cheap high-throughput DNA sequencing is going to change the world in a shocking way (by 2020, I think). at present, it's not crystal clear how; there's a lot of nonsense speculation being thrown around and it's not easy to separate the legit potential applications from the bogus. After all, there have been many new technologies in biology that have been touted as the technology that will cure disease.
For example, microarrays were supposed to inform differences in gene expression (i.e. how much of a given protein is being made from a given gene) between, for example, a normal tissue sample and a tumor sample, and thereby identify the cause(s) of cancer. The bogusness: 1) this reasoning requires that cancer is caused by change in gene expression (dubious), and 2) that there would be sufficient statistical power to distinguish such a change from the intrinsic measurement error (equally dubious).

More common diseases, like cancer, are thought to be caused by mutations in several genes, and finding the causes was the principal goal of the $3 billion human genome project. To that end, medical geneticists have invested heavily over the last eight years in an alluring shortcut.

But the shortcut was based on a premise that is turning out to be incorrect. Scientists thought the mutations that caused common diseases would themselves be common. So they first identified the common mutations in the human population in a $100 million project called the HapMap. Then they compared patients’ genomes with those of healthy genomes. The comparisons relied on ingenious devices called SNP chips, which scan just a tiny portion of the genome. (SNP, pronounced “snip,” stands for single nucleotide polymorphism.) These projects, called genome-wide association studies, each cost around $10 million or more.

The results of this costly international exercise have been disappointing. About 2,000 sites on the human genome have been statistically linked with various diseases, but in many cases the sites are not inside working genes, suggesting there may be some conceptual flaw in the statistics. And in most diseases the culprit DNA was linked to only a small portion of all the cases of the disease. It seemed that natural selection has weeded out any disease-causing mutation before it becomes common.

The finding implies that common diseases, surprisingly, are caused by rare, not common, mutations. In the last few months, researchers have begun to conclude that a new approach is needed, one based on decoding the entire genome of patients.

It's funny how the story is told. The author suggests that the HapMap project was intended to definitively determine the causes of cancer. But it is common knowledge that disease is determined not only by genotype and but also by environment--a pair of identical twins share the same genotype, but do not always share the same diseases.

The Illumina/Solexa technology requires only 1 g of DNA per library, enabling the study of primary tumour DNA rather than requiring the use of tumour cell lines, which may contain genetic changes and adaptations required for immortalization and maintenance in tissue culture conditions.