N24 Awareness Day 2016: Genetics, the new face of N24 and DSPS.23 November 2016 at 05:26 | Posted in Body clock, Circadian rhythm, Clock genes, DSPS, N24 | 3 Comments
I got my genes tested this month, and what I found out puts a new face on my understanding of N24 and DSPD.
The first human genome was sequenced in 2003 and cost 2.7 billion dollars. Over the years researchers have improved their technique and reduced the cost dramatically. Recently Veritas Genetics announced it had reached the goal of the under $1000 genome, offering a full genome sequence to anyone for $999. Still very expensive but quite a drop from 2.7 billion!
Other companies also offer a more limited but still useful form of genomic testing. One of these is 23andMe which offers testing for $99-$199. Rather than plunging into the deep end of whole genome sequencing, I thought I’d go with 23andMe to confirm that I could get useful information with less expense. I am very impressed with what I was able to find out from 23andMe.
The method of 23andMe is based on analysis of what are called single nucleotide polymorphisms (SNPs). Most of the human genome is identical from person to person, which is why we are all humans and not horses or banana trees. SNP analysis focuses on variations in the genome of a particular common type.
The genetic code is a sequence of DNA nucleotides which we label with the letters A,T,G or C. So part of the code might read like this: …CTGAATGCAGT… An SNP refers to a situation where one letter of the code differs from person to person. So while one person may have the sequence CTGAATGCAGT another may have the sequence CTGAATTCAGT. Notice the only change is that the letter G in the 7th place has become a T. Typically one SNP will be more common in the population than the other. So, for example 90% of the population may have a G, which would be referred to as the major (more common) allele. The T would be called the minor allele. (Allele is another word for genetic letters.)
So if you sign up for 23andMe you send them a vial of your spit, and 4-6 weeks later they send you a link to their site where they give you information about a selection of your SNPs and what they mean, as well as some other genetic information.
Most of the information you get from 23andMe, at first glance, seems pretty basic. They tell you where your ancestors came from and a list of various genetic traits: is your hair likely to be curly, can you taste bitter foods etc. Interesting but hardly world-shaking in most cases.
But in addition to this pre-analyzed information 23andMe also allows you to download a file containing the raw data: a long list of the actual SNPs and your results. These you can upload to certain web sites such as Promethease for detailed analysis, or if you know what you are doing and what you are looking for you can look through the raw data yourself. That’s when the fun begins.
And I knew just what I wanted to look for.
In 2014 Daniel Kripke et al. published an article called, Circadian Polymorphisms in Night Owls, in Bipolars, and in Non-24-Hour Sleep Cycles. You can get the full text at the link below.
The study identified several SNPs statistically associated with N24 or DSPS. Not all of the SNPs studied by Kripke et al were tested by 23andMe but three of the most important ones were.
In the case of N24, Kripke et al. were particularly interested in variations in a gene called BHLHE40, or basic helix-loop-helix protein E 40. The protein produced by this gene plays a major role in the molecular clock.
The study found that subjects with N24 were statistically more likely to have one or two C alleles instead of a T at a portion of the genome labelled rs908078, which is part of the regulatory sequence for this gene. Looking at my 23andMe data I found this line:
rs908078 3 5024771 CT
So, yes indeed I did have one C allele. It might have been even more impressive if I had two, as some of the N24 subjects did, but one C is still interesting.
But I developed N24 as an adult, following chronotherapy. Before that I had DSPD. So if there is a genetic predisposition it might be even more likely to show up in genes associated with DSPD. Kripke et al found two such genes and corresponding SNPS.
The first is a gene called NFIL3 (nuclear factor, interleukin 3 regulated). It also plays a role in the circadian clock.
The SNP for NFIL3 is rs2482705, and people with DSPS are more likely to have two G alleles. So looking at my data file I find this line.
rs2482705 9 94182502 GG
So, yes, GG. I can cross out another letter on my bingo card.
The other gene is RORC (retinoic acid receptor-related orphan receptor C). This gene has many functions and is not well understood, but one of its roles is also in clock regulation.
The associated SNP is designated rs3828057. People with DSPS are more likely to have a GG allele. Going back to my data file I search for that string and find this.
rs3828057 1 151780177 CC
You might at first think that was a miss, but remember the structure of DNA. It consists of two strands linked together in a helix, which run in opposite directions, the sense strand and the antisense strand. A C in the sense strand matches a G in the antisense strand, and vice versa. An A matches to a T. So CC is actually equivalent to a GG in this case. It simply means one group tested the sense strand and the other the antisense strand.
So we have another hit.
So for the SNPs that were tested by 23andMe I am 3 for 3 in having the alleles associated with N24 or DSPD. I don’t want to make too much of this. These are statistical associations. It’s entirely possible to have either disorder and not have these genes or to have the genes and not the disorder. Nonetheless, while I am not yet ready to shout BINGO!, I find the presence of these genes intriguing. We aren’t quite ready to trace their function directly to the disorder but that may come in time. The first step in that process is to know what genes are involved. The fact that these genes are ones we do know are intimately involved in regulating the circadian clock is a good omen for our future understanding.
But there is also more on the horizon. Recall I mentioned 23andMe only tests a limited number of SNPs. Kripke et al reported a total of 9 SNPs associated with N24. While rs908078 was the one they focused on the most, the other 8 are also significant. But 23andMe only tested for rs980078. They did not test the other 8. But a whole genome sequencing, if I am ever able to afford that, should give results for the other 8. That’s a lot more letters to put on the bingo card!
I don’t think we are likely to explain N24 or DSPD entirely based on genetics. Developmental and epigenetic factors almost certainly play a role. But the more we know about the genetic aspects, the better off we will be. I must also add that genetic studies are not always replicated and it may turn out that all of this is a Will-o’-the-wisp that I will have to retract next year. But eventually real data will come out. As one of my favorite fictional characters said, “the truth is out there.”
LivingWithN24 (James Fadden)
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