Immunochip v1

Manufactured by Illumina

The Immunochip-v1 is a custom-designed microarray that enables high-throughput genotyping of genetic variants associated with immune-mediated diseases. It allows for the efficient and cost-effective analysis of genetic markers related to the immune system and its functioning.

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Lab products found in correlation

Bead express platform, by Illumina (1 mentions) Immunochip, by Illumina (1 mentions)

Close spelling variants of this product

Immunochip (81 citations) Infinium ImmunoChip-v1 array (2 citations)

2 protocols using immunochip v1

Illumina Immunochip Genotyping Protocol

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Patients included in the study were genotyped using the Illumina Immunochip-v1 on the Illumina Bead Express platform at the Broad Institute (Cambridge, MA). The Immunochip is an Illumina genotyping platform containing 196,524 polymorphisms (718 small insertion deletions, 195,806 SNPs), with dense coverage of known major immune and inflammatory diseases loci.

Burke K.E., Khalili H., Garber J.J., Haritunians T., McGovern D.P., Xavier R.J, & Ananthakrishnan A.N. (2018). Genetic Markers Predict Primary Nonresponse and Durable Response to Anti–Tumor Necrosis Factor Therapy in Ulcerative Colitis. Inflammatory Bowel Diseases, 24(8), 1840-1848.

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Validating Sequencing Calls with Immunochip Genotyping

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A subset (n=536) of study samples was also genotyped with the Immunochipv1, an Illumina infinium genotyping chip which contains 196524 genomewide markers. SNP concordance analysis was done between sequencing and immunochip genotypes in order to validate the quality of sequencing calls. Raw image files from immunochip array were imported into Genome Studio (GS version 1.9.4) and SNPs were called. The genotype outputs from Genome Studio were then imported into SNP & Variation suite (SVS version 7.6.8 win64) for further quality control (QC) and downstream association analysis. In addition, about 35 SLE associated SNPs from various targeted genes were also confirmed by Sanger sequencing method.

Raj P., Rai E., Song R., Khan S., Wakeland B.E., Viswanathan K., Arana C., Liang C., Zhang B., Dozmorov I., Carr-Johnson F., Mitrovic M., Wiley G.B., Kelly J.A., Lauwerys B.R., Olsen N.J., Cotsapas C., Garcia C.K., Wise C.A., Harley J.B., Nath S.K., James J.A., Jacob C.O., Tsao B.P., Pasare C., Karp D.R., Li Q.Z., Gaffney P.M, & Wakeland E.K. (2016). Regulatory polymorphisms modulate the expression of HLA class II molecules and promote autoimmunity. eLife, 5, e12089.

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