I saw this as a great explanation to this question -
Given that each person's DNA is unique, can someone please explain what "complete mapping of the human genome" means?
"Think of the human genome like a really long set of beads on a string. About 3 billion beads, give or take. The beads come in four colors. We'll call them bases. When we sequence a genome, we're finding out the sequence of those bases on that string.
Now, in any given person, the sequence of bases will in fact be unique, but unique doesn't mean completely different. In fact, if you lined up the sequences from any two people on the planet, something like 99% of the bases would be the same. You would see long stretches of identical bases, but every once in a while you'd see a mismatch, where one person has one color and one person has another. In some spots you might see bigger regions that don't match at all, sometimes hundreds or thousands of bases long, but in a 3 billion base sequence they don't add up to much.
If you line up a bunch of different people's genome sequences, you can compare them all to each other. You'll find that the vast majority of beads in each sequence will be the same in everybody, but, as when we just compared two sequences, we'll see differences. Some of those differences will be unique to a single person- everybody else has one color of bead at a certain position, but this guy has a different color. Some of the differences will be more widespread, sometimes half the people will have a bead of one color, and the other half will have a bead of another color. What we can do with this set of lined up sequences is create a consensus sequence, which is just the most frequent base at every position in that 3 billion base sequence alignment. And that is basically what they did in the initial mapping of the human genome. That consensus sequence is known as the reference genome. When other people's genomes are sequenced, we line them up to the reference genome to see all the differences, in the hope that those differences will tell us something interesting.
As you can see, however, the reference genome is just an average genome*; it doesn't tell us anything about all the differences between people. That's the job of a lot of other projects, many of them ongoing, to sequence lots and lots of people so we can know more about what differences are present in people, and how frequent those differences are. One of those studies is the 1000 Genomes Project, which, as you might guess, is sequencing the genomes of a thousand (well, more like two thousand now I think) people of diverse ethnic backgrounds.
*It's not even a very good average, honestly. They only used 8 people, and there are spots where the reference genome sequence doesn't actually have the most common base in a given position. Also, there are spots in the genome that are extra hard to sequence, long stretches where the sequence repeats itself over and over; many of those stretches have not yet been fully mapped, and possibly never will be.
edit: I should also add that, once they made the reference sequence, there was still work to be done- a lot of analysis was performed on that sequence to figure out where genes are, and what those genes do. We already knew the sequence of many human genes, and often had a rough idea of their position on the genome, but sequencing the entire thing allowed us to see exactly where each gene was on each chromosome, what's nearby, and so on. In addition to confirming known sequences, it allowed scientists to predict the presence of many previously unknown genes, which could then be studied in more detail. Of course, 98% of the genome isn't genes, and they sequenced that as well -some scientists thought this was a waste of time, but I'm grateful the genome folks ignored them, because that 98% is what I study, and there's all sorts of cool stuff in there, like ancient viral sequences and whatnot."
