Thai PGx Landscape is a web-based pharmacogenomics platform dedicated to the Thai population. It serves as a centralized resource for exploring genetic variation data that influences individual and population-level drug responses, supporting researchers, clinicians, and policy makers in applying pharmacogenomic knowledge to real-world practice.
Background & Purpose
Genetic differences among individuals and populations are a principal determinant of variability in drug efficacy and safety. Characterizing these differences requires population-specific pharmacogenomic data, which is essential for the effective and evidence-based implementation of clinical pharmacogenomics. Comprehensive resources of this nature for the Thai population have, however, remained limited.
Thai PGx Landscape was developed to address this gap. The platform consolidates pharmacogenomic data derived from whole-genome sequencing (WGS) of Thai individuals into a structured, searchable system, enabling evidence-based exploration of how genetic variation shapes drug response and providing a foundation for precision medicine at both the individual and national level.
Data Generation
The platform's data is derived from a multi-stage genomic analysis pipeline applied to whole-genome sequencing data of Thai individuals. The pipeline encompasses three sequential phases, spanning raw sequencing data processing, individual-level pharmacogenomic analysis, and population-level aggregation with database integration.
Phase 1
NGS Data Processing
Raw WGS reads (FASTQ) undergo quality filtering, read mapping to GRCh38, base quality score recalibration (BQSR), and per-sample variant calling using GATK HaplotypeCaller, producing aligned BAM files and combined variant VCFs.
Phase 2
Individual-level PGx Analysis
HLA diplotypes are called using HLA-LA; CYP2D6 diplotypes using StellarPGx; and remaining pharmacogenes using the PharmVIP guideline module. Short variant analysis encompasses 3,239 pharmacogenes, with results formatted per individual sample.
Phase 3
Population-level Aggregation
Individual-level results are extracted, transformed into genotype summaries, drug recommendation reports, and HLA reports, then loaded into a central data warehouse and MongoDB database, enriched with curated data from DrugBank, GeneCards, HLA-ADR, and gnomAD.
Data Sources
In addition to the Thai WGS dataset, the platform integrates curated information from established external databases and reference resources:
DrugBank
Drug–gene interaction and pharmacology data
GeneCards
Comprehensive gene annotation and function
HLA-ADR database
HLA allele–adverse drug reaction associations
gnomAD
Population-level variant frequency reference
CPIC guidelines
Clinical dosing recommendations by genotype
PharmGKB
Pharmacogenomic variant and guideline annotations
Platform Modules
The platform is organized into six interconnected functional modules, each designed to address a specific dimension of pharmacogenomic data and to support distinct research or clinical use cases.
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Genes
Gene explorer
Enables users to search and explore pharmacogenes by gene name or associated properties. The module presents gene-level details including genetic analysis results, phenotype associations, and drug dosing guidance, facilitating a comprehensive understanding of each gene's role in pharmacogenomics.
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Drugs
Drug–gene links
Allows users to search for drugs and examine their associations with relevant pharmacogenes. The module presents drug details, genetic analysis results, phenotype information, and prescribing recommendations to support the clinical interpretation of pharmacogenomic data.
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Variants
Variant browser
Provides a searchable and filterable interface for genetic variant data. The module supports filtering by multiple variant properties, enabling efficient and targeted access to specific variants of interest, including short variants, SNPs, and functionally significant alterations in pharmacogenes.
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HLA-ADR
Drug safety
Presents associations between HLA gene alleles and adverse drug reactions (ADRs). Users may search and filter by HLA gene name and access the supporting research evidence underlying each association, providing critical information for pharmacovigilance and drug safety assessment.
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Samples
Population data
Facilitates exploration of population-level data by allowing users to define selection criteria for filtering sample groups. The module displays the total count and detailed characteristics of samples satisfying the specified conditions, supporting an understanding of the structure and composition of the underlying dataset.
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Statistics
Summary & visualization
Presents aggregated pharmacogenomic analysis results in the form of charts and statistical visualizations, enabling users to identify trends, patterns, and distributional characteristics across the dataset in an accessible and interpretable manner.
Scope of Use
Thai PGx Landscape is designed to serve a broad range of users across research, clinical, and health policy contexts. The platform supports pharmacogenomic research and data exploration, assists clinicians in interpreting genetic information relevant to drug prescribing decisions, and provides a data infrastructure for national genomics initiatives, including the Genomics Thailand program.
The six modules are designed to function in an integrated manner, enabling users to navigate fluidly across gene, drug, variant, and population perspectives, thereby facilitating a comprehensive and multi-dimensional understanding of the Thai pharmacogenomic landscape.