BeadStudio Portal
		Special Alert! Due to the precise clustering of the Infinium assay, we have always recommended a GenCall score cutoff of 0.15 and that is something we continue to recommend for the HumanCNV370-Duo and Human1M BeadChips. The user should adjust the GenCall score cutoff in BeadStudio3.1 from 0.25 to 0.15 when they are analyzing their data from these products. What's New? 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•connect illumina•connect is a software and hardware network connecting Illumina with researchers in the genomics, genetics, and sequencing communities. Our partners include: BioComputing Platforms, Ltd. • GenoLogics • Golden Helix, Inc. • InforSense, Inc. • Ingenuity Systems, Inc. • Partek Incorporated • Plink • Rosetta BioSoftware • Sapio Sciences, LLC • SAS Institute, Inc. • Stratagene, Inc. • VizX Labs/GeneSifter • The Wellcome Trust Centre for Human Genetics. Releases and Updates V3.1 Updater (EXE) V3.0 Updater (EXE) Plug-ins Illumina (provided and supported by Illumina) - ChromoZone (Autobookmarking Plug-in) - dChip Plug-in (Report Plug-in to dChip for CNV/LOH Analysis) / Documentation (PDF) - LOH Detector (Autobookmarking Plug-in) - cnvPartition (CNV Analysis Plug-in) / Documentation (PDF) - QuantiSNP Plug-in Coming Soon - LOH Score (Column Plug-in) Third-Party (provided and supported by their respective vendors) - Sapio Sciences - BeadStudio Plug-ins (Column Plug-in) - Golden Helix - DSF Helix Tree Report Plug-in (Report Plug-in) Documentation Release Notes - What's New in BeadStudio v3.1? (PDF) - BeadStudio v3.1 Release Notes (PDF) - BeadStudio v3.0.27 HotFix Release Notes (PDF) - BeadStudio v3 Release Notes (PDF) User Guides - BeadStudio Framework User Guide, Rev. C (PDF) - BeadStudio Genotyping Module User Guide, Rev. C (PDF) - BeadStudio Gene Expression Module User Guide, Rev. B (PDF) - BeadStudio Methylation Module User Guide, Rev. A (PDF) - BeadStudio Protein Analysis Module User Guide, BETA (PDF) Technical Notes - DNA Copy Number Analysis Algorithms (PDF) - Overview of CNV Analysis tools in BeadStudio (PDF) - TOP/BOT Strand (PDF) API - BeadStudio Plug in SDK FAQ Visit the Illumina Software FAQ page. Future Releases Coming soon… 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_R1 (BGX) - HumanWG-6_V2_0_R1 (BGX) - MouseRef-8_V1_1_R1 (BGX) - MouseWG-6_V1_1_R1 (BGX) - RatRef-12_V1_0_R1 (BGX) Please note: the new BGX files are not replacements for older manifest files. Analysis can still be obtained using the old versions for compatibility reasons, or user can choose the new version For other manifest or annotation files, contact techsupport@illumina.com.