PRODUCT BULLETIN TaqMan SNP Genotyping Assays

TaqMan SNP Genotyping Assays

Applied Biosystems™ TaqMan™ SNP
Genotyping Assays from Thermo 1. Assay components and DNA template

Fisher Scientific provide a highly flexible Forward primer

Probe Probe
Reverse primer
A
technology for detection of polymorphisms 5’
G
3’
DNA template [G/A]
within any genome. Applied Biosystems™
TaqMan™ Assays have the simplest 3’
[C/T]
5’

workflow available and are the quickest 5’ Legend

2. Denatured template and annealing assay components 3’
way to generate genotyping data. Based
VIC dye
on powerful Applied Biosystems™ TaqMan™ Probe Probe Reverse primer
FAM dye
probe and primer chemistry and designs, Forward primer
G A
Quencher
and coupled to dependable Applied 3’ [C/T]
5’ Minor Groove
Biosystems™ instruments and software, Binder

these made-to-order assays produce high- 3. Polymerization and signal generation 5’ 3’ AmpliTaq Gold
DNA Polymerase
Reverse primer
confidence results. TaqMan Assays are Probe Probe

ideal for genotyping applications, including Forward primer

A
Primer
G
screening, association, candidate region, Template

candidate gene, and fine-mapping studies. C

Match
Extended primer

Content-rich marker selection tools simplify Figure 1. Allelic discrimination is achieved by the selective annealing of TaqMan MGB probes.
study design and help you select from a
library of human and mouse assays. This probes, which incorporate minor groove quencher (NFQ) that virtually eliminates
library includes over 7 million genome-wide binder (MGB) technology at the 3´ end, the background fluorescence associated
human assays (of which 3.5 million are deliver superior allelic discrimination. with traditional quenchers, and provides
HapMap SNP-based assays, 160,000 are The MGB molecule binds to the minor a greater signal-to-noise ratio for superior
validated assays, and over 950,000 are groove of the DNA helix, improving assay sensitivity.
coding region assays) and 10,000 mouse hybridization-based assays by stabilizing
assays. We also offer 2,700 inventoried TaqMan SNP Genotyping Assays
the MGB probe–template complex. This
drug metabolism genotyping assays. collection
increased binding stability permits the
Additionally, with Applied Biosystems™ TaqMan SNP Genotyping Assays are
use of probes as short as 13 bases for
Custom TaqMan™ SNP Genotyping Assays the world’s largest collection of single-
improved mismatch discrimination and
you can confidentially submit target SNP tube, ready-to-use SNP assays available.
greater flexibility when designing assays for
sequences for any genome to create your The TaqMan SNP Genotyping Assays
difficult or variable sequences. In addition
own assays. Let TaqMan SNP Genotyping library consists of two collections of
to SNP detection, TaqMan probes can
Assays accelerate the pace of your human assays and one of mouse assays,
be designed to detect multiple nucleotide
discovery by eliminating time-consuming and can be supplemented with assays
polymorphisms (MNPs) and insertion/
experimental design and optimization. designed using our Custom TaqMan SNP
deletions (indels).
Genotyping Assays Service.
Powerful, proven chemistry Detection is achieved with proven
Whether your genotyping studies require 5´ nuclease chemistry by means of
targeted detection of essential SNPs, or exonuclease cleavage of an allele-
the flexibility to choose SNPs for mapping, specific 5´ dye label, which generates
TaqMan SNP Genotyping Assays are the the permanent assay signal (Figure 1). All
technology of choice. Proven TaqMan MGB probes include a nonfluorescent
Over 7 million human SNP the assay designs are aligned to the Quality design and manufacturing
genotyping assays human genome using BLAST to ensure Probes and primers used in TaqMan
This assay group contains over 7 that each assay binds uniquely to the SNP Genotyping Assays are designed
million genome-wide SNPs, providing intended polymorphism. As the Custom using our rigorous bioinformatics pipeline.
unprecedented marker coverage. Included TaqMan SNP Genotyping Assay Service This proprietary group of algorithms has
in this collection are 160,000 validated is confidential and secure, you simply generated millions of TaqMan Assay
assays that have approximately 10 kb perform your own bioinformatics analysis designs by utilizing heuristic design rules
spacing across gene regions. These prior to submitting your sequence for deduced from both manufacturing and
assays were subjected to an extensive assay design. assay performance data. All assays are
minor allele frequency test in 2–4 ethnic designed to perform under universal
populations (45 individual samples per Custom assay service for any reaction conditions, as calculated probe
ethnic group) and as a result, offer the possible SNP and primer melting temperatures are
highest success rate. Also included are Custom TaqMan SNP Genotyping Assays consistent and include contributions
over 600,000 assays for the detection of can be developed for any SNP in any from associated probe conjugates
nonsynonymous SNPs in coding regions, organism. This service can generate (i.e., dyes and MGB).
including many putative functional SNPs. assays for the detection of SNPs, MNPs,
Visit thermofisher.com/taqmansnp for indels of up to 6 bases, or QSY™-labeled After manufacturing, assay components
more information. probes for multiplexing SNP assays. undergo extensive laboratory testing
at our state-of-the-art manufacturing
Over 10,000 mouse SNP genotyping Custom TaqMan SNP Genotyping Assays facility. Quality-control testing includes
assays provide you with a complete service mass spectrometry for sequence
The Applied Biosystems™ Mouse TaqMan™ that includes secure and confidential verification and formulation assessments
Predesigned SNP Genotyping Assays ordering, assay design and manufacturing, of probe and primer concentrations.
collection consists of over 10,000 assays, and quality-control testing for synthesis Additionally, all human SNP genotyping
and can be supplemented with assays accuracy and formulation completeness. assays are functionally tested to ensure
designed using our Custom TaqMan SNP Additionally, custom human assays are allelic discrimination.
Genotyping Assays Service. subjected to a functional test on 20 unique
DNA samples. Simple workflow for quick results
TaqMan Drug Metabolism Genotyping TaqMan SNP Genotyping Assays constitute
Assays Use the free Applied Biosystems™ Custom the simplest SNP genotyping technology
The collection of Applied Biosystems™ TaqMan™ Assay Design Tool to input and available. We deliver your ready-to-
TaqMan™ Drug Metabolism Genotyping submit your sequence for assay design. use SNP genotyping assay at ambient
Assays includes 2,700 assays that target This easy-to-use online resource lets you temperature in a convenient, single-tube
high-value polymorphisms in 221 drug quickly submit your sequence information format. The rest is easy. Just combine the
metabolism genes. These assays have and start the ordering process securely assay with Applied Biosystems™ TaqMan™
proven performance in four different and confidentially. Access the Custom Genotyping Master Mix or TaqMan™
ethnic population samples, consisting TaqMan Assay Design Tool at Universal PCR Master Mix and your purified
of 45 individuals each. To enable easy thermofisher.com/snpcadt DNA sample (Figure 2). There is no need to
identification, these assays have been optimize probe, primer, salt concentrations,
mapped to the common public allele or temperature because all assays use
nomenclature websites where possible. universal reagent concentrations and
Visit thermofisher.com/taqmandme for thermal cycling conditions.
more information.

All TaqMan SNP Genotyping Assays are

1 2 3
generated using next-generation algorithms Combine sample with TaqMan Thermal cycle and read Analyze data
from the Thermo Fisher Scientific SNP Genotyping Assay in plate
A
B
C
1
A

A
A

A
2 3
A

A
4
A

A
5 6
A

A
A

A
7
A

A
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A

A
9 10 11
A

A
A

A
A

A
12 13 14 15 16 17 18 19 20 21 22 23 24
A

A
A

A
A

A
A

A
A

A
A

A
A

A
A

A
A

A
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A
A

A
A

A
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A
Setup InstrumentResults

7.0
Legend
Undetermined
Allele X
D A A A A A A A A A A A A A A A A A A A A A A A A Both

bioinformatics pipeline. For all predesigned

Allele Y
E A A A A A A A A A A A A A A A A A A A A A A A A
NTC
F A A A A A A A A A A A A A A A A A A A A A A A A

A A A A A A A A A A A A A A A A A A A A A A A A
G
A A A A A A A A A A A A A A A A A A A A A A A A
H
A A A A A A A A A A A A A A A A A A A A A A A A
I 6.0
A A A A A A A A A A A A A A A A A A A A A A A A
J
A A A A A A A A A A A A A A A A A A A A A A A A
K
A A A A A A A A A A A A A A A A A A A A A A A A
L
A A A A A A A A A A A A A A A A A A A A A A A A
M

assays, bioinformatics evaluation of target

A A A A A A A A A A A A A A A A A A A A A A A A
N
A A A A A A A A A A A A A A A A A A A A A A A A
O 5.0
A A A A A A A A A A A A A A A A A A A A A A A A
Allele Y (AL-6)

Position Sample Marker Allele X Rn Call Allelle Y Rn Passive Ref R Task Qua
A1
A2
A3
Assays
SNP Genotyping A4
Ta q M a n ® 4.0
Part No.:
A5
r:
Sales Orde
Plate ID: A6

SNP sequences includes the masking

A7
A8
A9
A10
A11
A12
A13
A14 3.0
A15
A16
A17
A18
A19
A20
A21

of adjacent SNPs and ambiguous bases

A22
A23
2.0
A24
Part No.: 4362691 B1 1.1 1.6 2.1 2.6 3.1 3.6
Allele X (AL-5)
Sales Order: 18524966

Plate ID: 1704370-1

so that assay design and subsequent

performance is not affected by the poor Figure 2. A simple workflow and reliable instruments combine to generate fast, high-
quality of the underlying sequence. Lastly, confidence results.
After generating an endpoint read using a Table 1. Applied Biosystems instrument capacities.
thermal cycler or real-time PCR instrument,
Instrument Capacity
no transfers, washes, or additional
reagents are required, and the plate 7500/7500 Fast Real-Time PCR System 96-well block (standard or Fast)

remains sealed; just read the plate and 7900HT Fast Real-Time PCR System 96- and 384-well blocks (standard or Fast)
analyze the genotypes. This reduces the 96-well (standard or Fast), 384-well, and
chance of contamination, sample mix-up, ViiA 7 Real-Time PCR System
TaqMan Array Card blocks
and sample loss. The simplicity of the StepOne Real-Time PCR System 48-well block (standard or Fast)
chemistry allows you to easily automate the
reaction for massively parallel genotyping StepOnePlus Real-Time PCR System 96-well block (standard or Fast)

studies, readily increasing the number QuantStudio 3 Real-Time PCR System 96-well block (standard or Fast)
of assays, number of samples, or both.
QuantStudio 5 Real-Time PCR System 96-well (standard or Fast) and 384-well blocks
Additionally, the analysis software allows
you to auto-call genotypes, minimizing QuantStudio 6 Real-Time PCR System 96-well (standard or Fast) and 384-well blocks
manual intervention. 96-well (standard or Fast), 384-well, and
QuantStudio 7 Real-Time PCR System
TaqMan Array Card blocks
Reliable real-time PCR platforms 96-well (standard or Fast), 384-well, TaqMan
QuantStudio 12K Flex Real-Time PCR System
A suite of superior Applied Biosystems Array Card, and OpenArray plate blocks
instrument platforms is available for
processing and analyzing TaqMan SNP
Genotyping Assays (Table 1). These
instruments, which meet all throughput
needs and budgets, include the 7500,
7500 Fast, 7900HT Fast, ViiA™ 7,
StepOne™, and StepOnePlus™ Real-Time
PCR Systems, and the QuantStudio™ 3, 5,
6, 7, and 12K Flex Real-Time PCR Systems
(Figure 3). Following PCR amplification, an
endpoint read can be performed on any
Applied Biosystems real-time PCR system.
All of these dependable instruments
Figure 3. The QuantStudio 5 Real-Time PCR System (left) and the QuantStudio 12K Flex
offer the advanced multicolor detection Real-Time PCR System (right), which offers the highest throughput of all Applied Biosystems
capabilities required for highly accurate and real-time PCR instruments.
reproducible allelic discrimination assays.

Data analysis software

The sophisticated SDS software package
provided with all Applied Biosystems real-
time PCR systems facilitates experimental
setup, data collection, and assay
performance analysis. The SDS software
uses an advanced multicomponent
algorithm to calculate the distinct signal
contribution of each allele of a marker
from the fluorescence measurements of
each sample well during the assay plate
read. The multicomponent data collected
from the plate read are stored as SDS
files, ready for genotype determination
by the SDS software or optional Applied
Biosystems™ TaqMan™ Genotyper Software
(Figure 4).
Figure 4. TaqMan Genotyper Software automatically determines sample genotypes and
displays data.
TaqMan Genotyper Software is a great Simple ordering Our Custom TaqMan SNP Genotyping
resource for fast and accurate genotype Selecting and ordering TaqMan SNP Assays supply you with SNPs that are
calling. It is a free SNP genotyping data Genotyping Assays is as simple as “point not available from our predesigned
analysis tool for use with TaqMan SNP and click.” Use SNPbrowser Software to assay collection, including those from
Genotyping Assays performed in 48-, 96-, select the most informative SNPs for your any nonhuman organism. This service
or 384-well microtiter plates or on Applied genotyping studies. As you identify SNPs designs assays for all possible SNP, MNP,
Biosystems™ TaqMan™ OpenArray™ Plates. of interest, simply upload your selected and indel targets but without the up-
It has a state-of-the-art genotype-calling TaqMan SNP Genotyping Assays to our front bioinformatic preparation used for
algorithm, an intuitive user interface, and online ordering tool. the predesigned made-to-order assays.
enhanced study-based analysis features. Our complementary Custom TaqMan
The software enables multi-plate data The TaqMan Assay online ordering tool Assay Design Tool conveniently formats
analysis for high-throughput workflows (Figure 5) enables you to search, select, your target sequence for submission
and improved accuracy in genotype and order from our catalog of over 7 million to our manufacturing facilities. To order
calling; versatile export features and made-to-order predesigned TaqMan SNP custom assays, simply prepare your
comprehensive quality-control features Genotyping Assays. You can search for target sequence according to the Design
facilitate streamlining of the entire SNPs using any of several criteria: National and Ordering Guide, and upload your
workflow. TaqMan Genotyper Software Center for Biotechnology Information submission file at
can be downloaded at (NCBI) gene ID, NCBI SNP reference ID thermofisher.com/snpcadt
thermofisher.com/taqmangenotyper (rs#), or gene symbol. You can further
refine your search by using SNP type (i.e.,
intragenic, 5´ or 3´ UTR, chromosome, etc.).

Figure 5. Our TaqMan Assay search and order tool makes online ordering easy. For convenient
online ordering and multiple search options for all our genotyping assays, including keyword, batch,
and location searches, visit thermofisher.com/taqmansnp
Ordering information

Human Nonhuman No. of 5 µL No. of 25 µL

Number of Assay mix
Size assays assays reactions reactions Assay type
SNPs formulation
(Cat. No.) (Cat. No.) (384-well plate) (96-well plate)

Predesigned TaqMan SNP Genotyping Assays for Human and Mouse

Small 4351379 4351384* >4.5 million 1,500 300 40X made-to-order

Medium 4351376 4351382* >4.5 million 5,000 1,000 40X made-to-order

Large 4351374 4351380* >4.5 million 12,000 2,400 80X made-to-order

Custom TaqMan SNP Genotyping Assays

Small 4331349 4332077 ∞ 1,500 300 40X made-to-order

Medium 4332072 4332075 ∞ 5,000 1,000 40X made-to-order

Large 4332073 4332076 ∞ 12,000 2,400 80X made-to-order

TaqMan Drug Metabolism Genotyping Assays

Small 4362691 NA 2,700 750 150 20X inventoried

All assays are quality-control tested using a mass spectrometer to verify sequence and yield. All assays have a VIC dye–labeled probe, a FAM dye–labeled probe, and two target-specific primers. All assays, excluding Custom TaqMan SNP Genotyping
™ ™

Assays, undergo bioinformatics evaluation of target SNP sequences.

Functional testing against 20 unique genomic DNA samples is performed on all custom and predesigned made-to-order human TaqMan SNP Genotyping Assays. Validation testing against four populations (45 samples/population) was performed on all
160,000 validated TaqMan SNP Genotyping Assays, and all TaqMan Drug Metabolism Genotyping Assays.
* Over 10,000 mouse assays available.
Find out more at thermofisher.com/taqmansnp

For Research Use Only. Not for use in diagnostic procedures. © 2016 Thermo Fisher Scientific Inc. All rights reserved. All trademarks
are the property of Thermo Fisher Scientific and its subsidiaries unless otherwise specified. TaqMan is a trademark of Roche Molecular
Systems, Inc., used under permission and license. CO020271 0116