Beadstudio genotyping module v 2.3.41

Manufactured by Illumina

The BeadStudio Genotyping Module (v. 2.3.41) is a software tool developed by Illumina for analyzing and interpreting genotyping data. It provides a platform for visualizing and managing the results of Illumina's genotyping arrays.

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Lab products found in correlation

Goldengate assay, by Illumina (2 mentions) Beadarray reader, by Illumina (2 mentions)

2 protocols using beadstudio genotyping module v 2.3.41

Genotyping of Candidate SNPs Using Illumina GoldenGate

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DNA samples from a total of 1274 participants were sent for genotyping. Genotyping of the candidate SNPs was performed using an Illumina GoldenGate assay (Illumina, San Diego, CA). Ninety-three percent of the SNPs analyzed had Illumina SNP scores of >0.6. Genotyping of DNA samples (250 ng) was conducted following Illumina's standard 3-day protocol. The BeadArray reader (Illumina, Inc.) was used to autocall data from the SNP array. Cluster definitions for each SNP were determined using Illumina BeadStudio Genotyping Module (v. 2.3.41). SNP genotype assignments (calls) were made when a genotype yielded a quality value (Gencall score) of 95% or higher. Among the markers included in this study, only 1.5% had a Gencall score less than 95% (10 of 672). Seventy blind duplicate pairs were included, and the overall concordance of SNP genotype calls was greater than 99%.

Archer N.P., Wilkinson A.V., Ranjit N., Wang J., Zhao H., Swann A.C, & Shete S. (2014). Genetic, psychosocial, and demographic factors associated with social disinhibition in Mexican-origin youth. Brain and Behavior, 4(4), 521-530.

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Genotyping SNPs Using Illumina GoldenGate

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An Illumina GoldenGate assay was designed for genotyping 672 SNPs (Illumina, Inc.). Ninety-three percent of the SNPs had Illumina SNP scores of >0.6. A total of 1,274 samples with DNA 250ng were genotyped following the standard 3-day Illumina protocol. The BeadArray Reader (Illumina, Inc.) was used to call the array data. Cluster definitions for each SNP were determined using Illumina BeadStudio Genotyping module v. 2.3.41. When a quality score (i.e., Gencall value) of a genotype is over 95%, genotype calls were made, and 1.2% of the calls (8 of 672) were missing. Therefore, we used 664 SNPs with genotype data for analysis. The concordance of SNP genotype calls was greater than 99% when examined with 70 blind duplicate pairs.

Song S., Marcum C.S., Wilkinson A.V., Shete S, & Koehly L.M. (2018). Genetic, Psychological, and Personal Network Factors Associated With Changes in Binge Drinking Over 2 Years Among Mexican Heritage Adolescents in the USA. Annals of Behavioral Medicine: A Publication of the Society of Behavioral Medicine, 53(2), 126-137.

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