An ambiguous NUDT15 signal in a child with B-cell acute lymphoblastic leukemia

Summary

https://doi.org/10.1093/clinchem/hvaf028

A pharmacogenetic test for variants in the TPMT and NUDT15 genes, which encode thiopurine methyltransferase (TPMT) and nudix hydroxylase 15 (NUDT15), respectively, was ordered on a 6-year-old female to guide thiopurine treatment.

Student discussion

Student Discussion Document (pdf)

Rosalie M. Sterner, Farha Sherani, Margaret A. DiGuardo, Patricia T. Greipp, and Ann M. Moyer

Case description

A pharmacogenetic test for variants in the TPMT and NUDT15 genes, which encode thiopurine methyltransferase (TPMT) and nudix hydroxylase 15 (NUDT15), respectively, was ordered on a 6-year-old female to guide thiopurine treatment. DNA was extracted from the patient’s whole blood specimen using a MagNA Pure system (Roche Diagnostics), followed by genotyping for 8 TPMT variants and 3 NUDT15 variants by real-time PCR on a Quant Studio 12K Flex Open Array (Thermo Fisher Scientific). Initial testing revealed a genotype of TPMT*1/*3A and an inconclusive NUDT15 c.415C > T (*3) assay signal shifted between the heterozygous and reference zones, which was still present upon repeat testing of the sample (data not shown). Next, Sanger sequencing was performed to troubleshoot the NUDT15*3 signal and revealed a weak NUDT15 c.415C > T peak (corresponding with *3), not consistent with the expected peak height for a heterozygote. Additionally, no nearby variants that could interfere with binding of the genotyping primers or probes were identified. The Sanger sequencing results suggested that the original genotyping signal was real (not artifact) and not due to allele drop-out.