Commit 466c6d46 authored by Laros's avatar Laros
Browse files

Added sv_validation slides.

parent 0cb75314
../../submodules/presentation/Makefile
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\setlength{\linethickness}{1.5pt}
\providecommand{\PCRPicture}{
\begin{center}
\fbox{
\begin{picture}(90, 20)(0, 0)
\put(0, 10){\line(1, 0){45}}
\put(45, 10){\color{red}\line(1, 0){45}}
\put(5, 12){\color{green}\vector(1, 0){10}}
%\put(5, 12){\color{yellow}\line(-1, 1){5}}
\color{yellow}\qbezier(5, 12)(5, 12)(1.5, 15.5)
\put(85, 8){\color{green}\vector(-1, 0){10}}
%\put(85, 8){\color{yellow}\line(1, -1){5}}
\color{yellow}\qbezier(85, 8)(85, 8)(88.5, 4.5)
\end{picture}
}
\end{center}
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\providecommand{\PCRPictureTwo}{
\begin{center}
\fbox{
\begin{picture}(90, 20)(0, 0)
\put(0, 10){\color{yellow}\line(1, 0){5}}
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\put(85, 10){\color{yellow}\line(1, 0){5}}
\end{picture}
}
\end{center}
}
\providecommand{\PrimerExtend}{
\begin{center}
\fbox{
\begin{picture}(90, 20)(0, 0)
\put(0, 10){\line(1, 0){45}}
\put(45, 10){\color{red}\line(1, 0){45}}
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\end{picture}
}
\end{center}
}
\providecommand{\PrimerExtendTwo}{
\begin{center}
\fbox{
\begin{picture}(90, 20)(0, 0)
\put(0, 10){\line(1, 0){45}}
\put(45, 10){\color{red}\line(1, 0){45}}
\put(5, 12){\color{green}\vector(1, 0){10}}
\put(15, 12){\line(1, 0){30}}
\put(45, 12){\color{red}\line(1, 0){30}}
\end{picture}
}
\end{center}
}
\providecommand{\PrimerExtendThree}{
\begin{center}
\fbox{
\begin{picture}(90, 20)(0, 0)
\put(0, 10){\color{yellow}\line(1, 0){5}}
\put(5, 10){\color{green}\line(1, 0){10}}
\put(15, 10){\line(1, 0){30}}
\put(45, 10){\color{red}\line(1, 0){30}}
\put(75, 10){\color{yellow}\line(1, 0){5}}
\end{picture}
}
\end{center}
}
\providecommand{\AmpliconSelect}{
\begin{center}
\fbox{
\begin{picture}(90, 20)(0, 0)
\put(0, 10){\line(1, 0){45}}
\put(45, 10){\color{red}\line(1, 0){45}}
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\end{center}
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\providecommand{\AmpliconClass}{
\begin{center}
\fbox{
\begin{picture}(90, 20)(0, 0)
\put(15, 10){\line(1, 0){30}}
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../../submodules/presentation/beamerthemelumc.sty
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../../submodules/presentation/gen2phen_logo.eps
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../../submodules/presentation/lgtc_logo.eps
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../../submodules/presentation/lumc_logo.eps
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../../submodules/presentation/lumc_logo_small.eps
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../../submodules/presentation/nbic_logo.eps
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../../submodules/presentation/ngi_logo.eps
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../../submodules/presentation/nwo_logo_en.eps
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../../submodules/presentation/nwo_logo_nl.eps
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\documentclass[slidestop]{beamer}
\title{SV validation proposal}
\providecommand{\myConference}{GoNL data analysis call}
\providecommand{\myDate}{Thursday, 28 February 2012}
\author{Jeroen F. J. Laros}
\providecommand{\myGroup}{Leiden Genome Technology Center}
\providecommand{\myDepartment}{Department of Human Genetics}
\providecommand{\myCenter}{Center for Human and Clinical Genetics}
\providecommand{\lastCenterLogo}{
\raisebox{-0.1cm}{
\includegraphics[height = 1cm]{lgtc_logo}
}
}
\providecommand{\lastRightLogo}{
\includegraphics[height = 0.7cm]{nbic_logo}
%\includegraphics[height = 0.8cm]{nwo_logo_en}
%\hspace{1.5cm}\includegraphics[height = 0.7cm]{gen2phen_logo}
}
\usetheme{lumc}
\input{amplicons}
\begin{document}
% This disables the \pause command, handy in the editing phase.
%\renewcommand{\pause}{}
% Make the title page.
\bodytemplate
% First page of the presentation.
\section{Introduction}
\begin{frame}
\frametitle{The samples}
Around $1000$ breakpoints selected by the SV group.
\begin{itemize}
\item The breakpoints have been fine mapped, so the location is known up to
the nucleotide level.
\item Allows for primer design close to the breakpoint.
\item Allows for sequencing of the PCR product.
\end{itemize}
\bigskip
\pause
We need a high throughput method for validation.
\begin{itemize}
\item Multiple samples.
\end{itemize}
\end{frame}
\section{Experimental design}
\begin{frame}
\frametitle{Traditional approach}
\begin{figure}
\PCRPicture
\caption{PCR the region of interest}
\label{fig:PCR}
\end{figure}
Legend:
\begin{itemize}
\item White and red parts represent the regions flanking the breakpoint.
\item Green parts represent the primers.
\item Yellow parts represent the sequencing adapters.
\end{itemize}
\end{frame}
\begin{frame}
\frametitle{Traditional approach}
\begin{figure}
\PCRPictureTwo
\caption{Product ready for sequencing}
\label{fig:PCR2}
\end{figure}
Not really high throughput or cheap.
\begin{itemize}
\item Cost: \euro$2.5$ to \euro$5$ per primer.
\item Work: $1000$ \emph{separate} PCR reactions.
\end{itemize}
\end{frame}
\begin{fframe}
\frametitle{Experimental approach}
\begin{figure}
\PrimerExtend
\caption{Primer extension}
\label{fig:Extend}
\end{figure}
Step one.
\begin{itemize}
\item Design one primer at either side of the breakpoint.
\item Extend the primer with a normal polymerase.
\end{itemize}
\vfill
\bs{H.P.J. Buermans}
\end{fframe}
\begin{fframe}
\frametitle{Experimental approach}
\begin{figure}
\PrimerExtendTwo
\caption{Extended primer}
\label{fig:Extend2}
\end{figure}
Step two.
\begin{itemize}
\item Do DNA end repair.
\item Ligate adapters.
\end{itemize}
\vfill
\bs{H.P.J. Buermans}
\end{fframe}
\begin{frame}
\begin{figure}
\PrimerExtendThree
\caption{Product ready for sequencing}
\label{fig:Extend3}
\end{figure}
The primer design is done only once.
\begin{itemize}
\item Primers can be made with FlexGen.
\begin{itemize}
\item Around $6000$ primers can be made.
\item Multiple primers can be used per locus.
\item Cost around \euro$1400$.
\end{itemize}
\item Sequencing on the Ion Torrent.
\begin{itemize}
\item Around $10$ samples can be multiplexed per run.
\item Cost around \euro$600$.
\end{itemize}
\end{itemize}
\end{frame}
\section{Data analysis}
\begin{fframe}
\frametitle{Combined analysis}
For the data analysis, there are several options.
\begin{itemize}
\item Map the sequences and use Pindel.
\item Do analysis on the raw data with a tool designed for STR analysis.
\begin{itemize}
\item Find two anchors in the flanking regions.
\item Classify the region between these regions.
\item No mapping needed.
\item Capable of finding heterozygous events.
\item Capable of finding mosaicism.
\end{itemize}
\end{itemize}
\vfill
\bs{K. Ye, J.W.F. van der Heijden}
\end{fframe}
\begin{frame}
\begin{figure}
\AmpliconSelect
\caption{Selecting the variable region}
\end{figure}
\end{frame}
\begin{frame}
\begin{figure}
\AmpliconClass
\caption{Classifying the STR}
\end{figure}
\end{frame}
\section{Questions?}
\lastpagetemplate
\begin{frame}
\begin{center}
Acknowledgements:
\bigskip
\bigskip
Henk Buermans
Jaap van der Heijden
Kai Ye
Johan den Dunnen
\end{center}
\end{frame}
\end{document}
../../submodules/presentation/ul_logo.eps
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