Sequencing / DNA Sequencing

The Genome Analyzer system's powerful combination of read-length and paired-end flexibility enables the broadest range of genomic sequencing applications. Illumina's robust sequencing chemistry supports a wide range of read lengths, allowing researchers to tailor each run to meet their needs.

Industry-leading raw read accuracy at 100+ bp single-reads, short- and long-insert paired-end reads enable whole-genome sequencing and resequencing, SNP discovery, identification of copy number variations, chromosomal rearrangements and the following:

De Novo Sequencing

  • Paired Reads - Generate long scaffolds and highly accurate contigs using multiple insert lengths with high library diversity.
  • Read Length - Use paired-end reads in excess of 2 x 100 bases for mammalian-scale de novo assembly.
  • Raw-Read Accuracy - Access the highest yield of perfect reads and Q35 data to generate long, error-free contigs.
  • Assembly Tools - Leverage a rapidly growing number of assemblers optimized for Genome Analyzer reads, such as Velvet, EULER-SR, and SSAKE.

Targeted Resequencing

The Genome Analyzer requires minimal sample input, allowing the sequencing of limited archival tissues, embryoid bodies, small model systems, and difficult-to-cultivate organisms. Targeted genomic regions can be isolated by a series of long PCR reactions or by hybridization-based approaches using oligonucleotide arrays.

Sequencing / Transcriptome Analysis

Explore the transcriptome like never before. Characterize all transcriptional activity, coding and non-coding, in any organism without a priori assumptions using the Genome Analyzer and achieve an unprecedented view of the transcriptome. 

Illumina's unique combination of long and short reads, strand specificity, and millions of counts allows you to annotate coding SNPs, discover transcript isoforms, identify regulatory RNAs, characterize splice junctions, and determine the relative abundance of transcripts.

Generate transcript profiles in a single day with the greatest daily system output. Align RNA sequencing reads across splice junctions and map to reference genomes. Identify and quantify both rare and common transcripts, with six orders of magnitude of dynamic range. Reveal the hidden world of non-coding RNA architecture without prior information.

Fully Supported Transcriptome Analysis Applications

  • mRNA-Seq: Identify and quantify full-length poly-A transcript isoforms
  • Tag Profiling: Sequence short 3' transcript fragments to quantify known and novel transcripts from any eukaryotic species
  • Small RNA Discovery and Analysis: Discover rare small RNA without previous sequence or secondary structure information in any organism; generate strand-specific reads with mRNA samples
LEARN MORE

Sequencing / Gene Regulation Analysis

Get a complete view of the epigenome at single-base resolution with the Genome Analyzer. Whether you are interested in CpG methylation, histone modifications, chromatin structure, or DNA-protein interactions, Illumina's unique sequencing chemistry gives you unbiased coverage of every base in the genome.

Use Illumina's ChIP-Seq protocol to generate accurate and precise DNA-protein interaction maps from a single chromatin immunoprecipitated sample. Map genome-wide methylation patterns by sequencing bisulfite-converted DNA, methylation-sensitive restriction digest-enriched fragments, anti-methyl-C precipitated fragments, or chromatin immunoprecipitates of methyltransferases trapped to aza-labeled DNA.

Learn more about ChIP-Seq and view publications demonstrating how researchers are using Genome Analyzer system to explore and characterize gene regulation and control.

Highlights

  • High Sequencing Accuracy: Achieve true base-by-base sequencing even through homopolymers created by bisulfite conversion

  • High Sensitivity: Identify a broad range of protein-DNA interactions with confidence, and use millions of counts to differentiate real events from spurious signal

  • Single-Site Resolution: Detect variations in methylation signatures at single-base resolution; pinpoint rare binding events to within 50 bases of the actual binding site

  • Mapping Accuracy: Correctly map more reads to the epigenome using accurate 100+ bp paired-end reads

SNP Genotyping and CNV Analysis / SNP Discovery and Structural Variation Analysis

Single nucleotide polymorphisms (SNPs) and structural variants are at the root of genetic variation among individuals and populations. This variation influences how individuals differ in their risk of disease and their response to therapeutic treatments.  SNPs and structural variants are discovered within the genome by comparing multiple genomic sequences from a diverse sample set of individuals. Illumina's industry-leading sequencing technology provides the sample throughput level and high-quality data required for accurate SNP discovery and structural variation analysis studies.


SNP Discovery and Structural Variation Analysis on the Genome Analyzer

Illumina's Genome Analyzer generates the highest quality data available to analyze any genome for any species, and every genetic variant. A flexible, convenient workflow allows you to combine both short-insert paired-end and long-insert mate pair libraries to create an optimal level of detail and accuracy for any study. Go rapidly from DNA to data with minimal hands-on effort to produce meaningful results, reliably and efficiently.

SNP Discovery and Genotyping

SNP discovery studies provide valuable allelic variation information that can be translated into content for genotyping experiments on BeadArray products. SNP discovery is at the heart of large world-wide collaborative studies like the HapMap Project and the 1000 Genomes Project, which aim to comprehensively catalog human genetic variation. The data generated by these cutting-edge studies is an important source of content for Illumina's broad portfolio of whole-genome genotyping BeadArray products. While the majority of SNP discovery studies and array-based products focus on human genetics, Illumina sequencing allows customized genotyping products to be created for any species of interest through the iSelect program.

SNP Genotyping and CNV Analysis / Custom Genotyping

For researchers who want to study focused genomic regions of interest, or are interested in organisms for which there are no standard products, Illumina offers a broad range of custom genotyping options.  Customized iSelect BeadChips can be easily developed to fit any experimental design, allowing customers to select the ideal solution for their loci multiplexing and sample throughput requirements. Convenient online tools and Illumina representatives are available to help you design and select your markers of interest, and choose the assay and customized products to best suit your research goals.


iSelect HD Custom Genotyping

The iSelect HD Custom Genotyping program enables easy, versatile design of custom arrays to investigate markers targeting:

  • Any species, with the flexibility of assaying virtually any marker in the genome
  • Disease or pathway specific markers
  • Rare variants, CNVs, and much more

Illumina's fully custom genotyping platform offers all of the benefits of standard Infinium products, including industry-leading data quality and call rates, streamlined workflow, and rational SNP selection with access to the entire genome of any species.

iSelect HD Custom BeadChips

Access the enhanced multiplexing capabilities of the Infinium HD Assay deployed on either the 12-sample format (60,801 to 200,000 attempted bead types), or the 24-sample format (3,000 to 68,000 attempted bead types). For array customization in human studies, add up to 60,800 markers to the standard whole-genome SNP genotyping and CNV content available on the semi-custom Human1M-Duo+ and HumanHap550-Quad+ BeadChips or up to 200,000 markers on the HumanOmniExpress+. 

SNP Genotyping and CNV Analysis / Focused Genotyping

Focused genotyping supports a variety of applications such as candidate-gene studies in cancer, cardiovascular disease, and admixture mapping. Illumina also works closely with major animal consortia to develop genome-wide genotyping products for non-human organisms, including both animal and plant species.


Infinium Focused Content

For focused content, Infinium BeadChips feature the same design as the whole-genome Infinium DNA Analysis BeadChips and are powered by our proven, PCR-free Infinium Assay. A number standard focused content Infinium BeadChips are available, or have the option to design your own high-density focused content panel.

Infinium BeadChips

Goldengate Focused Content

Illumina offers variety of standard GoldenGate focused content panels and the option to design your own GoldenGate Custom Panel for a wide range of genomes and experimental strategies. GoldenGate panels can be deployed on 32-, 16-, and 12-sample Universal BeadChips or the 96-sample Universal Array Matrix.

GoldenGate BeadChips

SNP Genotyping and CNV Analysis / Cytogenetic Analysis

Structural variability is a substantial source of genetic varia­tion that has a major influence on phenotypic variation. Cytogenetic analysis allows researchers to profile chromosomal aberrations such as amplifications, deletions, rearrangements, point mutations, copy number changes, and copy-neutral loss of heterozygosity (LOH) events.


Illumina offers a broad portfolio of genome-wide analysis BeadChips that enable researchers to analyze structural variation at varying levels of detail, from routine cytogenetic screening to sample profiling with up to 1.2 million markers.

Complete Genome-wide Coverage in Multi-Sample Array Formats

Illumina's revolutionary Infinium HD technology allows for the selection of any SNP or probe, enabling dense, uniform coverage across the genome and the ability to target any genomic region. From 300,000 markers on the HumanCytoSNP-12 BeadChip to over 1.1 million markers per sample on the HumanOmni-1 Quad, Infinium HD BeadChips support high-resolution copy number and LOH analysis with median marker spacing as low as 1kb.

Higher Resolution

The Infinium Assay simultaneously measures intensity differences and allelic ratios, enabling the profiling of intercellular mosaicism and copy-neutral LOH events such as uniparental disomy (UPD), mitotic recombination, or gene conversion events, all of which cannot be detected on array-CGH platforms.

Simplified Analysis

Analysis of Infinium HD BeadChip data is supported by Illumina's BeadStudio Genotyping Module and the standalone KaryoStudio data analysis software package, which was specifically designed by and for molecular cytogeneticists. In addition, through the illumina•connect program, Illumina data can be analyzed using common cytogenetics analysis programs.

Cytogenetic Analysis BeadChips

SNP Genotyping and CNV Analysis / Linkage Analysis

Linkage analysis provides researchers a powerful method for mapping the location of disease-causing loci by identifying genetic markers that are co-inherited with a phenotype of interest.  Illumina's linkage analysis BeadChips present the optimal solution for identifying regions of statistically unequivocal linkage by delivering the information content, call rates, and accuracy that enable discovery of links between familial genotype and phenotype in both monogenic and polygenic disorders.


Human Linkage Analysis

Available with the GoldenGate Assay, the HumanLinkage V Panel Set is optimized to detect recombination events. Linkage analysis is a powerful approach for mapping the location of disease-causing loci. The 6,056 HumanLinkage V Panel SNP markers were chosen from highly validated HapMap DNA assays to optimize information content, enabling researchers to extract the greatest amount of data from the least number of markers.

Mouse Linkage Analysis

For mouse genetics applications, two Mouse Linkage Panels — Mouse Low Density (LD) Linkage and Mouse Medium Density (MD) Linkage — are available. Both single nucleotide polymorphism (SNP) panels offer a low-cost, efficient method for attaining genome-wide genetic data to identify quantitative trait loci (QTLs), map candidate genes, and increase genotyping throughput. SNP sequences are optimized for Illumina's proven

SNP Genotyping and CNV Analysis / Whole-Genome Genotyping and Copy Number Variation Analysis

Genome-wide association studies (GWAS) map genetic variation across human populations to identify variants associated with human disease.  Infinium HD BeadChips offer GWAS researchers the flexibility to profile samples with 300,000 to 1.2 million markers in high-throughput format, and deliver dense genome-wide coverage with the most up-to-date content available from the scientific community. Strategically selected probes provide sensitive copy number variation analysis and target high-value regions of the genome associated with disease.

Illumina GWAS Roadmap

The Omni family of microarrays will soon allow researchers to assay up to 5 million markers per sample, including comprehensive coverage of both common and rare variants identified by 1000 Genomes Project. As novel SNP sets are released into the public database, researchers using Omni products will have exclusive access to supplemental arrays that build up to the full 5 million variants.

LEARN MORE

Infinium HD Technology

Illumina's revolutionary Infinium HD technology allows for the rational selection of any SNP or probe, enabling dense, uniform coverage across the genome and the ability to target any genomic region. Infinium BeadChips feature strategically selected tag SNPs, which offer greater statistical power, allowing you to find meaningful association faster using fewer samples. Sensitive CNV detection probes yield low overall noise for copy number measurements (average stdev log R ratios < 0.2) through built-in marker redundancy. Mulit-sample BeadChips let you to increase sample throughput with Duo (2-sample), Quad (4-sample), and 12-sample formats.

Integrated SNP and CNV Analysis

Illumina's GenomeStudio analysis software package offers integrated copy number tools and a Genome Viewer. GenomeStudio also provides an open plug-in interface that accepts other downstream analysis tools created in collaboration between Illumina and various partners. GenomeStudio plugins are available for download from illumina.Connect.

Infinium HD BeadChipsSamples per BeadChipMarkers per Sample
HumanOmni1-Quad 4 > 1 million*
Human1M-Duo 2 > 1 million
HumanOmniExpress 12 > 700,000
Human660W-Quad 4 > 658,000
HumanCytoSNP-12 12 ~ 300,000
Semi-Custom Human1M-Duo+, and HumanHap550-Quad+ 2 / 4 standard content and up to 60,800 customized SNPs per sample

*Completely redesigned array with aggressively selected SNPs and probes from all three HapMap phases, the 1,000 Genomes Project, and published studies.

SNP Genotyping and CNV Analysis / Custom Low- to Mid-plex Genotyping

For profiling and validation studies requiring low to mid-plex genotyping, Illumina provides customized solutions that allow researchers to optimize the number of loci per sample and throughput level to best suit their study goals. Custom assay panels can be easily developed for any species and deployed with either BeadArray or Veracode technology.


GoldenGate Custom Genotyping on BeadArray

Interrogate 96, or from 384 to 1,536, SNP loci simultaneously with the proven GoldenGate Genotyping Assay. The protocol can be performed manually or can be easily automated, with a streamlined workflow that allows a single technician to generate over 300,000 genotypes in just six hands-on hours. Custom Panels can be designed for many species with user-defined content.

GoldenGate Custom Genotyping on Veracode

Genotyping with VeraCode technology is available with three robust and customizable solutions that facilitate low- to mid-plex assays.

The GoldenGate Genotyping Assay is available in 48-384 multiplex kits for the VeraCode platform, providing a flexible customized solution for mid-level multiplexed assays. Universal Capture Bead Sets are an optimal solution for allele-specific primer extension (ASPE) assays. Carboxyl Bead Sets enable the immobilization of target-specific capture sequences on a coded carboxyl surface.

Gene Regulation and Epigenetic Analysis / Small RNA Discovery and Analysis

Small RNA sequencing is a powerful application on the Genome Analyzer,  enabling the discovery and profiling of microRNAs and other non-coding RNA on any organism without prior genome annotation. Using low RNA inputs, you can profile the differential expression of known microRNAs as well as detect novel microRNA targets and wide-ranging sequence variation or "iso-miRs" miRBase accessions. With unprecedented sensitivity and dynamic range, Illumina's industry-leading small RNA sequencing methods allow for the most accurate detection and quantification of rare small RNA sequences.

LEARN MORE

Highlights

  • Simple, Fast Workflow: One-day library preparation protocol allows for the fastest RNA-to-data solution for rapid analysis and publication
  • Strand-Specific Sequence Data: Retain the original strand orientation information of microRNAs and other small RNAs, including piwi-interacting RNAs
  • Low Input Requirements: Requires 1.0 µg or less of total RNA for analysis of precious samples with high sensitivity, detecting as low as a single copy per cell
  • Superior Data: Achieve the highest quality data with the most accurate sequence detection across greater than six orders of dynamic range
  • Broad Application: Use for other RNA sequencing methods, including CLIP-Seq, RIP-Seq, or analysis of messenger RNA fragments
  • Universal Platform: Analyze any small RNA sample from any species without any prior knowledge of sequence of secondary structure

Gene Regulation and Epigenetic Analysis / Sequencing-Based Methylation Analysis

Identify and track methylation patterns by directly sequencing bisulfite-converted DNA, methylation-sensitive restriction digest-enriched fragments, anti-methyl C-precipitated fragments, or chromatin immunoprecipitates of methyltransferases trapped to aza-labeled DNA on the Genome Analyzer.


Correctly map more reads to the methylated genome using accurate 100+ base paired-end reads. Easily prepare highly diverse libraries needed for comprehensive characterization of methylation status. Using Illumina sequencing technology, you can evenly sequence a repetitive bisulfite-converted genome and detect variations in methylation signatures at single-base resolution to pinpoint rare binding events to within 50 bases of the actual binding site.

 

Gene Regulation and Epigenetic Analysis / DNA-Protein Interaction Analysis (ChIP-Seq)

Accurately survey interactions between protein, DNA, and RNA to interpret regulation events central to many biological processes and disease states. Quantify in vivo protein-DNA interactions using the combination of chromatin immunoprecipitation with Illumina's sequencing technology (ChIP-Seq) on a genome-wide scale. Identify a broad range of interactions with confidence, and use millions of counts to differentiate real events from noise.


Illumina sequencing enables cost-effective and precise analysis of protein/nucleic acid interactions and gives you the freedom to interpret binding events without being confined to set number of array features or candidate sequences.

  • Open Platform: Study any immunoprecipitate from any organism with a sequenced genome without any prior assumptions
  • Comprehensive Access: Map in vivo binding sites across the entire genome
  • Cost-Effective Analysis: 1/10-1/30th cost of whole-genome ChIP-chip
  • Robust and Precise Detection: Obtain higher signal-to-noise ratios than array platforms, and map binding sites less than 50 bp
  • Optimized Kits: Accelerate whole-genome protein-nucleic acid interaction analysis with Illumina's easy-to-use protocols and analysis tools.

Related info:

Gene Regulation and Epigenetic Analysis / Array-Based Methylation Analysis

DNA methylation plays a critical role in the regulation of gene expression and has been implicated in the etiology of many human diseases including cancer. Methylation profiling with BeadArray technology allows researchers to analyze the effects of aberrant methylation (either hyper- or hypomethylation) for a variety of applications. Illumina has developed a robust methylation profiling platform that provides quantitative methylation measurement at the single-CpG-site level, providing the highest resolution for understanding epigenetic changes.


Infinium Methylation Assay

With the Infinium Methylation Assay, researchers can quantitatively interrogate 27,578 CpG loci, covering more than 14,000 genes at single-nucleotide resolution, per sample. The HumanMethylation27 BeadChip lets researchers profile up to 12 samples in parallel, providing high-throughput power while minimizing the cost per sample.

Gene Regulation and Epigenetic Analysis / Custom Low- to Mid-plex Methylation Analysis

For methylation profiling studies requiring low- to mid-plex analysis, Illumina provides a customized solution that allows researchers to target CpG loci within genes or regions of interest. With the proven GoldenGate Methylation Assay, customized probes can be easily developed for virtually any experimental design.


GoldenGate Customized Methylation Panels on VeraCode

Methylation profiling with Veracode technology provides a simplified workflow, high-throughput sample processing, and assay flexibility. A customized panel of 48-384 CpG regions can be profiled simultaneously, and hundreds of samples can be read per day with the BeadXpress Reader. Individual bead types can be combined in unlimited combinations to support flexible assay design tailored to specific applications. Submit your desired list of CpG regions, and Illumina scientists will help you create successful custom content for multiplexed GoldenGate Methylation assays.

GoldenGate Customized Methylation Panels on BeadArray

The Illumina GoldenGate Methylation Solution offers an array-based platform that uniquely combines high sample throughput, high multiplexing, single-site CpG resolution, and content flexibility for DNA methylation profiling. You can choose to target CpG loci within genes or regions of interest to meet specific research needs. Custom methylation is available in panels of 96 and 384-1,536 assays per Oligo Pool for Methylation Assay (OMA) tube. Larger panels can be accommodated with multiple OMA tubes and the appropriate GoldenGate reagents and arrays. Panels for 384-1,536 loci are available in multiples of 96.

Gene Expression Analysis / Custom Low- to Mid-plex Gene Expression Analysis

For researchers interested in RNA analysis of specific genes or regions of interest, a customized solution can be developed with the DASL Assay. The robust DASL assay chemistry can generate high-quality data from samples with low RNA abundance or partial RNA degradation, such as formalin-fixed, paraffin embedded (FFPE) samples.

Veracode DASL Assay

Customizable VeraCode gene expression kits developed for the DASL Assay allow maximal sample throughput for low- to mid-multiplex expression profiling. Customizable VeraCode DASL kits allow you to simultaneously profile 32-384 transcripts of choice, and hundreds of samples can be read per day with the BeadXpress Reader. Simply submit your desired gene list, and Illumina scientists will help you create successful custom content for multiplexed DASL assays.

Custom DASL Panel for BeadArray or Universal Array Matrix

Custom DASL Assay Panels (DAPs) can be generated for between 512 (three probe groups per gene) and 1,536 genes (one probe group per gene). Although a single probe group per gene can be used, more probe groups allow detection down to 1.3-fold changes. Custom DAP design is accomplished via a collaborative process that is included with DAP purchase. Oligo probes for both standard expression panels and custom sets are subjected to a rigorous bioinformatics screening procedure. This process assesses each target site for specificity in the transcriptome (RefSeq) and the genome, and also assesses predicted behavior in DASL biochemistry. Custom DASL Panels can be deployed on 16- and 12-sample Universal BeadChips or the 96-sample Universal Array Matrix.

Gene Expression Analysis / Transcriptome Analysis

Explore the transcriptome like never before. Characterize all transcriptional activity, coding and non-coding, in any organism without a priori assumptions using the Genome Analyzer and achieve an unprecedented view of the transcriptome. Illumina's unique combination of long and short reads, strand specificity, and millions of counts allows you to annotate coding SNPs, discover transcript isoforms, identify regulatory RNAs, characterize splice junctions, and determine the relative abundance of transcripts. Generate transcript profiles in a single day with the greatest daily system output. Align RNA sequencing reads across splice junctions and map to reference genomes. Identify and quantify both rare and common transcripts, with six orders of magnitude of dynamic range. Reveal the hidden world of non-coding RNA architecture without prior information.

Fully Supported Transcriptome Analysis Applications

  • mRNA-Seq: Identify and quantify full-length poly-A transcript isoforms
  • Tag Profiling: Sequence short 3' transcript fragments to quantify known and novel transcripts from any eukaryotic species
  • Small RNA Discovery and Analysis: Discover rare small RNA without previous sequence or secondary structure information in any organism; generate strand-specific reads with mRNA samples
LEARN MORE

Gene Expression Analysis / Whole-Genome Gene Expression Analysis

The Direct Hybridization Assay offers the highest level of multiplexing for whole-genome expression profiling available. With the most up-to-date expression content and high-throughput processing, Illumina's whole-genome expression arrays produce high-quality data for large gene expression studies, efficiently and economically.

Whole-Genome Expression Beadchips


Gene Expression Analysis / FFPE Sample Analysis

Formalin-fixed, paraffin-embedded (FFPE) samples are preserved tissue samples that are generally associated with disease. Many of these samples represent clinical outcomes, a potential gold mine of information when linked with underlying expression profiles. FFPE samples generally contain partially degraded RNA, so transcription analysis is a challenge for many gene expression assays. By using probe groups spanning approximately 50 bases, Illumina's DASL assays are able to provide high-quality data for degraded RNA samples. The availability of additional, unique probe sequences per gene increases the sensitivity of the assay, allowing the quantitation of low-abundance transcripts, even in partially degraded samples.


Whole-Genome DASL Assay

Covering more than 24,000 transcripts, the Whole-Genome DASL Assay is ideal for high-multiplex whole-genome profiling. The assay is based on a multi-sample BeadChip format, allowing reduced cost per sample and requiring low-sample input. Obtain qPCR-equivalent results with high reproducibility, as well as excellent correlation with matching fresh/frozen samples.

Veracode DASL Assay

The VeraCode DASL Assay combines the specificty of VeraCode technology with the proven DASL Gene Expression Assay to allow maximal sample throughput for custom, low- to mid-multiplex expression profiling. This is the ideal solution for researchers interested in focused RNA analysis for specific genes or regions of interest. The Veracode DASL Assay enables expression profiling of 96-384 transcripts per sample, providing the flexibility to meet diverse experimental designs.

Protein Analysis / Protein Screening

VeraCode technology provides a simple and flexible solution for multiplexed protein assays. With VeraCode Carboxyl Bead Sets, any protein or peptide can be covalently attached to the highly stable microbead surface, enabling the development of standard "sandwich" immunoassays. The 48 unique Carboxyl bead types can be pooled in varying combinations to perform up to 48 immunoassays in a single reaction in a standard 96-well microplate.

Analytes can be labeled with standard fluorescent reporters such as phycoerythrin (R-PE), Cy3, Cy5, or AlexaFluor dyes. During analysis, the fluorescence and code inscription for each microbead are detected by the BeadXpress Reader.

It has been demonstrated that the BeadXpress Reader can detect protein concentrations as low as 10 pg/ml in a multiplexed VeraCode Carboxyl bead assay.

The VeraScan Software that comes with the BeadXpress Reader System provides users the flexibility they need to customize scanning protocols. Illumina's BeadStudio software provides users a forum for simple to complex data analysis that can be easily exported to third-party data analysis programs.

Learn more about Carboxyl Bead Sets.

Agriculture / Discovery

Combining high throughput, accuracy, and flexibility, the Genome Analyzer and iScan Reader enable discovery of any variant in any species.

Gene and SNP Discovery
Whole-genome resequencing to discover genes and structural variants; simultaneously determine minor allele frequencies.

De Novo Sequencing
Sequence and assemble complex plants, animals, and pathogens.

Targeted Resequencing
Isolate and resequence regions of interest from association and linkage studies.

Whole-Genome Genotyping
Perform genome-wide association studies to discover quantitative trait loci, CNVs, rare variants, and other genetic variants.

RNA Expression Analysis
Discover coding SNPs and other genetic variations to reveal new aspects of the transcriptome.

Small RNA Discovery
Identify novel microRNAs and other small RNA targets at unprecedented depth.

Agriculture / Validation

For simple validation and confirmed decision making, use the Genome Analyzer, iScan Reader, and BeadXpress platforms.


Parentage Verification
Correct parentage misidentification and trace the parentage of any animal.

Confirm Genetic Identity
Identify plant varieties and correctly trace their pedigree.

Linkage Mapping
Locate genomic regions associated with a phenotype of interest.

Whole-Genome Selection
Identify informative markers to create focused screening panels.

Transcriptome Profiling
Discover coding SNPs and other genetic variations to reveal new aspects of the transcriptome.

Agriculture / Screening

Quickly and easily screen your markers of interest in large populations using the iScan and BeadXpress Readers.


Prediction of Genetic Merit
Improve breeding programs by identifying plants or animals that will produce progeny with the desired traits.

Marker-Assisted Breeding and Selection
Determine percent recurrent parent and select desirable traits.

Disease Susceptibility
Establish susceptibility to specific diseases or conditions by screening for associated markers.

Crop QC Testing
Identify DNA fingerprints to track samples and estimate inbred/hybrid purity and biotech (GMO) event purity.

Related Information

 

Cytogenetics / Array-Based Cytogenetics

Structural variability is a substantial source of genetic variation that has a major influence on phenotypic variation. Illumina products allow researchers to profile chromosomal aberrations such as amplifications, deletions, rearrangements, point mutations, copy number changes, and copy-neutral loss of heterozygosity (LOH) events. Illumina offers a broad portfolio of genome-wide analysis BeadChips that enable researchers to analyze structural variation at varying levels of resolution, from routine cytogenetic screening to sample profiling with up to 1.2 million markers to examine both known and novel variants.


Complete Genome-Wide Coverage in Multi-Sample Array Formats

Illumina's revolutionary Infinium HD technology allows for unconstrainted design of SNP or intensity-only markers, enabling dense, uniform coverage across the genome and the ability to target high-value genomic regions. From 300,000 markers on the HumanCytoSNP-12 BeadChip to more than 1.1 million markers per sample on the HumanOmni-1 Quad, Infinium HD BeadChips support high-resolution copy number and LOH analysis with median marker spacing down to 1.2 kb.

Better Detection

The Infinium Assay simultaneously measures intensity differences and allelic ratios, enabling the profiling of intercellular mosaicism and copy-neutral LOH events such as uniparental disomy (UPD), mitotic recombination, or gene conversion events, all of which cannot be detected on array-CGH platforms.

Simplified Analysis

Analysis of Infinium HD BeadChip data is supported by Illumina's BeadStudio Genotyping Module and the standalone KaryoStudio data analysis software package, which was developed in collaboration with molecular cytogeneticists. In addition, through the illumina•connect program, Illumina data can be analyzed using other common cytogenetics analysis programs.

Cytogenetics / DNA Sequencing

The Genome Analyzer system's powerful combination of read-length and paired-end flexibility enables the broadest range of genomic sequencing applications. Illumina's robust sequencing chemistry supports a wide range of read lengths, allowing researchers to tailor each run to meet their needs.

Industry-leading raw read accuracy at 75+ bp single-reads, short- and long-insert paired-end reads and long-insert mate pairs enable whole-genome sequencing and resequencing, SNP discovery, identification of copy number variations, chromosomal rearrangements and the following:

De Novo Sequencing

  • Paired Reads - Generate long scaffolds and highly accurate contigs using multiple insert lengths with high library diversity.
  • Read Length - Use paired-end reads in excess of 2 x 75 bases for mammalian-scale de novo assembly.
  • Raw-Read Accuracy - Access the highest yield of perfect reads and Q30 data to generate long, error-free contigs.
  • Assembly Tools - Leverage a rapidly growing number of assemblers optimized for Genome Analyzer reads, such as Velvet, EULER-SR, and SSAKE.

Targeted Resequencing

The Genome Analyzer requires minimal sample input, allowing the sequencing of limited archival tissues, embryoid bodies, small model systems, and difficult-to-cultivate organisms. Targeted genomic regions can be isolated by a series of long PCR reactions or by hybridization-based approaches using oligonucleotide arrays.