Star Allele-Based Haplotyping versus Gene-Wise Variant Burden Scoring for Predicting 6-Mercaptopurine Intolerance in Pediatric Acute Lymphoblastic Leukemia Patients

Abstract

Nudix Hydrolase 15 (NUDT15) and Thiopurine S-Methyltransferase (TPMT) are strong genetic determinants of thiopurine toxicity in pediatric acute lymphoblastic leukemia (ALL) patients. Since patients with NUDT15 or TPMT deficiency suffer severe adverse drug reactions, star (*) allele-based haplotypes have been used to predict an optimal 6-mercaptopurine (6-MP) dosing. However, star allele haplotyping suffers from insufficient, inconsistent, and even conflicting designations with uncertain and/or unknown functional alleles. Gene-wise variant burden (GVB) scoring enables us to utilize next-generation sequencing (NGS) data to predict 6-MP intolerance in children with ALL. Whole exome sequencing was performed for 244 pediatric ALL patients under 6-MP treatments. We assigned star alleles with PharmGKB haplotype set translational table. GVB for NUDT15 and TPMT was computed by aggregating in silico deleteriousness scores of multiple coding variants for each gene. Poor last-cycle dose intensity percent (DIP < 25%) was considered as 6-MP intolerance, resulting therapeutic failure of ALL. DIPs showed significant differences ( p < 0.05) among NUDT15 poor (PM, n = 1), intermediate (IM, n = 48), and normal (NM, n = 195) metabolizers. TPMT exhibited no PM and only seven IMs. GVB showed significant differences among the different haplotype groups of both NUDT15 and TPMT ( p < 0.05). Kruskal–Wallis test for DIP values showed statistical significances for the seven different GVB score bins of NUDT15 . GVB NUDT15 outperformed the star allele-based haplotypes in predicting patients with reduced last-cycle DIPs at all DIP threshold levels (i.e., 5%, 10%, 15%, and 25%). In NUDT15 -and- TPMT combined interaction analyses, GVB NUDT15 , TPMT outperformed star alleles [area under the receiver operating curve (AUROC) = 0.677 vs. 0.645] in specificity (0.813 vs. 0.796), sensitivity (0.526 vs. 0.474), and positive (0.192 vs. 0.164) and negative (0.953 vs. 0.947) predictive values. Overall, GVB correctly classified five more patients (i.e., one into below and four into above 25% DIP groups) than did star allele haplotypes. GVB analysis demonstrated that 6-MP intolerance in pediatric ALL can be reliably predicted by aggregating NGS-based common, rare, and novel variants together without hampering the predictive power of the conventional haplotype analysis.

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

“…22 Compared with other Asian ALL populations, 13,[23][24][25][26][27] the frequency of TPMT Ã 3C in this Thai pediatric ALL population was somewhat higher but did not reach statistical significance except with the Korean population. 28,29 In addition, the allele frequency TPMT Ã 3C in our study population was extremely higher than those reported in European ALL patients 30 (►Table 2). Among 10 NUDT15 variants investigated, NUDT15 Ã 3 is the most common variant in Thai ALL population, followed by NUDT15 Ã 6, NUDT15 Ã 2, and NUDT15 Ã 5 variants.…”

“…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).…”

PG-path: Modeling and personalizing pharmacogenomics-based pathways

“…[21] This method operates under the hypothesis that variants that potentially change protein function are not assured, but may cause deleterious phenotypes. [22] A lower GVB score represents an increased likelihood of a variant to be more deleterious to the function of the protein encoded by the gene. [21,22]…”

“…[22] A lower GVB score represents an increased likelihood of a variant to be more deleterious to the function of the protein encoded by the gene. [21,22]…”

Homozygote CRIM1 variant is associated with thiopurine-induced neutropenia in leukemic patients with both wildtype NUDT15 and TPMT

“…Since East Asian ancestry requires significantly lower 6-MP dose intensity compared to the other ethnic groups [5], patients who require less than 25% of the protocol planned dose were classified as MP-intolerant groups [6]. We have previously presented a detailed description of the subjects and a summary of the measurements [7]. The present study was approved by the SNUH, AMC, and SMC institutional review boards.…”