	Relatively inexpensive Rapid turnaround	Difficult to interpret complex resistance patterns Misses minority variants	Yes
Phenotypic	Avoids need to interpret complex mutational patterns Intuitive results	Expensive Slow turnaround time Limited availability outside Europe or United States and Canada Less sensitive than standard genotype testing	Yes
Ultrasensitive techniques
Allele-specific polymerase chain reaction	Highly sensitivea	Detects only a few targeted resistance mutations	No
Deep sequencingb	Moderately to highly sensitivea Evaluates entire region of interest.	Cost Need for computational support	Yesc
Oligonucleotide ligation assay	Moderately sensitivea Avoids expensive equipment or specialized technical expertise	Only detects a few targeted resistance mutations Assay is not quantitative	No

Adapted from [104].

^a Test sensitivity and limits of detection vary by testing site and patient-specific variables (eg, viral load, sample volume).

^b Refers to the Roche/454, Illumina, and other next-generation sequencing platforms.

^c The Roche/454 deep-sequencing system is currently used as part of a coreceptor tropism test developed by Quest Diagnostics (Madison, New Jersey).