1506 Tech Guide Molecular Probes Reagents Assays

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24 June 2015 | clpmag.com

Molecular Probes, Reagents, and Assays

guide

[ tech ]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 opti-

mal 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 micro-

array; 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.

clpmag.com | June 2015 25

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, paraffin-

embedded (FFPE) tissue; frozen tissue;

plasma; purified RNA; serum.

Genomic DNA extracted from a blood sample

FilmArray is an automated sample-

to-answer system for nucleic acid

extraction, nested polymerase chain

reaction amplification, and detection.

FilmArray is an automated sample-

to-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 sample-

to-answer system.

FilmArray is an automated sample-

to-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.

26 June 2015 | clpmag.com

Molecular Probes, Reagents, and Assays

guide

[ tech ]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 real-

time 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 pal-

lidum, 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 opti-

mal 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 tissue-

extraction 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.