WHOLE-GENOME SCANIn this initial step, an unbiased subsetof all SNPs are genotyped on a microar-ray to determine which are statisticallyassociated with a given phenotype—a predisposition to disease, drug response,diagnosis, or prognostic outcome.

FINE MAPPING/REPLICATIONIn this second step, additional SNPs inthe regions identified during the ini-tial whole genome scan are analyzed forstatistical association with the pheno-type. SNPs are re-genotyped in addi-tional sample populations, or in thesame population, to replicate the ini-tial discoveries.

SEQUENCE ANALYSISIn this third step, genomic regions arechosen for detailed sequence analysis toidentify all SNPs in these regions withina particular population. Regions arechosen based on proximity to statisticallysignificant SNPs and, often, functionalannotations. Those SNPs can then be ana-lyzed for statistical association with thephenotype and researchers can ultimatelypinpoint one or more causal variants.

FUNCTIONAL TESTINGIn this final step, researchers look to verifyand explore the association between thecausal variant that has been discoveredand the phenotypic effects.

Solutions for Each Step of anAssociation Study

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Application Note

Association Study

OverviewAffymetrix offers solutions for each step of a typical whole-genome associationstudy—from initial discovery, to replication and fine mapping, sequence analysis,and functional testing of genes. Researchers worldwide are now using these toolsto identify the genetic causes of a wide range of common diseases such as autism,obesity, cancer, asthma, and diabetes.

WHOLE-GENOME SCANScan whole-genome hypothesis free

Products:• GeneChip® Mapping 500K

Array Set

FINE MAPPING/REPLICATIONReduce to candidate region/genes; repeat in another population

Products:• Custom Targeted

Genotyping

SEQUENCE ANALYSISIdentify candidate nucleotide variants

Products:• GeneChip CustomSeq® Arrays

FUNCTIONAL TESTSUnderstand the function

Products:• Gene Expression• Exon Expression• Gene Regulation• Full Transcriptome

Study Design and GeneticPower

LOWER COSTS. MORE SAMPLES. HIGHERGENETIC POWER.

The number of samples genotyped in yourstudy is the single most important factorin powering your whole-genome scan. TheGeneChip® Human Mapping 500K ArraySet reduces genotyping costs to $250 persample,* which allows you to dramaticallyincrease the number of samples you canrun in a single study. More samples trans-late into higher genetic power to detecttrue associations (Figures 1 and 2).*U.S. list price

1,000,000 SNPS IN 2007Use a platform that will grow with yourfuture needs. Affymetrix will introduce a 1million-SNP product by the first quarter of2007. Additionally, by the end of 2006,Affymetrix will begin offering a single-array genotyping product for whole-genome association studies to replace theMapping 500K Array Set. This new prod-uct, developed in collaboration with theBroad Institute of MIT and Harvard, willallow researchers to increase throughput,devote more resources toward performinglarger experiments, and analyze more copynumber variation in their studies.

CONTROLS DATABASEAccess 6 billion control genotypes to sup-plement your data—without spending apenny more. Over 10 investigators world-wide have agreed to make their 500Kgenotyping data—more than 13,000 sam-ples from multiple ethnic backgrounds—accessible to other scientists.

Watch an Affymetrix UserForuminterview with Stefan Schreiber,Christian-Albrechts-University,lead investigator and contributor tothe database, at www.affymetrix.com/userForum/news/collabora-tions/schreiber.uf

Analysis has shown that doubling thenumber of control genotypes can result ina 20 percent increase in genetic power(Figure 3). Also, by accessing these freely

available data, you may be able to runfewer controls.

Researchers using the controls databasewill be able to select age- and sex-matchedcontrols from ethnic backgrounds similarto their cases, and add them to their cur-rent study.

COPY NUMBER AND SNP VARIATIONAnalyze SNP and copy number variationin a single assay. A growing number ofgeneticists are studying germ line copynumber variation in their association orlinkage studies. The Mapping 500K ArraySet allows you to identify disease-causingcopy number variation on the same arrays,with no additional cost. Genotype infor-mation, in addition to quantitative copynumber information, allows researchers todistinguish between copy-neutral events,such as Uniparental Disomy (UPD).

Listen to an AffymetrixMicroarray Bulletin sympo-sium with Stanley Nelson,UCLA, on disease-associatedcopy number variation atwww.microarraybulletin.com/community/article.php?p=134

More resolution provides more powerto detect chromosomal aberrations andbetter define boundaries and breakpoints. The Mapping 500K Array Setprovides a mean resolution of 5.8kb and

a median marker distance of 2.5kb,giving scientists the highest physicalcoverage of the genome for their study.

Affymetrix offers a growing family ofsoftware solutions for copy numberanalysis, including standardized third-party software providers:

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Better powerthan r2=0.8

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$180k study at $250 per sample = 720 samples

$180k study at $600 per sample = 300 samples

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Figure 2: This example power calculation illustrates how more samples impact geneticpower.

Whole-Genome Scan

• The Affymetrix® Copy NumberAnalysis Tool (CNAT) and theAffymetrix Integrated GenomeBrowser (IGB) are available for down-load at www.affymetrix.com. CNATsupports copy number and Loss ofHeterozygosity (LOH) analysis ofMapping Array data, including 10K,50K, and 100K. Look for expandedsupport for the 500K in late 2006.

• Partek® Genomics Solution™ is thefirst commercial software applicationavailable for copy number analysis insupport of Mapping 10K, 100K, and500K arrays.

• CNAG, from Dr. Seishi Ogawa at theUniversity of Tokyo, and dChip SNP,from Dr. Cheng Li at HarvardUniversity and the Dana FarberCancer Institute, are both academicsoftware tools available for copy num-ber and LOH analysis of AffymetrixMapping Arrays, including 10K,100K, and 500K.

Genotyping Software,Downstream Analysis, andSample Tracking

Affymetrix uses an open informatics plat-form and partners with a community ofover 25 software development partners, to

provide flexible and innovative genotyp-ing software solutions for researchers indifferent laboratory environments, withdifferent software development resources.

GENECHIP® OPERATING SYSTEM (GCOS)Affymetrix GeneChip® Operating Soft-ware (GCOS) uses a database structure forstorage and management of samples,sample attributes, associated arrays andthe resulting data. GCOS is an out-of-the-box software solution for primary datageneration. Using a standard MicrosoftWindows XP workstation, GCOS canassociate sample attributes with theresulting files. These data are stored in alightweight, freely available database.

INPUT DATA AND SAMPLE ATTRIBUTES QUICK-LY AND EASILY INTO GCOSToday, Affymetrix supports a number ofmethods to push data into GCOS througha variety of input data types—from simpleCSV or XML files, to ties to external data-bases through embedded libraries. Oncethe data reside within GCOS, sampleattributes are natively associated with theresulting files, and samples run on multi-ple arrays are properly associated.Researchers can use GCOS as the masterdata repository, or use existing methods topull data out of GCOS into another datarepository. To learn more about integration

options, please contact the AffymetrixDevelopers’ Network Mailbox: devnet@affymetrix.com.

GENECHIP GENOTYPING ANALYSISSOFTWARE (GTYPE)Affymetrix GeneChip® GenotypingAnalysis Software (GTYPE) is part of theGeneChip Mapping Array System, specif-ically designed to give highly accurate,automated SNP allele calls for GeneChipMapping Arrays. In addition, GTYPEwas developed to enable workflows for avariety of SNP-related applications, suchas whole-genome association, linkage, andcopy number studies.

GTYPE provides high-quality geno-typing, quality control reporting, andstreamlined data analysis for projectswith thousands of samples. GTYPEintegrates with the BRLMM genotypingalgorithm; BRLMM performs multiple-chip analysis, fitting probe effects toincrease precision on signal estimates forthe two alleles of each SNP. This is fol-lowed by a Bayesian classificationapproach to make genotype calls.

Learn more about BRLMM, the genotype callingalgorithm, at www.affymetrix.com/support/techni-cal/product_updates/brlmm_algorithm.affx

Watch a video with Greg Marcus, Affymetrix Sr.Product Manager, discussing the algorithmimprovements implemented in BRLMM atwww.affymetrix.com/userForum/news/collabora-tions/marcus.uf

Look at the GTYPE Data Analysis Workflow atwww.affymetrix.com/support/technical/other/gtype_workflow_diagram.pdf

GENECHIP-COMPATIBLE™™ SOFTWARE

Over 25 companies have built softwarethat is integrated with the GeneChipsystem. If you tend to “buy” rather than“build” software, Affymetrix has alreadytaken the first step to help you qualify yoursoftware vendors. Affymetrix’ GeneChip-compatible™ Application Program featurescommercial software vendors that haveintegrated their software products to workcleanly with the Affymetrix platform. TheGeneChip-compatible Software SolutionsCatalog (www.affymetrix.com/products/software/compatible/snp.affx) provides acomprehensive list of software packagesboth at the level of SNP analysis as well

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Figure 3: Doubling the number of controls can result in a 20 percent increase in geneticpower.

as laboratory management. Simply lookfor the GeneChip-compatible logo onany software package that you buy.

GeneChip-compatible providers forSNP Analysis:

• GGoollddeenn HHeelliixx’’ HHeelliixxTTrreeee®® GGeenneettiiccssAAnnaallyyssiiss SSooffttwwaarree View a recentGeneChip-compatible™ webcast illus-trating a complete analysis workflowof data from the Mapping 500K ArraySet at www.affymetrix.com/corpo-rate/events/processEventRegistrationArchive.jsp?event=71

• PPrrooggeennyy SSooffttwwaarree’’ss PPrrooggeennyy LLaabbView a recent webcast illustratinghow Progeny Lab can aid in datamanagement from the GeneChipHuman Mapping 500K Array Set.www.affymetrix.com/corporate/events/processEventRegistrationArchive.jsp?event=68

• SSaappiioo SScciieenncceess’’ EExxeemmppllaarr GGeennoottyyppiinnggAAnnaallyyssiiss SSuuiittee

• BBiiooccoommppuuttiinngg PPllaattffoorrmmss’’ BBCC//GGEENNEEJJMMPP®® GGeenneettiiccss ffrroomm SSAASS

INTEGRATE EXPRESSION AND GENOTYP-ING DATA

The Integrated Genome Browser (IGB, pro-nounced “ig-bee”) from Affymetrix allowsresearchers to visualize genomic data andannotations from multiple data sources.IGB enables researchers to integrate geno-typing and expression data into a singleview of the genome, on a single platform.

AFFYMETRIX GENECHIP® COMMANDCONSOLE™

Affymetrix has announced the upcomingrelease of the next generation of instru-ment control software—AffymetrixGeneChip® Command Console™ (AGCC),which will co-exist with GCOS.Command Console software will lever-age the latest software developmenttechnologies, including web-based userinterfaces, file indexing, and integra-tion via web services. Licenses toCommand Console software will befreely available to all currentAffymetrix customers. Learn more at:www.affymetrix.com/userForum/news/newProducts/GC_CommandConsole.uf

The Platform

PERFORM YOUR RESEARCH ON A PROVEN,STANDARDIZED PLATFORM

The Mapping 500K Array Set is being usedby over 200 investigators worldwide. Therehave been nearly 120 scientific publicationsin peer-reviewed journals, across multipleapplications based on Affymetrix genotypingtechnology—including ground-breakingassociation studies in sudden cardiac death(Arking, et al.), obesity (Christman, et al.)and macular degeneration (Klein et al).

Read over 120 Peer-reviewed Publications usingthe Mapping Assay at www.affymetrix.com/sup-port/technical/other/mapping_publications_august_2006.pdf

SUDDEN CARDIAC DEATH

Watch an interview with JohnsHopkins School of Medicine’s,Aravinda Chakravarti whoseteam has identified a genetic vari-ant associated with electocardio-graphic QT interval, a trait asso-ciated with increased risk ofsudden cardiac death at www.

microarraybulletin.com/community/article.php?p=241

OBESITY

Watch an interview with BostonUniversity Medical Center’s AlanHerbert and Michael Christmanon their discovery of a gene thatpredisposes individuals to obesityat www.microarraybulletin.com/community/article.php?p=133

Read an interview with HarvardUniversity School of PublicHealth’s Christoph Lange on algo-rithm development that enabledthis study at www.microarraybul-letin.com/community/article.php?p=206

The Mapping 500K Array Set is also beingused by many major pharmaceutical compa-nies conducting pharmacogenomics-basedtarget discovery and clinical development.

Read an interview with Allen Roses, SVP ofGenetics at GlaxoSmithKline, who is conductingpharmacogenomic studies in multiple steps of drugdiscovery and development at www.microarraybul-letin.com/community/article.php?p=242.

DIAGNOSTICS

Plan a diagnostic path for your study, andyour business. Affymetrix has the firstand only microarray instrument to becleared by the FDA for in vitro diagnos

tics (IVD) use, providing a standardizedplatform for nucleic acid diagnostics.Additionally, Affymetrix will soon bethe only microarray manufacturer tooffer a CLIA-approved laboratory fordevelopment of clinical assays and sam-ples. Under the Powered by Affymetrix™

program, companies can license technol-ogy from Affymetrix to develop innova-tive microarray products.

The Custom Genotyping Assay

50,000 CUSTOM SNPS AT YOUR FINGERTIPSUntil recently, researchers have beenpursuing just a handful of SNPs in thereplication or fine mapping phase of anassociation study because there was nohigh-throughput, affordable technologythat allowed them to genotype a cus-tomized set of SNPs. By applying arobust replication technology, the ini-tial discovery scan can be maximallyinformative.

With Affymetrix Custom TargetedGenotyping Panels, you no longer need tolet technology limit your study. Using thissystem, which is based on MolecularInversion Probe Technology, you can geno-type up to 50,000 SNPs of your choice,enabling large-scale fine mapping andreplication studies (Figures 4, 5, and 6).

THE TARGETED GENOTYPING ASSAYAffymetrix Custom Targeted Geno-typing allows you to genotype more ofthe SNPs you want. The conversion ratespecification for the assay (the percentageof working SNPs that make it into thefinal assay panel from what was submit-ted) is greater than 80 percent, and typi-cally greater than 90 percent. Thisconversion rate is considerably higherthan other custom SNP genotypingassays on the market. Guarantees fromother companies about conversion ratesare based on the number of SNPs thathave already passed a bioinformaticscreening step.

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Fine Mapping/Replication

QUALITY CHECKS EVERY STEP OF THE WAY Every Affymetrix Custom TargetedGenotyping oligo panel undergoesfunctional quality checks before itever leaves our facility. Additionally,only Affymetrix Custom TargetedGenotyping allows you to see raw datafrom all four possible genotype calls.This gives researchers a built-in qualitycheck for each SNP—you will know aSNP call has failed if there is too muchbackground signal. With allele-specificprobes, a researcher will not know thatis the case.

GET A STREAMLINED WORKFLOW There is one protocol for all custom assaypanels—from 3,000 to 50,000 SNPs; theassay leverages routine laboratory tech-niques, materials, and equipment.

CUSTOM ASSAY SPECIFICATIONS

Conversion Rate: >80 percentData Completeness: ≥97.0 percentRepeatability: ≥99.3 percentAccuracy: ≥99.3

The Custom GenotypingPlatform, Services, andThroughput

THE PLATFORM

Buy a standardized platform that’s proven inthe field. The Affymetrix Custom TargetedGenotyping Assay has already been used todiscover genetic associations in commondiseases such as juvenile diabetes.

JUVENILE DIABETES

Watch an interview with JohnTodd, from the JDRF/WellcomeTrust Diabetes Laboratory atwww.microarraybulletin.com/community/article.php?p=203

BOVINE TRAITS

Watch an interview with BaylorCollege of Medicine’s RichardGibbs at www.microarraybulletin.com/community/article.php?p=213

GENOTYPING SERVICES

Researchers can perform targeted genotyp-ing on their existing Affymetrix systemwith a simple upgrade, or have a serviceprovider do the work. Genotyping servicesoffer researchers a way to complete theirprojects quickly—simply send the samplesin and receive data back. Affymetrix canprovide this service, or researchers can workwith one of our expert service providers—they have years of experience, extensive sci-entific expertise, and tight process controls.Affymetrix works with scientists to deter-mine whether an in-house system or a serv-ice provider will best meet their needs.

THROUGHPUT

The Affymetrix Targeted Genotyping Assaygenotypes up to 50,000 SNPs* in 48 samplesper day (including controls) and 192 samplesper week. That is 2.4 million genotypes/day(Figure 7). Throughputs can be even higher

by using additional equipment.

Custom Genotyping Software

GET HIGHLY ACCURATE GENOTYPE CALLS

The Affymetrix GeneChip® TargetedGenotyping Analysis Software (GTGS)streamlines sample tracking and dataanalysis for Custom Targeted Genotyping.

GTGS implements an enhanced geno-type calling algorithm that improves therobustness and quality of genotyping. Theexpectation-maximization (E-M) algo-rithm handles the enormous number ofdata points (105-108) that need to be ana-lyzed in a typical targeted genotypingexperiment. It requires no manual inter-vention at the detailed level of a single call,sample, or marker. The algorithm performsdata normalization followed by the appli-cation of a clustering algorithm for geno-type calling. Optional marker filters arethen applied to the clustered data, and per-

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Universal 70K Array*50K services only

Universal 25K Array

Universal 10K Array

Universal 5K Array

Custom 50K SNP Kit*

Custom 20K SNP Kit

Custom 10K SNP Kit

Custom 5K SNP Kit

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 cross-hybridization and do not require redesign or recreation of custom GeneChip arrays.

Universal 3K ArrayCustom 3K SNP Kit

Figure 4: Custom Targeted Genotyping combines custom SNP assay panels withUniversal Tag Arrays.

An Affymetrix Project Manager is assigned to assist you with your custom panel project.

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.

On your approval, Affymetrix will manufacture your custom panel.

Your project manager will keep you updated with the status of your custom panel.

Your custom panel product is delivered.

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Figure 5: Affymetrix Targeted GenotypingCustom Panel Order Process.

formance metrics, including conversionrate, call rate, repeatability, data complete-ness, and Mendelian consistency (if pedi-gree information is supplied) are reported.

IMPROVE THE QUALITY OF YOUR GENO-TYPES BY INSPECTING MORE OF YOURDATA AT ONCEThe GTGS software can genotype up to5,000 samples in one batch. Genotypes foreach marker are determined only afterinspecting the distribution of signal inten-sities for all samples in the batch.Inspection of genotypes across samplesimproves genotyping quality. Rare alleles,like those in green, are more easily detectedwhen more samples can be analyzed at onetime (Figure 8).

MAKE QUALITY CONTROL CHECKS MOREEFFICIENTQuality control (QC) is streamlined withGTGS because the software automaticallyflags samples or markers that do not passquality control criteria. GTGS qualitychecks on three levels: for each call individ-ually (signals from all four nucleotides aremeasured), at the sample level (is the over-all data quality from a single array suffi-cient?), and at the marker level (is the dataquality for a marker across multiple sam-ples sufficient?). GTGS provides a visuali-zation of each QC step, such as trend chartsto look at QC metrics vs. time, and samplelocation, as well as a visual inspection ofeach array at each nucleotide channel.

TRACK YOUR SAMPLES FROM START TOFINISHThe complete custom genotyping assay isdivided into two major steps: pre-amplifica-tion and post-amplification. Dedicated labo-ratory space and computer stations arerecommended for both steps. The GTGSsoftware allows you to track your samplesfrom sample plate to GeneChip arraybetween these laboratory areas.

EXPORT YOUR DATA IN ONE OF MULTIPLETEXT-BASED FORMATSGenotypes are exported as a single file, col-lating the data across all of your samplesbelonging to a single-batch genotypingoperation. The tab-delimited output pro-vides the flexibility to reformat as desired.

The Affymetrix CustomSeq®

Resequencing Program

The Affymetrix CustomSeq® ResequencingProgram enables researchers to designcustom arrays for rapid identi f ica-t ion of a l l SNPs—common, rare, ornon-synonymous—in a specific genomicregion. Complete sequence analysis ensuresthe highest probability of finding causative

SNPs, since many causal variants are rareor heterogeneous in the population.CustomSeq Arrays provide a high-throughput method of SNP detection byenabling the analysis of large contiguouschromosomal regions, or multiple candi-date genes, on a single array.

Read an interview withUniversity of Connecticut’s, LindaStrausbaugh on array-based re-sequencing. www.microarraybul-letin.com/community/article.php?p=67

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Monday Tuesday Wednesday Thursday Friday

Per Day:- 20K Assay Panel- 46 Samples (48 - 2 Controls)- 46 Samples x 20,000 Genotypes/Sample~ 1 Million Genotypes/Day

Per Week:- 20K Assay Panel- 192 Samples (does not include controls)- 192 Samples x 20,000 Genotypes/Sample~ 3.8 Million Genotypes/Day

Scan 48 Samples(from Monday)

Scan 48 Samples(from Tuesday)

Scan 48 Samples(from Wednesday)

Scan 48 Samples(from Thursday)

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)

Anneal 48 Samples(for Tuesday)

Anneal 48 Samples(for Wednesday)

Anneal 48 Samples(for Thursday)

Anneal 48 Samples(for Friday)

Figure 7: Researchers can genotype up to 192 samples per week with Affymetrix CustomTargeted Genotyping. That’s 2.4 million genotypes per day.

Resequencing

Genomic DNA

Mix DNA andassay (SNP) panel

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queried by different dNTPs

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Identify the nucleotide at each assay locus (SNP locus) using

Universal Tag Array

WGA DNA

Assay Panel3K probes5K probes10K probes20K probes50K probes

Figure 6: The Custom Targeted Genotyping System is based on the Molecular InversionProbe Assay.

SEQUENCE MORE DNA FOR LESS THAN ATENTH OF A PENNY PER BASE

CustomSeq Arrays enable the analysis ofup to 300,000 bases of double-strandedsequence (600,000 bases total) on a singlearray, providing the most efficient andcost-effective method for interrogatinglarge amounts of sequence in a singleexperiment.

GET HIGH-QUALITY SEQUENCING DATA IN ASINGLE PASSAffymetrix CustomSeq Arrays call greaterthan 90 percent of bases at greater than99.9 percent accuracy and 99.9 percentreproducibility.

PERFORMANCE ON CEPH SAMPLESAffymetrix has characterized the per-formance of the 300kb resequencingarrays across multiple designs, represent-ing homozygous and heterozygous modelsystems. To demonstrate performance fora typical human region, resequencingarray data and dideoxy sequence datawere collected from 16 diploid CEPH(Centre d’etude du polymorphismehumaine) individuals across 115kb ofnon-repetitive sequence on Chromosome4—1.84 mega base pairs (Mb) in total.While the performance of every custom-designed array depends on the specific

genomic sequence, the overall call rate inthis study was found to be 96.56 per-cent; overall accuracy was 99.95 percent.

CUSTOMSEQ ARRAY THROUGHPUTCustomSeq Arrays give you data faster, soyou can find your SNPs faster. CustomSeqarrays deliver completed sequence in 48hours with minimal alignment, curation,or hand editing.

Put your time and money into yourexperiments, not your reagents. By lever-aging long-range PCR, the number ofamplification reactions required can bedramatically reduced, decreasing the costand time associated with PCR.

Do your resequencing, whole-genomescanning, and targeted genotyping on onereliable, integrated Affymetrix system.

CUSTOM RESEQUENCING PUBLICATIONSTake advantage of a proven, cutting-edgetechnology. The publications below high-light the advantages and system perform-ance in two candidate gene studies.

1. Sequencing Arrays for ScreeningMultiple Genes Associated with Early-Onset Human Retinal Degenerations ona High-Throughput Platform. MandalMN, et al. Invest Opthalmol Vis Sci.4466(9):3355-62(2005).

EXPERIMENT SUMMARY:• Sequenced 155 exons from 35 patients

(29,214 bp) from genes associatedwith autosomal recessive RetinitisPigmentosa (arRP), a condition lead-ing to irreversible blindness or severevisual impairment, and affecting onein 3500 individuals worldwide

• Retinitis Pigmentosa shows broadgenetic heterogeneity with at least 32genes known to be associated withvarious forms (autosomal dominant,autosomal recessive, and X-linked)

BASE CALLING PERFORMANCE• Average Call Rates=97.60 percent

(individual arrays ranged from 96.0percent to 98.5 percent)

• Accuracy >99 percent• Reproducibility >99 percent

SNP DETECTION• 506 sequence changes identified• Accurately detected 382 previously

reported SNPs and identified 113novel SNPs

• Accurately detected five previouslyreported mutations and identifiedseven novel rare mutations

2. A Transforming MET Mutation Discov-ered in Non-small Cell Lung Cancer UsingMicroarrray-based Resequencing. Tengs T.,et al. Cancer Lett. (2005).

EXPERIMENT SUMMARY:• Sequenced 164 exons (23,966 bp)

from genes associated with cancer in20 lung tumor samples with matchednormal controls

• Dideoxy sequencing was performedon a subset of exons in order to eval-uate the performance of the arrays

COMPARISON TO DIDEOXYSEQUENCING• Call rate=97.53 percent• Overall accuracy=99.99 percent• Only four SNP call errors reported• Three homozygous SNPs called het-

erozygous and one heterozygous SNPcalled reference

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Figure 8: A screen shot of the GeneChip®® Targeted Genotyping Analysis Software(GTGS).

Figure 9: Applications for Affymetrix Expression Products.

Part No. 702256 Rev. 1©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.

AFFYMETRIX UK Ltd

Voyager, Mercury Park,Wycombe Lane, Wooburn Green,High Wycombe HP10 0HHUnited KingdomUK and Others Tel: +44 (0) 1628 552550France Tel: 0800919505Germany Tel: 01803001334Fax: +44 (0) 1628 552585saleseurope@affymetrix.comsupporteurope@affymetrix.com

AFFYMETRIX, INC.

3420 Central ExpresswaySanta Clara, CA 95051 USATel: 1-888-DNA-CHIP (1-888-362-2447)Fax: 1-408-731-5441sales@affymetrix.comsupport@affymetrix.com

AFFYMETRIX JAPAN K.K.

Mita NN Bldg., 16 F 4-1-23 Shiba, Minato-ku, Tokyo 108-0014 Japan Tel: +81-(0)3-5730-8200 Fax: +81-(0)3-5730-8201 salesjapan@affymetrix.com supportjapan@affymetrix.com

www.affymetrix.com Please visit our web site for international distributor contact information.

For research use only. Not for use in diagnostic procedures.

Functional Testing ThroughExpression Analysis

Finding a causal variant or gene is just thebeginning—understanding how thataffects the entire biological system is thecritical next step to ultimately developinga therapeutic or diagnostic. A new genera-tion of expression microarrays allows youto examine all aspects of the genome—exons, introns, and other non-coding regu-latory regions—to decipher pathways andfunctional effects.

GeneChip® Exon Arrays enable you toidentify expression profiles affected by adisease-causing variant or gene, includingaltered splicing patterns. GeneChip®Tiling Arrays for ChIP-on-chip analysisallow you to identify regions of DNA withwhich your specific protein interacts—atthe highest resolution, and with the mostcomplete coverage of the human genome.Affymetrix 3'IVT Expression Arrays arethe industry standard and have been usedin thousands of studies.

Functional Tests