Indeed, there are plenty of things missing even from a "complete" DNA sequence. The methylation sites, as you mentioned, are just one of them. We still can't sequence the telomeres and centromeres even in the reference genome. This doesn't tell you about mitochondrial DNA, which is maternally inherited. Furthermore all cells in the body have their unique RNA and gene expression profiles, which must be painstakingly addressed with other special microarray techniques. Every cell division involves its own set of random mutations that occurred during DNA duplication, and there's no way to catalog these through the whole body. There are histones compacting the DNA and repressing expression in non-obvious ways, plus multiple sites on the histones for regulation through acetylation. The beauty of life is in its complexity and many layers of regulation, but it's still amazing to witness the pace at which we are demystifying it.
People frequently confuse microarray SNP (single nucleotide polymorphism) studies with an actual DNA scan that identifies all 3 billion A,C,T and G bases in the human genome. This $1000 option looks at about 2 million KNOWN sites which vary between people. These mutations are not the ones that actually code for a disease, but because they happen to be NEAR the actual ones that do on the chromosomes, it is assumed that if you have the SNP mutation, you will have the disease-prone variant in your genome as well. The problem with this technique is that it only measures variants that we know about, whereas a true complete DNA scan would be the "gold standard" and provide you with the most detailed information possible. Unfortunately, a true DNA sequencing of this variety runs about $100000.
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I'm not saying that it's a commercialized product yet, but 454 Life Sciences has the technology to do it at that price. Read the NYTimes article here: http://www.nytimes.com/2007/05/31/science/31cnd-gene.html
Indeed, there are plenty of things missing even from a "complete" DNA sequence. The methylation sites, as you mentioned, are just one of them. We still can't sequence the telomeres and centromeres even in the reference genome. This doesn't tell you about mitochondrial DNA, which is maternally inherited. Furthermore all cells in the body have their unique RNA and gene expression profiles, which must be painstakingly addressed with other special microarray techniques. Every cell division involves its own set of random mutations that occurred during DNA duplication, and there's no way to catalog these through the whole body. There are histones compacting the DNA and repressing expression in non-obvious ways, plus multiple sites on the histones for regulation through acetylation. The beauty of life is in its complexity and many layers of regulation, but it's still amazing to witness the pace at which we are demystifying it.
People frequently confuse microarray SNP (single nucleotide polymorphism) studies with an actual DNA scan that identifies all 3 billion A,C,T and G bases in the human genome. This $1000 option looks at about 2 million KNOWN sites which vary between people. These mutations are not the ones that actually code for a disease, but because they happen to be NEAR the actual ones that do on the chromosomes, it is assumed that if you have the SNP mutation, you will have the disease-prone variant in your genome as well. The problem with this technique is that it only measures variants that we know about, whereas a true complete DNA scan would be the "gold standard" and provide you with the most detailed information possible. Unfortunately, a true DNA sequencing of this variety runs about $100000.