Commit 3a66d750 authored by Laros's avatar Laros
Browse files

Added lecture.

parent 5d4f3d84
../../submodules/presentation/Makefile
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../../submodules/presentation/beamerthemelumc.sty
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../../submodules/presentation-pics/pics/network/flow.dia
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../../submodules/presentation/logos
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\documentclass[slidestop]{beamer} % Add 'handout' for printable slides.
\title{NGS data flow}
\providecommand{\myConference}{BDAM introduction meeting}
\providecommand{\myDate}{Monday, September 7, 2015}
\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]{logos/lgtc_logo}
%\includegraphics[height=0.7cm]{logos/ngi_logo}
}
}
\providecommand{\lastRightLogo}{
%\includegraphics[height=0.7cm]{logos/nbic_logo}
%\includegraphics[height=0.8cm]{logos/nwo_logo_en}
%\hspace{1.5cm}\includegraphics[height=0.7cm]{logos/gen2phen_logo}
\includegraphics[height=0.7cm]{logos/generade_logo}
}
\usetheme{lumc}
\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{NGS data flow}
\subsection{Overview}
\begin{pframe}
\begin{figure}[]
\begin{center}
\includegraphics[height=0.85\textheight]{flow}
\end{center}
\caption{Data flow for NGS of clinical samples.}
\end{figure}
\end{pframe}
\begin{pframe}
Before sequencing:
\begin{itemize}
\item Miracle receives pedigree information and an order for sequencing.
\item Miracle makes a batch for the sequencing company using its own IDs.
\begin{itemize}
\item DNA is extracted and put in a test tube, barcode is linked to ID.
\item Digital sample sheet is made for the sequencing company.
\begin{itemize}
\item ID.
\item Test (exome / target / array / NIPT).
\end{itemize}
\end{itemize}
\end{itemize}
\end{pframe}
\begin{pframe}
Primary data analysis:
\begin{itemize}
\item Miracle checks that sequencing does not take too long.
\item Raw data arrives.
\begin{itemize}
\item Miracle gets a signal that the raw data is available.
\end{itemize}
\item Miracle sends pedigree information and the test to the
pipeline.
\item Primary data analysis on the cluster.
\begin{itemize}
\item Miracle gets a signal when the primary data analysis is finished or
has failed.
\end{itemize}
\end{itemize}
\end{pframe}
\begin{pframe}
Secondary data analysis:
\begin{itemize}
\item Miracle sends IDs to the analysis program.
\item Annotated varianten are analysed with the analysis program.
\begin{itemize}
\item Miracle gets a signal when the data is loaded.
\end{itemize}
\item Secondary data analyse in starts.
\begin{itemize}
\item Miracle receives list of variants for validation.
\item Miracle receives primers.
\end{itemize}
\item Validation tests are done and reported back to Miracle.
\item Miracle sends results back to analysis program.
\item Miracle reports back to patient registration system.
\end{itemize}
\end{pframe}
\section{Questions?}
\lastpagetemplate
\begin{pframe}
\begin{center}
Acknowledgements:
\bigskip
\bigskip
Peter Taschner
Christi van Asperen
Adri Krol
\end{center}
\end{pframe}
\end{document}
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