Large scale medical sequencing
The National Human Genome Research Institute (NHGRI) announced recently that it's going to divert some of the throughput of its large scale sequencing program towards medical genetics.
Despite falling costs, large scale sequencing is still far beyond the budget of your everyday researcher, especially those researchers working on obscure Mendelian disorders that commercially minded funders aren't really interested in.
NHGRI is planning on tackling some of those obscure disorders first. If a disease is particularly rare then it's difficult to assemble a big enough family of patients for linkage analysis to be able to pinpoint the gene in a useful way and investigators can be left knowing only that the "broken" gene responsible for the disease lies somewhere in a stretch of the genome many megabases long. NHGRI's approach is to simply step in and sequence the whole stretch in all of the patients, then pass on the data to the relevant researchers.
NHGRI's also planning on looking at unmapped X-linked disorders; they say that there are at least 130 of these, based on data from OMIM. This would involve sequencing all of the exons on the X chromosome from patients afflicted by a particular disorder and looking for the variations that they had in common, on the basis that those variations might be worthy of further study.
Even more ambitiously, they outline a plan to sequence the loci surrounding and containing genes involved in common complex disorders like epilepsy and diabetes from samples taken from thousands of patients whose physiological parameters have been accurately measured. Variants with medically interesting correlations can then be detected with statistical methods.
Much of the work that they talk about is presumably designed more to drive technology and to generate protocols and methods for similar work in the future, with any potentially positive outcomes (i.e. mapping some disease genes) being simply a bonus. It seems unlikely that NHGRI would invest so much money on a brute force approach in an area like Mendelian disorders otherwise. There'll be a lot of very happy M.Ds whose pet Mendelian trait is just about to benefit from federal funding.
A lot of data is going to be generated from projects like this and the various national Biobanks. A top tip, if you're just finishing up your undergraduate degree (or looking for a career switch): there was never a better time to become a biostatistician.
Despite falling costs, large scale sequencing is still far beyond the budget of your everyday researcher, especially those researchers working on obscure Mendelian disorders that commercially minded funders aren't really interested in.
NHGRI is planning on tackling some of those obscure disorders first. If a disease is particularly rare then it's difficult to assemble a big enough family of patients for linkage analysis to be able to pinpoint the gene in a useful way and investigators can be left knowing only that the "broken" gene responsible for the disease lies somewhere in a stretch of the genome many megabases long. NHGRI's approach is to simply step in and sequence the whole stretch in all of the patients, then pass on the data to the relevant researchers.
NHGRI's also planning on looking at unmapped X-linked disorders; they say that there are at least 130 of these, based on data from OMIM. This would involve sequencing all of the exons on the X chromosome from patients afflicted by a particular disorder and looking for the variations that they had in common, on the basis that those variations might be worthy of further study.
Even more ambitiously, they outline a plan to sequence the loci surrounding and containing genes involved in common complex disorders like epilepsy and diabetes from samples taken from thousands of patients whose physiological parameters have been accurately measured. Variants with medically interesting correlations can then be detected with statistical methods.
Much of the work that they talk about is presumably designed more to drive technology and to generate protocols and methods for similar work in the future, with any potentially positive outcomes (i.e. mapping some disease genes) being simply a bonus. It seems unlikely that NHGRI would invest so much money on a brute force approach in an area like Mendelian disorders otherwise. There'll be a lot of very happy M.Ds whose pet Mendelian trait is just about to benefit from federal funding.
A lot of data is going to be generated from projects like this and the various national Biobanks. A top tip, if you're just finishing up your undergraduate degree (or looking for a career switch): there was never a better time to become a biostatistician.
posted by Stew @ 10:51 AM
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