Model for assessment of proficiency of human immunodeficiency virus type 1 sequencing-based genotypic antiretroviral assays.
Use of sequencing-based genotyping as a diagnostic assay for human immunodeficiency virus (HIV) antiretroviral resistance is increasing. Periodic evaluation of the proficiency of laboratories performing this assay should be established. It is important to identify components of the assay that influence the generation of reliable sequencing data and that should and can be monitored. A model was developed to determine what parameters were reasonable and feasible for assessing the performance of genotyping assays. Ten laboratories using the genotyping platform, HIV-1 Genotyping System (HGS) v. 1 and software versions 1.1 or 2.0, participated in two rounds of testing. For each round, each group was sent a panel consisting of three clinical samples to sequence in real time. Six months later, seven laboratories using the TRUGENE HIV-1 Genotyping Kit participated in a separate round, working with both panels at the same time. Analysis of the data showed that one main indicator of genotyping proficiency was achievement of > or =98% sequence homology of a sample tested to a group consensus sequence for that sample. A second was concordant identification of codons at sites identified with resistance mutations in the sample, although scoring of these criteria is still undetermined from this study. These criteria are applicable to all sequence-based genotyping platforms and have been used as a baseline for assessing the performance of genotyping for the determination of antiretroviral resistance in our ongoing proficiency program.
Huang
Diana D
DD
Department of Immunology/Microbiology, Rush Medical College, 1653 W. Congress Parkway, Chicago, IL 60612, USA. diana_huang@rush.edu
Bremer
James W
JW
Brambilla
Donald J
DJ
Palumbo
Paul E
PE
Aldrovandi
Grace
G
Eshleman
Susan
S
Brown
Clark
C
Fiscus
Susan
S
Frenkel
Lisa
L
Hamdan
Hasnah
H
Hart
Stephen
S
Kovacs
Andrea
A
Krogstad
Paul
P
LaRussa
Phillip
P
Sullivan
John
J
Weinberg
Adriana
A
Zhao
Yu Qi
YQ
D019380:Anti-HIV Agents / Q000494:pharmacology*; D003062:Codon; D024882:Drug Resistance, Viral; D005838:Genotype; D015497:HIV-1 / Q000187:drug effects / Q000235:genetics*; D009154:Mutation; D017422:Sequence Analysis, DNA; D013698:Templates, Genetic
D019380:Anti-HIV Agents; D003062:Codon