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| Clinical
and Research Laboratory |
HIV
Genotyping Lab |
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HIV
Genotyping Lab
The HIV genotyping lab has one of the advanced
DNA sequencing platforms currently in the market. The
Genotyping Lab was set-up for the purpose of various
clinical trials funded by NIH (ACTG and HPTN) and establishing
the HIV drug resistance database in India.
ABI Avant 3100 DNA Sequencer
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ABI Avant 3100 Sequencer is one of the advanced DNA
sequencing platforms available today, supported by robotic
automation with advanced bioinformatics software to
ensure high quality, unparalleled accuracy, and fast
sample turnaround. |
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| Currently,
the lab offers large-scale HIV genotyping services using
Homebrew HIV Genotyping technique since 2002. The test
is intended for use in detecting HIV-1 genomic mutations
that confer resistance to specific types of antiretroviral
drugs. This lab services are extended to the referral
cases from other centers / hospitals from different
parts of the country.The Homebrew Assay detects mutations
in the entire protease gene and two thirds of RT gene
(nested product of 700bp RT and 400 bp of PI). The nested
product is generated and sequenced bidirectional. |
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| ABI
Avant 3100 DNA Sequencer |
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The softwares used are ABI Data Collection v1.0, ABI
Sequence Analysis v 3.7 and multiple sequence alignment Seqscape
v2.5, to assembles, edit and identify the mutations within
the pol region of HIV-1. The consensus sequence finally compared
with Stanford HIV Drug Resistance Online Database, to determine
mutations present in the virus.
The Viroseq™ HIV-1 Genotyping System version 2.0 from
Celera Diagnostics is commercially available kit and licensed
from US-FDA. Currently, this kit is standardized in our lab
for certifications from Johns Hopkins University and VQA (US)
for the participation in international clinical trials. The
Viroseq HIV-1 Genotyping system detects mutations in the RT
and Protease region of the pol gene and provides the information
on the genetic evidence of viral resistance. The entrie protease
gene and two third of RT gene are amplified to generate 1.8
kb amplicon. The amplicon is used as a sequencing template
for 7 primers that generate an approximately 1.3 kb consensus
sequence. The Viroseq HIV-1 genotyping system software assembles
edits and identifies mutations within this 1.3 kb sequence.
The software compares the consensus sequence with a known
reference, HXB-2, to determine mutations present in the sample.
Finally, the Viroseq software uses proprietary algorithm to
analyze the mutations and generate the drug resistance report.
The facility maintains a team of expert professionals who
specialize in the area of molecular virology, cutting-edge
research and development, education, and training especially
in the area of HIV genotyping. |
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