With the completion of the HapMap and its commercialization by Illumina and Affymetrix, it should be possible for researchers to find susceptibility alleles which have an odds ratio of >2 for any disorder, including Alzheimer disease, over the next couple of years. The expense will be high: Sample sizes of about 500 cases and 500 controls will be needed, and the cost per sample is on the order of $900. But if there are anymore genes with the effect size of ApoE out there, for AD or other diseases, we should now be able to find them.

View all comments by John Hardy

Q: Does the map provide enough resolution?
A: On average, the haplotype map has investigated about 1 SNP every 5,000 bases (i.e., 5 kb). For most applications this density should be sufficient to allow linkage disequilibrium mapping of common variants with at least moderate effects in genetically complex diseases. However, a phase 2 of the HapMap is planned which will probably more than quadruple this resolution.

Q: Will the HapMap help in complex diseases, where several variants on different chromosomes must interact, for example?
A: While the HapMap has many valuable uses in designing and interpreting future genetic association in AD and other diseases, it will unfortunately not help to better understand interactions between different genetic loci or non-genetic factors, because such interactions likely vary from phenotype to phenotype.

Q: Will the HapMap help in...  Read more

Q: Does the map provide enough resolution?
A: On average, the haplotype map has investigated about 1 SNP every 5,000 bases (i.e., 5 kb). For most applications this density should be sufficient to allow linkage disequilibrium mapping of common variants with at least moderate effects in genetically complex diseases. However, a phase 2 of the HapMap is planned which will probably more than quadruple this resolution.

Q: Will the HapMap help in complex diseases, where several variants on different chromosomes must interact, for example?
A: While the HapMap has many valuable uses in designing and interpreting future genetic association in AD and other diseases, it will unfortunately not help to better understand interactions between different genetic loci or non-genetic factors, because such interactions likely vary from phenotype to phenotype.

Q: Will the HapMap help in diseases where gene silencing, mRNA splicing, and other post-transcriptional and post-translational modifications are key to the pathophysiology?
A: If these pathophysiological changes are actually caused by common genetic variants in the genome, HapMap will definitely help us find them. It will still require a good number of experiments, though, to actually prove the causal relationship between associated SNPs on the one hand, and differences in mRNA splicing (for instance) on the other hand.

Q: Is the principle of tagging haplotypes scientifically sound, or does it run the risk of missing out on haplotypes that are low in frequency but high in consequence?
A: The principle of tagging haplotypes to cover untyped common genetic variants is certainly sound, and—with the data provided by the current HapMap release—has just become a whole lot easier. As everything in science, it does have limitations (such as finding very low-frequency polymorphisms or haplotypes). However, this is a rapidly evolving field and the planned phase 2 release of the HapMap, together with novel analytic strategies, should facilitate even the search for such uncommon variants in the near future.

The completion of the HapMap is a major advance for science, and one which will particularly benefit the field of psychiatry. Schizophrenia research has been hampered by a failure to replicate genetic linkage and association studies, and this may in part owe to population differences in allele frequency, haplotype structure, and the inability to select the proper genes and polymorphisms for analysis. The HapMap reduces the "search space" for genetic markers that will show associations with complex diseases, like schizophrenia, across samples, and will thus facilitate the causal polymorphisms that may be shared across these populations. The completion of the first phase of the HapMap is not just important as a milestone marking progress in mapping the human genome, but also it is important for the enhanced level of scientific inquiry it can enable.

View all comments by Stephen J. Glatt