Application of long-read sequencing to elucidate complex pharmacogenomic regions: a proof of principle

Lee, Maaike van der; Rowell, William J.; Menafra, Roberta; Guchelaar, Henk‐Jan; Swen, Jesse J.; Anvar, Seyed Yahya

doi:10.1038/s41397-021-00259-z

Cited by 18 publications

(11 citation statements)

References 42 publications

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“…For a detailed overview of the technological basis of long‐read sequencing, we refer the interested reader to excellent reviews on this matter 19,20 . Long‐read sequencing facilitates the exact identification of CNVs and structural rearrangements and has already demonstrated considerable advantages compared to short‐read methods for the profiling and phasing of complex pharmacogenomic loci 21 . Both short‐read and long‐read sequencing have contributed to the identification of pharmacogenomic variant and allele distributions at the population scale 22,23 .…”

Section: Advances In Genetic and Genomic Profiling Methods That Enabl...mentioning

confidence: 99%

“… 19 , 20 Long‐read sequencing facilitates the exact identification of CNVs and structural rearrangements and has already demonstrated considerable advantages compared to short‐read methods for the profiling and phasing of complex pharmacogenomic loci. 21 Both short‐read and long‐read sequencing have contributed to the identification of pharmacogenomic variant and allele distributions at the population scale. 22 , 23 These projects have resulted in the identification of tens of thousands of different single‐nucleotide variations (SNVs), indels and CNVs.…”

Section: Advances In Genetic and Genomic Profiling Methods That Enabl...mentioning

confidence: 99%

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A paradigm shift in pharmacogenomics: From candidate polymorphisms to comprehensive sequencing

Zhou

Koutsilieri

Eliasson

et al. 2022

Basic Clin Pharma Tox

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Genetic factors have long been recognized as important determinants of interindividual variability in drug efficacy and toxicity. However, despite the increasing number of established gene-drug associations, candidate polymorphisms can only explain a fraction of the genetically encoded functional variability in drug disposition. Advancements in genetic profiling methods now allow to analyse the landscape of human pharmacogenetic variations comprehensively, which opens new opportunities to identify novel factors that could explain the "missing heritability." Here, we provide an updated overview of the landscape of pharmacogenomic variability based on recent analyses of population-scale sequencing projects. We then summarize the current state-of-the-art how the functional consequences of variants with unknown effects can be quantitatively estimated while discussing challenges and peculiarities that are specific to pharmacogenes. In the last sections, we discuss the importance of considering ethnogeographic diversity to provide equitable benefits of pharmacogenomics and summarize current roadblocks for the implementation of sequencing-based guidance of clinical decision-making.Based on the current state of the field, we conclude that testing is likely to gradually shift from the interrogation of selected candidate polymorphisms to comprehensive sequencing, which allows to consider the full spectrum of pharmacogenomic variations for a true personalization of genomic prescribing.

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Section: Advances In Genetic and Genomic Profiling Methods That Enabl...mentioning

confidence: 99%

Section: Advances In Genetic and Genomic Profiling Methods That Enabl...mentioning

confidence: 99%

A paradigm shift in pharmacogenomics: From candidate polymorphisms to comprehensive sequencing

Zhou

Koutsilieri

Eliasson

et al. 2022

Basic Clin Pharma Tox

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“…Although genome sequencing has become affordable for precision medicine programs focusing on cancer and the diagnosis of rare diseases, its costeffectiveness has not been proven yet for broader application such as population scale implementation of pharmacogenetics. Targeted sequencing of pharmacogenes with short or long-read sequencing 69 are more within reach, and particularly the latter has several advantages over other methods that cannot uniquely align reads or probes in the high homology regions of the Cytochrome P450 family of genes. 70 For population-scale programs, microarrays remain important for the rapid and ideally pre-emptive screening of millions of individuals at a low cost.…”

Section: Methods For Pharmacogenetic Testingmentioning

confidence: 99%

Pharmacogenomics in Stroke and Cardiovascular Disease: State of the Art

Ross

Krebs

Paré

et al. 2023

Stroke

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There is considerable interindividual variability in the response to antiplatelet and anticoagulant therapies, and this variation may be attributable to genetic variants. There has been an increased understanding of the genetic architecture of stroke and cardiovascular disease, which has been driven by advancements in genomic technologies and this has raised the possibility of more targeted pharmaceutical treatments. Pharmacogenetics promises to use a patient’s genetic profile to treat those who are more likely to benefit from a particular intervention by selecting the best possible therapy. Although there are numerous studies indicating strong evidence for the effect of specific genotypes on the outcomes of vascular drugs, the adoption of pharmacogenetic testing in clinical practice has been slow. This resistance may stem from sometimes conflicting findings among pharmacogenetic studies, a lack of stroke-specific randomized controlled trials to test the effectiveness of genetically-guided therapies, and the practical and cost-effective implementation of genetic testing within the clinic. Thus, this review provides an overview of the genetic variants that influence the individual responses to aspirin, clopidogrel, warfarin and statins and the different methods for pharmacogenetic testing and guidelines for clinical implementation for stroke patients.

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“…However, until relatively recently, these SMRT technologies had a lower accuracy than short-read NGS. In 2019, circular consensus sequencing (CCS) was optimized to generate highly accurate (99.8%) long high fidelity (HiFi) reads 46 , with a median length of 13.4 kb 47 . At this accuracy level, SNVs and short indels may be identified as well as structural variants.…”

Section: Introductionmentioning

confidence: 99%

Single molecule long-read real-time amplicon-based sequencing ofCYP2D6: a proof-of-concept with hybrid haplotypes

Dong

Thamilselvan

et al. 2022

Preprint

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CYP2D6 is a widely expressed human xenobiotic metabolizing enzyme, best known for its role in the hepatic phase I metabolism of up to 25% of prescribed medications, which is also expressed in other organs including the brain, where its potential role in physiology and mental health traits and disorders is under further investigation. Owing to the presence of homologous pseudogenes in the CYP2D locus and transposable repeat elements in the intergenic regions, the gene encoding the CYP2D6 enzyme, CYP2D6, is one of the most hypervariable known human genes - with more than 140 core haplotypes. Haplotypes include structural variants, with a subtype of these known as fusion genes comprising part of CYP2D6 and part of its adjacent pseudogene, CYP2D7. The fusion genes are particularly challenging to identify. The CYP2D6 enzyme activity corresponding to some of these fusion genes is known, while for others it is unknown. The most recent (high fidelity, or HiFi) version of single molecule real-time (SMRT) long-read sequencing can cover whole CYP2D6 haplotypes in a single continuous sequence read, ideal for structural variant detection. In addition, the accuracy of base calling has increased to a level sufficient for accurate characterization of single nucleotide variants. As new CYP2D6 haplotypes are continuously being discovered, and likely many more remain to be identified in populations that are relatively understudied to date, a method of characterization that employs sequencing with at least this degree of accuracy is required. The aim of the work reported herein was to develop an efficient and accurate HiFi SMRT amplicon-based method capable of detecting the full range of CYP2D6 haplotypes including fusion genes. We report proof-of-concept for 20 amplicons, aligned to fusion gene haplotypes, with prior cross-validation data. Amplicons with CYP2D6-D7 fusion genes aligned to *36, *63, *68, and *4 (*4-like; *4N, or *4.013) hybrid haplotypes. Amplicons with CYP2D7-D6 fusion genes aligned to the *13 subhaplotypes predicted (e.g., *13F, *13A2). Data analysis was efficient, and further method development indicates that this technique could suffice for the characterization of the full range of CYP2D6 haplotypes. Although included in drug labelling by regulatory bodies (the U.S. Food and Drug Administration, the European Medicines Agency, the Pharmaceuticals and Medical Devices Agency) and prescribing recommendations by consortia (Clinical Pharmacogenetics Implementation Consortium and the Dutch Pharmacogenetics Working Group), the identification of CYP2D6 variants is not yet routine in clinical practice. The HiFi sequencing method reported herein is suitable for high throughput, efficient, identification of the full range of known CYP2D6 haplotypes and novel haplotypes, and can be completed in a week or less. Moreover, the method that we have developed could be extended to other complex loci and to other species in a multiplexed high throughput assay.

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Application of long-read sequencing to elucidate complex pharmacogenomic regions: a proof of principle

Cited by 18 publications

References 42 publications

A paradigm shift in pharmacogenomics: From candidate polymorphisms to comprehensive sequencing

A paradigm shift in pharmacogenomics: From candidate polymorphisms to comprehensive sequencing

Pharmacogenomics in Stroke and Cardiovascular Disease: State of the Art

Single molecule long-read real-time amplicon-based sequencing ofCYP2D6: a proof-of-concept with hybrid haplotypes

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