Determination of NUDT15 variants by targeted sequencing can identify compound heterozygosity in pediatric acute lymphoblastic leukemia patients

Mercaptopurine intolerance is an adverse effect of mercaptopurine administration in childhood acute lymphoblastic leukemia. NUDT15 variants were recently identified as a major determinant of mercaptopurine intolerance. Two NUDT15 variants, c.36_37insGGAGTC and c.415C>T, are located on exons 1 and 3, respectively. Sanger sequencing cannot distinguish heterozygous patients with both variants on the same allele from compound heterozygous patients with two variants on different alleles. Because patients with biallelic NUDT15 variants are extremely sensitive to mercaptopurine, clinical identification of the diplotype of NUDT15 would be advantageous. A cohort of 37 patients with c.36_37insGGAGTC and c.415C>T NUDT15 variants were selected for haplotyping using targeted sequencing. NUDT15 complementary DNA was amplified and sequenced by 300-bp paired-end sequencing on an Illumina MiSeq. Of the 37 patients carrying NUDT15 variants, 35 were heterozygous NUDT15*1/*2 variants and two were compound heterozygous NUDT15*3/*6 and NUDT15*2/*7 variants. These two patients with compound heterozygous variants could only tolerate low doses of mercaptopurine, similar to patients with homozygous NUDT15 variants. Targeted sequencing of NUDT15 cDNA can be used to determine the diplotype of NUDT15 and identify patients with compound heterozygous NUDT15 variants.