Scientists Complete Map of Human Genetic Variation

UltimaGuy writes "A major scientific step in the field of genetics is set to speed up the search for the causes of common illnesses ranging from heart disease and cancer to Alzheimer's and asthma. Scientists have mapped patterns of tiny DNA differences that distinguish one person from another, a step that will speed up the search for genes that promote common illnesses such as heart disease and diabetes."

Comments

Podcast from nature

[Oxen]

Here is a link to the mp3 of the Nature podcast on this.

I always think it is ridiculous how these genomic announcements happen. They choose to announce that they have ONE MILLION SNPs with big press release, but this data is available online as soon as its sequenced.

Re:Podcast from nature

[mr_stinky_britches]

Parent makes an interesting point. Here is a link a website where one can find additional information and even tab-delimited datafiles of SNPs variation and linkage.

Here is an additional site with even more information and datasets available. I'm going to download these and see what I can find.

They only analyzed DNA of 269 people

[backslashdot]

so if there are SNP mutations that only have a 1 in 270 or lesser chance of being present ..it's not going to be in their Map. You could be walking around with an SNP they missed cause the mutation happened recently (unique to you or maybe your grandparents etc) or is rare or whatever.

Re:They only analyzed DNA of 269 people

[espressojim]

You can measure SNPs that are undetected by this method by measuring haplotypes that those rare snps might occur on. Once you see an effect, then you can home in on the causal SNP.

Something that's interesting about your statement: if you look at a very rare SNP (less than 1%, for example), then you have very little power to see an effect on disease for this SNP. By definition, 99% of your sample size is not contributing power to your study. Thus, you can't statistically find effects unless you have a) massive sample size or b) massive mendelian effects.

The goal of this data is to study COMMON polymorphisms. That's why it's callled the common variant hypothesis.

And yes, I do work with these people.

RTFHM

[Anonymous Coward]

Read the friendly Haplotype Map, that is:
http://www.hapmap.org/.
You can even browse the project data: Gbrowse

Re:Patented

[lockefire]

First of all, most SNPs are free information. dbSNP contains ~5 million validated SNPs and ~27 million reported SNPs in humans. Celera owns a lot of SNP finds, but most are junk (sequencing errors) and they will be giving them to the free databases soon.

However, the importance of this article has nothing to do with the number of SNPs available or the fact that the SNPs are common (because of the low sample size). The whole point is to have SNPs that exist in ~50% of the population so that the haplotype can be determined. The Haplotype shows which segments of the genome tend to be inherited together. This can be traced back for multiple generations of inheritance - essentially there are ancient haplotypes and more modern haplotypes. The importance of looking at haplotypes is that it allows researchers to see which region an important mutation relating to a disease may occur in. Note that just by knowing which haplotype the disease causing mutation occurs in does not let us know which SNP or insertion/deletion event causes the disease.

A Human Geneticist's Point Of View

[kid_icarus75]

There are so many things incorrectly implied about this finding that it's almost hard to begin:

1) The headline and idea: "New DNA Map Will Help Find Bad Genes". There are no bad genes. Evolution didn't just come around and place some miscreant gene in your body just to give you a hard time after living off a diet of pizza and Mt. Dew for ten years. Every gene has its own function. Genetic research is based more upon finding which variation of a gene is more beneficial to an individual and how to change/block the non-beneficial variations. Genes are either more or less successful, but definitely (minus the case or rare genetic diseases) not evil or bad.

2) "The project analyzed DNA samples from 269 people from Nigeria, Beijing, Tokyo and Utah." Well, this would be fine if everyone was of a direct Nigeria, Beijing, Tokyo or Utah decent similar to the test subjects. As for real world population, they probably contain mutations not near those found in any of these people. A native american, a man from agentina, and a guy from India I guarantee you would have completely different results. And that's assuming pure-bread people. Where would someone like Tiger Woods fit in? As an interesting side note, why do you think they picked Utah? Could it be that one of the principal investigators of the study is Mormon and thought it might be nice to bring government funds to his own people? I think that most of us can agree that politics and science rarely mix to give good results...

3) 269 People? You're telling me that out of 3 billion DNA basepairs, we can find all the parts that have changed over the last few hundred thousand (and more) years in only 269 people?

4) "This clustering greatly simplifies the task of analyzing what variations a person carries, because not all of them have to be identified." and "A person with one particular version of a SNP is highly likely to carry particular versions of other SNPs as well." When you begin to think about the error rates contained in "highly likely" and then start to cluster those rates togeter, your model falls apart.

Basically, from my own experience of working with data of thousands of whites, blacks, both male and female, the rates at which certain areas of DNA are linked vary directly upon the strata one looks at and the number of individuals in that strata. This project is a neat theorhetical idea, but until we can sequence the entire genomes of thousands of people overnight for a small fee, there is not enough realy data to really do anything with.

We are not trying to trick nature.

[hackwrench]

Nature doesn't have goals to be tricked out of. Nature doesn't have beliefs to be fooled out of believing.

Coordinators

Abh

No rare alleles in data

[John Hawks]

Actually, the HapMap is basically useless for "rare" genetic variants, because it intentionally is screening for common ones. Hence, it may actually be useful for common susceptibility alleles for heart disease or stroke but it isn't going to find the rare variants that affect only a few people.

From my weblog:

The HapMap is an incredible step forward in characterizing human genetic variation. It's a challenging dataset to work with, though. It's like an old map showing continent margins and little else -- we can see many of the common SNPs, but for most we have no idea which ones are functional or what they might do.

--John