LabAutomation 2006 - SLAS

TP79
Sutian Zhu
Quest Diagnostics
Irvine, California
sutian.x.zhu@questdiagnostics.com
Where Laboratory Technologies Emerge and Merge
Co-Author(s)
Jamie Platt
Greg Putignani
Michelle McGill
Kevin Chen
Hasnah Hamdan
Quest Diagnostics Nichols Institute
Validation of HIV-1 Genotype on the Protedyne BioCube
HIV-1 Genotype, Virtual Phenotype is a semi-automated assay having automated steps at several points in the assay (RNA extraction and
sequence detection) interspersed with many manual procedures. More fully automating the assay should allow us to improve the assay in
terms of throughput, turn-around-time, labor and reagent savings, and quality.
To achieve this goal we have automated this assay by using Protedyne’s BioCubeÔ system, which is a customized robotic platform. The
customized BioCubeÔ provide automation through steps from Reverse Transcription PCR (RT-PCR), nested PCR (PCR2), PCR product
purification, gel check, cycle sequencing, and dye terminator clean-up.
For method Comparison Amplification rates were compared across methods and analyzed using a paired t-test. No significant difference
in amplification rates was observed between the current method and the BioCubeÔ method (Mean = 82.9%; SD = 0.03; p = 0.40; n =
1334). Recovery on BioCube was 100% concordant with recovery by manual method. No significant difference in sequence data between
the current method and the BioCubeÔ method. 99.99% concordance was observed at the inferred amino acid level (n = 12475). All
sequencing controls gave the expected result.
We project that multiple new assays can be configured on the BioCube in the future by the addition of modules or robotic attachments.
The BioCube designed for Molecular Microbiology at Quest Diagnostics will be the first to be configured for molecular diagnostic testing
and will serve as a prototype for use of industrial-grade automation in the clinical laboratory.
TP80
Zhu Zhu
Beckman Coulter, Inc.
Fullerton, California
zzhu@beckman.com
Zhu Zhu
Laura Pajak
Automated Target Preparation for GeneChip* Arrays Using the ArrayPlex Application
on Beckman Coulter’s Biomek ® 3000 Laboratory Automation Workstation
Microarray technology enables the simultaneous parallel analysis of changes in gene expression across the whole genome. However, the
process of target preparation for the gene expression analysis is time consuming and labor intensive. We present here the development
of the automated target preparation process using the ArrayPlex application on Beckman Coulter’s Biomek 3000 Laboratory Automation
Workstation with Affymetrix’ GeneChip Expression 3’-Amplification reagents and Agencourt ® RNAClean. This highly automated process
is comprised of three methods, cDNA Synthesis, in vitro Transcription (IVT) and Fragmentation. It allows for the processing of a partial or
a full 96-well plate of samples from total RNA to the biotin-labeled complementary RNA (cRNA). The target cRNA generated using these
methods was analyzed on Agilent’s 2100 Bioanalyzer and hybridized to Affymetrix’ Human Genome U133 Plus 2.0 Array.
The information provided here includes:
• The description of the automated methods
• The results obtained when using the methods.
*All trademarks are property of their respective owners.
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