TY - JOUR
T1 - Automated sequence analysis and editing software for HIV drug resistance testing
AU - Struck, Daniel
AU - Wallis, Carole L.
AU - Denisov, Gennady
AU - Lambert, Christine
AU - Servais, Jean Yves
AU - Viana, Raquel V.
AU - Letsoalo, Esrom
AU - Bronze, Michelle
AU - Aitken, Sue C.
AU - Schuurman, Rob
AU - Stevens, Wendy
AU - Schmit, Jean Claude
AU - Rinke de Wit, Tobias
AU - Perez Bercoff, Danielle
N1 - Funding Information:
This work is supported by a grant of the Netherlands Organisation for Scientific Research/Science for Global Development (NWO/WOTRO) , under the Netherlands-African Partnership for Capacity Development and Clinical Interventions against Poverty related Diseases (NACCAP) for the Affordable Resistance Test for Africa (ART-A) project (grant: W.07.05.204.00). CRP-Santé PR–RT sequencing, sequence analysis and interpretation were supported by the Fondation Recherche sur le SIDA, Luxembourg.
PY - 2012/5
Y1 - 2012/5
N2 - Background: Access to antiretroviral treatment in resource-limited-settings is inevitably paralleled by the emergence of HIV drug resistance. Monitoring treatment efficacy and HIV drugs resistance testing are therefore of increasing importance in resource-limited settings. Yet low-cost technologies and procedures suited to the particular context and constraints of such settings are still lacking. The ART-A (Affordable Resistance Testing for Africa) consortium brought together public and private partners to address this issue. Objectives: To develop an automated sequence analysis and editing software to support high throughput automated sequencing. Study design: The ART-A Software was designed to automatically process and edit ABI chromatograms or FASTA files from HIV-1 isolates. Results: The ART-A Software performs the basecalling, assigns quality values, aligns query sequences against a set reference, infers a consensus sequence, identifies the HIV type and subtype, translates the nucleotide sequence to amino acids and reports insertions/deletions, premature stop codons, ambiguities and mixed calls. The results can be automatically exported to Excel to identify mutations. Automated analysis was compared to manual analysis using a panel of 1624 PR-RT sequences generated in 3 different laboratories. Discrepancies between manual and automated sequence analysis were 0.69% at the nucleotide level and 0.57% at the amino acid level (668,047 AA analyzed), and discordances at major resistance mutations were recorded in 62 cases (4.83% of differences, 0.04% of all AA) for PR and 171 (6.18% of differences, 0.03% of all AA) cases for RT. Conclusions: The ART-A Software is a time-sparing tool for pre-analyzing HIV and viral quasispecies sequences in high throughput laboratories and highlighting positions requiring attention.
AB - Background: Access to antiretroviral treatment in resource-limited-settings is inevitably paralleled by the emergence of HIV drug resistance. Monitoring treatment efficacy and HIV drugs resistance testing are therefore of increasing importance in resource-limited settings. Yet low-cost technologies and procedures suited to the particular context and constraints of such settings are still lacking. The ART-A (Affordable Resistance Testing for Africa) consortium brought together public and private partners to address this issue. Objectives: To develop an automated sequence analysis and editing software to support high throughput automated sequencing. Study design: The ART-A Software was designed to automatically process and edit ABI chromatograms or FASTA files from HIV-1 isolates. Results: The ART-A Software performs the basecalling, assigns quality values, aligns query sequences against a set reference, infers a consensus sequence, identifies the HIV type and subtype, translates the nucleotide sequence to amino acids and reports insertions/deletions, premature stop codons, ambiguities and mixed calls. The results can be automatically exported to Excel to identify mutations. Automated analysis was compared to manual analysis using a panel of 1624 PR-RT sequences generated in 3 different laboratories. Discrepancies between manual and automated sequence analysis were 0.69% at the nucleotide level and 0.57% at the amino acid level (668,047 AA analyzed), and discordances at major resistance mutations were recorded in 62 cases (4.83% of differences, 0.04% of all AA) for PR and 171 (6.18% of differences, 0.03% of all AA) cases for RT. Conclusions: The ART-A Software is a time-sparing tool for pre-analyzing HIV and viral quasispecies sequences in high throughput laboratories and highlighting positions requiring attention.
KW - Automated-sequence-analysis
KW - HIV genotyping
KW - HIV resistance
KW - Software
UR - http://www.scopus.com/inward/record.url?scp=84861885800&partnerID=8YFLogxK
UR - https://www.ncbi.nlm.nih.gov/pubmed/22425336
U2 - 10.1016/j.jcv.2012.01.018
DO - 10.1016/j.jcv.2012.01.018
M3 - Article
C2 - 22425336
AN - SCOPUS:84861885800
SN - 1386-6532
VL - 54
SP - 30
EP - 35
JO - Journal of Clinical Virology
JF - Journal of Clinical Virology
IS - 1
ER -