Constellation: a tool for rapid, automated phenotype assignment of a highly polymorphic pharmacogene, CYP2D6, from whole-genome sequences.

Greyson P Twist,Andrea Gaedigk,Josh E Petrikin,Stephen F Kingsmore,Emily G Farrow,Suzanne Herd,Margaret Gibson,Amanda K Riffel,Darrell L Dinwiddie,J Steven Leeder,Neil A Miller,Sarah E Soden,Deendayal Dinakarpandian,Julie A Cakici,Laurel K Willig

doi:10.1038/npjgenmed.2015.7

Greyson P Twist, Andrea Gaedigk + Show 13 more

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https://doi.org/10.1038/npjgenmed.2015.7

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An important component of precision medicine—the use of whole-genome sequencing (WGS) to guide lifelong healthcare—is electronic decision support to inform drug choice and dosing. To achieve this, automated identification of genetic variation in genes involved in drug absorption, distribution, metabolism, excretion and response (ADMER) is required. CYP2D6 is a major enzyme for drug bioactivation and elimination. CYP2D6 activity is predominantly governed by genetic variation; however, it is technically arduous to haplotype. Not only is the nucleotide sequence of CYP2D6 highly polymorphic, but the locus also features diverse structural variations, including gene deletion, duplication, multiplication events and rearrangements with the nonfunctional, neighbouring CYP2D7 and CYP2D8 genes. We developed Constellation, a probabilistic scoring system, enabling automated ascertainment of CYP2D6 activity scores from 2×100 paired-end WGS. The consensus reference method included TaqMan genotyping assays, quantitative copy-number variation determination and Sanger sequencing. When compared with the consensus reference Constellation had an analytic sensitivity of 97% (59 of 61 diplotypes) and analytic specificity of 95% (116 of 122 haplotypes). All extreme phenotypes, i.e., poor and ultrarapid metabolisers were accurately identified by Constellation. Constellation is anticipated to be extensible to functional variation in all ADMER genes, and to be performed at marginal incremental financial and computational costs in the setting of diagnostic WGS.

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Cytochrome P450 family 2, subfamily D, polypeptide 6, CYP2D6, is one of the most important enzymes of bioactivation or elimination of endogenous and exogenous biochemicals
Mothers categorised as CYP2D6 ultrarapid metabolisers (OMIM#608902), and taking normal doses of codeine for post-partum pain relief, while breast feeding, convert codeine to morphine quickly resulting in high levels of morphine in breast milk that can lead to death in nursing infants.[4]
Variant-free reads were tiled across the 37-kb CYP2D6*2 region at 5-nt spacing and aligned to the CYP2D6*2-containing reference genome (GRCh37) with the algorithm Genomic Short-read Nucleotide Alignment Program (GSNAP) (Figure 2)

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Cytochrome P450 family 2, subfamily D, polypeptide 6, CYP2D6, is one of the most important enzymes of bioactivation or elimination of endogenous and exogenous biochemicals. To evaluate the performance of Constellation, CYP2D6 alleles were ascertained in 61 samples by manual integration of results obtained by quantitative copy-number assessment, a panel of TaqMan genotype assays, and Sanger sequencing of long-range genomic PCR products (the combination of these constitute the ‘consensus reference’) and probabilistic WGS analysis by Constellation (Table 1, Supplementary Table 2 and Supplementary Figure 3).

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