How Much Neanderthal DNA Do You Have? A Free Count From Your Raw DNA File

You can count your Neanderthal variants free from the raw DNA file you already have. At healthosx.com/dna, choose your 23andMe, AncestryDNA, MyHeritage, FamilyTreeDNA, Living DNA, WeGene or whole-genome file. Your browser checks it against 251,234 Neanderthal-matching sites, counts the Neanderthal variants you carry, and ranks you against the people outside Africa in the 1000 Genomes study: "You carry more of them than about 22% of people outside Africa." The count is done on your device, so nothing about it is uploaded.

What the number is

Everyone whose ancestors lived outside Africa carries some DNA from Neanderthals, inherited from interbreeding roughly 50,000 years ago. A study by Browning and colleagues (Cell, 2018) found the stretches of modern genomes that came from them, and the variants inside those stretches. Those variants are the reference list.

For your file, the report shows:

• The count: how many Neanderthal-matching variants you carry, at the sites your file covers.
• Your rank against people outside Africa in 1000 Genomes, overall and within Europe, East Asia, South Asia and the Americas.
• A range around the rank, because a chip reads only a small share of the sites. The report says so instead of printing one confident number.

healthosx.com/dna

Your Neanderthal variants, counted on your device and ranked against 1000 Genomes.

Why it isn't a percentage

23andMe and others have trained everyone to expect "2.1% Neanderthal". This report won't print that, for a plain reason: a percentage of your genome needs your whole genome compared with an archaic reference genome, and a chip reads a few thousand of these sites out of hundreds of thousands. What a chip can support honestly is a count and a rank.

The rank is also the more interesting statement. The share of Neanderthal DNA barely varies between people outside Africa, roughly 1 to 2% for almost everyone. Where you sit among them does vary, and that is what the percentile tells you.

Chip or whole genome?

Both work. A whole genome covers all 251,234 sites and pins your rank down. A chip covers a few thousand, enough to rank you once it covers at least 1,500, but with a wider range. To make the two comparable, the report ranks a ratio rather than a raw count: the variants you carry divided by the number expected at the sites your file covers. Every one of the 2,504 reference people has the same ratio computed, so a chip and a genome are placed on the same scale.

The count needs your file on genome build GRCh37, which is what 23andMe, AncestryDNA and MyHeritage deliver. A whole genome on GRCh38 skips it in the browser. The free file checker tells you your build and whether the count will run, without uploading anything.

If much of your ancestry is African

The Neanderthal-matching sites were found by comparing non-African genomes against an African outgroup, because Neanderthal ancestry entered the human line outside Africa. So the study has no African group to measure against, and a person with mostly African ancestry will see a low count. The report says why, rather than handing over a rank that reads like a shortfall.

Where else to get one

23andMe's report is the best known: it counts variants and ranks you among its own customers, but it needs a 23andMe kit and its Ancestry Service. Living DNA adds a Denisovan score, which this report doesn't have. GEDmatch's archaic matching looks for shared segments with specific archaic genomes, a different measure. The free option here is a count and a rank from any file you already own.

How to get your count

1. 1.Download your raw data (23andMe, AncestryDNA, MyHeritage or a whole-genome VCF).
2. 2.Choose it at healthosx.com/dna. The count runs in your browser while the file is read.
3. 3.Open your full report, which is free and needs a one-time code sent to your email. Your Neanderthal variants are counted on your device from the file and shown beside your ancestry and the ancient people you're closest to.

FAQ

Does more Neanderthal DNA mean anything for my health?

Some Neanderthal variants are linked in studies to traits such as skin, hair and immune responses, but a count across all of them isn't a health measure. Read it as history, not as a risk.

Why is my number different from 23andMe's?

Different sites, a different yardstick. 23andMe counts its own set of variants on its chip and ranks you among its customers. This counts Browning's sites and ranks you against 1000 Genomes. The two ranks can disagree and both be right about what they measure.

Count your Neanderthal variants, free, on your own device: healthosx.com/dna