Dataset Information

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

ABSTRACT:

Background

With 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.

Methods

Genomic 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 findings

Over 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.

Conclusions

The 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.

SUBMITTER: Salleh MZ

PROVIDER: S-EPMC3751891 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Publications

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

Salleh Mohd Zaki MZ Teh Lay Kek LK Lee Lian Shien LS Ismet Rose Iszati RI Patowary Ashok A Joshi Kandarp K Pasha Ayesha A Ahmed Azni Zain AZ Janor Roziah Mohd RM Hamzah Ahmad Sazali AS Adam Aishah A Yusoff Khalid K Hoh Boon Peng BP Hatta Fazleen Haslinda Mohd FH Ismail Mohamad Izwan MI Scaria Vinod V Sivasubbu Sridhar S

PloS one 20130823 8

<h4>Background</h4>With 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.<h4>Methods</h ...[more]

PMID: 24009664

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Dataset Information

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

Background

Methods

Principal findings

Conclusions

Publications

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

Similar Datasets

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