Diplotype analysis of NUDT15 variants and 6-mercaptopurine sensitivity in pediatric lymphoid neoplasms

Tsujimoto, Shin‐ichi; Osumi, Tomoo; Uchiyama, Meri; Shirai, Ryota; Moriyama, Takaya; Nishii, Rina; Yamada, Yuji; Kudo, Ko; Sekiguchi, Mutsuo; Arakawa, Yuki; Yoshida, Masanori; Uchiyama, Toru; Terui, Kiminori; Ito, Shuichi; Koh, Katsuyoshi; Takita, Junko; Ito, Etsuro; Tomizawa, Daisuke; Manabe, Atsushi; Kiyokawa, Nobutaka; Yang, Jun J.; Kato, Motohiro

doi:10.1038/s41375-018-0190-1

Cited by 22 publications

(51 citation statements)

References 15 publications

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“…Our study and that of Tsujimoto et al 32 showed that most patients with the NUDT15 c.36_37insGGAGTC and c.415C > T variants harbored heterozygous NUDT15 *1/*2. Tsujimoto et al defined the diplotypes of 14 patients carrying the two variants (i.e., c.415C > T and c.36_37insGGAGTC) by droplet digital PCR (ddPCR) and restriction enzyme-PCR (RE-PCR) 32 . We developed another method using NUDT15 cDNA-targeted sequencing.…”

Section: Discussionsupporting

confidence: 76%

“…From a cost and benefit perspective, it might be difficult to use cDNA NGS to determine the diplotype of NUDT15 in clinical practice; moreover, the incidence of compound heterozygous mutations, such as NUDT15 *3/*6, is very rare 18 . Sanger sequencing remains the most convenient and cost-effective method for the analysis of genetic variants of NUDT15 17 , 18 , 20 , 25 , 27 , 28 , 31 , 32 , 35 . However, to improve clinical outcomes and reduce adverse effects in pediatric patients with ALL, appropriate preemptive diagnosis of pharmacogenetic variants might be warranted 31 , 36 , 37 .…”

Section: Discussionmentioning

confidence: 99%

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

Chang

Wang

et al. 2020

Sci Rep

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Mercaptopurine intolerance is an adverse effect of mercaptopurine administration in pediatric acute lymphoblastic leukemia. Recently, NUDT15 variants were 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. Patients with heterozygous c.36_37insGGAGTC and c.415C > T can be either compound heterozygous with two variants on different alleles or heterozygous with both variants on the same allele. Because patients with biallelic NUDT15 variants are extremely sensitive to mercaptopurine, clinical identification of NUDT15 diplotype would be advantageous. A cohort of 37 patients with c.36_37insGGAGTC and c.415C > T NUDT15 variants were selected for haplotyping by targeted sequencing. NUDT15 complementary DNA was amplified and sequenced by 300-bp paired-end sequencing on Illumina MiSeq. Of the 37 patients carrying NUDT15 variants, 35 had heterozygous NUDT15 *1/*2 variants and two had compound heterozygous NUDT1 5*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 NUDT15 diplotype and identify patients with compound heterozygous NUDT15 variants .

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Section: Discussionsupporting

confidence: 76%

Section: Discussionmentioning

confidence: 99%

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

Chang

Wang

et al. 2020

Sci Rep

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“…Other known loss-of-function alleles were not detected in this study population. Compared with other Asian ALL populations, 4,21,24,28,[31][32][33] the frequency of the NUDT15 Ã 3 in Thai pediatric ALL patients was comparable, whereas NUDT15 Ã 6 was significantly higher. In contrast, the allele frequency of NUDT15 Ã 3 observed in this study was higher than those reported in European, 14 Hispanic-American, 14 Native-American, 4 and African 14 ALL populations (►Table 4).…”

Section: Discussionmentioning

confidence: 59%

Genetic Polymorphisms of Drug-Metabolizing Enzymes Involved in 6-Mercaptopurine-Induced Myelosuppression in Thai Pediatric Acute Lymphoblastic Leukemia Patients

et al. 2020

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Genetic polymorphisms of thiopurine S-methyltransferase (TPMT) and nucleoside diphosphate-linked moiety X-type motif 15 (NUDT15) genes have been proposed as key determinants of 6-mercaptopurine (6-MP)-induced myelosuppression in pediatric acute lymphoblastic leukemia (ALL). In the present study, genotypes of TPMT and NUDT15 were investigated in 178 Thai pediatric patients with ALL by the TaqMan SNP genotyping assay and DNA sequencing. The frequency of TPMT*3C was 0.034. Among NUDT15 variants, NUDT15*3 is the most common variant with the allele frequency of 0.073, whereas those of NUDT15*2, NUDT15*5, and NUDT15*6 variants were 0.022, 0.011, and 0.039. These data suggest that a high proportion of Thai pediatric ALL patients may be at risk of thiopurine-induced myelosuppression.

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“…Experimentally linking SNPs over distances exceeding those that can be amplified by long-range PCR (up to approximately 20 kb) remains a challenge. Although technologies such as 10X Genomics Linked-Reads (discussed in more detail below) are establishing themselves as powerful tools, cost is a major barrier for their use in routine clinical and research applications and the vendor has recently announced that support for the platform will end in July, 2020. ddPCR is increasingly utilized for DNA and RNA quantification, detection of tumor-derived DNA and pathogen detection to name a few (Li et al, 2018;Liao et al, 2019;Nyaruaba et al, 2019;O'Hara et al, 2019;Oscorbin et al, 2019;Valpione and Campana, 2019), but can also be employed for linkage analysis (Roberts et al, 2014;Karlin-Neumann and Bizouarn, 2018;Lunenburg et al, 2018;Regan and Karlin-Neumann, 2018;Tsujimoto et al, 2018). Since assays can easily be developed by the user and cost-effectively performed, DropPhase2D6 was established to experimentally determine linkage between the "enhancer" SNP and known CYP2D6 haplotypes.…”

Section: Dropphase2d6mentioning

confidence: 99%

“…In droplet digital PCR (ddPCR), a reaction is divided into up to 20,000 nanoliter-sized droplets, enabling PCR amplification from a single DNA molecule; this technology, combined with allele-specific TaqMan® probes, can rapidly phase two SNP loci that are thousands of bases apart (Roberts et al, 2014;Karlin-Neumann and Bizouarn, 2018;Lunenburg et al, 2018;Tsujimoto et al, 2018). This method is a robust and scalable molecular phasing approach that allowed Regan et al to perform haplotype analysis of loci up to 200 kb apart (Regan et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

Long-Distance Phasing of a Tentative “Enhancer” Single-Nucleotide Polymorphism With CYP2D6 Star Allele Definitions

et al. 2020

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Background: The CYP2D6 gene locus has been extensively studied over decades, yet a portion of variability in CYP2D6 activity cannot be explained by known sequence variations within the gene, copy number variation, or structural rearrangements. It was proposed that rs5758550, located 116 kb downstream of the CYP2D6 gene locus, increases gene expression and thus contributes to variability in CYP2D6 activity. This finding has, however, not been validated. The purpose of the study was to address a major technological barrier, i.e., experimentally linking rs5758550, also referred to as the "enhancer" single-nucleotide polymorphism (SNP), to CYP2D6 haplotypes >100 kb away. To overcome this challenge is essential to ultimately determine the contribution of the "enhancer" SNP to interindividual variability in CYP2D6 activity. Methods: A large ethnically mixed population sample (n=3,162) was computationally phased to determine linkage between the "enhancer" SNP and CYP2D6 haplotypes (or star alleles). To experimentally validate predicted linkages, DropPhase2D6, a digital droplet PCR (ddPCR)-based method was developed. 10X Genomics Linked-Reads were utilized as a proof of concept. Results: Phasing predicted that the "enhancer" SNP can occur on numerous CYP2D6 haplotypes including CYP2D6*1, *2, *5, and *41 and suggested that linkage is incomplete, i.e., a portion of these alleles do not have the "enhancer" SNP. Phasing also revealed differences among the European and African ancestry data sets regarding the proportion of alleles with and without the "enhancer" SNP. DropPhase2D6 was utilized to confirm or refute the predicted "enhancer" SNP location for individual samples, e.g., of n=3 samples genotyped as *1/*41, rs5758550 was on the *41 allele of two samples and on the *1 allele of one sample. Our findings highlight that the location of the "enhancer" SNP must not be

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Diplotype analysis of NUDT15 variants and 6-mercaptopurine sensitivity in pediatric lymphoid neoplasms

Cited by 22 publications

References 15 publications

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

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

Genetic Polymorphisms of Drug-Metabolizing Enzymes Involved in 6-Mercaptopurine-Induced Myelosuppression in Thai Pediatric Acute Lymphoblastic Leukemia Patients

Long-Distance Phasing of a Tentative “Enhancer” Single-Nucleotide Polymorphism With CYP2D6 Star Allele Definitions

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