BeadStudio Portal

Special Alerts!

The CN Estimate algorithm has been replaced by newer and more accurate algorithms for copy number analysis. The newer algorithms we recommend are ChromoZone and cnvPartition for autobookmarking and CNV analysis, respectively. The user may also consider several 3rd party CNV algorithms with plug-ins to BeadStudio from our iConnect partners.

Due to a recent change in the LTM antibody lot, the optimal temperature requirement for the XStain procedure has changed. Please check all LTM tube labels for the proper temperature setting.

Due to the precise clustering of the Infinium^® Assay, Illumina recommends a GenCall score cutoff of 0.15 for all Infinium products, including the HumanCNV370-Duo and Human1M BeadChips. Be sure to adjust the GenCall score cutoff in BeadStudio from the default 0.25 to 0.15 when you are analyzing data from Infinium products.

What's New?

BeadStudio FW v3.1.3, GT v3.2, GX v3.2.6, and ChIP Sequencing v1.0 (EXE) were released on January 17, 2008.

Partners

illumina•connect

illumina•connect is a software and hardware network connecting Illumina with researchers in the genomics, genetics, and sequencing communities. Our partners include:

Ariadne • BioComputing Platforms, Ltd. • BioDiscovery • dChip • GeneData • GenoLogics • Golden Helix, Inc. • InforSense, Inc. • Ingenuity Systems, Inc. • LUMI • Partek Incorporated • Plink • Progeny • Rosetta BioSoftware • Sapio Sciences, LLC • SAS Institute, Inc. • Stratagene, Inc. • VizX Labs/GeneSifter • The Welcome Trust Centre for Human Genetics.

Releases and Updates

Updates

BeadStudio FW v3.1.3, GT v3.2, GX v3.2.6, and new ChIP Sequencing (CS) Module v1.0 Full Installer (EXE)
BeadStudio GX Module v3.2 Full Installer (EXE)
BeadStudio v3.1 Updater (EXE)
BeadStudio v3.0 Updater (EXE)

HotFix Release

BeadStudio GT v3.1.14 Full Installer (download and install this if upgrading from BeadStudio GT v3.0.x)
BeadStudio GT v3.1.14 Updater (download and install this if upgrading from BeadStudio GT v3.1.12)

Plug-ins

APIs for Genotyping and Gene Expression Analysis

BeadStudio Custom Report

New APIs for genotyping and gene expression analysis allow you to create DLL plug-ins for custom BeadStudio reports and columns. Get the BeadStudio API SDK (Application Programming Interface / Software Development Kit).

Illumina Plug-ins (provided and supported by Illumina)

- cnvPartition v1.0.1 (CNV Analysis Plug-in) / Documentation (PDF)
- Universal CNV Adapter Plug-in v1.0.4 for BeadStudio (compatible with QuantiSNP algorithm) / Documentation (PDF)
- ChromoZone (Autobookmarking Plug-in)
- LOH Detector (Autobookmarking Plug-in)
- LOH Score (Column Plug-in)
- dChip Plug-in (Report Plug-in to dChip for CNV/LOH Analysis) / Documentation (PDF)
- ArrayExpress Data Submission Report Plug-in for GX / Documentation (PDF)
- GEO Data Submission Report Plug-in for GX / Documentation (PDF)

Third-Party Plug-ins (provided and supported by their respective vendors)

- OverUnder Plug-in / Documentation
- Partek Custom Report for CNV analysis
- ArrayAssist Explorer v1.0 / Documentation
- Nexus CGH Custom report Plug-in
- Golden Helix Report Plug-ins for CNV Analysis / Documentation
- Sapio Sciences - BeadStudio Plug-ins (Column Plug-in)
- Golden Helix - DSF Helix Tree Report Plug-in (Report Plug-in)

Documentation

Release Notes

- January 2008 BeadStudio Release Notes (PDF)
- BeadStudio Gene Expression (GX) Module v3.2 Release Notes (PDF)
- BeadStudio v3.1.14 HotFix Release Notes (PDF)
- BeadStudio v3.1 Release Notes (PDF)
- BeadStudio v3.0.27 HotFix Release Notes (PDF)
- BeadStudio v3 Release Notes (PDF)

User Guides

- BeadStudio Framework v3.1.3 User Guide, Rev. A (PDF)
- BeadStudio Genotyping Module v3.2 User Guide, Rev. A (PDF)
- BeadStudio Gene Expression Module v3.2 User Guide, Rev. A (PDF)
- BeadStudio Methylation Module User Guide, Rev. A (PDF)
- BeadStudio Protein Analysis Module User Guide, Rev. A (PDF)
- ChIP Sequencing Module v1.0 User Guide, Rev. A (PDF)

Technical Notes

- Gene Expression Data Quality Control (PDF)
- Merging Gene Expression and Methylation Data (PDF)
- CNV Analysis Tutorial (PDF)
- DNA Copy Number Analysis Algorithms (PDF)
- Copy Number Variation (CNV) Analysis with BeadStudio v3.1 (PDF)
- "TOP/BOT" Strand and "A/B Allele" (PDF)
- Infinium Genotyping Data Analysis (PDF)
- BeadStudio Normalization Algorithms for Gene Expression Data (PDF)

BeadStudio Application Support

- BeadStudio Script Interface
- BeadStudio Plug in SDK

FAQ

Visit the Illumina Software FAQ page.

New Manifests/Annotation Files

Genotyping

- GoldenGate
   » Linkage Panel

- Infinium
   » Human-1M (Please note that for Infinium-LIMS customers, this new manifest requires LIMS software v1.2.0.18)
   » HumanCNV370Duo_v1-0 (Please note that for Infinium-LIMS customers, this new manifest requires LIMS software v1.2.0.18)

Gene Expression

- HumanRef-8_V2_0_R2 (BGX)
- HumanWG-6_V2_0_R2 (BGX)
- MouseRef-8_V1_1_R2 (BGX)
- MouseWG-6_V1_1_R2 (BGX)
- RatRef-12_v1_0_R2 (BGX)

microRNA

- Human (BGX)
- Mouse (BGX)

VeraCode Assay

- Sample manifest file

Please note: New BGX files are not replacements for older manifest files. You can perform analyses using the older versions for compatibility reasons, or you can choose to use the new versions.

For other manifest or annotation files, contact techsupport@illumina.com.