The MGC Services: BeadArray SNP Genotyping

BeadArray SNP Genotyping Service

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Whole Genome Genotyping
Infinium SNP Genotyping on single BeadChip.

humanhap240S
240,000 tag SNPs derived from HapMap data.
humanhap300-duo
318,000 tag SNPs derived from HapMap data, in a two-sample format.
humanhap300-duo+
HumanHap300-Duo (318,000 tag SNPs) + custom SNP content (60,800 SNPs per sample), in a two-sample format.
humancnv370-duo
HumanHap300-Duo (318,000 tag SNPs) + 52,167 markers that target nearly 14,000 copy number variant regions, in a two-sample format.
humanExon510S-Duo
510,000 markers, in a two-sample format: gene-centric SNPs and non-synonymous SNPs, addtional Tag SNPs, CNV probes, ADME, MHC and Sex Chromosomes SNPs.
humanhap550-duo
555,000 tag SNPs from both the humanhap240S and humanhap300, in a two-sample format.
humanhap550+
humanhap550 (555,000 tag SNPs) + custom SNP content (120,600 SNPs)
human610-quad NEW!
>98% overlap of HumanHap550-Duo(555,000 tag SNPs) + HumanCNV-12(52k CNV probes), in a four-sample format.
human650Y
humanhap550 (555,000 tag SNPs) + 100,000 Yoruba-specific tag SNPs
human 1M
humanhap550-duo (555,000 tag SNPs) + humanExon510S-Duo.
human1M-duo NEW!
>98% overlap with the Human1M, plus recently identified disease-associated SNPs and intelligently selected high-density SNPs in coding regions, in a two-sample format.

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Focused Content
Standard SNP Panels

african american admixture panel
1,509 SNPs optimized for admixture mapping studies in African American populations.
cancer snp panel
1,421 SNP loci chosen from the National Cancer Institute’s (NCI) Cancer Genome Anatomy Project SNP500 Cancer Database. Covers over 400 genes.
dna test panel
360 SNP loci chosen from Illumina’s LinkageIVb Panel. May be used as a genomic control or to assess potential stratification in study samples.
mhc panel set
· MHC Exon-Centric Panel: (>1200 SNPs within 10 kb of coding sequences of genes in the MHC)
· MHC Mapping Panel: (>1250 SNPs with average spacing of 3.8 kb)
· Combine both panels for dense MHC coverage (2 kb average spacing)
bovinesnp50 beadchip NEW!
54,000 evenly spaced SNPs at average spacing of 51.5 Kb, 12 samples per BeadChip.
canineSNP20 BeadChip NEW!
22,362 evenly spaced SNPs (eight SNPs per Mb), 12 samples per BeadChip.

Custom-designed SNP Panels

SNPs are selected by customer, assistance available.
Illumina provides custom SNP design Tool templates and training materials.
Submit RS list, Sequence list, Regions (by coordinate), or Gene List to Illumina.
Design score, design rank, minor allele frequency (MAF), and validation status will be given by Illumina for each SNP submitted.
SNPs must be ordered at 96-plex increments.
It is more cost-effective when SNPs are ordered at 384-plex increments such as 384, 768 and 1536.

iselect Infinium custom panels : From 7,600 to 60,800 attempted bead types on a 12-sample BeadChip format.

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human

Infinium Linkage-12: cost-effective, 12 samples per BeadChip.
GoldenGate Linkage V: choice for degraded samples such as FFPE and WGA samples.

Mouse low density (LD) linkage panel: Consists of 377 loci, optimized for application to N2 and F2 mouse genetics crosses. These crosses can be used for mapping quantitative trait loci.
Mouse medium density (MD) linkage panel: Consists of 1,449 loci, optimized for various mapping applications including characterization of transgenic, congenic and knockout animals, and genetic mapping in advanced intercross mouse lines.