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Inferring germline pharmacogenomics from tumor transcriptome.

Wenjian Yang1, Gang Wu2, Jeffery M Klco3

  • 1Department of Pharmacy and Pharmaceutical Sciences.

Pharmacogenetics and Genomics
|September 25, 2025
PubMed
Summary

Whole transcriptome sequencing (WTS) of leukemia tumors can accurately determine germline pharmacogenomic genotypes for treating pediatric acute lymphoblastic leukemia (ALL). This method provides reliable thiopurine dosing guidance for patients with ALL.

Keywords:
leukemiapharmacogeneticspharmacogenomicssequencingtranscriptome

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Area of Science:

  • Genomics
  • Pharmacogenomics
  • Pediatric Oncology

Background:

  • Pharmacogenomic testing is increasingly standard for pediatric acute lymphoblastic leukemia (ALL) treatment.
  • Risk stratification in ALL can be achieved using whole transcriptome sequencing (WTS) of diagnostic tumor samples.

Purpose of the Study:

  • To assess the feasibility of inferring germline pharmacogenomic genotypes from tumor transcriptome data in pediatric ALL patients.
  • To evaluate the accuracy of WTS-derived pharmacogene genotypes compared to germline sequencing.

Main Methods:

  • Collected transcriptome and paired tumor-germline genome sequencing data from clinical testing.
  • Utilized a rule-based algorithm on WTS data to determine genotypes for TPMT, NUDT15, and G6PD.
  • Compared WTS-derived genotypes with those from whole genome sequencing (WGS) and clinical assays.

Main Results:

  • WTS provided thiopurine dosing guidance for 83.8% of patients by determining TPMT and NUDT15 diplotypes.
  • Accurate G6PD genotyping was achieved in 367 male patients.
  • Demonstrated >99% concordance between WTS-derived and germline WGS diplotypes for TPMT, NUDT15, and G6PD.

Conclusions:

  • The leukemia transcriptome is a viable source for accurate germline pharmacogene genotyping in pediatric ALL.
  • This approach supports pharmacogenomic testing and personalized treatment strategies for pediatric ALL.