Sequencing.com Pharmacogenetics: Turn Your WGS Data Into a PGx Report

Sequencing.com gives you your full genome: whole genome sequencing data you can download as a VCF, alongside a marketplace of third-party apps that interpret raw data. What it does not give you directly is a comprehensive, guideline-based report on how those genes affect your medications. That is what Gene2Rx adds. Download your VCF from your Sequencing.com account and upload it to gene2rx.com, and Gene2Rx turns it into a pharmacogenetics report covering 110 medications, built on the same CPIC and FDA guidelines clinicians use. It runs in minutes, costs $5 for a starter report or $49 for the full report, plus a $15 surcharge for WGS and VCF uploads because they take more processing, so the full WGS report is $64. It needs no doctor's order and never expires, because your DNA does not change. You already paid to have your whole genome sequenced; this unlocks the part of it that affects prescriptions.

Whole genome sequencing reads every position, which is where your Sequencing.com data has a real edge. Genotyping chips (23andMe, AncestryDNA) tag variants at fixed positions, so they miss the rare variants that matter most for patients who do not fit the common phenotype bins; a VCF includes those. Gene2Rx reads the variant calls in your VCF, so one limit to know is that it does not detect copy-number changes such as CYP2D6 gene duplications or deletions, which require raw alignment files. And because the report is anchored to published guidelines, you can re-run it as those guidelines evolve.

Gene2Rx parses your VCF, extracts genotypes at every clinically relevant pharmacogenetic position, calls your metabolizer phenotype for each pharmacogene (poor, intermediate, normal, rapid, or ultrarapid), resolves star alleles from the variants in your VCF, and maps each phenotype to specific recommendations for 110 medications, with every recommendation traceable to its CPIC or FDA guideline. The report spans psychiatry (antidepressants, antipsychotics, ADHD medications), cardiology (clopidogrel, warfarin, statins, metoprolol), pain (codeine, tramadol), chemotherapy (capecitabine, fluorouracil), transplant, and gastrointestinal drugs. It is delivered in minutes, no new sample and no prescriber required.

Sequencing.com pairs whole genome sequencing with a marketplace of third-party apps that interpret your data. Gene2Rx is not listed in that marketplace; the workflow is simply to download your VCF from your Sequencing.com account and upload it to gene2rx.com, where the pharmacogenetic analysis runs. That keeps the process the same whether your data came from Sequencing.com or anywhere else, and it gives you a comprehensive CPIC- and FDA-anchored report across all major drug classes rather than a narrower built-in summary.

Clinical pharmacogenetic tests like GeneSight run from a few hundred to a few thousand dollars, need a new DNA sample, and require a provider order. Because you already have Sequencing.com WGS data, none of that applies: a Gene2Rx report is $5 for the starter tier or $49 for the full report, plus a $15 surcharge for WGS and VCF uploads (so the full WGS report is $64), with no lab work to repeat. Your pharmacogenetic profile does not change over time, so a single report is a reference you will use for decades of prescribing decisions.

These are the main genes Gene2Rx reads out of your Sequencing.com VCF and what each one affects. The biology is the same no matter which data source you start from; what Sequencing.com provides is the raw sequence at these positions.

Your Sequencing.com VCF contains the sequence for all of these genes; the only thing standing between that and actionable guidance is interpretation. Gene2Rx translates your genotypes into metabolizer phenotypes for each gene, then maps those phenotypes to specific medication recommendations anchored to CPIC^[8] and FDA^[9] guidelines, so the output reads the same way a clinical pharmacogenetic report would.

If you already have Sequencing.com WGS data, there is little reason to wait: the data exists and the starter report is $5 (plus the $15 WGS surcharge). It is most valuable if you are starting or already taking a medication with pharmacogenetic guidelines, if you have had side effects or poor response in the past, or if you simply want the information on file for future prescribing. Because your genotype never changes, one report serves you for life.

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No, Gene2Rx is not listed in the Sequencing.com App Market. The workflow is to download your VCF from your Sequencing.com account and upload it to gene2rx.com, where the pharmacogenetic analysis runs.

Download your VCF file from your Sequencing.com account, then upload it to gene2rx.com. The analysis covers 110 medications and supports both GRCh37 and GRCh38 reference genomes, auto-detecting which build your file uses.

Yes. Sequencing.com offers different sequencing depths; 30x coverage WGS is the clinical standard and the best substrate for pharmacogenetic analysis, resolving more than a genotyping chip can, especially complex genes like CYP2D6. The interpretation Gene2Rx derives from it follows the same CPIC and FDA guidelines a clinical lab would use. Lower-coverage sequencing can still produce useful calls but with less confidence on rare variants.

The starter report is $5 and the full 110-medication report is $49. WGS and VCF uploads carry a $15 surcharge because they take more processing, so the full WGS report is $64. You can start with the starter tier and upgrade later.