Thiopurine pharmacogenomic landscape in India: TPMT and NUDT15 allele frequencies Free

Thiopurines—such as azathioprine, mercaptopurine, and thioguanine—are commonly used in hematology as immunosuppressants and chemotherapeutic agents. However, they carry a risk of myelosuppression, potentially leading to treatment delays or discontinuation. Genetic variants in TPMT and NUDT15, which increase toxicity risk by causing cytotoxic metabolite accumulation, are well-recognized, but their prevalence in the Indian population remains unknown.

Identifying with this goal, we analyzed anonymized whole-exome sequencing data (GRCh38) processed with the Illumina DRAGEN pipeline from 1,742 individuals tested at a collaborative tertiary laboratory in India, including 609 hematology cases evaluated for both benign and malignant indications. TPMT and NUDT15 variants were curated from Clinical Pharmacogenetics Implementation Consortium (CPIC) and annotated in VarSeq ((Golden Helix, Inc.) using 1000 Genomes Project, IndiGen, gnomAD v4.1, RefSeq, and ClinVar; variants with high population frequency, synonymous/nonfunctional annotations, or benign ClinVar classifications were excluded and the remainder classified according to ACMG/AMP guidelines. Allele frequencies in the hematology cohort were compared to the broader pan-India non-hematology cohort and benchmarked across major ancestry groups, with enrichment assessed by contingency testing.

Across the full dataset of 1,742 samples, two clinically actionable TPMT no-function variants—c.719A>G (p.Tyr240Cys) and c.460G>A (p.Ala154Thr)—were detected. In the pan-India cohort, 54 individuals carried at least one no-function TPMT allele: c.719A>G in 44 (allele frequency 1.26%) and c.460G>A in 10 (allele frequency 0.29%), all heterozygous and designated no-function by CPIC. By contrast, in the single-center hematology sub-cohort (n=609), only one c.719A>G carrier was identified (AF 0.08%) and no c.460G>A carriers, representing a significant depletion compared to the non-hematology group (Fisher's exact p=1.62×10⁻⁷ and p=0.018, respectively). When benchmarked against gnomAD, IndiGen, and 1KGP, the pan-India TPMT frequencies remained comparable to South Asian references (c.719A>G: 1.26% versus gnomAD_SAS 1.68% and 1KGP_SAS 1.74%; c.460G>A: 0.29% versus gnomAD_SAS 0.65% and 1KGP_SAS 0.41%) and were much rarer in East Asian and African populations. Broad TPMT interrogation identified 1,101 rare variants after filtering, including three pathogenic/likely pathogenic changes (chr6:18143722T>TTC, chr6:18139038C>T, chr6:18149083A>ATC) that were absent or extremely rare in gnomAD and IndiGen, suggesting possible population-specific relevance.

For NUDT15, the variant c.415C>T (p.Arg139Cys, *2/*3) was common in the full cohort, identified in 245 individuals (237 heterozygous, 8 homozygous; AF 7.26%) and closely matched South Asian frequencies in gnomAD_SAS (6.47%) and 1KGP_SAS (6.95%), though it differed modestly from IndiGen (8.37%; p=0.003), suggesting regional substructure. In the hematology subset, c.415C>T was enriched, with 105 carriers (100 heterozygous, 5 homozygous; AF 9.03%) versus 7.26% in non-hematology (p=0.00396), contrasting with the depletion of actionable TPMT alleles in the same group. Additional rare functional NUDT15 alleles were observed: c.50_55delGAGTCG (*9) and c.55_56insGAGTCG (*2/*6) in two heterozygotes each (AF 0.062%), and c.52G>A (*5) in one individual (AF 0.031%); c.50_55delGAGTCG is annotated as non-functional by CPIC.

In conclusion, actionable TPMT and NUDT15 alleles are present in India. TPMT no-function variants, which reduce or abolish TPMT activity and increase the risk of thiopurine-induced myelosuppression, were seen at expected South Asian frequencies in the broader cohort but were markedly depleted in our single-center hematology subset, likely reflecting referral/regional sampling bias. In contrast, the NUDT15 risk allele c.415C>T was common nationally and enriched in hematology patients, including homozygotes at high risk for severe thiopurine toxicity. We also identified rare, potentially deleterious TPMT variants that are absent or underrepresented in global reference datasets, underscoring the value of population-specific pharmacogenomic profiling. Our findings support pre-treatment NUDT15 genotyping (and TPMT where indicated) with genotype-informed dose adjustment and early monitoring to reduce myelosuppression-related treatment interruptions.