1. Discussion and Conclusion (mtDNA)
2. References (mtDNA)
3. Chrm 9 Hrt Rate
- Run QTLD (All)
- SNP LD (AZ, ALL)
- Run polygenic screen (13 variables)
- Run bivariate screens (16 variables)
- Run trivariate on Visits 1 and 3 and differences (25 variables)
6. E-mail regarding MAPP hrt rate correlation
Get to work and start doing the polygenic screens. Also, I need to read an upcoming paper from a fellow postdoc and how to do a gene centric significance testing for association vs. genome wide. A general problem with genome-wide association is that most of the variables you find won't meet significance after using a correction. So if you have 2,000 SNPs then you have a correction p-value of 0.00002, so imaging if you are using 500K or 1M SNPs, not very likely. An alternate way to do this is to a gene specific or gene centric approach. Then what you need to do is measure the number of SNPs in a given gene, then the effective number of SNPs (the number not in LD) - then base your correction value on that. Then you can bring in transcript data and p-values associated, then combine them to come up with a z-score (formally known as Stouffer's method). This will give you a better idea of the weight and you will also be able to determine if the SNP is correlated with the phenotype you are interested in. This way you get around a number of replication issues often required in GWAS studies. Of course you need expression data but the combination of expression and GWAS is much better than just the SNPs alone. So that took up a good portion of the morning.
I have a healthscreen at 10:23, very specific so I go over to get my blood pressure, a sample for lipids taken, and measured and weighed. My blood pressure is good 120/78, I've shrunk an inch - must be the gravity of living so far south, and I've put on a good deal of weight 165.4. So I'm offically overweight according to my BMI - 25.5. I'm not a fan of BMI because it is terrible predictor of obesity because it doesn't take into account body fat vs. muscle mass. However, some more exercise wouldn't hurt and J and I have talked about it. My body is also de-stressing from the last year. The two worst years of grad school are the first and the last in my opinion. There is a tremendous amout of worry about landing a job, finishing - passing, and becoming a real working member of society rather than an academic serf. The first year is stressful because you wonder, what the frack did I just do and can I make it. Throw in a new baby and a move, plus all the interviews etc from last year and I was one stressed primate. Now that stress is easing a bit and I'm getting more comfortable in Tejas del Sur, my body is of the opinion that I should eat and be Merry.
I also run about four of the polygenic screens, only one of which is heritable of 0.35 -so these are differences, which means that more than one third of the explained variation in this particular phenotype is due to genetics. So I run a linkage on that and nothing exciting comes up. I also begin to prepare the AZ SNPs for LD, this can be a little time consuming. J also edited the Mennonite manuscript or most of what I have. It is nice to have a wife who can read through things and offer advice. At some point I set up a meeting for tomorrow to talk about the SNP stuff. I need to pick up milk, honey, and mild green chilis from the grocery store. So off I go. I pick up the necessary items as well as some pink carnations for J - because I have that Stevie Wonder song stuck in my head "Isn't she lovely, isn't she beautiful" and the mutant flowers from Target died.
I head home and the kids are outside playing in the yard, so I pour us a glass of wine. A burgundy. Say what you want about the French and I usually do, they make excellent wine and supposedly cheese, but I'm not a fan of the cheese. I walk outside to say hello and X and S get into a full on fist fight over somthing trivial. Both J and I break it up and S goes to his room, X is uber-emotional about it but they are both at fault. I check on the garden and the new composter J built while I was at work (pictures forthcoming). J traded some homemade yogurt and cottage cheese for the worms and we used two rubber containers deystroyed in the move. Right now we have lettuce coming up, pumpkins, watermelon, radishes, and cantaloupe. Blossom deystroyed one of the radish plants and it doesn't look well for either the carrots or cucumbers.
We have a delightful dinner (as X calls it) then J goes for her walk - she has to return the movie. I give X his bath, play with S. Then it is milk and story time. I'm impressed at how well they read their ABCs, it appears S knows most of them along with their associated sounds and X is right behind. C being a girl and advanced mentally will probably know them by the time she is 3. J calls and ask is she should pick up The Day the Earth Stood Still and I say yes. She gets back as the kids are finishing watching their ABC video that I burned for them. Then bedtime, I take X upstairs and read a little Harry Potter to him and we both fall asleep. J comes in and wakes me up and I try to stay up through the movie to no avail. We will try and watch it tomorrow morning.
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