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Helix Sequencing vs Promethease
Promethease has been the go-to cheap SNP lookup for a decade. Helix Sequencing represents what comes next. Here is a fair comparison of both approaches.
Last updated March 30, 2026 · 9 min read
Promethease and Helix Sequencing both accept raw DNA data from 23andMe, AncestryDNA, and other consumer tests. But they do fundamentally different things with that data. Promethease runs your SNPs against SNPedia, a community-edited wiki of genetic variant associations, and returns a list of matches. Helix Sequencing runs a full computational pipeline — deep imputation, 3,550+ polygenic risk scores, 34-gene pharmacogenomics, ClinVar scanning, and an AI-generated health protocol.
The price difference reflects the scope difference: Promethease costs $12 and gives you a variant lookup. Helix costs $50 and gives you a clinical-grade health analysis with AI integration. Understanding what each service actually does helps you decide which — or both — makes sense for you.
Quick Comparison
| Feature | Helix Sequencing | Promethease |
|---|---|---|
| Approach | Full analysis pipeline: imputation + PRS + PGx + ClinVar + AI | Individual SNP lookup against SNPedia wiki |
| Polygenic Risk Scores | 3,550+ models (PGS Catalog) | None |
| Pharmacogenomics | 34 genes, CPIC star allele calling | Individual SNP mentions only (no star alleles) |
| Deep Imputation | Yes (Beagle 5.5, 700K → 28M+ variants) | No |
| ClinVar Scanning | 400,000+ variants | Individual variant mentions via SNPedia |
| AI Integration | MCP server for Claude + JSON export for any AI | None |
| Report Quality | Interactive report + Doctor's PDF + longevity protocol | Color-coded SNP list (green/red/grey) |
| Actionable Guidance | Personalized health protocol with supplements, diet, training | None — raw research citations only |
| Report Synthesis | Prioritized by clinical significance | Thousands of entries to sort through manually |
| Accepted Files | 23andMe, Ancestry, MyHeritage, VCF, most chips | 23andMe, Ancestry, MyHeritage, FTDNA, VCF, WES |
| Data Retention | Zero (SHA-256 deletion certificate) | Temporary; owned by MyHeritage |
| Price | $50 one-time or $10+$5/mo | $12 one-time |
| Best For | Comprehensive health analysis + AI integration | Quick, cheap individual variant lookup |
What Promethease Actually Does
Promethease is a literature retrieval service. It takes your raw DNA file, matches each SNP against the SNPedia database, and returns a list of your variants alongside published research findings. Each entry shows your genotype, a summary from SNPedia, a “magnitude” score (0-10 scale of interestingness), frequency data, and links to source publications.
Entries are color-coded: green (potentially beneficial), red (potentially concerning), and grey (neutral or unclear). A typical report contains several thousand entries that you scroll through and filter manually.
SNPedia contains information on roughly 100,000+ SNPs, curated as a wiki by community editors. This means quality varies — some entries are well-sourced from large genome-wide association studies, while others reference small, unreplicated findings. There is no systematic curation standard, and some entries reference outdated or superseded research.
The fundamental limitation: Promethease reports individual SNP associations. It does not combine variants into polygenic risk scores, does not perform star allele calling for pharmacogenomics, does not prioritize findings by clinical actionability, and does not provide recommendations. You get data. What you do with it is entirely up to you.
The Polygenic Risk Score Gap
This is the single largest difference between the two services. Promethease does not calculate polygenic risk scores. It reports individual variant associations — one SNP at a time.
Polygenic risk scores combine thousands of variants into a single risk prediction. Heart disease risk, for example, depends on hundreds or thousands of genetic positions working together. Looking at any single variant gives you almost no useful information about your overall risk. A PRS integrates all of them.
Helix Sequencing runs all 3,550+ modelsin the PGS Catalog — the peer-reviewed repository maintained by EMBL-EBI and the University of Cambridge. Each model was developed by research institutions and published in scientific journals. This is the same scoring methodology being adopted by research hospitals worldwide for clinical risk stratification.
Promethease might tell you that you carry a variant associated with slightly increased heart disease risk in one study. Helix tells you where you fall on the population distribution for coronary artery disease risk based on all known contributing variants, with a percentile and confidence level.
Pharmacogenomics: Individual SNPs vs Clinical Star Alleles
Promethease will flag individual pharmacogenomic SNPs that appear in SNPedia — for example, it might highlight rs4244285 (CYP2C19*2). But it does not perform star allele calling, does not assign diplotype status, and does not generate a metabolizer phenotype. You see individual variants but not the clinical interpretation that makes them useful.
Helix Sequencing analyzes 34 pharmacogenesusing CPIC (Clinical Pharmacogenetics Implementation Consortium) star allele calling — the same methodology used in hospital pharmacogenomic testing. This means you get actual metabolizer status (poor, intermediate, normal, rapid, ultrarapid) for each gene, with specific drug-gene interaction reports that are actionable by physicians.
The difference matters clinically. Knowing you carry one CYP2C19 variant is not the same as knowing you are a CYP2C19 poor metabolizer who should avoid clopidogrel. The first is trivia. The second can prevent a heart attack.
Report Quality: Data Dump vs Health Analysis
The most common criticism of Promethease is that reports are overwhelming and difficult to interpret. You receive thousands of variant entries with minimal guidance on what matters, what is actionable, and what is based on weak evidence. Many users report anxiety from seeing dozens of “red” variants without understanding that most have tiny effect sizes or come from unreplicated studies.
Helix Sequencing produces an interactive HTML report organized by clinical category, with risk scores presented as percentiles on population distributions. A doctor-ready PDF summarizes findings for healthcare providers. A personalized longevity protocol provides actionable supplement, diet, and training recommendations based on your actual risk profile. And structured JSON export lets you connect everything to AI assistants for conversational follow-up.
When Promethease Makes Sense
You want a quick, cheap first look
At $12, Promethease is the cheapest way to see which of your individual variants have been studied. It's a reasonable starting point if you're curious about your DNA and want to browse published associations without committing to a deeper analysis.
You enjoy reading primary research
If you're the kind of person who reads GWAS papers and understands odds ratios, Promethease gives you direct links to the source literature for each variant. It's essentially a research bibliography personalized to your genotype.
You want broad file compatibility
Promethease accepts nearly every consumer DNA format including whole genome sequencing VCF files. If you have an unusual file format, Promethease is likely to accept it.
When to Choose Helix Sequencing
You want actionable health insights, not a data dump
Helix synthesizes your data into prioritized findings: risk percentiles across 3,550+ conditions, a pharmacogenomic profile for 200+ medications, and a personalized health protocol. You get answers, not homework.
Polygenic risk scores matter to you
Promethease cannot calculate PRS. Helix runs the full PGS Catalog — the most comprehensive PRS analysis available to consumers. For conditions like heart disease, diabetes, and cancer, PRS provides dramatically more predictive power than individual SNP lookups.
You need clinical-grade pharmacogenomics
Helix's 34-gene CPIC star allele calling gives you actual metabolizer status for major drug-metabolizing enzymes. This is the information your doctor needs to adjust medications. Promethease's individual SNP flags don't provide this level of clinical utility.
You want to connect your DNA to AI
Helix's MCP server and JSON export let you ask Claude or ChatGPT questions about your genetic data in natural language. Promethease has no AI integration — you're on your own interpreting thousands of entries.
Data privacy matters
Helix deletes your data after analysis with cryptographic proof. Promethease is owned by MyHeritage, which experienced a 92-million-account data breach in 2018 (before the acquisition, but under the same corporate umbrella).
You can use both. Run Promethease for $12 to browse individual variant associations, then upload the same file to Helix for comprehensive risk scoring, pharmacogenomics, and AI integration. The $62 combined cost is still less than most single genomic services.
Frequently Asked Questions
Does Promethease calculate polygenic risk scores?
No. Promethease only performs individual SNP lookups against the SNPedia database. It does not aggregate variants into polygenic risk scores. Helix Sequencing runs 3,550+ PRS models from the peer-reviewed PGS Catalog, providing composite risk predictions for thousands of conditions.
Is Promethease still worth using in 2026?
Promethease provides a quick, affordable ($12) look at individual genetic variants with published research associations. It's a reasonable starting point for curious users. However, for comprehensive health analysis with polygenic risk scores, proper pharmacogenomics, and actionable recommendations, it has been surpassed by services like Helix Sequencing.
Who owns Promethease?
Promethease was acquired by MyHeritage in June 2019. MyHeritage is a genealogy company that experienced a data breach in 2018 affecting 92 million accounts. Promethease data is governed under MyHeritage's broader privacy policy.
Why are Promethease reports hard to read?
Promethease reports contain thousands of individual variant entries with minimal synthesis or prioritization. Each entry is a raw SNPedia match — you must manually determine which findings are clinically significant, which are based on strong evidence, and which are actionable. This requires genetics expertise most consumers don't have.
Can I upload my 23andMe data to both services?
Yes. Both Promethease and Helix Sequencing accept raw data files from 23andMe, AncestryDNA, MyHeritage, and most other consumer DNA services. You can upload the same file to both for complementary analysis.
Go Beyond Individual SNPs
Get 3,550+ polygenic risk scores, 34-gene pharmacogenomics, and a personalized longevity protocol from the same DNA file. Connect your genome to Claude or ChatGPT. Zero data retention.
Upload Your DNA FileAccepts the same files as Promethease. Results in minutes.
Key Takeaways
Promethease is a $12 variant lookup tool that matches your SNPs against the SNPedia wiki. It does not calculate polygenic risk scores, perform star allele calling, or provide health recommendations.
Helix Sequencing runs a full analysis pipeline: deep imputation to 28M+ variants, 3,550+ PRS models, 34-gene pharmacogenomics with CPIC star alleles, 400,000+ ClinVar variants, and a personalized health protocol.
The biggest gap is polygenic risk scores. Individual SNP lookups miss the combined effect of thousands of variants working together. PRS provides dramatically more predictive power for complex diseases.
Promethease reports are widely criticized for being overwhelming — thousands of entries with minimal synthesis. Helix delivers prioritized, actionable findings with interactive reports and doctor-ready PDFs.
Promethease is owned by MyHeritage (acquired 2019). Helix operates on zero data retention with SHA-256 deletion certificates.
The services are complementary. Promethease for $12 gives you a quick variant browse. Helix for $50 gives you the deep analysis. Both accept the same DNA files.