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Polymorphism discovery in 51 chemotherapy pathway genes.

Robert R Freimuth1, Ming Xiao, Sharon Marsh

  • 1Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.

Human Molecular Genetics
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Area of Science:

  • Pharmacogenetics
  • Genomics
  • Cancer Research

Background:

  • Pharmacogenetic studies rapidly assess predictive markers for therapeutic response.
  • Understanding genetic variations is crucial for optimizing cancer chemotherapy.

Purpose of the Study:

  • To identify common genetic polymorphisms in 51 candidate genes involved in antineoplastic agent pathways.
  • To assess the frequency and distribution of these polymorphisms across African-American, Asian-American, and European-American populations.

Main Methods:

  • Resequencing of 51 candidate genes across 120 DNA samples (40 per population group).
  • Genomic sequence analysis covering approximately 378 kb per sample.
  • Comparison of identified variants with public databases and prediction of functional impact using PolyPhen.

Main Results:

  • Identified 904 genetic variants, including 139 coding single nucleotide polymorphisms (cSNPs).
  • Found 40% of polymorphisms were common across all three populations, while 41% were population-specific.
  • 38% of variants were novel, not found in public databases. 35% of non-synonymous cSNPs were predicted as damaging, with frequency decreasing as predicted severity increased.

Conclusions:

  • Provides experimental validation and allele frequencies for polymorphisms in key cancer chemotherapy-related genes.
  • Facilitates the development of pharmacogenetic strategies for personalized cancer treatment.
  • Highlights the importance of population-specific genetic variation in drug response.