1000 genomes

Having discussed some of the issues I think it’s worth considering before deciding whether to get your own genome sequenced, I thought I would follow it up with why it is a good idea to sequence lots of people’s genomes!

Image from Leeds teaching hospital cytogenetics website

The 1000 genome project is actually a slightly misleading name for it as they actually plan to sequence 2500 genomes by the end of this year. Unfortunately (Or perhaps fortunately for my blog post!) they don’t provide any convenient sound-bites about why it’s a good idea apart form to say that “These methods and public data will support the next phase of human genetic research”. In fact the paper begins by saying it will “provide a foundation for investigating the relationship between genotype and phenotype” yet on the website they state that most samples were collected anonymously and no associated medical or phenotype data was recorded. So I think you could be forgiven for being a little confused by that!

(In case you’re wondering genotype refers to the version of the gene and phenotype refers to the physical characteristic that gene is responsible for.)

When the human genome project was first begun one of the criticisms of the project was whose genome would be sequenced?  A white male scientist? As I suggested in my last blog post “What’s in your genome?” having 3.3 gigabases of As, Ts, Cs and Gs doesn’t necessarily tell you anything, you need to be able to interpret it. Whilst there are reasons that getting your whole genome sequenced may not be such a good idea there are also times when genetic tests are invaluable. If there is a single gene disease that runs in your family, knowing whether you carry that version of the gene or not allows you to make informed choices, as does testing during pregnancy.

The 1000 genome project is one of a few projects designed to provide us with the user manual for the human genome. It provides a reference, a strong indication of how much genetic variation there is in the human race. Some conditions are quite complex and have both environmental and genetic components. For these many different genes can be involved and often regions of a chromosome are known to be associated with the condition but it isn’t known which changes or which genes exactly are involved. Knowing how much natural variation there is in the region will help to narrow down which changes are actually involved and help us to achieve a better understanding of the disease.

As well as it’s use in medical research this information could be used in forensics to narrow down the identity of a person.

Such detailed information about genetic variation could give us more information about our history and evolution. For instance, it has provided us with an indication of the rate of changes between generations by including some mother-father-child trios.

The 2500 genomes are made up of: 500 European, 500 East Asian, 500 West African, 500 from The Americas and 500 from South Asia. You can see a more detailed breakdown here. Whilst this doesn’t cover the whole world it does provide quite a bit of breadth.

Now we just have to read and understand the user manual and of course that’s going to take a little more time, and yes, you guessed it, more research before we fully understand the data. It is only by starting to use the manual that we’ll come to understand how well written it is and grasp fully the complexities and implications of the data.

This project is a world-wide effort and funding was provided by 29 different sources, so if you’re not convinced this project was worth the money, don’t worry you only paid for a tiny bit of it!

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5 Responses to 1000 genomes

  1. liz Alsbury says:

    This and the previous article have been both useful to my understanding and well written so that someone like me who has no knowledge of this subject is able to comprehend the main themes.

    Thanks for this most appropriate education

    Liz

  2. Laura clarke says:

    Hi

    I just thought i would clarify something. The reason the samples are anonymised with no information beyond family relationships and gender is to enable us to distribute everything about them from cell lines from their samples to the final discovered variants withou restriction

    The people who are sampled at at least at the time if collection are phenotypically normal so the assumption is made that at variant discovers is normal or at least not very pathogenic

    There are newer projects like uk10k which is sequencing very deeply phenotyped individuals to enable better genotype to phenotype discoveries to be made but the data from these projects will have restricted access due to the identifiable nature of the samples

    • Welcome to the blog Laura and thanks for your comment which is really enlightening.

      I guessed that was probably why more history wasn’t included and to be fair the paper was obviously aimed at other scientists so the ‘genotype to phenotype’ comment probably didn’t need expanding for that audience, but for a member of the public reading it that wouldn’t necessarily be very clear.

      One of the reasons I started this blog was to try and open the world of science up to more people and I’ve noticed that as scientists we don’t always do a great job of explaining why a particular piece of research is worth the money it costs to do it. I’m totally including myself in that but I’m hoping that writing a blog will help me to get better at it!

      Anyway, thanks again.

      • Laura says:

        Thanks

        I appreciate those of us in the know don’t always explain what we consider to be obvious details so I am glad my explaintation helped.

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