New way of viewing genetic variations

Dec 21 2004

Human geneticists can now see which variations on the human genome are inherited together, thanks to a new way of viewing genetic variations in the latest release of the Ensembl genome browser [a joint project between EMBL's EBI and the Wellcome Trust Sanger Institute]. The new viewer will help researchers to understand susceptibility to complex diseases such as heart disease, diabetes, cancer and many psychiatric diseases.

Any two people share 99.9% of their DNA sequence but tiny variations, often in a single letter of the DNA code, can greatly affect an individual's susceptibility to disease. These 'single nucleotide polymorphisms' [SNPs] are inherited in blocks, and if two SNPs have a greater than random chance of being inherited together, they are said to be in linkage disequilibrium. "If you imagine the human genome as a pack of cards, with one SNP on each card, it's as though some cards are always shuffled together," explains Ensembl team leader Ewan Birney. "The upshot of this is that you only need to look at some of the cards to know what hand you've been dealt. The new view in Ensembl allows you to work out which cards you need to look at in any region of the sequence to predict which cards are in any individual's genetic 'hand.'"

This information will be extremely useful to human geneticists who are looking for genetic markers for disease. The likelihood that each SNP will be inherited with another is colour coded and indicated as a score. This helps researchers to pinpoint which SNPs they need to sequence in any population to find out whether inheritance of certain combinations of SNPs are associated with a certain disease.

Information from several large experiments to measure genetic variation in different populations is available through Ensembl's new linkage disequilibrium view. It's important to include different populations because two SNPs that are always inherited together in one population might not be in another. More information on genetic variation will be added to Ensembl in the near future because the HapMap consortium, an international group of scientists that is doing a global study of genetic variation, has just lifted all restrictions on the use of its data, allowing it to be incorporated into the major public databases for the first time.

"Understanding genetic variation is the next frontier in genomic research," concludes Birney; "Now that we have to tools to track variation effectively, we're much closer to fulfilling the promise of genomics, in terms of better ways of diagnosing and treating disease."

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