Monday, February 15, 2016

DNA


Here are some notes about DNA, taken from a series of introductory videos produced by 23andMe and the Khan Academy.
  • The human body is made up of about 50 trillion cells. Almost every cell contains a nucleus which holds 99.9% of our genes (cell mitochondria store a few more genes).
  • The coiled DNA in a nucleus is about 6 foot long.
  • All told, we have around 20,000 genes. Together, these form our DNA.
  • DNA comprises sugar, phosphate and four bases (adenine, thymine, cytosine and guanine).
  • The bases spell out the genetic code. The numbering and ordering determines the organism and its characteristics.
  • Most genes are recipes for making specific proteins. They tell a cell how to function (e.g. whether to become a hair follicle, a brain cell or a heart cell). 
  • Gene regulators turn different genes on and off to control cell functions. 
  • The long pieces of DNA containing your genes are organised into pieces called chromosomes. Humans have two sets of 23 chromosomes. 
  • The entire set of chromosomes is call the genome. The genome comprises around 3 billion base pairs. It would take a person over 9 years to read these out without stopping.
  • When a new cell is made, a single base pair may get added, substituted or left out. These variations (single-nucleotide polymorphisms, or SNPS, also knowns as 'snips') are what us make us different from one another. 
  • Most variations produce unobservable differences, but some lead to observable changes in traits (e.g. curly hair) or to the development of various conditions. As these differences are passed on to future generations, looking at differences and similarities in genomes can tell you how closely two people are related.
  • You can get your whole genome sequenced for around $1,000. 23andMe conducts genotyping analysis, looking at around 600,000 variations of base pairs (these are called SNPs or 'snips', the locations where variations are known to occur). 23andMe focuses on those snips, which have well studied contributions to particular traits.
  • We share 99.5% of our DNA with other humans.
  • Ancestry analysis is easier using the Y chromosome for the male line (passed down from father to son) or mitochondrial DNA from the female line, as both of these sets of DNA are more likely to have stayed intact across many generations.This analysis assigns a haplogroup to the maternal and paternal lineage, relating to a particular point and place in history when a specific mutation arose and has been passed along in future generations.
  • Phenotypes = observable traits (e.g. weight, height, etc) that result from the interaction between you and your environment. Some traits are more determined by the environment than others.

Wednesday, February 10, 2016

A myopia epidemic - an excellent article from Nature


Nature reports on the rise of myopia (short-sightedness). The quoted statistics are astounding:
East Asia has been gripped by an unprecedented rise in myopia, also known as short-sightedness. Sixty years ago, 10–20% of the Chinese population was short-sighted. Today, up to 90% of teenagers and young adults are. In Seoul, a whopping 96.5% of 19-year-old men are short-sighted.

...Other parts of the world have also seen a dramatic increase in the condition, which now affects around half of young adults in the United States and Europe — double the prevalence of half a century ago. 
The thinking is that it isn't book work and staring at ipads that causes myopia but time spent indoors. The correlation may be due to exposure to bright day light, which is thought to have protective benefits for the yes, or it could be some other factor that acts as a preventative. For now, it's another reason to spend some time outdoors.
In 2009, Regan Ashby, Arne Ohlendorf and Frank Schaeffel from the University of Tübingen's Institute for Ophthalmic Research in Germany showed that high illumination levels — comparable to those encountered outside — slowed the development of experimentally induced myopia in chicks by about 60% compared with normal indoor lighting conditions. Researchers elsewhere have found similar protective effects in tree shrews and rhesus monkeys.
Based on epidemiological studies, Ian Morgan, a myopia researcher at the Australian National University in Canberra, estimates that children need to spend around three hours per day under light levels of at least 10,000 lux to be protected against myopia. This is about the level experienced by someone under a shady tree, wearing sunglasses, on a bright summer day. (An overcast day can provide less than 10,000 lux and a well-lit office or classroom is usually no more than 500 lux.) Three or more hours of daily outdoor time is already the norm for children in Morgan's native Australia, where only around 30% of 17-year-olds are myopic. But in many parts of the world — including the United States, Europe and East Asia — children are often outside for only one or two hours.
...In some places, children cannot get any more outdoor light: there are too few hours of daylight, the sun is too fierce, or the cold too intense. Animal research10 has suggested that powerful indoor lights could do the trick instead: light boxes currently sold to treat seasonal affective disorder, for example, can deliver up to 10,000 lux illumination, but their effects on myopia have not been tested extensively in humans.

Saturday, February 06, 2016

23andme - a review

Just before Christmas I sent a vial of my saliva to a company called 23andMe, the world's largest personal genetics company. 23andMe extracts and analyses the DNA to provide a raft of detailed information covering aspects of ancestry and health. The ancestry information is pretty interesting but it's the health information that has made the exercise worth the £125 fee, several times over. The health info includes reports on inherited conditions, traits, likely drug responses and genetic risk factors.

Here's a short video of how 23andMe processes the DNA. In a nutshell, the saliva only holds 0.5% DNA, so they amplify it, embed it into a special chip, and analyse it.



Here's my ancestry breakdown at the highest certainty level of 90%:

Things get more interesting when the strictness is reduce. Here's my ancestry breakdown at the lowest certainty level of greater than 51%:
Here's some information on traits:

And here's the neanderthal DNA report. Finally, I'm above average in something!

Note, this is just small sampling of the information provided.

Monday, February 01, 2016