Pharmacogenomics Impacts Patient Care
Pharmacogenomics (PGx) utilizes genomic information to assess an individual’s response to certain medications. PGx can be used to predict adverse drug reactions or decreased efficacy, leading to improved health outcomes and decreased costs. An estimated 99% of people have actionable variants in PGx genes[1,2], and studies have shown that up to 55% of adults are prescribed drugs for which there are PGx guidelines available.
Using HiFi reads to advance pharmacogenomics research
In the following webinar, Dr. Stuart Scott and Dr. Yao Yang from Stanford University Medical Center discuss different approaches utilizing HiFi sequencing to interrogate CYP2D6 and other PGx regions.
HIFI TARGET ENRICHMENT WITH TWIST PROBES
Why choose HiFi sequencing with Twist target enrichment?
• End-to-end workflow optimized for HiFi reads
• Custom design for any panel size
• Small and large cohorts on a single SMRT® Cell
• High-accuracy variant calls, including SVs
• Direct phasing, unambiguous haplotypes, ancestry-agnostic discovery
HiFi Sequencing for Pharmacogenomics
Highly accurate long-read sequencing, known as HiFi sequencing, provides high-resolution insight into PGx loci, which include complex variants such as pseudogenes, tandem repeats, and CNVs. Compared to other technologies, long-read HiFi sequencing allows for accurate detection of structural and complex variants, direct haplotype phasing, and coverage of rare variants. With read lengths of up to 25 kb and >99.9% accuracy, HiFi sequencing enables PGx discovery and translational research to help drive personalized medicine and potentially improve patient care.
- McInnes G, Lavertu A, Sangkuhl K, Klein TE, Whirl-Carrillo M, Altman RB. Pharmacogenetics at Scale: An Analysis of the UK Biobank. Clin Pharmacol Ther. 2021 Jun;109(6):1528-1537. doi: 10.1002/cpt.2122. Epub 2020 Dec 17. PMID: 33237584; PMCID: PMC8144239.
- Chanfreau-Coffinier C, Hull LE, Lynch JA, DuVall SL, Damrauer SM, Cunningham FE, Voight BF, Matheny ME, Oslin DW, Icardi MS, Tuteja S. Projected Prevalence of Actionable Pharmacogenetic Variants and Level A Drugs Prescribed Among US Veterans Health Administration Pharmacy Users. JAMA Netw Open. 2019 Jun 5;2(6):e195345. doi: 10.1001/jamanetworkopen.2019.5345. PMID: 31173123; PMCID: PMC6563578.
Botton et al. described the inability of short-read sequencing approaches (B, C) to interrogate the promotor region of SLC6A4 (A), a gene involved with serotonin reuptake and antidepressant response, with high tandem repeat variability in this region affecting gene expression. Using PacBio technology, they were able to fully resolve and phase this region in the NA12156 Coriell sample (D). Read more about this study in this blog post on highly accurate variant calling with SMRT sequencing
Adapted from Figure 1 in Botton MR, Yang Y, Scott ER, Desnick RJ, Scott SA. Phased Haplotype Resolution of the SLC6A4 Promoter Using Long-Read Single Molecule Real-Time (SMRT) sequencing. Genes (Basel). 2020; 11(11):1333
HiFi amplicon sequencing for pharmacogenetics: CYP2D6
With PacBio® HiFi sequencing, CYP2D6 variation can be captured using highly accurate long reads on a single platform. Amplicon-based HiFi sequencing fully and directly resolves and phases complex loci like CYP2D6 without assembly or inference, allowing for ancestry agnostic haplotype assignment. In this CYP2D6 application note, we propose a streamlined PCR amplicon workflow that characterizes full-length CYP2D6 alleles with PacBio HiFi sequencing.
Whole Genome Sequencing
Generate reference-quality de novo genome assemblies
Comprehensively detect all variants in the human genome
Focus on variation in even the most difficult regions of the genome.
Get a complete view of transcript isoform diversity — no assembly required
Highly scalable pharmacogenomic panel testing with hybrid capture and long-read sequencing
Legacy low-cost technologies can be biased towards known variants and/or populations and may result in data that are incomplete or difficult to phase, potentially affecting phenotype prediction and subsequent clinical utility. With long-read PacBio HiFi sequencing and Twist Bioscience hybrid capture technology, we describe a pre-designed PGx panel that is comprehensive and cost-efficient, allowing for scalable application to precision medicine research programs.
Enabling research in pharmacogenomics
In the drive for precision medicine, enabling pharmacogenomics (PGx) research to investigate how an individual’s genetic variants can impact their response to medication is critical. With robust coverage of difficult-to-sequence and difficult-to map regions, combined with high accuracy variant calling and unambiguous haplotype resolution through direct phasing, HiFi sequencing is a powerful tool in PGx.
Full-length sequencing of CYP2D6 variants with PacBio HiFi reads
Explore our ACMG poster explaining how our recently developed streamlined end-to-end workflow enables the more accurate detection of highly polymorphic CYP2D6 loci.
From sample to star alleles: a long-read pharmacogenomics pipeline powered by Twist target enrichment and PacBio HiFi sequencing
We demonstrate the use of the Twist Alliance Long-Read PGx panel for use with PacBio HiFi sequencing systems, with an analysis pipeline that includes primary analysis (on-instrument), bioinformatics tools for secondary and tertiary analysis, star allele calling with Pangu and PharmCAT, and interpretation and reporting with PharmCAT and custom EHR clinical decision support (CDS) (e.g. Epic Best Practice Alerts).