Genotyping of NUDT15 Variants

Genotyping of three variant NUDT15 alleles [*2 (*3) (rs116855232), *4 (rs147390019) and *5 (rs186364861)] was performed using a comprehensive pharmacogenetic genotyping panel (S. A. Scott et al., 2020 (link)), which employs multiplex PCR and single base extension (SBE) using the Agena^® SpectroCHIP^® II and MassARRAY^® Analyzer 4 platform as per manufacturer instructions (Agena Biosciences, San Diego, CA). Genotypes at the targeted loci were determined by SBE peak intensity and Typer software v4.1 (Agena Biosciences), and NUDT15 diplotypes were inferred by a haplotype translation table and Typer software v4.1. Of note, the Agena chemistry was unable to interrogate the c.50_55dup (rs746071566) variant, which independently defines *6 and is found in cis with c.415C>T (rs116855232) on the *2 haplotype. Given that c.415C>T (rs116855232) is found on both *2 and *3, the Agena genotyping panel is unable to distinguish between NUDT15*2 and *3 when c.415C>T (rs116855232) is detected (S. A. Scott et al., 2020 (link)).

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Scott E.R., Yang Y., Botton M.R., Seki Y., Hoshitsuki K., Harting J., Baybayan P., Cody N., Nicoletti P., Moriyama T., Chakraborty S., Yang J.J., Edelmann L., Schadt E.E., Korlach J, & Scott S.A. (2022). Long-read HiFi sequencing of NUDT15: Phased full-gene haplotyping and pharmacogenomic allele discovery. Human mutation, 43(11), 1557-1566.

Publication 2022

SpectroCHIP® II MassARRAY® Analyzer 4

Alleles Haplotype Multiplex pcr

Corresponding Organization : Sema4 (United States)

Other organizations : St. Jude Children's Research Hospital, University of Pittsburgh, Pacific Biosciences (United States)

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Variable analysis

independent variables

Genotyping of three variant NUDT15 alleles (*2 (*3) (rs116855232), *4 (rs147390019) and *5 (rs186364861))

dependent variables

Genotypes at the targeted loci
NUDT15 diplotypes

control variables

Comprehensive pharmacogenetic genotyping panel (S. A. Scott et al., 2020)
Multiplex PCR and single base extension (SBE) using the Agena® SpectroCHIP® II and MassARRAY® Analyzer 4 platform
Typer software v4.1 (Agena Biosciences) for genotype and diplotype determination

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