Name: Xiaoqi Geng

Class Year: 2016

Internship Placement: I am researching in the statistics department in UPenn this summer. I will be working on adapting a newly developed statistical method called CODEX for a large alzheimer’s disease sequencing project.

What’s happening? We’d love to hear how your internship is going!

I spent my summer with Professor Nancy Zhang in statistics department in UPenn. Before my research experience started, one of her Ph.D. students already developed a statistical method called CODEX, which is a normalization and copy number variation detection method for whole Exome Sequencing. Whole Exome Sequencing has been a trend of research area in recent years in the field of bioinformatics. The goal of this sequencing method is to identify genetic variation that is responsible for both mendelian and common diseases, such as Miller syndrome and Alzheimer’s disease, with lower cost than Whole Genome Sequencing. Along with my partner, we examined CODEX model during this summer by using data of blood samples of the same 110 individuals collected and processed from three medical centers. By doing this, we hoped to perfect CODEX so that it could serve as a better tool for Alzheimer’s Disease Sequencing Project (ADSP). 

When approaching CODEX for the first time, my partner and I had no idea what the results really meant. However, after consulting with Professor Zhang, we gradually understood how to visualize data. If we realized any signal missed from the final result, we looked into the model and detected which step the signal was lost and its reason. Though we still have not finish the project, we completed running the model on 22 chromosomes of all three centers and made comparison between the results of three centers on each chromosome. We have already figured out our next goal after examining the results; we hoped to lower the threshold of the normalization and segmentation process so that the model would not be too stringent on the detected signals.

I have never thought I could do academic research before this summer. This summer’s experience provided me confidence to go into academia. Besides, I got more information of what I can do and contribute for the area of bio-statistics and bio-informatics. I really look forward to seeing this research project being applied in real life and I believe many people will be benefited if they can know at an early stage if they will have the tendency of being attacked by Alzheimer’s Disease.