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TaqMan SNP Genotyping Assays

TaqMan SNP Genotyping Assays from

Applied Biosystems provide a highly
flexible technology for detection of poly-
morphisms within any genome. With
the simplest workflow available, TaqMan
Assays are the quickest way to generate
genotyping data. Based on powerful
TaqMan probe and primer chemistry
and designs, and coupled to dependable
Applied Biosystems instruments and
software, these Made-to-Order assays
produce high-confidence results. These
TaqMan Assays are ideal for genotyping
applications including screening, associa-
tion, candidate region, candidate gene, Powerful, Proven Chemistry (MGB) technology at the 3 end,
or fine-mapping studies. Whether your genotyping studies deliver superior allelic discrimination.
require targeted detection of essential The MGB molecule binds to the minor
Content-rich marker-selection tools
SNPs, or the flexibility for choosing groove of the DNA helix, improving
simplify study design and help you
SNPs for mapping, TaqMan SNP hybridization-based assays by stabilizing
select from a library of human and
Genotyping Assays are the technology the MGB-probe/template complex. The
mouse assays. This library includes
of choice. Proven TaqMan probes, which increased binding stabilization permits
over 4.5 million genome-wide human
incorporate minor groove binder the use of probes as short as 13 bases
assays (of which 3.5 million are
HapMap SNP-based assays, 160,000
are validated assays, and over 70,000
are coding region assays) and 10,000
mouse assays. We also offer over
2,600 Inventoried Drug Metabolism
Genotyping Assays. Additionally, Custom
TaqMan SNP Genotyping Assays let you
create your own confidential assays by
submitting target SNP sequences for any
genome. Let TaqMan SNP Genotyping
Assays accelerate the pace of your
discovery by eliminating time-consuming
experimental design and optimization.

Figure 1. Allelic discrimination is achieved by the selective annealing of TaqMan MGB probes.
for improved mismatch discrimination
and greater flexibility when designing
assays for difficult or variable sequences.
In addition to SNP detection, TaqMan
probes can be designed to detect
multiple nucleotide polymorphisms
(MNPs) and insertion/deletions (InDels).
Detection is achieved with proven 5 nuc-
lease chemistry by means of exonuclease
cleavage of a 5 allele-specific dye label,
which generates the permanent assay
signal (Figure 1). All MGB probes include
a nonfluorescent quencher (NFQ) that
virtually eliminates the background
fluorescence associated with traditional
quenchers and provides a greater signal-
to-noise ratio for superior assay sensitivity.
TaqMan SNP Genotyping
Assays Collection
TaqMan SNP Genotyping Assays are the
worlds largest collection of single-tube,
ready-to-use SNP assays available.
The TaqMan SNP Genotyping Assays Visit snp.appliedbiosystems.com
library consists of two human and one for more information.
mouse assay collections, and can be
Over 10,000 Mouse SNP
supplemented with assays designed
Genotyping Assays
using our Custom TaqMan SNP
The Mouse TaqMan Pre-Designed SNP
Genotyping Assays Service (Table 1).
Genotyping Assays collection consists
Over 4.5 Million Human SNP of over 10,000 assays, and can also be
Genotyping Assays supplemented with assays designed
This assay group contains over 4.5 using our Custom TaqMan SNP
million genome-wide SNPs providing Genotyping Assays Service.
unprecedented marker coverage.
TaqMan Drug Metabolism
Included in this collection are 160,000
Genotyping Assays Collection
validated assays that have roughly
Over 2,600 assays that target high
10-kb spacing across gene regions.
value polymorphisms in over 220 drug
These assays were subjected to a minor
metabolism genes. These assays have
allele frequency test in 24 ethnic
proven performance in four different
populations (45 individual samples per
ethnic populations, comprised of 45
ethnic group) and offer the highest
individuals each. To enable easy
success rate because of this extensive
identification, these assays have been
testing. Over 70,000 assays are also
mapped to the common public allele
included for the detection of nonsyn-
nomenclature Web sites where possible.
onymous SNPs in coding regions, includ-
Visit dme.appliedbiosystems.com for
ing many putative functional SNPs.
more information.

Table 1. TAQMAN SNP GENOTYPING ASSAYS

Human assays Non-human Number of Reactions at Reactions at Assay mix Availability

part numbers assays part SNPs 5 L volume 25 L volume formulation
numbers (384-well plate) (96-well plate)

TaqMan Pre-Designed SNP Genotyping Assays for Human and Mouse

Small-scale 4351379 4351384* >4,500,000 1,500 300 40X Made-to-Order

Medium-scale 4351376 4351382* >4,500,000 5,000 1,000 40X Made-to-Order

Large-scale 4351374 4351380* >4,500,000 12,000 2,400 80X Made-to-Order

TaqMan Drug Metabolism SNP Genotyping Assays

Small-scale 4362691 N/A >2,600 750 150 20X Inventoried

Custom TaqMan SNP Genotyping Assays

Small-scale 4331349 4332077 1,500 300 40X Made-to-Order

Medium-scale 4332072 4332075 5,000 1,000 40X Made-to-Order

Large-scale 4332073 4332076 12,000 2,400 80X Made-to-Order

All assays are quality control tested using a mass spectrophotometer to verify sequence and yield. All assays have one VIC and one FAM
dye-labeled probe and two target-specific primers. All assays, except Custom Assays, undergo bioinformatics evaluation of target SNP
sequences.

Functional testing against 20 unique genomic DNAs is performed on all human SNP Genotyping Assays. Validation testing against three
populations with ~45 samples/population was performed on all Validated and Drug Metabolism Assays.

All Validated and Coding Assays that were previously held in inventory are now available as Made-to-Order Pre-Designed Assays. Their assay
IDs remain unchanged.

*Over 10,000 mouse assays available.

All TaqMan SNP Genotyping Assays
were generated using next-generation
algorithms from the Applied Biosystems
bioinformatics pipeline. Bioinformatics
evaluation of target SNP sequences
includes the masking of adjacent SNPs
and ambiguous bases so that assay
design and subsequent performance
is not affected by underlying sequence
quality. Lastly, the assay designs are
aligned to the human genome using
BLAST to ensure the assay is uniquely
binding and targets only the intended
polymorphism. As the Custom TaqMan
SNP Genotyping Assay Service is a
confidential and secure service, custom-
ers perform their own bioinformatics
analysis prior to submission of sequence
for assay design.
Free Marker Selection Tools
SNPbrowser Software for Human SNPs
SNPbrowser Software for human SNPs
simplifies study design by facilitating
easy and intuitive selection of the optimal
SNP assay set for each project. You can
download free SNPbrowser Software at
www.allsnps.com/snpbrowser
SNPbrowser Software provides a physical
map view of the human genome.
Two different genotype data sources
are incorporated into the software to
generate unique linkage disequilibrium
(LD) maps and haplotype block informa-
tion. These two sources are the public
HapMap Project and Applied Biosystems
20+ million genotypes generated during
the development of the 160,000 TaqMan
Validated SNP Genotyping Assays.
This genotyping data also facilitates the
use of tagging SNP methods, which allow
more affordable study design by reducing
the number of SNPs while conserving
study statistical power (Figure 2).
SNPbrowser Software allows you to
optimize study design based on LD
patterns, minor allele frequency require-
ments, total number of cases and
controls, and statistical power. Finally,
the software includes a SNP density
tool that prioritizes the selection of
validated SNPs while supplementing
A.
B.
Figure 2. Identifying Optimal Subsets of SNPs with the SNP Wizard. (A) Search and visualize your gene of
interest, then activate the SNP Wizard. (B) Choose a tagging SNP method and set parameters to reduce
the number of SNPs needed to represent common haplotypes. A summary panel appears that displays
algorithm results and allows you to easily adjust your parameter selection. Selected tagging SNPs are shown
in red on the graphical map.
with additional SNPs to fulfill the marker Mouse SNPbrowser selects from
density requirements for your study. Pre-Designed SNP Genotyping assays
using either TaqMan Assay or SNPlex
When you have identified your SNPs
Genotyping System Assay collections
of interest, order TaqMan SNP
available from the Applied Biosystems
Genotyping Assays by directly uploading
online store. You can download free
Assay IDs from the software to the
Mouse SNPbrowser Software from
Applied Biosystems Web site by going
www.allsnps.com/mousesnpbrowser
to snp.appliedbiosystems.com
Mouse SNPbrowser Software supports
Mouse SNPbrowser Software
genetic monitoring, genetic mapping,
Complimentary Mouse SNPbrowser
and speed congenics applications by
Software enables efficient and easy
offering a variety of tools to search, view,
selection of appropriate SNP sets
export SNP information, and purchase
to discriminate between strains of
assays. The software displays the mouse
interest, with specific applications in
chromosome map so users can view
genotype/phenotype mapping and strain
SNP location and obtain National Center
verification. It visualizes informative
for Biotechnology Information (NCBI)
SNPs that distinguish two selected
data for SNPs of interest. The software
mouse strains at a user-definable
allows SNP selection for two applications:
resolution. There are ~10,000 mouse
genetic monitoring and genetic mapping.
SNPs genotyped in 44 of the most
common strains.
For genetic monitoring, the software and primer melting temperatures After manufacturing, assay components
selects optimal SNPs to distinguish are consistent and include contributions undergo extensive laboratory testing at
between any number of strains. SNPs from associated probe conjugates our state-of-the-art manufacturing facility
can be selected for each chromosome (i.e., dyes, MGB). (Figure 3). Quality-control testing includes
or across the genome. For genetic mass spectrometry for sequence
mapping, the software segments each
chromosome into evenly sized blocks
based on user-specified mapping resolu-
tion, and searches for distinguishing SNP
in each block to generate evenly-spaced
SNP coverage throughout the genome.
Mouse SNPbrowser Software also
features a SNP wizard to assist defining
search criteria. A help text file is provided
within the tool to assist in familiarizing
users of the extensive functionality
offered.

Custom Assay Service for Any Figure 3. Applied Biosystems high-throughput manufacturing facility.

Possible SNP
Custom TaqMan SNP Genotyping Assays
are available for any possible SNP in any
organism. This service can generate
assays for the detection of SNPs, MNPs,
or insertions/deletions of up to six bases.

Custom TaqMan SNP Genotyping Assays

provide customers with a complete
service that includes secure and
confidential ordering, assay design and
manufacturing, quality-control testing
for synthesis accuracy and formulation
completeness. Additionally, custom
human assays are subjected to a func-
tional test on 20 unique DNA samples.

Our complimentary File Builder Software

makes it easy to submit your targets
for design through our custom assay
service. Download the latest version
of File Builder Software at
www.appliedbiosystems.com/filebuilder

Quality Design and Manufacturing

Probes and primers used in TaqMan SNP
Genotyping Assays are designed by
our rigorous bioinformatics pipeline.
This proprietary group of algorithms has
generated millions of TaqMan Assay
designs by utilizing heuristic design rules
deduced from both manufacturing and
assay performance data. All assays are
designed to perform under universal
reaction conditions, as calculated probe
Figure 4. A simple workflow and reliable instruments combine to generate fast, high-confidence results.
 verification and formulation assessments
of probe and primer concentrations.
Additionally, we functionally test all
human SNP genotyping assays with an
allelic discrimination test.

Simple Workflow for Quick Results

TaqMan SNP Genotyping Assays
constitute the simplest SNP genotyping
technology available. Applied Biosystems
delivers your ready-to-use SNP geno-
typing assay in a convenient, single-tube
format. The rest is easy. Just combine
the assay with TaqMan Genotyping
Master Mix or TaqMan Universal PCR
Master Mix and your purified DNA
sample. There is no need to optimize
temperature or concentrations of probes,
primers, or salts, because all assays run
under universal reagent concentrations
Figure 5. The SNP auto-caller feature automatically determines sample genotypes and displays data. and thermal cycling conditions.

After thermal cycling, no transfers, wash-

Table 2. Instrument Capacity es, or addition of reagents is required,
and the plate remains sealed; just read
Instrument Platforms Capacity
the plate and analyze the genotypes
Applied Biosystems GeneAmp 60-, 96-, Dual 96-, or Dual 384-well (Figure 5). This reduces the chance
PCR System 9700 Thermal Cycler blocks
of contamination, sample mix-up, and
Applied Biosystems Veriti Thermal Cycler 60-, 96- (Standard or Fast), sample loss. Because of the simplicity in
or 384-well block chemistry, you can easily automate the
Applied Biosystems 7300 Real-Time PCR System 96-well block reaction for massively parallel genotyping
Applied Biosystems 7500/7500 Fast 96-well block (Standard and Fast) studies, readily increasing the number
Real-Time PCR System of assays, number of samples, or both.
Additionally, the analysis software allows
Applied Biosystems 7900HT Fast 384-well block (Standard and Fast)
Real-Time PCR System you to auto-call genotypes, minimizing
manual intervention.
Applied Biosystems StepOne 48-well block (Standard and Fast)
Real-Time PCR System Reliable Real-Time PCR Platforms
Applied Biosystems StepOnePlus
96-well block (Standard and Fast) Applied Biosystems offers a suite
Real-Time PCR System of superior instrument platforms for
processing and analyzing TaqMan SNP
Genotyping Assays. These instruments,
which meet all throughput needs and
budgets, include the GeneAmp PCR
System 9700 and Veriti Thermal Cyclers
and the Applied Biosystems 7300, 7500,
7500 Fast, 7900HT Fast, StepOne or
StepOnePlus Real-Time PCR Systems.
Following PCR amplification, an endpoint
read can be performed on any Applied
Biosystems Real-Time PCR System. All of
these dependable instruments offer the
advanced multicolor detection capabilities
required for highly accurate and reproduc-
Figure 6. The flexible, high-throughput Applied Biosystems 7900HT Fast Real-Time PCR System. ible allelic discrimination assays.
 simplify high volume data transfer and
analysis with the optional SDS version
2.2 Enterprise Edition Software Suite.

Ordering Information
Selecting and ordering TaqMan SNP
Genotyping Assays is as simple as
point and click. Use SNPbrowser
Software to select the most informative
SNPs for your genotyping studies. As
you identify SNPs of interest, simply
upload your selected TaqMan SNP
Genotyping Assays to the Applied
Biosystems Web site for ordering.

The Applied Biosystems Web site (Figure

Figure 7. The Applied Biosystems Web site (www.appliedbiosystems.com) facilitates convenient online
ordering and multiple search options for all our genotyping assays, including keyword, batch, and location searches.
Data Analysis Software
The sophisticated software package
provided with all Applied Biosystems
Real-Time PCR Systems facilitates
experimental set-up, data collection,
and assay performance analysis.
The SDS software uses an advanced
multi-component algorithm to calculate
distinct allele/marker signal contributions
from fluorescence measurements for
each sample well during the assay
plate read. The SNP auto-caller feature
automatically determines sample
genotypes and generates a cluster plot
that helps you visualize data across
samples or populations (Figure 5).
For large-scale studies, you can cycle
samples on multiple Dual 384-Well
GeneAmp 9700 or Veriti Thermal
Cyclers and then analyze them on a
7900HT System. The 7900HT System
(Figure 6) facilitates high-throughput
applications by allowing large sample
batches (up to eighty-four 384-well
plates) to be processed without
manual intervention using the optional
Automation Accessory. Following data
collection, you can accelerate and
7) enables you to search for, select,
and order from our catalog of over 4.5
million TaqMan SNP Genotyping Assays.
You can search for SNPs using several
criteria options: National Center for
Biotechnology Information (NCBI) gene
ID, NCBI SNP reference ID (rs#) and gene
symbol. You can further refine your search
by using SNP type (i.e., intragenic, 5 or 3
UTR, chromosome, etc.).
Our Custom TaqMan SNP Genotyping
Assays Service is provided to supply
you with any SNP not available from our
catalog, including any non-human
organism. This service designs assays
for all possible SNP, MNP, and InDel
targets. Our complementary File Builder
Software conveniently formats your
target sequence for submission to our
manufacturing facilities. To order any
custom assays, simply upload your
submission file to our Web site, or email
the file to your local sales office.

For Research Use Only. Not for use in diagnostic procedures. NOTICE TO PURCHASER: LIMITED LICENSE
A license to perform the patented 5 Nuclease Process for research is obtained by the purchase of (i) both Licensed Probe and Authorized 5 Nuclease Core Kit, (ii) a Licensed 5
Nuclease Kit, or (iii) license rights from Applied Biosystems.
TaqMan SNP Genotyping Assays contain Licensed Probes. Use of these products is covered by one or more of the following US patents and corresponding patent claims outside
the US: 5,538,848, 5,723,591, 5,876,930, 6,030,787, 6,258,569, and 5,804,375 (claims 1-12 only). The purchase of these products includes a limited, non-transferable immunity
from suit under the foregoing patent claims for using only the amount of product specified for the purchasers own internal research. Separate purchase of an Authorized 5
Nuclease Core Kit would convey rights under the applicable claims of US Patents Nos. 5,210,015 and 5,487,972, and corresponding patent claims outside the United States, which
claim 5 nuclease methods. No right under any other patent claim and no right to perform commercial services of any kind, including without limitation reporting the results of
purchasers activities for a fee or other commercial consideration, is conveyed expressly, by implication, or by estoppel. These products are for research use only. Diagnostic uses
under Roche patents require a separate license from Roche. Further information on purchasing licenses may be obtained from the Director of Licensing, Applied Biosystems, 850
Lincoln Centre Drive, Foster City, California 94404, USA.
2008. Applied Biosystems. All Rights Reserved. Information subject to change without notice. Applera, Applied Biosystems, AB (Design), GeneAmp, and VIC are registered
trademarks and FAM, StepOne, StepOnePlus, and Veriti are trademarks of Applera Corporation in the US and/or certain other countries.
AmpliTaq Gold and TaqMan are registered trademarks of Roche Molecular Systems, Inc.
Printed in the USA. 06/2008 Publication 135PB03-02

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