Gene2Rx CYP2D6 Structural Analysis from your whole genome
Deletions, duplications and gene fusions, measured from the reads behind your whole genome VCF.
Your genome stays on your computer: your browser sends only the sections the analysis needs: CYP2D6 and a few dozen short comparison regions.
Who it's for
Anyone with whole genome sequencing who has, or can download, the BAM or CRAM file behind their VCF. CYP2D6 handles codeine, tramadol, many antidepressants, atomoxetine, metoprolol and tamoxifen, and its structure (how many copies you carry, and whether one is fused with a neighboring gene) can change your result for all of them.[1] A VCF lists variants, not copies or fusions, so your Gene2Rx report from a VCF says CYP2D6 copy number isn't measured. This add-on analyzes CYP2D6's structure and regenerates the report. It is not available for consumer DNA chips (23andMe, AncestryDNA and others) or for results entered from GeneSight or Genomind.
Our most complete analysis
$80A Full Report from your whole genome VCF and CYP2D6 Structural Analysis from your BAM or CRAM, together. All in, nothing else to buy:
- $50
- Full Report. Every medication we cover, with guidance from CPIC, the FDA and DPWG.
- $20
- Whole genome data. Every gene and variant we report on, read from your genome, including rare variants a DNA test chip doesn't read.
- $10
- CYP2D6 Structural Analysis. CYP2D6's deletions, duplications and gene fusions, measured from your reads, which a VCF can't show.
The whole genome example
Its VCF alone said CYP2D6 *2/*2, a normal metabolizer. The reads show *2/*2x2: three copies of CYP2D6, so an ultrarapid metabolizer. That changes guidance for 28 of the report's medications, including codeine and tramadol.
What's included
Your full CYP2D6 result measured from your reads: which alleles you carry, how many copies, and any fusion, including whole-gene deletions (*5), duplications and multiplications (such as *2x2), and CYP2D6-CYP2D7 hybrids (*36, *36+*10, *68+*4).[2] Its activity score and metabolizer status follow CPIC's standard translation.[3] Your report is then regenerated from your VCF on file. Every result shows its confidence; when your reads fit the best result less clearly than most, you also see the next most likely result and which of your medications it would change.
Example results
Real results from public benchmark samples: a duplication, a close call with the result that came close (we thinned this sample to 5x to show one; your file needs at least 20x), and an allele without an agreed function. For a whole report with it, see the whole genome example.
CYP2D6, measured from your reads
Measured*1/*4x2
Intermediate Metabolizer
Confidence: DecisiveStructure measured: deletions, duplications and gene fusions are part of this result, and your report's CYP2D6 medications use it.
CYP2D6, measured from your reads
Close call*1/*1
Normal Metabolizer
Structure measured: deletions, duplications and gene fusions are part of this result, and your report's CYP2D6 medications use it.
It was a close call: your reads fit this result best, but another came close. The next most likely result is *1/*1x2 (Ultrarapid Metabolizer).
If it were, guidance would change for 28 medications:
- Amitriptyline
- Amphetamine
- Aripiprazole
- Brexpiprazole
- Clomipramine
- Clozapine
- Codeine
- Desipramine
and 20 more
- Doxepin
- Eliglustat
- Fluvoxamine
- Haloperidol
- Hydrocodone
- Imipramine
- Meclizine
- Metoprolol
- Nortriptyline
- Oliceridine
- Ondansetron
- Paroxetine
- Pimozide
- Risperidone
- Tramadol
- Trimipramine
- Tropisetron
- Venlafaxine
- Vortioxetine
- Zuclopenthixol
Your file has fewer reads at CYP2D6 than a typical 30x genome, which makes the call less certain.
CYP2D6, measured from your reads
Unknown function*2x2/*71
One of these alleles has an unknown function: nobody yet knows how it changes the enzyme, so we can't predict your drug response from it. Your report keeps the CYP2D6 result from your VCF for now.
We don't refund a result like the last one, because the analysis ran and found your alleles. If it can't reach a result at all, we refund it automatically.
What's not included
It looks at CYP2D6 only. It reads BAM and CRAM files aligned to GRCh37 or GRCh38. Before you buy, your browser checks that your file has enough data to measure, so you never pay for a file we can't use. Low read depth makes calls less certain, and your result says so. A few rare alleles don't yet have an agreed function: if you carry one, you see the measured result, your report keeps the result from your VCF, and we don't refund it, because the analysis ran and found your alleles. If the analysis can't reach a result at all, we refund it automatically.
How it works
Your browser does the heavy lifting. Choose your BAM or CRAM file and its index on the CYP2D6 Structural Analysis page: your browser sends only the sections the analysis needs (CYP2D6 and a few dozen short comparison regions, a tiny fraction of your genome). The rest of your genome never leaves your computer. The measurement takes a few minutes, and we email you when your report is updated. Add it at checkout for $10 when you order a report from a whole genome VCF, or later from your account page for $10.
References
- Nofziger C et al., Clinical Pharmacology & Therapeutics. PharmVar GeneFocus: CYP2D6 (2020). doi.org
- Pharmacogene Variation Consortium (PharmVar). CYP2D6 allele definitions, including structural variants. pharmvar.org
- Caudle KE et al., Clinical and Translational Science. Standardizing CYP2D6 Genotype to Phenotype Translation: CPIC and DPWG Consensus Recommendations (2020). pmc.ncbi.nlm.nih.gov
Analyze your CYP2D6 structure
Order a report from your whole genome VCF and add it at checkout, or add it from your account if you already have a report.