PLoS ONE (Jan 2013)

Systematic pharmacogenomics analysis of a Malay whole genome: proof of concept for personalized medicine.

  • Mohd Zaki Salleh,
  • Lay Kek Teh,
  • Lian Shien Lee,
  • Rose Iszati Ismet,
  • Ashok Patowary,
  • Kandarp Joshi,
  • Ayesha Pasha,
  • Azni Zain Ahmed,
  • Roziah Mohd Janor,
  • Ahmad Sazali Hamzah,
  • Aishah Adam,
  • Khalid Yusoff,
  • Boon Peng Hoh,
  • Fazleen Haslinda Mohd Hatta,
  • Mohamad Izwan Ismail,
  • Vinod Scaria,
  • Sridhar Sivasubbu

DOI
https://doi.org/10.1371/journal.pone.0071554
Journal volume & issue
Vol. 8, no. 8
p. e71554

Abstract

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BackgroundWith a higher throughput and lower cost in sequencing, second generation sequencing technology has immense potential for translation into clinical practice and in the realization of pharmacogenomics based patient care. The systematic analysis of whole genome sequences to assess patient to patient variability in pharmacokinetics and pharmacodynamics responses towards drugs would be the next step in future medicine in line with the vision of personalizing medicine.MethodsGenomic DNA obtained from a 55 years old, self-declared healthy, anonymous male of Malay descent was sequenced. The subject's mother died of lung cancer and the father had a history of schizophrenia and deceased at the age of 65 years old. A systematic, intuitive computational workflow/pipeline integrating custom algorithm in tandem with large datasets of variant annotations and gene functions for genetic variations with pharmacogenomics impact was developed. A comprehensive pathway map of drug transport, metabolism and action was used as a template to map non-synonymous variations with potential functional consequences.Principal findingsOver 3 million known variations and 100,898 novel variations in the Malay genome were identified. Further in-depth pharmacogenetics analysis revealed a total of 607 unique variants in 563 proteins, with the eventual identification of 4 drug transport genes, 2 drug metabolizing enzyme genes and 33 target genes harboring deleterious SNVs involved in pharmacological pathways, which could have a potential role in clinical settings.ConclusionsThe current study successfully unravels the potential of personal genome sequencing in understanding the functionally relevant variations with potential influence on drug transport, metabolism and differential therapeutic outcomes. These will be essential for realizing personalized medicine through the use of comprehensive computational pipeline for systematic data mining and analysis.