Illumina Genotyping Protocol for DNA Samples

Genomic DNA was extracted from peripheral blood using the High Pure PCR Template Preparation Kit (Roche Diagnostics GmbH, Mannheim, Germany). DNA samples were genotyped using the Illumina BeadXpress platform based on Golden Gate chemistry. A 192-plex and 48-plex Illumina VeraCode GoldenGate Genotyping Assay (Illumina, Inc., San Diego, CA) was developed using the Assay Design Tool (ADT) available through Technical Support on the Illumina website (https://illumina.com). Details about the workflow for assay design, laboratory sample processing, data analysis, and quality control were reported previously (16 (link)). The genetic polymorphisms that did not pass quality control in the BeadXpress workflow were tested using an allelic discrimination method by predesigned TaqMan SNP genotyping assays. All commercial TaqMan assays were purchased from Applied Biosystems (https://www.appliedbiosystems.com) and the analyses performed using the Applera TaqMan Universal Master mix on an ABI 7500 (AB Applied Biosystems, Foster City, CA) according to the manufacturer's instructions. Positive and negative control samples were included in each analysis.

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De Mattia E., Polesel J., Roncato R., Labriet A., Bignucolo A., Dreussi E., Romanato L., Guardascione M., Buonadonna A., D'Andrea M., Lévesque E., Jonker D., Couture F., Guillemette C., Cecchin E, & Toffoli G. (2019). Germline Polymorphisms in the Nuclear Receptors PXR and VDR as Novel Prognostic Markers in Metastatic Colorectal Cancer Patients Treated With FOLFIRI. Frontiers in Oncology, 9, 1312.

Publication 2019

High Pure PCR Template Preparation Kit BeadXpress platform VeraCode GoldenGate Genotyping Assay Applera TaqMan Universal Master mix ABI 7500

Allelic Assays Blood Diagnostics Discrimination Genetic polymorphisms Genomic Genotyping method

Corresponding Organization :

Other organizations : Centro di Riferimento Oncologico, Istituti di Ricovero e Cura a Carattere Scientifico, Centre hospitalier universitaire de Québec, Université Laval, Ospedale San Filippo Neri, Ottawa Hospital, University of Ottawa

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Variable analysis

independent variables

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Positive and negative control samples were included in each analysis.

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