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SURF: Announcements of Opportunity

Below are Announcements of Opportunity posted by Caltech faculty and JPL technical staff for the SURF program. Additional AOs for the Amgen Scholars program can be found here.

Specific GROWTH projects being offerred for summer 2018 can be found here.

Each AO indicates whether or not it is open to non-Caltech students. If an AO is NOT open to non-Caltech students, please DO NOT contact the mentor.

Announcements of Opportunity are posted as they are received. Please check back regularly for new AO submissions! Remember: This is just one way that you can go about identifying a suitable project and/or mentor.

Announcements for external summer programs are listed here.

Students pursuing opportunities at JPL must be
U.S. citizens or U.S. permanent residents.

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Project:  Impact of demographic and genetic history on the pattern of variation in humans
Disciplines:  Biology, Computer Science
Mentor:  Charleston Chiang, Assistant Professor of Preventive Medicine, (BBE), charleston.chiang@med.usc.edu, Phone: 323-442-8052
Mentor URL:  http://chianglab.usc.edu  (opens in new window)
Background:  NOTE: This project will be conducted at the Center for Genetic Epidemiology, Keck School of Medicine USC, in Los Angeles, California.

A major effort in human genetics is to understand the genetic architecture of complex traits, such as the effect sizes and frequencies of the alleles underlying of these traits. The past history of a human population could exert a noticeable impact to the distribution of alleles in that population. For example, demographic events such as past population bottleneck is known to enrich functionally deleterious alleles in human populations. As another example, recent exponential expansions in human population sizes have increased the number of rare variations in human populations, many of which are deleterious as selection has not had time to remove these variation from population. As such, it is important to better understand the demographic and genetic history of a population, particularly given the public releases of ancient DNA samples that now allow investigations into the connections between populations of the present and the past.
Description:  In general, investigations of the population size history of a population using genetics require large-scale genetic data. In this project, the student will take advantage of the genetic sequencing data of ~20,000 Finnish individuals to investigate the fine-scale structure and genetic history of Finland. The student will identify locations in the genome that are most likely neutrally evolving and use that to infer the population size history in Finland. Then, the student will also assemble and curate from literature an updated collection of ancient DNA data, and utilize population genetic approaches to investigate the relationships between modern Finland individuals and ancient individuals across time and space.
References:  Lim ET, W├╝rtz P, Havulinna AS, et al. Distribution and medical impact of loss-of-function variants in the Finnish founder population. PLoS Genet. 2014 Jul 31;10(7):e1004494. doi: 10.1371/journal.pgen.1004494. eCollection 2014 Jul.

Wang SR, Agarwala V, Flannick J, Chiang CW, Altshuler D; GoT2D Consortium, Hirschhorn JN. Simulation of Finnish population history, guided by empirical genetic data, to assess power of rare-variant tests in Finland. Am J Hum Genet. 2014 May 1;94(5):710-20. doi: 10.1016/j.ajhg.2014.03.019. Epub 2014 Apr 24.

Nielsen R, Akey JM, Jakobsson M, Pritchard JK, Tishkoff S, Willerslev E. Tracing the peopling of the world through genomics.
Nature. 2017 Jan 18;541(7637):302-310. doi: 10.1038/nature21347. Review.
Student Requirements:  Proficiency in programming (e.g. python, perl, C++, R, etc.) is essential. Backgrounds in genetics principles and statistics necessary. Good organizational skills.
Programs:  This AO can be done under the following programs:

  Program    Available To
       SURF    Caltech students only 

Click on a program name for program info and application requirements.


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