Enlarging a training set for genomic selction by imputation of un-genotyped animals in populations of varying genetic architecture

Background: The most common application of imputation is to infer genotypes of a high-density panel of markers on animals that are genotyped for a low-density panel. However, the increase in accuracy of genomic predictions resulting from an increase in the number of markers tends to reach a plateau beyond a certain density. Another application of imputation is to increase the size of the training set with un-genotyped animals. This strategy can be particularly successful when a set of closely related individuals are genotyped. ----- Methods: Imputation on completely un-genotyped dams was performed using known genotypes from the sire of each dam, one offspring and the offspring’s sire. Two methods were applied based on either allele or haplotype frequencies to infer genotypes at ambiguous loci. Results of these methods and of two available software packages were compared. Quality of imputation under different population structures was assessed. The impact of using imputed dams to enlarge training sets on the accuracy of genomic predictions was evaluated for different populations, heritabilities and sizes of training sets. ----- Results: Imputation accuracy ranged from 0.52 to 0.93 depending on the population structure and the method used. The method that used allele frequencies performed better than the method based on haplotype frequencies. Accuracy of imputation was higher for populations with higher levels of linkage disequilibrium and with larger proportions of markers with more extreme allele frequencies. Inclusion of imputed dams in the training set increased the accuracy of genomic predictions. Gains in accuracy ranged from close to zero to 37.14%, depending on the simulated scenario. Generally, the larger the accuracy already obtained with the genotyped training set, the lower the increase in accuracy achieved by adding imputed dams. ----- Conclusions: Whenever a reference population resembling the family configuration considered here is available, imputation can be used to achieve an extra increase in accuracy of genomic predictions by enlarging the training set with completely un-genotyped dams. This strategy was shown to be particularly useful for populations with lower levels of linkage disequilibrium, for genomic selection on traits with low heritability, and for species or breeds for which the size of the reference population is limited.

Retargeting of pre-set regions on chromosome for high gene expression in mammalian cells

We have developed a system to hunt and reuse special gene integration sites that allow for high and stable gene expression. A vector, named pRGFP8, was constructed. The plasmid pRGFP8 contains a reporter gene, gfp2 and two extraneous DNA fragments. The gene gfp2 makes it possible to screen the high expression regions on the chromosome. The extraneous DNA fragments can help to create the unique loci on the chromosome and increase the gene targeting frequency by increasing the homology. After transfection into Chinese hamster ovary cells (CHO) cells, the linearized pRGFP8 can integrate into the chromosome of the host cells and form the unique sites. With FACS, 90 millions transfected cells were sorted and the cells with strongest GFP expression were isolated, and then 8 stable high expression GFP CHO cell lines were selected as candidates for the new host cell. Taking the unique site created by pRGFP8 on the chromosome in the new host cells as a targeting locus, the gfp2 gene was replaced with the gene of interest, human ifngamma, by transfecting the targeting plasmid pRIH-IFN. Then using FACS, the cells with the dimmest GFP fluorescence were selected. These cells showed they had strong abilities to produce the protein of interest, IFN-gamma. During the gene targeting experiment, we found there is positive correlation between the fluorescence density of the GFP CHO host cells and the specific production rate of IFN-gamma. This result shows that the strategy in our expression system is correct: the production of the interesting protein increases with the increase fluorescence of the GFP host cells. This system, the new host cell lines and the targeting vector, can be utilized for highly expressing the gene of interest. More importantly, by using FACS, we can fully screen all the transfected cells, which can reduce the chances of losing the best cells.

When a data set can be considered compositional?

Traditionally, compositional data has been identified with closed data, and the simplex has been considered as the natural sample space of this kind of data. In our opinion, the emphasis on the constrained nature of compositional data has contributed to mask its real nature. More crucial than the constraining property of compositional data is the scale-invariant property of this kind of data. Indeed, when we are considering only few parts of a full composition we are not working with constrained data but our data are still compositional. We believe that it is necessary to give a more precise definition of composition. This is the aim of this oral contribution

Quantified set inversion with applications to control

This paper describes a new reliable method, based on modal interval analysis (MIA) and set inversion (SI) techniques, for the characterization of solution sets defined by quantified constraints satisfaction problems (QCSP) over continuous domains. The presented methodology, called quantified set inversion (QSI), can be used over a wide range of engineering problems involving uncertain nonlinear models. Finally, an application on parameter identification is presented

Point Set Topology

Lecture notes about point set toplogy

Team Quintinlessness: Open source software resource set

INFO2009 Assignment 2 reference list for team "Quintinlessness" - Subject: Open source software

Green ICT Resource Set - INFO2009 Coursework, Bobs' Finest Group

Online resource set which details in full the Green ICT topic and associated areas. Online multiple choice quiz also included to test readers knowledge of topic once the tutorial has been read.

INFO2009 Academic Year 09-10: Luc Moreau's Tutor Group's Accessibility Resource Set

Our resource set

Annotated Bibliographies Notes Set

Slides, handouts and links covering relevant topics including how to create an annotated bibliography, exemplar bibliography, reference managers etc. The coursework specification with assessment criteria is available as a single item from http://www.edshare.soton.ac.uk/6044/

INFO2009 Group 21 - A Poster and set of Resources on Computer Security

This contains a poster advertising the resources. The resource is a profile folder on five topics, as well as a website, a quiz, and an interactive game.

Entire set of working mu-specific plugins for WP3.1.3

Entire set of working mu-specific plugins to create a structured/secure/LDAP-authenticated WP-multisite environment in WP3.1.3

ALPS Workshop 2 p3 Atom Chart

Animation

Show Set up Induction 2014

A recorded version of Adam Procter's show induction for students that due to legitimate reasons where unable to attend this compulsary setting - once viewed an email should be sent to adam.procter@soton.ac.uk to confirm you have watched, understand and will comply with the information presented.

How do I set up Landscape sections in a Word thesis?

This video shows how to create a Landscape Section in a Word 2010 file. Users of Word 2013 will find the steps almost identical. Users of Word 2011 for Mac will find this useful, steps can be found in the Word 2011 Sections manual. See how to: • Create a Landscape section • Set up margins for the Landscape section • Create Headers and Footers that retain the orientation of the text in Portrait section

How do I set up Headers and Footers in a Word thesis?

This video shows how to: • Set up Headers for each section, on the outside edge for both odd and even pages • Set up Footers with Page Numbering, on the outside edge for both odd and even pages Although this video shows the steps in Word 2010, the steps are virtually the same in Word 2013. Those using Word 2011 for Mac will find this useful and can find the details of where buttons are located in the Word Section manual.