Renewable Revolution

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Opinion: What Is the Human Genome?


The human genome that researchers sequenced at the turn of the century doesn’t really exist as we know it.

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The Human Genome project sequenced “the human genome” and is widely credited with setting in motion the most exciting era of fundamental new scientific discovery since Galileo. That’s remarkable, because in important ways “the human genome” that we have labeled as such doesn’t actually exist.
 
Plato essentially asserted that things like chairs and dogs, which we observe in this physical world, and even concepts like virtues, are but imperfect representations or instances of some ideal that exists, but not in the material world. Such a Platonic ideal is “the human genome,” a sequence of about 3 billion nucleotides arrayed across a linear scale of position from the start of chromosome 1 to the end of the sex chromosomes. Whether it was obtained from one person or several has so far been shrouded in secrecy for bioethical reasons, but it makes no real difference. What we call the human genome sequence is really just a reference: it cannot account for all the variability that exists in the species, just like no single dog on earth, real or imagined, can fully incorporate all the variability in the characteristics of dogs.
 
Nor is the human genome we have a “’normal” genome. What would it mean to be “normal” for the nucleotide at position 1,234,547 on chromosome 11?  All we know is that the donor(s) had no identified disease when bled for the cause, but sooner or later some disease will arise. Essentially all available whole genome sequences show potentially disease-producing variants, even including nonfunctional genes, in donors who were unaffected at the time.
 
Furthermore, the current reference genome sequence is haploid, which means that even if it were compiled from just one donor, the single reference sequence does not report the variation at millions of nucleotide positions between the donor’s two copies (except for X and Y) that we know exist. I understand that the DNA template is being resequenced, to be reported as a diploid sequence, which is progress. Hopefully this will be done in a way that produces phased sequence, in which each chromosome is reported separately, rather than just identifying the two alleles at each variable site along the genome without specifying on which chromosome it lies. Only the former format will represent sequences as they actually exist in the sequenced person, identifying which alleles go together on a chromosome, and are thus linked evolutionarily.
 
Even so the reference human genome will keep changing!

http://the-scientist.com/2012/08/17/opinion-what-is-the-human-genome/