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GTR Home > Tests > SmartMeds+ Pharmacogenomic Testing By Innovative GX Health

Methodology

Methodology

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Molecular Genetics
TTargeted variant analysis
NGS Amplicon sequencingSNP Detection
  • Other

Test comments

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Patients with a past medical history of the following conditions have limitations for PGX testing: Presence of hematological malignancy affecting white blood cells; Recent (<20 days) whole blood transfusion; Bone marrow or stem cell transplant.

Test development

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Test developed by laboratory (no manufacturer test name)

Test procedure

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The assays principle is to capture a robust and diverse amount of targets to generate a comprehensive Pharmacogenomics panel with the implementation of Next Generation Sequencing (NGS). The method of library preparation is Targeted Amplicon based sequencing, which was designed in collaboration with Paragon Genomics. The product of the Library prep is then sequenced using Illumina MiSeq Dx sequencers, and run through an in-house designed bioinformatic pipeline to handle variant calling and interpretation. The purpose of the qPCR is to supplement the NGS PGx Panel with additional variants not covered within our panel. These variants will be genotyped via qPCR using Thermofisher TaqMan genotyping assay. In addition to added variants, it will also act as a backup for variants that may fall below QC metrics to confirm genotyping. Data obtained from NGS will be processed by a validated internal bioinformatic pipeline for calling variants. These data will be combined with the data generated from qPCR for making clinical reports.

Citations
  • https://www.paragongenomics.com/targeted-sequencing/amplicon-sequencing/cleanplex-ngs-amplicon-sequencing/cleanplex_workflow/

Confirmation of results

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The PGX test was fully validated with >99.99% accuracy. In each run, 4 positive control samples obtained from Coriell are used to confirm the accuracy of the test in terms of copy number variant and SNP/variant calling.

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