Infinium iscan platform

Manufactured by Illumina

The Infinium iScan platform is a high-throughput microarray scanner designed for the analysis of genomic data. It is capable of scanning Infinium BeadChips, which are used for genotyping and gene expression studies. The iScan system provides rapid and accurate data acquisition for a wide range of genomic applications.

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Lab products found in correlation

Dnaeasy plant mini kit, by Qiagen (1 mentions) Genomestudio, by Illumina (1 mentions) Fluostar omega, by BMG Labtech (1 mentions) Hoechst, by Thermo Fisher Scientific (1 mentions)

Spelling variants of this product

IScan platform (30 citations) Infinium platform (29 citations)

2 protocols using infinium iscan platform

DNA Extraction and Genotyping in Plant Study

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Total genomic DNA was isolated from 100 mg of each leaf sample using the DNAeasy Plant Mini Kit (Qiagen, Germany). For SSR genotyping, 135 markers from our previous study were selected [18 ]. In the same study, we have shown that these SSRs, from an average of 10 cM mapping interval provided sufficient power for QTL detection. The SSR amplification was carried out using a M13-tailed forward primer with a four-color fluorescent detection technique [23 (link), 24 (link)]. The SSRs with more than two alleles were interpreted as two or more markers in order to convert all genotype values to −1, 0 or 1, an approach similar as published [10 (link)], without loss of information. Therefore, the informative SSRs used in this study were represented as 221 markers.
SNP genotyping on the same family was carried out using the OP200K array (170,860 SNPs) [15 (link)]. The process was done on the Infinium iScan platform (Illumina Inc., San Diego, CA) according to the manufacturer’s recommendations. The raw intensity SNP data was analyzed and auto-clustered using GenomeStudio version 20,011.1 (Illumina Inc., San Diego, CA) with genotyping module version 1.8.4. A total of 46,933 SNPs were identified to be polymorphic. These genotypes were coded into −1 (AA), 0 (AB) and 1 (BB) format. Missing genotype data were imputed using the na.roughfix function of the randomForest package [25 ] in R.

Kwong Q.B., Teh C.K., Ong A.L., Chew F.T., Mayes S., Kulaveerasingam H., Tammi M., Yeoh S.H., Appleton D.R, & Harikrishna J.A. (2017). Evaluation of methods and marker Systems in Genomic Selection of oil palm (Elaeis guineensis Jacq.). BMC Genetics, 18, 107.

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Genotyping of Commercial Oil Palm Populations

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The OP200K arrays were used to genotype a panel of 312 accessions from commercial oil palm populations of UR 3 AVROS and JL 3 AVROS (66 and 33 individuals), a semi-wild population of Nigerian 3 AVROS (101 individuals), and breeding populations of GM 3 DA and JL 3 DA (13 and 99 individuals).
For each of the accessions, gDNA was extracted using the same method as described under the resequencing step. Prior to hybridization to the bead arrays, DNA was diluted to 25 ng/ml and DNA quantification was obtained with Hoechst (33258 pentahydrate; Invitrogen), using the FLUOstar Omega (BMG Labtech). DNA quality was assessed on a 0.8% agarose gel. The genotyping was carried out using the designed array on the Infinium iScan platform (Illumina) according to the manufacturer's recommendations.
The raw intensity SNP data were analyzed using GenomeStudio version 20011.1 by Illumina with genotyping module version 1.8.4. Using a GenCall score cut-off of 0.15, autocluster of the SNPs was done. Cluster refining of the SNP clusters was done manually by visual inspection so that identifiable and scorable clusters were generated. The SNP calls were ex- ported into the PLINK program for MAF and callrate filtering (Purcell et al., 2007) . A minimal call rate of 90% and an MAF filter of 0.01 were set as baseline cut-offs.

Kwong Q.B., Teh C.K., Ong A.L., Heng H.Y., Lee H.L., Mohamed M., Low J.Z., Apparow S., Chew F.T., Mayes S., Kulaveerasingam H., Tammi M, & Appleton D.R. (2016). Development and Validation of a High-Density SNP Genotyping Array for African Oil Palm. Molecular plant, 9(8).

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