Southern California Genotyping Consortium

For detailed pricing calculations of genotyping, gene expression or whole genome genotyping projects please contact Joe DeYoung, facility manager, at jdeyoung@mednet.ucla.edu.

GoldenGate genotyping assays are a cost effective way to generate genotypes from small to moderate pools of custom snp markers in very large collections of samples. Per genotype costs can be as low as $0.03. Snp pools can be designed with as few as 96 snps but typically include 1536 snps in a single pool. Multiple pools can be designed such that the number of snps in a project is essentially unlimited (of course beyond a certain scale GoldenGate assays become less cost effective than alternate whole genome approaches such as Infinium assays)

Each SAM can process 96 samples at the stated snp “plex” level. It’s possible to design oligo pools (OPA’s) containing any number of snps between 96 and 1536 and the choice of array is dictated by the number of snps in an OPA. However, though it’s possible to design OPA’s with any number of snps (within certain stated limits) it’s generally most cost effective to design them to use the full capacity of the various array formats.

Currently available formats are:

• 96 plex (genotypes 96 snps)
• 384 plex (genotypes up to 384 snps)
• 768 plex (genotypes up to 768 snps)
• 1536 plex (genotypes up to 1536 snps)

Custom oligo pools can be designed for any organism for which adequate genomic information is available. We’ve successfully designed OPA’s for Arabidopsis, Mouse, Barley and Maize as well as Human. Illumina provides complete support for the design of custom OPA’s. OPA’s can be designed to contain from 96 to 1536 snps per pool. Larger projects requiring more than 1536 snps can be designed to utilize multiple OPA’s such that the number of snps that can be screened in a project is essentially limitless. Off the shelf Linkage, fine mapping and MHC snp panels are also available.

www.illumina.com

Sentrix Human-6 Expression BeadChip 48k transcripts per sample V.2.0	
Human whole Genome BeadChip for the analysis of 48,000 gene targets including all RefSeq genes and known alternative splice regions. Processes 6 samples per chip.
Sentrix HumanRef-8 Expression BeadChip	24k transcripts per sample V.2.0
Human whole genome BeadChip for the analysis of 24,000 RefSeq-curated gene targets. Processes 8 samples per chip.

Sentrix Mouse-6 Expression BeadChip  48K transcripts per sample V.1.0
Mouse Whole genome expression BeadChip for the analysis of 48k gene targets. Processes 6 samples per chip.
Sentrix MouseRef-8 Expression BeadChip  24K transcripts per sample V.1.0
Mouse whole genome expression BeadChip for the analysis of 24k gene targets per sample. Processes 8 samples per chip. 
Sentrix RatRef-12 Expression BeadChip	22k transcripts per sample V.1.0
Rat Whole genome expression BeadChip for the analysis of 22k gene targets per sample. Processes 12 samples per chip.

Custom content gene expression products are also available. Please enquire.

The Infimium Whole Genome Genotyping assay provides exceptionally accurate and reproducible genotyping of 100K, 317K, 550K or 650K snp markers in a single reaction. Exceptionally low per genotype cost, industry leading call rates, assay conversion rates and volume discounts make this assay extremely cost effective.

• Human 100k: Human-1 BeadChip enables whole-genome genotyping of over 100,000 SNP markers, 70% of which are located in exons or within 10kb of transcripts.
• HumanHap300 and HumanHap300 Duo: 317 tag snps chosen from Phase I HapMap release. This chip comes in a single and a two sample per chip format. Price per sample are equivalent between the two options but the Duo format provides improved processing efficiency.
• Humanhap550: 550K Tag snps chosen from HapMap Phase II data release.
• HumanHap650Y: 550K phase II Tag snps with an additional 100k Yoruban specific snps.

• HumanHapMap300Duo+: add 60K custom snps to the 300K Duo chips. Enables you to process 756,606 snps on two samples with a single chip.
• HumanHapMap550+: Add 120K custom snps to the 550K chips. Enables you to process 670k snps per sample on a single chip.
• iSelect: iSelect custom content chips allow you to design custom content chips containing between 7600 and 60,000 snps per sample. Each chip can process 12 samples.

Minimum scales apply for all custom products. Please inquire.

www.illumina.com