Tag Archives: personal-genomics

My attempts at explaining personal genomics

random hapmap graphicThe other day I was talking to my parents about the fascinating world of personal genomics and I ventured to write up my description of some of the ideas behind the hapmap and personal genomics in an email.

I am reproducing the email here and hoping that I can get pointers on explaining things better ( I am after all only a biochemist/structural biologist) 

The world of personal genomics is upon us. Companies like 23andMe and deCode will run your genetic sample against a known list of variation markers and tell you things about yourself as suggested by your genes. or they will tell you what markers you share with what groups of people. Although this sounds amazing , a lot of this is very nuanced and understanding it is a fun exercise. Also all of this will change evrything or atleast it has the potential to.

Lets start at the begining , when you ask yourself to be “typed” or what do my genes have? What is this stuff all about
We are all quite different, i.e you and me will probably have several hundreds of thousands of  differences between the two of us. To actually estimate exactly how different you and me are , this will require a full sequencing of our genomes . This is quite expensive and takes a lot of time . 
Instead imagine if I told you that that scientists have figured out that these differences occur in groups i.e they are linked together. Very crudely..if one of these jumps from you to your child..it will take a few thousands of its neighbors along for the ride.  So now instead of getting information about the several hundred thousand actual differences , we can learn a lot by just looking at the tens of thousands of these labels . In each case for a particular label ( or marker or SNP) we can look at all the variation determined this far. i.e at position 59 all know human variation has either a A or a T. So you can belong to one of those two groups. Now, Once you get this or any such  label you can infer the rest that such a label is tied to. Collecting information on these labels is what projects like the hapmap do ( see hapmap.org) and it is exactly the identity of these labels that a genotyping service will provide you with ( for an example see http://www.snpedia.com/files/promethease/outputs/promethease-ngnomics.html).  

SO whats the big deal? . All of science is trying to figure out, what makes a person A die of a heart-attack before he was 20 , while person B lives till he was 80. As well all know , there are two parts to this story “Nature : or your genes” and “Nurture – or your liefetsyle”. Science can easily attempt to understand your genes. Because that is “hard” information. And in the case of person A and B , science asks the question, whats in their genes that might have led to the outcome.
So coming back to the point I made in the prevous few paras , instead of looking at the entire genome  for differences between person A and B , we can start by asking what markers or labels do they share and what do they not share. Then, taking the markers they dont share . Which among those are common with people who had heart-attacks early. So,  looking at this information may lead to some clues about which genes A or B had led to their resultant life-expectancies.

Lets take another example , say you want to test in advance  “what genes cause allergies to Sulfur drugs ” . So what you would do is give many people sulfur drugs and then check all the people who were allergic and look at what groups their genes belong to. At the end of which you ask the obvious question..all those people who came up with severe allergies to sulfur , what group ( or markers ) did they have in common. In most cases this is not a single gene or single number  , but  for simplicity, the answer you get is something like : if you have group A59C (also known as single nucleotide polymorphism or SNP) then you have a 20% chance of being allergic . Also , since most traits dont depend on only one label or marker , the answers are quite diffused and are given in terms of probabilities. Say a 20% chance of A59C may be converted to a 80% chance in combination with label G456A and a 0.2 % chance if you had F555A . Do you get the point? If you dont dont worry as you can tell it is quite complicated!

Regardless. The chances are that, the more we ask such questions , the more we learn about these probabilities and that  is what most genetic research is looking to do.
So instead of studying say 10000 mostly white americans , things become more meaningful if you study 1000,000 people from every corner of this earth . Then the numbers may all add up and give us a more clear label to associate with any given outcome , like a heart-attack . Thats what the hapmap is all about.

Anyways getting back to the point,  Such studies are what give rise to the field of  personal genomics i.e look at what markers you have and then compare them with known marker-result associations or known drug-effect associations.

As I have already hopefuly convinced you : these studies are very nuanced. People expect  cut-and-dry answers and many may  return disappointed. Also people prone to hypochondria , should definitely stay away , lest that 2% chance that you will have a heart-attack will be converted to a very high percent chance of you getting it , actually because of the stress you put yourself through as a result of this knowledge ( the nurture  or lifestyle part).

Also this points to how these studies if carried out correctly will  change a lot of things , medicine , health-care , the very nature of how we view ourselves.
These studies can attempt to answer questions like how similar are south and north Indians genetically . And as I just told you , nature is not cut and dry and neither is human history!. So interpreting especially these results with social or political  implications is a double edged sword! 

Before I end , you can check out one of these reports as is given by companies like 23andme .
http://www.snpedia.com/files/promethease/outputs/promethease-ngnomics.html

So are you excited? Do you want to find out whether you have a 10% chance of arthritis ? or a 40% chance that you have descended from a caucasian lineage?

more Reading on this topic:
http://www.hapmap.org/

For the medically inclined . You can read an article in science that talks about the implications of these studies for healthcare studies published in the science magazine