CLP08 Tech Guide

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Molecular Testing

1) What is the name of your company’s
molecular diagnostics testing product?

www.clpmag.com

Abbott Molecular

Avellino Lab USA Inc

bioTheranostics

Des Plaines, Ill
(800) 554-7042
www.abbottmolecular.com

Menlo Park, Calif
(650) 396-3741
www.avellinolab.com/us

San Diego
(877) 886-6739
www.biotheranostics.com

Abbott RealTime m2000 System

Avellino-GENE Detection System (AGDS) Test

CancerTYPE ID

2) For what purpose/condition/disease is
the product designed?

Rapid and highly automated PCRbased molecular diagnostic testing for
infectious diseases

The Avellino-GENE Detection System (AGDS)
Test was developed to detect Avellino Corneal
Dystrophy (ACD) - a disease that causes greywhite granular deposits on the cornea, which
over time can lead to blindness. It is the
world’s first genetic test to detect and identify
the gene mutation with 100% accuracy.

CancerTYPE ID uses the differential
expression of 92 genes to aid in the
determination of tumor site of origin
in patients with metastatic cancer of
uncertain, indeterminate, or differential
diagnosis.

3) What is the specimen type (eg, serum,
cultured cell lines, tissue, etc)?

Plasma, serum, whole blood, urine,
spinal fluid, tissue, and mucosal
swabs

Buccal swab with swipes taken from the
inside of both cheeks. Ten swipes each cheek
collects sufficient epithelial cells for analytical
and diagnostic purposes.

Formalin-fixed, paraffin embedded (FFPE)
tissue from fine needle aspirations, cytologic
specimens, core needle biopsies, excisional
biopsies, and/or surgical samples

4) Please note the platforms used (eg,
bead arrays, microarrays, PCR, RT-PCR,
etc).

The Abbott RealTime system employs
real-time polymerase chain reaction
(PCR) technology for DNA and RNA
amplification and detection.

Real-Time PCR

qRT-PCR

5) What is the turnaround time for test
results, and how much tech time is
required per assay setup?

Results are available in between
4.5 hours and 6.5 hours, and the
automated system eliminates many
manual steps associated with sample
transfer and preparation for PCR
analysis, which minimizes technician
time required to perform PCR assays.

6) How many channels/specimen
samples are tested per run (per plate,
etc)?

96 specimens can be performed in a
single RealTime m2000 run

Up to 90 samples per run

N/A

7) Is this an automated or manual
system, and what are the space/
environmental requirements?

The Abbott RealTime m 2000 is
fully automated and compact. The
m2000sp measures 66.2 inches x
69.5 inches x 31.3 inches.

The company is currently using a manual
method. The testing requires an ampliconfree environment. This fall, the analytical
process will become semiautomated (liquid
handling and data processing), which will
quadruple sample throughput.

N/A

8) Is the product FDA-cleared/pending/
approved?

Yes, the RealTime m2000 system is
FDA-approved to perform assays for
HIV viral load, HCV viral load, HBV viral
load, HCV Genotyping, and CT/NG.

Avellino Lab USA’s molecular testing lab
was validated with inspection received by
the California Department of Public Health –
Laboratory Field Services representatives and
approved (and subsequently certified) as a
CLIA licensure in 2012.

No

9) Can the system be incorporated in the
LIS?

Yes

Yes. In progress and scheduled for completion
this fall.

Yes

10) Is this unit acquired by purchase,
lease, or reagent rental, and what is the
cost per assay?

Information regarding system
acquisition plans and pricing is
available from local Abbott sales
representatives.

Most clinics choose to incorporate the cost of
the Avellino-GENE Detection System (AGDS)
Test into the total cost of the LASIK surgery.
The AGDS Test is affordable and a small
fraction of the total cost of refractive surgery
(LASIK, LASEK, PRK, etc).

CancerTYPE ID is offered as a
laboratory-developed test (LDT) through
bioTheranostics’ CLIA-certified, CAPaccredited diagnostic laboratory in
San Diego.

11) How is QC handled? Is it internal,
external, or both? Is this part of the
reagent supplied, or is an external source
required?

The RealTime m2000 system utilized
an internal control for sample
preparation and PCR validity control,
and also utilizes onboard external
controls. Realtime m2000 system
software also performs quality control
checks and reporting.

Avellino Lab uses both in-house and external
QC materials. QC materials are not supplied
by the reagent kit. One of the QC materials
requires cloning by an external company.

N/A

20

August 2013 | clpmag.com

The sample(s) are sent by the clinic within
7 days of collection and sent by overnight
courier to Avellino Lab USA (a certified CLIA
diagnostic facility). Test results are typically
sent to the requesting physician at the end
of the same day of sample receipt, with
guaranteed 48 hours turnaround.

Turnaround time is 5 business days.

bioTheranostics

EKF Molecular
Diagnostics Lts

GenMark Diagnostics

GenMark Diagnostics

San Diego
(877) 886-6739
www.biotheranostics.com

Cardiff, Wales UK
www.ekfdiagnostics.com

Carlsbad, Calif
(760) 448-4300
www.genmarkdx.com

Carlsbad, Calif
(760) 448-4300
www.genmarkdx.com

PRÉCIS Precision Medicine

PointMan DNA Enrichment Kits

eSensor Cystic Fibrosis Genotyping Test

eSensor Respiratory Viral Panel (RVP)

PRÉCIS Precision Medicine includes
biomarker profiles for non-small cell lung
cancer, colorectal cancer, breast cancer,
gastric cancer, melanoma, and GIST.

PointMan DNA Enrichment Kits are
designed to enrich rare mutated gene
sequences in the KRAS, BRAF, and
EGFR T790M sequences that are
associated with melanoma, lung, and
colorectal cancers.

The eSensor Cystic Fibrosis Genotyping
Test simultaneously detects and identifies
a panel of mutations and variants in the
CFTR gene.

The eSensor RVP is designed to detect
14 respiratory virus types and subtypes
to drive informed clinical decisions
regarding respiratory infection.

Formalin-fixed paraffin embedded (FFPE)
tissue from fine needle aspirations,
cytologic specimens, core needle biopsies,
excisional biopsies, and/or surgical
samples

PointMan DNA Enrichment Kits will
enrich mutant DNA from many sample
types including formalin-fixed paraffin
embedded (FFPE) and fresh frozen
tissue, whole blood and plasma, and
cultured human cell lines.

CF Genotyping Test specimen type is
whole blood collected using EDTA as the
anticoagulant.

The eSensor RVP specimen type is a
nasopharyngeal swab (NPS) obtained
from individuals exhibiting signs and
symptoms of respiratory infection.

qRT-PCR, IHC, FISH

PointMan DNA Enrichment kits can be
used on all RT/Q-PCR platforms.

The test is a qualitative nucleic acid
multiplex test designed for use on the
eSensor XT‐8 system.

The eSensor Respiratory Viral Panel
(RVP) is a qualitative nucleic acid
multiplex in vitro diagnostic test
intended for use on the eSensor XT‐8
system.

Turnaround time is 7 to 10 business days

Run times for PointMan kits typically
take less than 2 hours depending
on Q-PCR platform. Setup time is
limited only by the user’s ability and
experience with pipetting into 96-well
plates.

The eSensor turnaround time is a total of
4 hours from initiation of the test to result
reporting. Total hands-on time is less
than 40 minutes, including nucleic acid
extraction.

The eSensor turnaround time is a total
of 6 hours from initiation of the test to
result reporting. Total hands-on time is
less than 60 minutes, including nucleic
acid extraction.

N/A

Each PointMan DNA Enrichment Kit
includes sufficient reagent for 24
reactions.

The eSensor CF Genotyping Test can
process one to 24 specimens in 4 hours
and up to 96 specimens in 6 hours.

The eSensor RVP workflow can process
one to 24 specimens in 6 hours and up
to 96 specimens in under 8 hours.

N/A

PointMan DNA Enrichment Kits are
consumable products for use on
existing Q-PCR platforms.

The eSensor XT-8 system is a randomaccess electrochemical detection system,
which generates a single-page objective
result report. Prior to detection, specimens
require automated or manual nucleic acid
extraction and RT-PCR amplification.

The eSensor XT-8 system is a
random-access electrochemical
detection system that generates a
single-page objective result report.
Prior to detection, specimens require
automated or manual nucleic acid
extraction and RT-PCR amplification.

No

THE KITS ARE AVAILABLE
FOR RESEARCH-USE ONLY.
FDA clearance expected in 2014.
Clinical labs can assess the kits and
submit them for external quality
assessment (eg, NEQAS).

GenMark’s eSensor Cystic Fibrosis
Genotyping Test is FDA-cleared for use on
the eSensor XT-8 system.

GenMark’s eSensor Respiratory Viral
Panel is FDA cleared for use on the
eSensor XT-8 system.

Yes

N/A

The eSensor XT-8 system is capable of
being networked and transferring text file
data to the LIS.

The eSensor XT-8 system is capable of
being networked and transferring text
file data to the LIS.

PRÉCIS biomarker testing is offered as a
laboratory-developed test (LDT) through
bioTheranostics’ CLIA-certified, CAPaccredited diagnostic laboratory in
San Diego.

PointMan DNA Enrichment kits cost
between $1,314 and $1,500 per
kit, giving a per reaction cost of
approximately $55 to $62 per reaction.

GenMark offers programs for purchase and
reagent rental with cost per test based on
contracted test volume.

GenMark offers programs for purchase
and reagent rental with cost per test
based on contracted test volume.

PointMan DNA Enrichment Kits are
currently manufactured to ISO 9001.
Additionally, internal controls are
provided with each kit so that PCR
conditions and sample quality can be
confirmed.

Each CF Genotyping Test cartridge
contains onboard positive and negative
controls to monitor for proper performance
of the test. It is recommended that a PCR
blank, or negative control, be included
with each run of the CF Genotyping
Test. External controls are commercially
available through vendors such as the
Coriell Institute and MMQCI.

eSensor RVP is supplied with
bacteriophage MS2 internal control
to monitor test processing from
viral nucleic acid isolation through
detection. An external negative and
positive control should be included
with each batch. External respiratory
viral panel controls are offered by
Zeptometrix.

N/A

	

clpmag.com | August 2013

21

[ tech ]

guide

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Great Basin
Corp

Life Technologies
Corp

Life Technologies
Corp

Meridian
Bioscience Inc

Salt Lake City
(801) 990-1055
www.gbscience.com

Carlsbad, Calif
(800) 955-6288
www.lifetechnologies.com

Carlsbad, Calif
(800) 955-6288
www.lifetechnologies.com

Cincinnati
(513) 271-3700
www.meridianbioscience.com

Portrait Benchtop Analyzer and the
Portrait Toxigenic C. diff Assay

Applied Biosystems 7500 Fast Dx
Real-Time PCR Instrument

QuantStudio Dx Real-Time PCR
Instrument

illumigene Group A Streptococcus

For the detection of toxigenic Clostridium
difficile

The Applied Biosystems 7500 Fast Dx
Real-Time PCR Instrument is a real-time
nucleic acid amplification and detection
system that measures nucleic acid signals
from reverse transcribed RNA and converts
them to comparative quantitative readouts
using fluorescent detection of dual-labeled
hydrolysis probes.

The QuantStudio Dx Real-Time PCR
Instrument is intended to perform
fluorescence-based PCR to provide
detection of FDA-cleared and approved
nucleic acid sequences in humanderived specimens.

Detects Streptococcus pyogenes in
throat swab specimens.

Human stool samples collected from
patients suspected of having Clostridium
difficile infection

Any human-derived specimens from which
DNA or RNA can be extracted

Any human-derived specimens from
which DNA or RNA can be extracted

Throat swab sample (Liquid Amies,
without charcoal; Liquid Stuart)

Automated thermophilic blocked primer
helicase-dependent (bpHDA) amplification
technology coupled with chip-based
detection

RT-PCR/qPCR

RT-PCR/qPCR

Loop-Mediated Isothermal Amplification
(LAMP) technology

Turnaround time is 65 to 90 minutes;
tech time is about 3 minutes.

Typical qPCR runs can range from
30 minutes to 2 hours.

Typical qPCR runs can range from
30 minutes to 2 hours.

Less than 1 hour, with 2- to 3-minute
tech time

One

Up to 96 tests per run

Up to 96 tests per run

10

Automated. The Portrait analyzer
dimensions are 6.3 inches x 17.2 inches
x 21.4 inches.

7500 Fast Dx Real-time PCR Instrument
is a manual system. Dimensions are 13.4
inches x 17.8 inches x 49 inches.

Dimensions: 35.7 inches x 29.4 inches x
44.3 inches

Not applicable

Yes, as of May 1, 2013

FDA-cleared

FDA-cleared

FDA-cleared

Not at this time

Yes

Yes

No

Reagent rental, assays are ~$25,
depending on volume

Purchased, lease, or reagent rental.
Cost per test depends on the test being
provided.

Purchased, lease, or reagent rental.
Cost per test depends on the test being
provided.

Based on volume commitments

Both: Test cartridge has integrated
control features that are automatically
performed with every assay. External
positive and negative controls should be
used to monitor for correct procedural
technique and reagent integrity. Positive
external controls are not provided. The
negative control is run without adding
any sample to the assay.

Preventive maintenance is available from
Life Technologies. QC protocol is defined
by the test or by the user, and functionality
is provided by the Instrument software.

Preventive maintenance is available
from Life Technologies. QC protocol
is defined by the test or by the user,
and functionality is provided by the
Instrument software.

Both internal and external controls.
External controls may be purchased
separately.

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August 2013 | clpmag.com

[ tech ]

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Meridian
Bioscience Inc

Randox

Roche
Diagnostics

Siemens Healthcare
Diagnostics

Cincinnati
(513) 271-3700
www.meridianbioscience.com

Kearneysville, WVa
(866) 472-6369
www.randox.com

Indianapolis
(317) 521-2000
www.mylabonline.com

Tarrytown, NY
(877) 229-3711
usa.healthcare.siemens.com

illumigene Mycoplasma

cobas HPV Test

Siemens Tissue Preparation Solution

Simultaneous detection of 10 sexually
transmitted infections from one single
patient sample

The test provides individual genotyping
results for HPV 16 and 18, while
simultaneously reporting 12 other highrisk HPV types as a pooled result.

The Siemens Tissue Preparation
Solution includes a Tissue Preparation
System and the VERSANT Tissue
Preparation Reagents kit. Together,
this solution provides a more efficient
and reproducible process for the
isolation of high-quality nucleic
acids from formalin-fixed paraffinembedded (FFPE) tissue samples.

Throat and nasopharyngeal swab
specimens (0.85% Saline, M4,
M4-RT, M5, UTM-RT)

Genomic DNA is extracted from urine or
urogenital swab samples.

Cervical specimens collected in PreservCyt
solution using an endocervical brush/
spatula. The test is also FDA-approved
for the use of primary vial samples after
cytology processing on either the ThinPrep
3000 (T3000) system or the ThinPrep
2000 (T2000) system.

Formalin-fixed paraffin-embedded and
fresh frozen tissue samples

Loop-Mediated Isothermal
Amplification (LAMP) technology

The array utilizes Biochip Array
Technology, a unique multiplexing
method. It is based on a combination
of multiplex PCR, probe hybridization,
and chemiluminescence detection to
allow screening of viral, bacterial, and
protozoan STIs.

The test is performed on the cobas 4800
System. The system is also cleared/
approved for the cobas CT/NG (Chlamydia
trachomatis/Neisseria gonorrhoeae), the
cobas BRAF V600 Mutation Test, and the
cobas EGFR Mutation Test.

The Siemens Tissue Preparation
Solution uses magnetic particle-based
isolation and proprietary iron oxide
bead technology.

Less than 1 hour for turnaround
time after extraction

The STI Multiplex Array has a rapid
turnaround time from sample to result in
less than 5 hours.

The setup time is about 30 minutes
for a test run, and test turnaround time
(sample-in, results out) is less than
5 hours.

The turnaround time is dependent on
the number of samples loaded and the
protocol chosen (DNA, RNA, or Split
Method). This is from 3 to 4 hours. The
hands-on-time is 15 minutes, including
loading reagents and samples.

10

One biochip is required per patient sample
and one negative control is required per
run. This will vary between assays.

The cobas 4800 System can run up to
94 patient specimens and two control
samples per run.

The system runs up to 48 samples per
run.

N/A

The Evidence Investigator is a
semiautomated, benchtop biochip
analyzer that offers complete patient
profiling.

The cobas 4800 System offers automation
of nucleic acid purification, PCR
(polymerase chain reaction) setup, and
real-time PCR amplification and detection.
It can also be used with manual specimen
preparation kits.

The Siemens Tissue Preparation
Solution employs a fully automated
tissue extraction process. The
dimensions are 0.903 m x 1.124 m
x 1.2 m. The required environment
conditions are 18º to 30ºC; 24% to 80%
relative humidity, noncondensing; 0 to
2,000 m altitude.

FDA-cleared

FDA approval is pending

Yes

The system is listed with the FDA as
Class 1 exempt, and the reagents are
IVD.

Based on volume commitments

The Evidence Investigator is LIMSintegrated for convenient reporting.

Yes, it is designed for bidirectional LIS
communication to simplify test ordering
while supporting integrity of results (no
manual data entry required).

No LIS capabilities are available.

Both internal and external controls.
External controls may be purchased
separately.

Any of the above purchasing options can
be considered.

The cobas 4800 System can be leased or
purchased; the cost per assay depends
on a variety of contract-related factors,
including test volume.

Contact local Siemens representative

Both internal and external controls.
External controls may be purchased
separately.

QC for biochip is handled both internally
and externally. Randox has reference and
correction spots at the same location on
each chip to ensure that the CCD camera
within the Evidence Investigator is aligned
properly. For each run, Randox has a
negative control. Randox also has an
internal extraction control.

The cobas HPV Test includes a ß-globin
(cellular) internal control for sample
adequacy, to provide confidence in
negative results, and two kit quality
controls that are available from Roche.

This is a sample-handling platform
and does not require onboard quality
control.

Detects Streptococcus pyogenes in
throat swab specimens.

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August 2013 | clpmag.com

STI Multiplex Array

KRdbts.2thirdvCLP1308_x1a.pdf

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8:52 AM

Thermo Fisher Scientific
Portage, Mich
(800) 346-4364
www.thermoscientific.com
ImmunoCAP Allergen Components

ImmunoCAP Allergen Components are intended for in
vitro diagnostic use as an aid in the clinical diagnosis of
IgE-mediated allergic disorders. ImmunoCAP Allergen
component testing reveals sensitization to unique proteins
of the whole allergen test to help the clinician diagnose
and optimize management.

Human serum or plasma (EDTA or Na-Heparin)

Closed system. ImmunoCAP Allergen Components can
only be run on Phadia 100, Phadia 250, Phadia 1000,
Phadia 2500, and Phadia 5000.

Setup time approximately 15 to 20 minutes. First result
in 103 minutes, and depending on platform, a result is
produced every minute (Phadia 250) or a result every
15 seconds (Phadia 1000, 2500) after the first result is
generated.
Depends on instrument size; can range from 48 tests to
4,800 tests. Random access to load samples.

Automated platform varies based on size–specifications
can be provided per instrument upon request.

ImmunoCAP allergen components are FDA-cleared for
milk, egg, peanut, peach, Timothy grass, and birch. Many
more allergen components are in submission for FDA
clearance or are getting ready to be packaged for review.
See website for complete list available to your region.

Yes

Purchase or instrument use agreement. For pricing,
contact your Fisher Healthcare or Thermo Scientific
representative.

QC is external and run as a patient sample; available
separately from Thermo Fisher Scientific. The automated
instruments also have a number of built-in, internal
checks to help ensure quality assay results.

	

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