Tuesday, September 21, 2010

A moment of peace between busyworks

Jammed between works. Deadline came, changed, and working on the final version. I'm done the feedback modification boss brought to me. His meeting is still going on. What can I do now? Other works... too less time for too much work. Lunch... God, forgot the wallet at home this morning. Maybe just a moment of break... so precious. Print another small picture for my baby. Always happy to see his smiling and heartless face.

Sunday, September 19, 2010

So just dance

I feel I am pretty productive recently, though still have pressure to get papers published. It's already Sep. I got one rather good work rejected, mainly because they feel the topic is not so right to their journal. I have another finished work under modification. I have another rejected paper ready to polish. I just finished the work for GAW 17. Of course, I have some other collaborating works going.

It looks everything is busy, but I need to push them, make progress and get things done. Hard work, sadness, mixed of hope. Sometimes, I feel I can't keep things alive, and just want to have a good break. But who can't tell that everyone who keeps good wishes is not experiencing the similar feeling.

A moment of numb. Maybe, I can just ignore the details. Have a moment of peace, with my little sweet man, to listen to the piano. So why not just dance, and maybe you may find you can be just ok or just be wonderful without the need of counting the good and the bad.

Saturday, September 11, 2010

Methods of collapsing rare/common variants for mapping the assocition to traits in next generation sequencing

The time of next generation sequencing (NGS) comes so quick, and all of the sudden all the meetings and journals are ready to welcome for NGS time. This reflects to our research as well. I submitted a grant with transferring the concept of joint analysis of family and unrelated data to NGS. Then we quickly merged to 3 NGS projects.

Non-enough of explaining the most mapped common alleles to common diseases, people swarmed to rare variants. However, some rare variants will explain the disease, some may not since many of them are maybe only the results of evolution. Besides, due to its rare occurrence, larger sample size is needed to draw statistical conclusions. Yet many of the rare variants may occur as random mutations and be rare to repeat in population. All of these made the association study more difficult.

We reviewed the recent papers about rare variants. But most used the simulated data including Li and Neal,AJHG, 2008, Madsen and Browning, PLOS genetics, 2009 and Price et al. AJHG, 2009. The basic idea is that people are trying to upweight the rare variants that have true associations. It also seems that a bunch of GAW17 people are working on the same or similar topic. Obviously, it is worth to dig something here. But I have some little concerns whether it's worthy to draw so much attention?

Thursday, September 9, 2010

Analysis of GAW 17 data

GAW 17 data comes late this year. So people were rushing to make the coming deadline. We proposed a rather conservation method to analyze the data, however, the results do not look good in the first place. It took a while to observe from every aspect that it doesn't turn out the signal, with the accompany of the feeling of missing the deadline.

As more and more tests turned out not to be positive. I started to examine and analyze all the possible reasons. Though, all types of analysis look reasonable, but people don't have good ways to solve these problems. For example the influence of low heritability to the mapping of snp variations especially including the rare ones in NGS to traits.

This morning, I felt I may need to start a series of tests that may enlarge the signal units. Instead of genes, maybe signal pathways, since so many genes have only one or two rare variants, and it doesn't make sense to get anything from them.

Then, may change the view of extracting information. Not only use one rule, but may use multiple rules to collect information. Cross my figures...