The following documents contain information related to the instruments and
software required to perform the Axiom 2.0 Genotyping Assay:
GeneTitan® Multichannel Instrument User’s Manual, P/N 08-0306
GeneTitan® Multichannel Instrument Site Preparation Guide, P/N 08-0305
Affymetrix® GeneChip® Command Console® Software User Manual,
Axiom™ Genome-Wide CHB 1 Array Plate
Affymetrix® Genotyping Console™ 4.1 User Manual, P/N 702982
Biomek® Liquid Handler User’s Manual, Beckman Coulter P/N 987834
Biomek® Software User’s Manual, Beckman Coulter P/N 987835
The Axiom™ Genome-Wide CHB 1 Array Plate consists of peg arrays designed for
the genotyping of single nucleotide polymorphisms (SNPs) and simple insertion/
deletions (in/dels). These arrays were designed to maximize coverage of common
alleles in the Han Chinese population. This array plate, when used with the
Axiom™ 2.0 Reagent Kit (see Ordering Information for further details) enables
researchers to perform large-scale genotyping studies with minimal hands-on
processing per plate.
Each plate consists of 96 microarrays and is offered as a part of a complete
automated solution from Affymetrix that includes instrumentation for sample
preparation, and array washing, staining and scanning.
The array plate is available in a single configuration:
96-Array Plate — Twelve (12) columns of 8 microarrays in each column for
a total of 96 identical microarrays on the same plate.
Each microarray on the Axiom Genome-Wide CHB 1 Array Plate enables the
genotyping of 640,673 SNPs and 3,122 simple indels. SNPs on this array were
chosen from the Axiom Genomic database. These SNPs are present on short
randomly generated fragments of genomic DNA (25 to 125 basepair), and are
amplified using the Axiom 2.0 Reagent Kit. The reagents for processing Axiom
arrays are also included in this reagent kit.
SNPs were chosen and represented on the array in part based upon genotyping
reproducibility and call rate, with accuracy determined using genotypes from the
International HapMap Project. These SNPs have been validated across multiple
samples, including the original 270 HapMap Phase I samples as well as additional
extended HapMap Phase 3 populations.
Identical to the cartridge array manufacturing process, the oligonucleotide
probes on Axiom Genome-Wide CHB 1 Array Plates are synthesized in situ using
Affymetrix’ photolithographic process.
Library files contain information about the probe array design characteristics,
probe use and content, and scanning and analysis parameters. These
files are unique for each probe array type. Additional information can be
located under the specific array product on the Affymetrix web site at
Reagents, Instrumentation and Software Required
Axiom™ 2.0 Reagent Kit
Axiom™ Genome-Wide and/or myDesign Array Plates
Biomek FXP Target Prep Express by Beckman Coulter
GeneTitan™ Multichannel Instrument
Affymetrix GeneChip® Command Console® Software
Affymetrix Genotyping Console
For a complete list of reagents and consumables required, please refer to the
Axiom™ 2.0 Assay Automated Workflow Site Prep Guide, P/N 702984, or the
Axiom™ 2.0 Assay Manual Workflow Site Prep Guide, P/N 702991.
Axiom™ Genome-Wide CHB 1
One 96-Array Plate
Contains all GeneTitan consumables
required to process an Axiom array plate
Axiom™ 2.0 Reagent Kit
1 kit of 96 reactions
1. One Hyb Tray, one Scan Tray, and five Stain Trays with covers are included for use with each
array plate. These consumables are required for processing Axiom array plates on the GeneTitan
Instructions for Use
Affymetrix® products can be purchased directly from Affymetrix in the United
States, and many European and Asian countries. For all other territories,
please view a list of our distribution partners, which can be located at
Refer to the following documents for instructions on processing samples using
the Axiom™ 2.0 Assay.
Storage, Handling and Stability
Axiom 2.0 Assay Automated Workflow User Guide, P/N 702963
Axiom™ 2.0 Assay Automated Workflow Site Prep Guide, P/N 702984
Axiom™ 2.0 Assay Automated Target Prep Protocol QRC, P/N 702962
Axiom™ 2.0 Assay Manual Workflow User Guide, P/N 702990
Axiom™ 2.0 Assay Manual Workflow Site Prep Guide, P/N 702991
Axiom™ 2.0 Manual Target Prep Protocol QRC, P/N 702989
Axiom™ 2.0 gDNA Sample Prep Protocol QRC, P/N 702987
GeneTitan® MC Protocol for Axiom 2.0 Array Plate Processing QRC,
Axiom Genome-Wide CHB 1 Array Plates should be stored at 2 to 8 °C and must
not be frozen. Refer to the expiration date on the package label. Do not use
arrays or reagents after the expiration date.
When Handling the Axiom Array Plate
Remove the Array Plate from the pouch with gloved hands. The plate is packaged
with a blue plastic base. Do not remove the Array Plate from this protective base,
or touch the Array Plate directly. Keep the Array Plate in the protective base at all
times, including when placed on the GeneTitan Multichannel Instrument.
When Handling the 96 Plate Scan Tray
Remove the 96 Plate Scan Tray (Scan Tray) from the pouch with gloved hands.
The Scan Tray is packaged with a black protective base and cover. Keep the
Scan Tray in the protective base with the cover at all times prior to loading into
the GeneTitan Multichannel Instrument. Do not touch the bottom of the Scan
The Scan Tray has protruding guide posts that may be sharp and can puncture
the pouch if not handled carefully. Take the necessary precautions to avoid injury.
1. AXIOM™ GENOME-WIDE CHB 1 ARRAY PLATES ARE FOR RESEARCH USE
ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.
Avoid microbial contamination, which may cause erroneous results.
WARNING: All biological specimens and materials with which they
come into contact should be handled as if capable of transmitting
infection and disposed of with proper precautions in accordance with
federal, state, and local regulations. This includes adherence to the
OSHA Bloodborne Pathogens Standard (29 CFR 1910.1030) for bloodderived and other samples governed by this act. Never pipet by
mouth. Avoid specimen contact with skin and mucous membranes.
CAUTION: Exercise standard precautions when obtaining, handling, and
disposing of potentially carcinogenic reagents.
Exercise care to avoid cross-contamination of samples during all steps of this
procedure, as this may lead to erroneous results.
Use powder-free gloves whenever possible to minimize introduction of
powder particles into sample or probe array plates.
CAUTION: Use care when handling the Scan Tray as it has protruding guiding
posts that may be sharp and can stick out of the pouch if not handled
Subject to the Affymetrix terms and conditions that govern your use of
Affymetrix products, Affymetrix grants you a non-exclusive, non-transferable,
non-sublicensable license to use this Affymetrix product only in accordance with
the manual and written instructions provided by Affymetrix. You understand and
agree that except as expressly set forth in the Affymetrix terms and conditions,
that no right or license to any patent or other intellectual property owned or
licensable by Affymetrix is conveyed or implied by this Affymetrix product.
In particular, no right or license is conveyed or implied to use this Affymetrix
product in combination with a product not provided, licensed or specifically
recommended by Affymetrix for such use.
Affymetrix®, Axiom™, myDesign™, Command Console®, DMET™, GeneAtlas™,
GeneChip®, GeneChip-compatible™, GeneTitan®, Genotyping Console™,
NetAffx®, and Powered by Affymetrix™ are trademarks or registered trademarks
of Affymetrix Inc.
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Products may be covered by one or more of the following patents: U.S. Patent
Nos. 5,445,934; 5,744,305; 6,399,365; 6,733,977; and other U.S. or foreign
patents. Products are manufactured and sold under license from OGT under
5,700,637 and 6,054,270.
© 2011 Affymetrix, Inc. All rights reserved.
All other trademarks are the property of their respective owners.
Axiom™ Genome-Wide CHB 1 Array Plate For Research Use Only
Not for use in diagnostic procedures.
P/N 702986 Rev. 3