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Future of Pharmacogenomics
The debate about pharmacogenomics (PGx) as a future tool in healthcare divides the clinical research community today. Some researchers doubt the benefit while others see huge potential. In fact, the evidence shows that the real question is how PGx should be deployed, not if, as a white paper by Bruce Quinn Associates indicates.
The boldest vision of the future is preemptive screening of populations to provide physicians with on-demand treatment decision support. Research today is focused on solving many challenges and exploring potential preemptive PGx (PPGx) strategies.
It's clear that well-designed, well-powered clinical research studies have been lacking[1] but this is rapidly changing, led by pioneers like Dr. Philip Empey from University of Pittsburgh.
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The vision for pharmacogenomics
Research programs are trialling preemptive pharmacogenomics (PPGx) strategies to unlock health and economic benefits at population scale. For example, U-PGx Consortium in Europe is targeting commonly prescribed drugs [2] [3]; pediatric treatment is the focus of Boston Children's Hospital and a collaboration between Medical University of Wisconsin and St. Jude's Children’s Research Hospital.
In addition to who to screen and why, choice of variants is also critical. Missing clinically important SNPs, CNVs or HLA types can radically change interpretation [4]. But final choice of variants will depend on outcomes of the research to define how best to deploy PPGx.
Genotyping strategy in the past has been a choice of going big with many variants, or taking a very targeted, hypothesis-led approach. Recently, we have developed a more dynamic way to select pharmacogenomic variants for clinical research genotyping that combines benefits of both. You can learn more about this by exploring our new Axiom PharmacoFocus Assay.
PPGx research genotyping strategies
Testing large variant panels, reporting subsets
Pros:
- Comprehensive data
- Flexible across therapeutic research areas
- Potential for PRS* integration
*requires a genotyping solution that includes genome-wide markers to enable development of Polygenic Risk Scores (PRS). Learn more at thermofisher.com/predictivegenomics.
Cons:
- Risk of data overload
- Cost of unused data
- Complex interpretation; secondary findings
As implemented on Axiom PharmacoFocus Assay
Pros:
- Flexible across therapeutic research areas
- Manage data load
- Manage cost
- Manage interpretation
Testing and reporting a small, fixed variant panel
Pros:
- Low data load
- Manage cost
- Simple interpretation
Cons:
- Low flexibility across applications
- Multiple panels likely
- No futureproofing
Testing large variant panels, reporting subsets
Pros:
- Comprehensive data
- Flexible across therapeutic research areas
- Potential for PRS* integration
*requires a genotyping solution that includes genome-wide markers to enable development of Polygenic Risk Scores (PRS). Learn more at thermofisher.com/predictivegenomics.
Cons:
- Risk of data overload
- Cost of unused data
- Complex interpretation; secondary findings
As implemented on Axiom PharmacoFocus Assay
Pros:
- Flexible across therapeutic research areas
- Manage data load
- Manage cost
- Manage interpretation
Testing and reporting a small, fixed variant panel
Pros:
- Low data load
- Manage cost
- Simple interpretation
Cons:
- Low flexibility across applications
- Multiple panels likely
- No futureproofing
The top priority for effective preemptive PGx research is high accuracy coverage of SNPs, CNVs and HLA variants that are potentially clinically relevant. Practical needs also influence choice of genotyping solution.
"The coverage that best aligned with our genes of interest for a clinical return was highest on our list. Other important attributes included ease of implementation, the ability to have product support, and understanding how the platform could be used by our research team."
— Dr. Philip Empey, University of Pittsburgh
Applied Biosystems Axiom Genotyping Solution is trusted worldwide by leaders in genomics, generating billions of genotypes for studies like UK Biobank and FinnGen Study.
For pharmacogenomic research, our Axiom PGx microarrays and Axiom Plus assay provide choice of coverage and high data quality, with global support to ensure success.
Content for PGx:
- SNPs, CNVs and HLA
- Targeted or genome-wide
- High-evidence PGx variants
- Complex ADME genes
Consistent data quality:
- No random variant loss during array manufacture
- ≥99.9% genotype accuracy with a single assay workflow
Collaboration for success:
- Global service and support
Customization service:
- Supported by our bioinformatics experts
Sample processing
- Automated GeneTitan Instrument or via our Service Lab network
- Scalable throughput
Data analysis and reporting
- Axiom Analysis Suite
- Integrated star alleles with metabolizer status
- Compatible with 3rd party reporting software
Explore Axiom microarrays for pharmacogenomics research
NEW! Axiom PharmacoFocus Assay
For population-scale preemptive pharmacogenomic clinical research
Configurable, targeted, high-evidence PGx content: up to 2,000 variants in 150 genes.
Content:
- 88% coverage of variants in PharmGKB annotation levels 1A-2B
- Includes difficult variants in CYP2D6, CYP2B6, CYP2A6, CYP2C19, CYP2C8, CYP1A2 GSTM1, SULT1A1
- SNPs, CNVs and HLA on one assay
Configure your content:
- Access only the content you want up to a maximum of 150 genes and 2,000 variants
- Unlock more content when needed, no need to re-run the assay!
Flexibility across therapeutic research areas:
- Including psychiatry, oncology, cardiology, neurology, pain management, peri-operative
Star alleles/ metabolizer status reporting:
- Over 970 haplotypes in 66 gene regions
Axiom PharmacoScan Assay
For comprehensive translational pharmacogenomic research
High-evidence and putative PGx variants: 4,627 variants in 1,191 genes.
Content:
- Comprehensive coverage of variants: PharmGKB levels 1A-4, CPIC, PharmaADME
- Includes difficult variants in CYP2D6, CYP2B6, CYP2A6, CYP2C19, CYP2C8, CYP1A2, GSTM1, SULT1A1
- SNPs, CNVs and HLA on one assay
Flexibility across therapeutic research areas:
- Including psychiatry, oncology, cardiology, neurology, pain management, peri-operative
Star alleles/ metabolizer status reporting:
- Over 880 haplotypes in 66 gene regions
Axiom Precision Medicine Diversity Research Array
For deeper research insights into genetic risk factors (PRS) and PGx profiling
Genome-wide including high-evidence and putative PGx variants: >900K markers.
Content:
- 92K variants in ADME genes including >5,000 variants with known PGx value
- Sourced from CPIC, PharmGKB, PharmaADME
- SNPs, CNVs and HLA on one assay
- Includes difficult variants in CYP2D6, CYP2B6, CYP2A6, CYP2C19, CYP2C8, CYP1A2, SULT1A1
- Genome-wide imputation-optimized design: access millions of additional markers
Flexibility for Polygenic Risk Score development, pharmacogenomics research, ancestry etc
- Broad coverage of disease and therapeutic research areas
- Simple Mendelian and complex heritable disease research
Star alleles/ metabolizer status reporting
- 831 haplotypes in 66 gene regions
Thermo Fisher Scientific also offers PGx research solutions for single to low-plex genotyping and targeted sequencing via TaqMan qPCR Assays and Ion Torrent next-generation sequencing.
Preemptive pharmacogenomics research is focused on defining how on-demand actionable insights could be delivered in the future at the point of decision making. Interpretation and integration into EHRs are major focuses with research programs either developing their own infrastructure or outsourcing. Integrating a participant's genetics, lifestyle information and health history can identify research insights on potential drug-drug interactions and drug response.
Applied Biosystems Axiom Analysis Suite can translate genotypes into functional star alleles when analyzing data from Axiom Genotyping Solution for pharmacogenomics research.
Star Alleles are curated from:
- PharmGKB (Stanford University)
- Pharmacogene Variation Consortium
- Database of NAT genes (Democritus University of Thrace)
- UGT SNPs and haplotypes (Laval University)
- TPMT nomenclature (Linkoping University)
- PubMed (National Library of Medicine)
Data from Axiom Genotyping Solution can also be integrated into third-party interpretation, for example Coriell Life Sciences (www.coriell.com) and Translational Software (www.translationalsoftware.com).
References:
1. https://jamanetwork.com/journals/jamapsychiatry/article-abstract/2680809
2. https://ascpt.onlinelibrary.wiley.com/doi/full/10.1002/cpt.1489
3. www.upgx.eu
4. www.nature.com/articles/s41436-019-0614-y
For Research Use Only. Not for use in diagnostic procedures.
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