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The Whole Two Yards

March 21, 2012

I’ve seen a number of participants write us emails asking: “Where’s my genome?” Believe me, we’re working on it! What we’re trying to do is pretty big, though — and Rome wasn’t built in a day.

Whole genomes vs. genotypes

If you’re familiar with services like 23andme or FamilyTreeDNA, you might not realize that there are important differences between these “direct to consumer genetic testing” companies and the Personal Genome Project. One major difference is the technology being used. These companies perform genome-scale genotyping: a technology which analyzes a subset of genome positions known to vary between people. In contrast, the Personal Genome Project is interested in performing “whole genome sequencing” to gather information for all positions in the genome.

Each technology has some benefits and disadvantages…

Genome-scale genotyping Whole genome sequencing
0.03% of the genome 90-100% of the genome
Known variations (usually common) All variations
(common and rare, known and unexpected)
Ideal for ancestry, usefulness
for health & traits is debated
Ideal for both ancestry and health
Interpretation is facilitated –
there are already many published
studies for known variations
Interpretation is currently very difficult
for rare and unexpected variations
$200-$3001 $4,000-$5,0002
Weeks to produce Months to produce
5-10MB of data 40-400GB of data

Currently, genome-scale genotyping has an excellent cost-benefit ratio. There’s a good reason it’s so popular — whole genome sequencing simply costs too much! But the whole genome is 6 billion positions, any of which could potentially hold a rare and uniquely personal variation. If you stretch a single human genome’s DNA out like a string, this is a bit more than 2 yards in length (or 2 meters for the metric folks). In comparison, a molecule with 2 million positions (the number of positions typically genotyped) would only be about 1/40th of an inch (or 2/3 of a millimeter)!

The Personal Genome Project is dedicated to sequencing the whole two yards of each genome: the rare and the unique along with the common variations. We think it’s likely that analyzing only the common points of variation is going to miss out on the most dramatic, rare variations that affect our health and traits.

Whole genome sequencing technology is new. Rapid improvements are still being made, but it still takes a lot more of both time and money to get a whole genome. Right now it takes a couple of months to produce a genome, and it costs thousands of dollars. It’s expensive, but the price has finally decreased to a point where we decided it was time to get started.3 And so we are sequencing genomes.

Research starts small

Those of you who have been watching our project for a while might already know this… it literally took years for the first ten PGP participants (known as the “PGP-10”) to get their genomes after signing up and donating samples. We’re at an exciting point right now as we expand the project, but we can’t go from 10 to 1,000 in the blink of an eye!

Sample collection was one of the large barriers we had to overcome as we moved beyond the PGP-10. With the help of Pete Estep we now have saliva samples from nearly 1,000 people. Most participants who sent us samples won’t receive their whole genomes for a while yet, but it’s important that we have them. 200 genomes are currently queued up for sequencing in the coming months. Once we’ve done these we’ll have learned a lot about how to move forward, and we’ll be raising more funding to sequence our other samples.

Rather than receiving a polished service using existing published research, Personal Genome Project participants are on the cutting edge of creating new research discoveries. Even the way our study is organized (in particular, releasing personal genetic data publicly) is unprecedented in many ways. Working at the “cutting edge” of research is the opposite of “polished”: we’re venturing into uncharted territory. There’s a lot of unexpected decisions to make, trial and error, and false leads. It’s exciting stuff — but sometimes it’s also frustrating! Many thanks to the individuals who have chosen to work together with us in this pioneering research.


Footnotes
1 Links: Info on pricing for 23andme and FamilyTreeDNA.
2 Links: Info on pricing for Illumina and Complete Genomics.
3 In the early days of the PGP, the cost of a whole genome sequence was as expensive as buying a nice house or a yacht!

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