Download Solutions for Each Step of An Association Study

Association Study
Application Note
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Solutions for Each Step of an
Association Study
WHOLE-GENOME SCAN
Overview
Scan whole-genome
hypothesis free
Affymetrix offers solutions for each step of a typical whole-genome association
study—from initial discovery, to replication and fine mapping, sequence analysis,
and functional testing of genes. Researchers worldwide are now using these tools
to identify the genetic causes of a wide range of common diseases such as autism,
obesity, cancer, asthma, and diabetes.
Products:
• GeneChip® Mapping 500K
Array Set
FINE MAPPING/
REPLICATION
WHOLE-GENOME SCAN
Products:
• Custom Targeted
Genotyping
In this initial step, an unbiased subset
of all SNPs are genotyped on a microarray to determine which are statistically
associated with a given phenotype—
a predisposition to disease, drug response,
diagnosis, or prognostic outcome.
SEQUENCE ANALYSIS
FINE MAPPING/REPLICATION
Reduce to candidate region/
genes; repeat in another
population
Identify candidate
nucleotide variants
Products:
• GeneChip CustomSeq® Arrays
FUNCTIONAL TESTS
Understand the function
Products:
• Gene Expression
• Exon Expression
• Gene Regulation
• Full Transcriptome
In this second step, additional SNPs in
the regions identified during the initial whole genome scan are analyzed for
statistical association with the phenotype. SNPs are re-genotyped in additional sample populations, or in the
same population, to replicate the initial discoveries.
SEQUENCE ANALYSIS
In this third step, genomic regions are
chosen for detailed sequence analysis to
identify all SNPs in these regions within
a particular population. Regions are
chosen based on proximity to statistically
significant SNPs and, often, functional
annotations. Those SNPs can then be analyzed for statistical association with the
phenotype and researchers can ultimately
pinpoint one or more causal variants.
FUNCTIONAL TESTING
In this final step, researchers look to verify
and explore the association between the
causal variant that has been discovered
and the phenotypic effects.
LOWER COSTS. MORE SAMPLES. HIGHER
GENETIC POWER.
The number of samples genotyped in your
study is the single most important factor
in powering your whole-genome scan. The
GeneChip® Human Mapping 500K Array
Set reduces genotyping costs to $250 per
sample,* which allows you to dramatically
increase the number of samples you can
run in a single study. More samples translate into higher genetic power to detect
true associations (Figures 1 and 2).
U.S. list price
*
1,000,000 SNPS IN 2007
Use a platform that will grow with your
future needs. Affymetrix will introduce a 1
million-SNP product by the first quarter of
2007. Additionally, by the end of 2006,
Affymetrix will begin offering a singlearray genotyping product for wholegenome association studies to replace the
Mapping 500K Array Set. This new product, developed in collaboration with the
Broad Institute of MIT and Harvard, will
allow researchers to increase throughput,
devote more resources toward performing
larger experiments, and analyze more copy
number variation in their studies.
CONTROLS DATABASE
Access 6 billion control genotypes to supplement your data—without spending a
penny more. Over 10 investigators worldwide have agreed to make their 500K
genotyping data—more than 13,000 samples from multiple ethnic backgrounds—
accessible to other scientists.
Watch an Affymetrix UserForum
interview with Stefan Schreiber,
Christian-Albrechts-University,
lead investigator and contributor to
the database, at www.affymetrix.
com/userForum/news/collaborations/schreiber.uf
Analysis has shown that doubling the
number of control genotypes can result in
a 20 percent increase in genetic power
(Figure 3). Also, by accessing these freely
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GENOTYPING
Figure 1: This chart illustrates the influence of sample size on genetic power
for varying percentages of genome
coverage.
Mapping 500K Mapping 500K
Array Set
Array Set
2X Samples
1X Samples
550K Tag
Product
1X Samples
100%
COPY NUMBER AND SNP VARIATION
Analyze SNP and copy number variation
in a single assay. A growing number of
geneticists are studying germ line copy
number variation in their association or
linkage studies. The Mapping 500K Array
Set allows you to identify disease-causing
copy number variation on the same arrays,
with no additional cost. Genotype information, in addition to quantitative copy
number information, allows researchers to
distinguish between copy-neutral events,
such as Uniparental Disomy (UPD).
90%
80%
70%
Genome Coverage
Study Design and Genetic
Power
available data, you may be able to run
fewer controls.
Researchers using the controls database
will be able to select age- and sex-matched
controls from ethnic backgrounds similar
to their cases, and add them to their current study.
60%
50%
40%
30%
20%
10%
0%
Using three marker analysis
Listen to an Affymetrix
Microarray Bulletin symposium with Stanley Nelson,
UCLA, on disease-associated
copy number variation at
www.microarraybulletin.com/
community/article.php?p=134
More resolution provides more power
to detect chromosomal aberrations and
better define boundaries and break
points. The Mapping 500K Array Set
provides a mean resolution of 5.8kb and
Better power
than r2=0.8
Equivalent
power r2=0.8
Worse power
than r2=0.8
a median marker distance of 2.5kb,
giving scientists the highest physical
coverage of the genome for their study.
Affymetrix offers a growing family of
software solutions for copy number
analysis, including standardized thirdparty software providers:
Figure 2: This example power calculation illustrates how more samples impact genetic
power.
Power: Multiplicative Genetic Relative Risk 1.3
1
0.9
Power to detect association at 0.05
Whole-Genome Scan
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
200
300
400
$180k study at
$600 per sample
= 300 samples
500
600
700
800
900 1000 1100 1200 1300 1400 1500
$180k study at
$250 per sample
= 720 samples
Number of cases (for 1:1 case:control study)
· The Affymetrix ® Copy Number
Analysis Tool (CNAT) and the
Affymetrix Integrated Genome
Browser (IGB) are available for download at www.affymetrix.com. CNAT
supports copy number and Loss of
Heterozygosity (LOH) analysis of
Mapping Array data, including 10K,
50K, and 100K. Look for expanded
support for the 500K in late 2006.
· Partek® Genomics Solution™ is the
first commercial software application
available for copy number analysis in
support of Mapping 10K, 100K, and
500K arrays.
· CNAG, from Dr. Seishi Ogawa at the
University of Tokyo, and dChip SNP,
from Dr. Cheng Li at Harvard
University and the Dana Farber
Cancer Institute, are both academic
software tools available for copy number and LOH analysis of Affymetrix
Mapping Arrays, including 10K,
100K, and 500K.
Genotyping Software,
Downstream Analysis, and
Sample Tracking
Affymetrix uses an open informatics platform and partners with a community of
over 25 software development partners, to
provide flexible and innovative genotyping software solutions for researchers in
different laboratory environments, with
different software development resources.
GENECHIP® OPERATING SYSTEM (GCOS)
Affymetrix GeneChip® Operating Software (GCOS) uses a database structure for
storage and management of samples,
sample attributes, associated arrays and
the resulting data. GCOS is an out-ofthe-box software solution for primary data
generation. Using a standard Microsoft
Windows XP workstation, GCOS can
associate sample attributes with the
resulting files. These data are stored in a
lightweight, freely available database.
INPUT DATA AND SAMPLE ATTRIBUTES QUICKLY AND EASILY INTO GCOS
Today, Affymetrix supports a number of
methods to push data into GCOS through
a variety of input data types—from simple
CSV or XML files, to ties to external databases through embedded libraries. Once
the data reside within GCOS, sample
attributes are natively associated with the
resulting files, and samples run on multiple arrays are properly associated.
Researchers can use GCOS as the master
data repository, or use existing methods to
pull data out of GCOS into another data
repository. To learn more about integration
Figure 3: Doubling the number of controls can result in a 20 percent increase in genetic
power.
options, please contact the Affymetrix
Developers’ Network Mailbox: devnet@
affymetrix.com.
GENECHIP GENOTYPING ANALYSIS
SOFTWARE (GTYPE)
Affymetrix GeneChip® Genotyping
Analysis Software (GTYPE) is part of the
GeneChip Mapping Array System, specifically designed to give highly accurate,
automated SNP allele calls for GeneChip
Mapping Arrays. In addition, GTYPE
was developed to enable workflows for a
variety of SNP-related applications, such
as whole-genome association, linkage, and
copy number studies.
GTYPE provides high-quality genotyping, quality control reporting, and
streamlined data analysis for projects
with thousands of samples. GTYPE
integrates with the BRLMM genotyping
algorithm; BRLMM performs multiplechip analysis, fitting probe effects to
increase precision on signal estimates for
the two alleles of each SNP. This is followed by a Bayesian classification
approach to make genotype calls.
Learn more about BRLMM, the genotype calling
algorithm, at www.affymetrix.com/support/technical/product_updates/brlmm_algorithm.affx
Watch a video with Greg Marcus, Affymetrix Sr.
Product Manager, discussing the algorithm
improvements implemented in BRLMM at
www.affymetrix.com/userForum/news/collaborations/marcus.uf
Look at the GTYPE Data Analysis Workflow at
www.affymetrix.com/support/technical/other/gtyp
e_workflow_diagram.pdf
GENECHIP-COMPATIBLE™ SOFTWARE
1.0
IMPACT OF NUMBER OF CONTROLS ON GENETIC POWER
0.6
0.4
0.2
Control: Case=1:1
Control: Case=2:1
Control: Case=3:1
Control: Case=4:1
0.0
Power
0.7
20%
Increase
0.0
0.2
0.4
r2
0.6
0.8
1.0
Over 25 companies have built software
that is integrated with the GeneChip
system. If you tend to “buy” rather than
“build” software, Affymetrix has already
taken the first step to help you qualify your
software vendors. Affymetrix’ GeneChipcompatible™ Application Program features
commercial software vendors that have
integrated their software products to work
cleanly with the Affymetrix platform. The
GeneChip-compatible Software Solutions
Catalog (www.affymetrix.com/products/
software/compatible/snp.affx) provides a
comprehensive list of software packages
both at the level of SNP analysis as well
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as laboratory management. Simply look
for the GeneChip-compatible logo on
any software package that you buy.
GeneChip-compatible providers for
SNP Analysis:
· Golden Helix’ HelixTree® Genetics
An a l y si s So f tw a r e View a recent
GeneChip-compatible™ webcast illustrating a complete analysis workflow
of data from the Mapping 500K Array
Set at www.affymetrix.com/corporate/events/processEventRegistration
Archive.jsp?event=71
· Progeny Software’s Progeny Lab
View a recent webcast illustrating
how Progeny Lab can aid in data
management from the GeneChip
Human Mapping 500K Array Set.
www.affymetrix.com/corporate/events
/processEventRegistrationArchive.jsp
?event=68
· Sapio Sciences’ Exemplar Genotyping
Analysis Suite
· Biocomputing Platforms’ BC/GENE
JMP® Genetics from SAS
The Platform
PERFORM YOUR RESEARCH ON A PROVEN,
STANDARDIZED PLATFORM
The Mapping 500K Array Set is being used
by over 200 investigators worldwide. There
have been nearly 120 scientific publications
in peer-reviewed journals, across multiple
applications based on Affymetrix genotyping
technology—including ground-breaking
association studies in sudden cardiac death
(Arking, et al.), obesity (Christman, et al.)
and macular degeneration (Klein et al).
Read over 120 Peer-reviewed Publications using
the Mapping Assay at www.affymetrix.com/support/technical/other/mapping_publications_august
_2006.pdf
Watch an interview with Johns
Hopkins School of Medicine’s,
Aravinda Chakravarti whose
team has identified a genetic variant associated with electocardiographic QT interval, a trait associated with increased risk of
sudden cardiac death at www.
microarraybulletin.com/community/article.php?p=2
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OBESITY
Watch an interview with Boston
University Medical Center’s Alan
Herbert and Michael Christman
on their discovery of a gene that
predisposes individuals to obesity
at www.microarraybulletin.com/
community/article.php?p=133
The Integrated Genome Browser (IGB, pronounced “ig-bee”) from Affymetrix allows
researchers to visualize genomic data and
annotations from multiple data sources.
IGB enables researchers to integrate genotyping and expression data into a single
view of the genome, on a single platform.
Read an interview with Harvard
University School of Public
Health’s Christoph Lange on algorithm development that enabled
this study at www.microarraybulletin.com/community/article.ph
p?p=206
AFFYMETRIX GENECHIP ® COMMAND
CONSOLE ™
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GENOTYPING
Fine Mapping/Replication
The Custom Genotyping Assay
50,000 CUSTOM SNPS AT YOUR FINGERTIPS
SUDDEN CARDIAC DEATH
INTEGRATE EXPRESSION AND GENOTYPING DATA
Affymetrix has announced the upcoming
release of the next generation of instrument control software—Affymetrix
GeneChip® Command Console™ (AGCC),
which will co-exist with GCOS.
Command Console software will leverage the latest software development
technologies, including web-based user
interfaces, file indexing, and integration via web services. Licenses to
Command Console software will be
freely available to all current
Affymetrix customers. Learn more at:
www.affymetrix.com/userForum/news/new
Products/GC_CommandConsole.uf
tics (IVD) use, providing a standardized
platform for nucleic acid diagnostics.
Additionally, Affymetrix will soon be
the only microarray manufacturer to
offer a CLIA-approved laboratory for
development of clinical assays and samples. Under the Powered by Affymetrix™
program, companies can license technology from Affymetrix to develop innovative microarray products.
The Mapping 500K Array Set is also being
used by many major pharmaceutical companies conducting pharmacogenomics-based
target discovery and clinical development.
Read an interview with Allen Roses, SVP of
Genetics at GlaxoSmithKline, who is conducting
pharmacogenomic studies in multiple steps of drug
discovery and development at www.microarraybulletin.com/community/article.php?p=242.
DIAGNOSTICS
Plan a diagnostic path for your study, and
your business. Affymetrix has the first
and only microarray instrument to be
cleared by the FDA for in vitro diagnos
Until recently, researchers have been
pursuing just a handful of SNPs in the
replication or fine mapping phase of an
association study because there was no
high-throughput, affordable technology
that allowed them to genotype a customized set of SNPs. By applying a
robust replication technology, the initial discovery scan can be maximally
informative.
With Affymetrix Custom Targeted
Genotyping Panels, you no longer need to
let technology limit your study. Using this
system, which is based on Molecular
Inversion Probe Technology, you can genotype up to 50,000 SNPs of your choice,
enabling large-scale fine mapping and
replication studies (Figures 4, 5, and 6).
THE TARGETED GENOTYPING ASSAY
Affymetrix Custom Targeted Genotyping allows you to genotype more of
the SNPs you want. The conversion rate
specification for the assay (the percentage
of working SNPs that make it into the
final assay panel from what was submitted) is greater than 80 percent, and typically greater than 90 percent. This
conversion rate is considerably higher
than other custom SNP genotyping
assays on the market. Guarantees from
other companies about conversion rates
are based on the number of SNPs that
have already passed a bioinformatic
screening step.
JUVENILE DIABETES
Watch an interview with John
Todd, from the JDRF/Wellcome
Trust Diabetes Laboratory at
www.microarraybulletin.com/
community/article.php?p=203
BOVINE TRAITS
Watch an interview with Baylor
College of Medicine’s Richard
Gibbs at www.microarraybulletin.
com/communit y/article.php?
p=213
Figure 5: Affymetrix Targeted Genotyping
Custom Panel Order Process.
An Affymetrix Project Manager is
assigned to assist you with your
custom panel project.
GENOTYPING SERVICES
There is one protocol for all custom assay
panels—from 3,000 to 50,000 SNPs; the
assay leverages routine laboratory techniques, materials, and equipment.
Conversion Rate: >80 percent
Data Completeness: ³97.0 percent
Repeatability: ³99.3 percent
Accuracy: ³99.3
The Custom Genotyping
Platform, Services, and
Throughput
You will be required to submit
your gene list or SNP list by
either CD or email.
A preliminary QC is performed
and the list of SNPs is returned
for customer approval.
Affymetrix will only make your panel when
you are happy that the SNPs you want are
included.
Custom Panel Manufacturing Process
CUSTOM ASSAY SPECIFICATIONS
Researchers can perform targeted genotyping on their existing Affymetrix system
with a simple upgrade, or have a service
provider do the work. Genotyping services
offer researchers a way to complete their
projects quickly—simply send the samples
in and receive data back. Affymetrix can
provide this service, or researchers can work
with one of our expert service providers—
they have years of experience, extensive scientific expertise, and tight process controls.
Affymetrix works with scientists to determine whether an in-house system or a service provider will best meet their needs.
On your approval, Affymetrix will
manufacture your custom panel.
Approximately 8-12 weeks
GET A STREAMLINED WORKFLOW
Custom Panel Design Process
Every Affymetrix Custom Targeted
Genotyping oligo panel undergoes
functional quality checks before it
ever leaves our facility. Additionally,
only Affymetrix Custom Targeted
Genotyping allows you to see raw data
from all four possible genotype calls.
This gives researchers a built-in quality
check for each SNP—you will know a
SNP call has failed if there is too much
background signal. With allele-specific
probes, a researcher will not know that
is the case.
Approximately 2-4 weeks
QUALITY CHECKS EVERY STEP OF THE WAY
Your project manager will keep you
updated with the status of your
custom panel.
Your custom panel product is
delivered.
THROUGHPUT
THE PLATFORM
Buy a standardized platform that’s proven in
the field. The Affymetrix Custom Targeted
Genotyping Assay has already been used to
discover genetic associations in common
diseases such as juvenile diabetes.
The Affymetrix Targeted Genotyping Assay
genotypes up to 50,000 SNPs* in 48 samples
per day (including controls) and 192 samples
per week. That is 2.4 million genotypes/day
(Figure 7). Throughputs can be even higher
by using additional equipment.
Figure 4: Custom Targeted Genotyping combines custom SNP assay panels with
Universal Tag Arrays.
Custom SNP Assays
You can genotype 3,000 to
50,000 SNPs on the same
system and the same type
of assay.
Universal Tag Array
Custom assays don’t require custom arrays. Universal Tag
Arrays contain novel, bioinformatically designed tag
sequences that result in minimal potential for crosshybridization and do not require redesign or recreation of
custom GeneChip arrays.
Custom 3K SNP Kit
Universal 3K Array
Custom 5K SNP Kit
Universal 5K Array
Custom 10K SNP Kit
Universal 10K Array
Custom 20K SNP Kit
Universal 25K Array
Custom 50K SNP Kit*
Universal 70K Array
*50K services only
Custom Genotyping Software
GET HIGHLY ACCURATE GENOTYPE CALLS
The Affymetrix GeneChip ® Targeted
Genotyping Analysis Software (GTGS)
streamlines sample tracking and data
analysis for Custom Targeted Genotyping.
GTGS implements an enhanced genotype calling algorithm that improves the
robustness and quality of genotyping. The
expectation-maximization (E-M) algorithm handles the enormous number of
data points (105-108) that need to be analyzed in a typical targeted genotyping
experiment. It requires no manual intervention at the detailed level of a single call,
sample, or marker. The algorithm performs
data normalization followed by the application of a clustering algorithm for genotype calling. Optional marker filters are
then applied to the clustered data, and per-
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formance metrics, including conversion
rate, call rate, repeatability, data completeness, and Mendelian consistency (if pedigree information is supplied) are reported.
IMPROVE THE QUALITY OF YOUR GENOTYPES BY INSPECTING MORE OF YOUR
DATA AT ONCE
The GTGS software can genotype up to
5,000 samples in one batch. Genotypes for
each marker are determined only after
inspecting the distribution of signal intensities for all samples in the batch.
Inspection of genotypes across samples
improves genotyping quality. Rare alleles,
like those in green, are more easily detected
when more samples can be analyzed at one
time (Figure 8).
Figure 6: The Custom Targeted Genotyping System is based on the Molecular Inversion
Probe Assay.
Assay Panel
3K probes
5K probes
10K probes
20K probes
50K probes
Genomic DNA
WGA DNA
Mix DNA and
assay (SNP) panel
together
Aliquot into four
reactions to be
queried by
different dNTPs
Identify the nucleotide
at each assay locus
(SNP locus) using
Universal Tag Array
Label each
aliquot with a
different color
MAKE QUALITY CONTROL CHECKS MORE
EFFICIENT
Quality control (QC) is streamlined with
GTGS because the software automatically
flags samples or markers that do not pass
quality control criteria. GTGS quality
checks on three levels: for each call individually (signals from all four nucleotides are
measured), at the sample level (is the overall data quality from a single array sufficient?), and at the marker level (is the data
quality for a marker across multiple samples sufficient?). GTGS provides a visualization of each QC step, such as trend charts
to look at QC metrics vs. time, and sample
location, as well as a visual inspection of
each array at each nucleotide channel.
TRACK YOUR SAMPLES FROM START TO
FINISH
The complete custom genotyping assay is
divided into two major steps: pre-amplification and post-amplification. Dedicated laboratory space and computer stations are
recommended for both steps. The GTGS
software allows you to track your samples
from sample plate to GeneChip array
between these laboratory areas.
EXPORT YOUR DATA IN ONE OF MULTIPLE
TEXT-BASED FORMATS
Genotypes are exported as a single file, collating the data across all of your samples
belonging to a single-batch genotyping
operation. The tab-delimited output provides the flexibility to reformat as desired.
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GENOTYPING
Figure 7: Researchers can genotype up to 192 samples per week with Affymetrix Custom
Targeted Genotyping. That’s 2.4 million genotypes per day.
Monday
Tuesday
Wednesday
Thursday
Friday
Anneal 48 Samples
(for Tuesday)
Anneal 48 Samples
(for Wednesday)
Anneal 48 Samples
(for Thursday)
Anneal 48 Samples
(for Friday)
Hyb 48 Samples
(from last Friday
for Tuesday)
Process & Hyb
48 Samples
(for Wednesday)
Process & Hyb
48 Samples
(for Thursday)
Process & Hyb
48 Samples
(for Friday)
Process & Hyb
48 Samples
(for next Monday)
Scan 48 Samples
(from Monday)
Scan 48 Samples
(from Tuesday)
Scan 48 Samples
(from Wednesday)
Scan 48 Samples
(from Thursday)
Per Day:
Per Week:
- 20K Assay Panel
- 46 Samples (48 - 2 Controls)
- 46 Samples x 20,000 Genotypes/Sample
~ 1 Million Genotypes/Day
- 20K Assay Panel
- 192 Samples (does not include controls)
- 192 Samples x 20,000 Genotypes/Sample
~ 3.8 Million Genotypes/Day
Resequencing
The Affymetrix CustomSeq®
Resequencing Program
The Affymetrix CustomSeq® Resequencing
Program enables researchers to design
custom arrays for rapid identification of all SNPs—common, rare, or
non-synonymous—in a specific genomic
region. Complete sequence analysis ensures
the highest probability of finding causative
SNPs, since many causal variants are rare
or heterogeneous in the population.
CustomSeq Arrays provide a highthroughput method of SNP detection by
enabling the analysis of large contiguous
chromosomal regions, or multiple candidate genes, on a single array.
with
an
interview
Read
University of Connecticut’s, Linda
Strausbaugh on array-based resequencing. www.microarraybulletin.com/community/article.
php?p=67
Figure 8: A screen shot of the GeneChip® Targeted Genotyping Analysis Software
(GTGS).
®
EXPERIMENT SUMMARY:
· Sequenced 155 exons from 35 patients
(29,214 bp) from genes associated
with autosomal recessive Retinitis
Pigmentosa (arRP), a condition leading to irreversible blindness or severe
visual impairment, and affecting one
in 3500 individuals worldwide
· Retinitis Pigmentosa shows broad
genetic heterogeneity with at least 32
genes known to be associated with
various forms (autosomal dominant,
autosomal recessive, and X-linked)
BASE CALLING PERFORMANCE
· Average Call Rates=97.60 percent
(individual arrays ranged from 96.0
percent to 98.5 percent)
· Accuracy >99 percent
· Reproducibility >99 percent
SEQUENCE MORE DNA FOR LESS THAN A
TENTH OF A PENNY PER BASE
CustomSeq Arrays enable the analysis of
up to 300,000 bases of double-stranded
sequence (600,000 bases total) on a single
array, providing the most efficient and
cost-effective method for interrogating
large amounts of sequence in a single
experiment.
GET HIGH-QUALITY SEQUENCING DATA IN A
SINGLE PASS
Affymetrix CustomSeq Arrays call greater
than 90 percent of bases at greater than
99.9 percent accuracy and 99.9 percent
reproducibility.
PERFORMANCE ON CEPH SAMPLES
Affymetrix has characterized the performance of the 300kb resequencing
arrays across multiple designs, representing homozygous and heterozygous model
systems. To demonstrate performance for
a typical human region, resequencing
array data and dideoxy sequence data
were collected from 16 diploid CEPH
(Centre d’etude du polymorphisme
humaine) individuals across 115kb of
non-repetitive sequence on Chromosome
4—1.84 mega base pairs (Mb) in total.
While the performance of every customdesigned array depends on the specific
genomic sequence, the overall call rate in
this study was found to be 96.56 percent; overall accuracy was 99.95 percent.
CUSTOMSEQ ARRAY THROUGHPUT
CustomSeq Arrays give you data faster, so
you can find your SNPs faster. CustomSeq
arrays deliver completed sequence in 48
hours with minimal alignment, curation,
or hand editing.
Put your time and money into your
experiments, not your reagents. By leveraging long-range PCR, the number of
amplification reactions required can be
dramatically reduced, decreasing the cost
and time associated with PCR.
Do your resequencing, whole-genome
scanning, and targeted genotyping on one
reliable, integrated Affymetrix system.
CUSTOM RESEQUENCING PUBLICATIONS
Take advantage of a proven, cutting-edge
technology. The publications below highlight the advantages and system performance in two candidate gene studies.
1. Sequencing Arrays for Screening
Multiple Genes Associated with EarlyOnset Human Retinal Degenerations on
a High-Throughput Platform. Mandal
MN, et al . Invest Opthalmol Vis Sci.
46 (9):3355-62(2005).
SNP DETECTION
· 506 sequence changes identified
· Accurately detected 382 previously
reported SNPs and identified 113
novel SNPs
· Accurately detected five previously
reported mutations and identified
seven novel rare mutations
2. A Transforming MET Mutation Discovered in Non-small Cell Lung Cancer Using
Microarrray-based Resequencing. Tengs T.,
et al. Cancer Lett. (2005).
EXPERIMENT SUMMARY:
· Sequenced 164 exons (23,966 bp)
from genes associated with cancer in
20 lung tumor samples with matched
normal controls
· Dideoxy sequencing was performed
on a subset of exons in order to evaluate the performance of the arrays
COMPARISON TO DIDEOXY
SEQUENCING
· Call rate=97.53 percent
· Overall accuracy=99.99 percent
· Only four SNP call errors reported
· Three homozygous SNPs called heterozygous and one heterozygous SNP
called reference
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Functional Tests
Figure 9: Applications for Affymetrix Expression Products.
Functional Testing Through
Expression Analysis
Finding a causal variant or gene is just the
beginning—understanding how that
affects the entire biological system is the
critical next step to ultimately developing
a therapeutic or diagnostic. A new generation of expression microarrays allows you
to examine all aspects of the genome—
exons, introns, and other non-coding regulatory regions—to decipher pathways and
functional effects.
GeneChip® Exon Arrays enable you to
identify expression profiles affected by a
disease-causing variant or gene, including
altered splicing patterns. GeneChip®
Tiling Arrays for ChIP-on-chip analysis
allow you to identify regions of DNA with
which your specific protein interacts—at
the highest resolution, and with the most
complete coverage of the human genome.
Affymetrix 3'IVT Expression Arrays are
the industry standard and have been used
in thousands of studies.
AFFYMETRIX, INC.
AFFYMETRIX UK Ltd
AFFYMETRIX JAPAN K.K.
3420 Central Expressway
Santa Clara, CA 95051 USA
Tel: 1-888-DNA-CHIP (1-888-362-2447)
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www.affymetrix.com Please visit our web site for international distributor contact information.
For research use only. Not for use in diagnostic procedures.
Part No. 702256 Rev. 1
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2006 Affymetrix, Inc. All rights reserved. Affymetrix®,
, GeneChip®, HuSNP®, GenFlex®, Flying Objective™, CustomExpress®, CustomSeq® , NetAffx™, Tools To Take You As Far As Your Vision®, The Way Ahead™, Powered by Affymetrix™,
GeneChip-compatible™, and Command Console™ are trademarks of Affymetrix, Inc. Products may be covered by one or more of the following patents and/or sold under license from Oxford Gene Technology: U.S. Patent Nos.
5,445,934; 5,700,637; 5,744,305; 5,945,334; 6,054,270; 6,140,044; 6,261,776; 6,291,183; 6,346,413; 6,399,365; 6,420,169; 6,551,817; 6,610,482; 6,733,977; and EP 619 321; 373 203 and other U.S. or foreign patents.