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Genes-R-Us — The ‘signature’ within

Genes-R-Us — The ‘signature’ within

Posted: Wednesday, September 28, 2011 5:02 pm

Have you ever had the scientific rug pulled out from under you? Remember when margarine was healthier for you than butter? Is coffee good for you or bad for you? 
While the goal of science is absolute truth, science can only approximately explain our physical world, of which we are a part. Science deals with things that can be observed and measured. For example, while science can uncover an association between moderately high coffee consumption and lower rates of Alzheimer’s, science can neither prove nor disprove the existence of God as that is outside the realm of what can be observed and measured.
Science is data driven. Data have measurement errors and are only as good as the acquisition instruments. As better instruments come along, we refine our understanding of the “facts” and perhaps realize that we were asking the wrong question. One of the most dramatic improvements in the last decade has been in our ability to take genomic measurements.  This coupled with a mind-boggling decrease in price is the foundation of personalized medicine. 
Even a rudimentary understanding of this genomic “stuff” could help you receive better medical care, especially in cancer treatment, by asking proactive questions. My challenge in this column is to make this “stuff” as simple as possible without the “microbiology-lynch-squad” showing up at my front door.
Last week, I used an analogy that is worth repeating-especially since I plan to add onto it. Your genome is simply the complete set of your genetic instructions — your DNA “book” — written, amazingly, with only four “letters.”  Yes, the letters only represent the chemical bases that are glued onto a spirally chemical scaffold — but I will speak of letters (as my husband assures me that otherwise I am competing with baseball).
With some biological editing, we identified genes with “words,” proteins with “sentences” and chromosomes with “chapters.” For males, that last chapter or Y-Chromosome contained a “signature” that could be used to track paternal ancestry. To access our maternal history, we must look outside the book’s chapters. The maternal signature lives within a tiny piece of circular DNA, mtDNA, whose job it is to boss the cell around — I mean to supply energy to the cell. 
These two signatures, comprised of a small portion of the total letters on the Y-Chromosome and the mtDNA, are very stable over long periods of time, such as tens of thousands of years. But some changes do eventually creep in. These changes can be associated with the movement of human populations resettling into different geographical areas.
Now stop here. Close your eyes, unwind a super long strand of DNA, get out your biological scissors, and snip out a single letter. Ah, a SNP (pronounced snip), for short. But not every letter gets to be a SNP. SNPs are only in places where we have different letters in their genomes. Right now that is less than 0.5 percent of the total number of letters. Moreover, just a small fraction of SNPs are used in the paternal and maternal signatures.
Why do you care about SNPs? The “Mommy and Daddy Signatures” are comprised of SNPs. SNPs are what Direct-To-Consumer Genetic Testing companies use to trace your ancestry and disease vulnerabilities.
Computer programs compare these ancestry-predicting SNPs across large number of individuals within and across different geographical areas. The letter patterns that emerge are identified with various population groups moving over time and are summarized into what are called haplogroups.
Wow, look how far you have come in only three weeks. You now know that your genomic maternal and paternal ancestries are captured in haplogroups that are comprised of special SNPs somewhere in your mtDNA and your Y-Chromosome, respectively. 
Next week we are ready to jump into a real example. 
Editor’s note: Nancy Miller Latimer has worked in scientific research and development for 27 years. She blogs at neuronalbeauty.blogspot.com. Published in The Messenger 9.28.11

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