1506 Tech Guide Molecular Probes Reagents Assays

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guide

Molecular Probes, Reagents, and Assays

Affymetrix

Alere

Alere

Santa Clara, Calif
(888) 362-2447;
www.affymetrix.com

Waltham, Mass
(877) 441-7440;
www.alere.com

Waltham, Mass
(877) 441-7440;
www.alere.com

1. What is the brand name of your
company’s molecular diagnostic
probe, reagent, or assay?

CytoScan Dx assay

Alere i Influenza A & B

Alere i Strep A

2. What year was the product first
released to market (US, OUS)?

2014

2014

2015

3. Specify the authorizing agency,
type, and year of the product’s
regulatory authorizations (eg, TUV
CE mark, 2013; FDA 510(k), 2015).

CE IVD, 2014; FDA 510(k), 2014; CFDA
Class I, 2015

FDA 510(k), 2014

FDA 510(k), 2015

4. What is the intended use or primary
function of the product?

Intended for the postnatal detection
of chromosomal copy number
variants (CNVs) in genomic DNA obtained
from peripheral whole blood in patients
referred for chromosomal testing based
on clinical presentation; intended to be
used on the GeneChip 3000 Dx system
and analyzed by Chromosome Analysis
Suite Dx software.

Uses molecular diagnostic technology to
detect influenza A and B viruses.

Uses molecular diagnostic technology to
detect group A Streptococcus bacteria.

5. What type of specimen/sample does
the product employ?

Genomic DNA isolated from peripheral
blood

Nasal swab

Throat swab

6. What platform technologies does the
product employ?

Chromosomal microarray analysis

Molecular diagnostic test utilizing
isothermal nucleic acid amplification
technology.

Molecular diagnostic test utilizing
isothermal nucleic acid amplification
technology.

7. What tests can be performed using
the named product?

Detection of CNVs associated with
developmental delay and intellectual
disability, congenital anomalies, and
dysmorphic features.

Influenza A and B

Group A Streptococcus

8. How much time is required for setup
and preanalytical processing; what
is the time to first result under optimal conditions?

Turnaround time for a run of up to 24
patients is 3.5 days.

Set up is less than 1 minute; results in
less than 15 minutes.

Set up is less than 1 minute; results in
less than 8 minutes.

9. How many channels/specimens/
samples are tested per run (per
plate, etc)?

Each array is designed for a single
patient sample. Each run can process six
to 24 samples.

One

One

10. Describe any automation options
that pertain to the product.

GeneChip 3000 Dx system automates the
washing, staining, and scanning steps of
the CytoScan Dx assay.

Graphical user interface walks through
the simple six-step procedure with
animated graphics.

Graphical user interface walks through
the simple six-step procedure with
animated graphics.

11. How is quality control performed
for the product?

Quality control materials are included.

Internal quality control run with each
test. External quality control supplied
with each kit.

Internal quality control run with each
test. External quality control supplied
with each kit.

12. Describe the capabilities, features,
or accessories that distinguish this
product from others on the market.

Only FDA-cleared chromosomal microarray; can analyze the entire genome
at one time and detect chromosomal
variations of different types, sizes, and
genomic locations; provides all reagents
required to perform the test, including
an easy-to-use and intuitive analysis and
reporting software. Not intended to be
used for standalone diagnostic purposes,
preimplantation, or prenatal testing or
screening, population screening, or
for the detection of, or screening for,
acquired or somatic genetic aberrations.

First CLIA-waived molecular influenza
test; employs proprietary isothermal
nucleic acid amplification technology,
providing highly sensitive and specific
results within 15 minutes.

First Group A Streptococcus test to use
molecular technology; employs
proprietary isothermal nucleic acid
amplification technology, providing highly
sensitive and specific results within 8
minutes.

24

June 2015 | clpmag.com

BioFire Diagnostics LLC

BioFire Diagnostics LLC

HTG Molecular
Diagnostics Inc

Randox Biosciences-US Ltd

Salt Lake City
(800) 735-6544;
www.biofiredx.com

Salt Lake City
(800) 735-6544;
www.biofiredx.com

Tucson, Ariz
(877) 289-2615;
www.htgmolecular.com

Kearneysville, Wva
(866) 472-6369;
www.randoxbiosciences.com

FilmArray respiratory panel

FilmArray gastrointestinal panel

HTG Edge system

Familial hypercholesterolemia (FH) arrays I
and II

2011

2014

2013

2014

FDA 510(k), 2011

FDA 510(k), 2014

UL/CSA, 2014; CE mark, 2014

CE marked; FDA approval is pending

Detection and identification of
infectious diseases for upper
respiratory disease syndrome
caused by viruses or bacteria.

Detection and identification of
gastrointestinal infections.

The system is a 96-well plate-based
liquid handler and hybridization unit
designed to automate next-generation
sequencing library preparation.

In cases of suspected FH, simultaneous
detection of 40 FH-causing mutations within
the ApoB, LDLR, and PCSK9 genes.

Nasopharyngeal swabs in viral
transport medium

Stool in Cary-Blair transport medium

Cell lines; formalin-fixed, paraffinembedded (FFPE) tissue; frozen tissue;
plasma; purified RNA; serum.

Genomic DNA extracted from a blood sample

FilmArray is an automated sampleto-answer system for nucleic acid
extraction, nested polymerase chain
reaction amplification, and detection.

FilmArray is an automated sampleto-answer system for nucleic acid
extraction, nested polymerase chain
reaction amplification, and detection.

The system uses the company’s qNPA
chemistry system from post sample
preparation up to the addition of
molecular barcodes and sequencing tags.

Biochip array technology, a unique
multiplexing method that combines PCR,
probe hybridization, and chemiluminescence
detection.

20 upper respiratory disease targets
consisting of 17 viruses and three
bacteria.

22 of the most common
gastrointestinal pathogens, including
bacteria, parasites, and viruses.

miRNA and mRNA gene expression

The arrays enable simultaneous detection of
40 FH-causing mutations (20 mutations per
array) within the ApoB, LDLR, and PCSK9
genes.

2 minutes set-up time; test
turnaround time is about 1 hour.

2 minutes set-up time; test
turnaround time is about 1 hour.

Sample preparation takes 2 hours (30
minutes hands-on), with a total
turnaround time of 36 hours.

PCR setup is 5 to 15 minutes, depending on
batch size. DNA extraction time is typically
1 hour, depending on the laboratory method
employed. Time to first result from extracted
blood DNA sample is approximately 3 hours.

One patient sample tested per run for
20 assay targets.

One patient sample tested per run for
22 assay targets.

Eight to 96 samples may be run per
plate.

One negative control is required per run;
minimum batch of three biochips, maximum
batch of 54 in a single imaging run; 54
biochips per kit.

FilmArray is an automated sampleto-answer system.

FilmArray is an automated sampleto-answer system.

Receives lysed samples and automates
target capture and protection to produce
an untagged sequencing library.

FH multiplex PCR reactions performed off
board on thermal cycler; amplicon
hybridization and conjugation steps are
automated using Electronics International
analyzer package thermoshakers.

Test panels contain internal controls.

Test panels contain internal controls.

Assays use positive and negative
controls, and in some instances,
External RNA Controls Consortium
(ERCC) probes.

Quality control performed internally and
externally. Internally on each biochip:
reference and correction spots ensure the
analyzer charged-coupled device camera
is precisely aligned; additionally, extraction
controls are included for sample adequacy.
Externally: each run should include a
non-template or negative control; positive
controls are not supplied with the kit.

Sample-to-answer system that
requires minimal hands-on time;
reports results for a comprehensive
list of pathogens, depending on the
syndrome, in about 1 hour, which
helps physicians better manage their
patients.

Sample-to-answer system that
requires minimal hands-on time;
reports results for a comprehensive
list of pathogens, depending on the
syndrome, in about 1 hour, which
helps physicians better manage their
patients.

Targeted NGS sample and library prep
is simplified using a lysis-only chemistry,
with no nucleic acid extraction
necessary, and a simple, automated
workflow. Sample input amounts are
very low (eg, a single 5 μm FFPE slide
section), and the easy-to-use data output
streamlines analysis.

The FH 40-mutation panel identifies roughly
80% of the most commonly occuring
FH-causing mutations and can be used
as a rapid qualifier for deeper sequencing
approaches. The panel is split across two
biochips, allowing cost-effective subsequent
cascade mutation screening in the family
members of index cases.

clpmag.com | June 2015

25

[ tech ]

guide

Molecular Probes, Reagents, and Assays

Randox Biosciences-US Ltd

Roche Diagnostics Inc

Siemens Healthcare
Diagnostics

Kearneysville, Wva
(866) 472-6369;
www.randoxbiosciences.com

Indianapolis
(800) 428-5076;
www.usdiagnostics.roche.com

Tarrytown, NY
(877) 229-3711; usa.healthcare.
siemens.com/laboratory-diagnostics

1. What is the brand name of your
company’s molecular diagnostic
probe, reagent, or assay?

STI multiplex array

Cobas Strep A test for use on the Cobas
Liat analyzer

Siemens tissue preparation solution

2. What year was the product first
released to market (US, OUS)?

2014

2014 (US, OUS)

2011

3. Specify the authorizing agency,
type, and year of the product’s
regulatory authorizations (eg, TUV
CE mark, 2013; FDA 510(k), 2015).

CE marked; FDA approval is pending

FDA 510(k), 2014

FDA Class I exempt, 2011; CE-IVD mark
(reagents and system), 2011

4. What is the intended use or primary
function of the product?

Multiplex polymerase chain reaction
(PCR)-based biochip array for
simultaneous detection of 10 sexually
transmited infections from one single
patient sample.

The qualitative in vitro diagnostic test
detects Streptococcus pyogenes (group
A -hemolytic Streptococcus, Strep A)
in throat swab specimens from patients
with signs and symptoms of pharyngitis.

Provides a fully automated process,
including onboard deparaffinization and
lysis, for the isolation of high-quality
nucleic acids (both DNA and RNA with one
IVD reagent kit).

5. What type of specimen/sample does
the product employ?

Genomic DNA extracted from urine or
urogenital swab samples

Throat swabs collected in a liquid amies
collection and transport system

Formalin-fixed, paraffin-embedded (FFPE)
or fresh-frozen (FF) tissue samples

6. What platform technologies does the
product employ?

Biochip array technology, a unique
multiplexing method that combines
PCR, probe hybridization, and
chemiluminescence detection.

Nucleic acid purification and realtime polymerase chain reaction (PCR)
technology, targeting a segment of the
Streptococcus pyogenes genome.

Uses magnetic nanoparticle-based isolation
and proprietary iron oxide coated with a
nanolayer of silica.

7. What tests can be performed using
the named product?

Chlamydia trachomatis, Haemophilus
ducreyi, Herpes simplex virus 1 and 2,
Mycoplasma genitalium, Mycoplasma
hominis, Neisseria gonorrhoea,
Trichomonas vaginalis, Treponema pallidum, and Ureaplasma urealyticum.

Cobas Liat Strep A assay

Any molecular tests, including end-point
and real-time polymerase chain
reaction (PCR) and reverse transcription
PCR; Sanger and next-generation
sequencing, microarrays.

8. How much time is required for setup
and preanalytical processing; what
is the time to first result under optimal conditions?

PCR setup is 5 to 15 minutes,
depending on batch size. DNA extraction
time is typically 1 hour, depending on
the laboratory method employed. Time
to first result using extracted swab or
urine DNA is 6 hours.

A result can be obtained in less than 20
minutes.

Dependent on the number of samples
loaded and the protocol chosen (DNA,
RNA, or split method); ranges from 3 to 4
hours for 48 samples. Hands-on time is
15 minutes, including loading reagents
and samples.

9. How many channels/specimens/
samples are tested per run (per
plate, etc)?

One negative control is required per run;
minimum batch of three biochips,
maximum batch of 54 in a single imaging
run; 108 biochips per kit.

The analyzer can run one sample at a
time.

From one to 48 samples per run; sample
kit can be split into four runs within 2
weeks.

10. Describe any automation options
that pertain to the product.

Sexually transmitted infection (STI)
multiplex PCR reactions performed
off board on thermal cycler; amplicon
hybridization and conjugation steps are
automated using Electronics International
analyzer package thermoshakers.

The Cobas Liat automates and
integrates sample purification, nucleic
acid amplification, and detection of the
target sequence in biological samples
using real-time PCR. The assay targets
a well-conserved region of the Strep
A genome. An internal process control
processes target bacteria through all
steps of the assay process and monitors
the presence of inhibitors in the sample
preparation and PCR.

Employs a fully automated tissueextraction process; 0.903 m x 1.124 m x
1.2 m benchtop; requires environmental
conditions of 18°C to 32°C; 24% to 80%
relative humidity, noncondensing; 0 to
2,000 m altitude.

11. How is quality control performed
for the product?

Quality control performed internally and
externally. Internally on each biochip:
reference and correction spots ensure
the analyzer charged-coupled device
camera is precisely aligned; additionally,
extraction controls are included for
sample adequacy. Externally: each run
should include a non-template or
negative control; positive controls are not
supplied with the kit.

A positive and negative control kit
is available to run quality control for
the Strep A assay. Additionally, in
less than 3 minutes, the Cobas Liat
performs a full system check at power
on, including configuration and check of
all subsystems.

This is a sample-handling platform and
does not require Siemens onboard quality
control; customers have their own control
samples.

12. Describe the capabilities, features,
or accessories that distinguish this
product from others on the market.

The STI panel is the most
comprehensive multiplex PCR
microarray-based test, including primary,
secondary, and asymptomatic
coinfections for a complete sexual health
profile.

Ability to run real-time PCR tests and
receive results in 20 minutes or less.

The only fully automated solution for the
extraction of nucleic acids from FFPE and
FF tissue samples. It includes a tissue
preparation system and the Versant tissue
preparation reagents kit.

26

June 2015 | clpmag.com



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