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Commit f9eb7abb authored by Laros's avatar Laros
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Finished most figures.

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lectures/data_sharing/data_sharing.tex
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\subsection{Types of variants}
\begin{pframe}
% Data sharing at the LUMC:
% - Variant interpretations.
% - Variant frequencies.
Society for Clinical Genetic Laboratory Diagnostics (VKGL).
\bigskip
Two types of variants:
\begin{itemize}
\item Bulk data (frequencies, VCF files).
\item Interpretations (typically a few per analysis).
\end{itemize}
\end{pframe}
\section{Bulk data}
\subsection{Requirements}
\begin{pframe}
We aim for a solution that has the following properties:
......@@ -44,24 +50,13 @@
Labels allow for queries like:
\begin{itemize}
\item How many times have we seen this variant in non-diabetes patients?
\item How many times was this variant observed in Nijmegen?
\item How many times was this variant observed in institute X?
\end{itemize}
\bigskip
Timestamps are essential for \emph{reproducibility}.
\end{pframe}
\begin{pframe}
\begin{figure}[]
\vspace{-0.5cm}
\begin{center}
\includegraphics[height=0.8\textheight]{gq}
\end{center}
\vspace{-0.3cm}
\caption{Callable region ($584$--$1596$).}
\end{figure}
\end{pframe}
\begin{pframe}
\begin{figure}[]
\vspace{-0.5cm}
......@@ -79,58 +74,15 @@
\begin{pframe}
\begin{figure}[]
\vspace{-0.5cm}
\begin{center}
\Large\texttt{TTGAATCCT \color{red}TGCTC \color{black}TGCGATGGA}
\end{center}
\caption{\bt{NM\_003002.2:c.262\_266del}.}
\end{figure}
\begin{figure}[]
\begin{center}
\Large\texttt{TTGAATCCT \color{red}TGCTC \color{black}TGCGATGGA}\\
\Large\texttt{TTGAATCCTT \color{red}GCTCT \color{black}GCGATGGA}\\
\Large\texttt{TTGAATCCTTG \color{red}CTCTG \color{black}CGATGGA}\\
\Large\texttt{TTGAATCCTTGC \color{red}TCTGC \color{black}GATGGA}
\end{center}
%\caption{\bt{NM\_003002.2:c.262\_266del}.}
\end{figure}
\begin{figure}[]
\begin{center}
\Large\texttt{TTGAATCCTTGC \color{red}TCTGC \color{black}GATGGA}
\end{center}
\caption{\bt{NM\_003002.2:c.265\_269del}.}
\end{figure}
\end{pframe}
\begin{pframe}
\begin{figure}[]
\begin{center}
Genome\\
{\Large\texttt{AACTTAGGA \color{red}ACGAG \color{black}ACGCTACCT}}\\
{\Large\texttt{TTGAATCCTTGC \color{red}TCTGC \color{black}GATGGA}}\\
Transcript
\includegraphics[height=0.8\textheight]{gq}
\end{center}
\caption{}
\vspace{-0.3cm}
\caption{Callable region ($584$--$1596$).}
\end{figure}
\end{pframe}
\subsection{Options}
\begin{pframe}
Choices for the database layout:
\begin{itemize}
\item \emph{Sample} oriented.
\item \emph{Variant} oriented.
\end{itemize}
\bigskip
Choices for the infrastructure:
\begin{itemize}
\item Centralised.
\item Decentralised.
\end{itemize}
\end{pframe}
\subsection{Basic client set up}
\begin{pframe}
\begin{minipage}[t]{0.47\textwidth}
......@@ -146,28 +98,49 @@
From a \emph{gVCF}:
\begin{itemize}
\item Variants.
\item Regions with sufficient ``coverage''.
\begin{itemize}
\item We use \emph{genotype quality}.
\end{itemize}
\item Regions with sufficient \emph{genotype quality}.
\end{itemize}
\bigskip
Metadata:
\begin{itemize}
\item Labels.
\item Time stamp.
\end{itemize}
\end{minipage}
\end{pframe}
%\subsection{Concerns}
%\begin{pframe}
% Sample identification:
% \begin{itemize}
% \item The Netherlands: $17 \times 10^6$ inhabitants, $24$ SNPs.
% \item Global: $108 \times 10^9$ inhabitants, $37$ SNPs.
% \end{itemize}
%\end{pframe}
\subsection{Options}
\begin{pframe}
Choices for the database layout:
\begin{itemize}
\item \emph{Sample} oriented.
\item \emph{Variant} oriented.
\end{itemize}
\bigskip
Choices for the infrastructure:
\begin{itemize}
\item Centralised.
\item Decentralised.
\end{itemize}
\end{pframe}
\subsection{Technical issues}
\begin{pframe}
\begin{figure}[]
{\Large\texttt{
\begin{tabular}{llll}
\#CHROM & POS & REF & ALT\\
\onslide<1->{1 & 884551 & GAGA\color{red}AAGA & GAGA}\\
\onslide<2->{1 & 884552 & AGA\color{red}AAGA & AGA}\\
\onslide<3->{1 & 884553 & GA\color{red}AAGA & GA}\\
\onslide<4->{1 & 884554 & A\color{red}AAGA & A}
\end{tabular}
}}
\caption{Deletion of \bt{AAGA}.}
\end{figure}
\end{pframe}
\section{Sample oriented server}
\subsection{Database layout}
......@@ -381,6 +354,69 @@
\end{itemize}
\end{pframe}
\section{Interpreted data}
\begin{pframe}
\begin{figure}[]
\begin{center}
{\Large\texttt{
\only<1>{TTGAATCCT \color{red}TGCTC \color{black}TGCGATGGA\\}%
\only<2>{TTGAATCCTT \color{red}GCTCT \color{black}GCGATGGA\\}%
\only<3>{TTGAATCCTTG \color{red}CTCTG \color{black}CGATGGA\\}%
\only<4->{TTGAATCCTTGC \color{red}TCTGC \color{black}GATGGA\\}%
\vspace{1cm}
\begin{tabular}{l}
\onslide<1->{NM\_003002.2:c.262\_266del}\\
\onslide<2->{NM\_003002.2:c.263\_267del}\\
\onslide<3->{NM\_003002.2:c.264\_268del}\\
\onslide<4->{NM\_003002.2:c.265\_269del}
\end{tabular}
}}
\end{center}
\caption{Deletion of \bt{TCTGC}.}
\end{figure}
\end{pframe}
\begin{pframe}
\begin{figure}[]
\begin{center}
Genome\\
{\Large\texttt{%
3' AACTTAGGA \color{red}ACGAG \color{black}ACGCTACCT 5'\\
5' TTGAATCCTTGC \color{red}TCTGC \color{black}GATGGA 3'\\
}}
Transcript
\end{center}
\caption{3' rule.}
\end{figure}
\end{pframe}
\begin{pframe}
\begin{figure}[]
{\Large\texttt{%
\only<1>{%
ATGGCTCC \color{red}TG- \color{black}CCATGGAA\\
ATGGCTCC \color{red}TGC \color{black}CCATGGAA\\
}%
\only<2>{%
ATGGCTCCTG \color{red}- \color{black}CCATGGAA\\
ATGGCTCCTG \color{red}C \color{black}CCATGGAA\\
}%
\only<3->{%
ATGGCTCCTGCC \color{red}- \color{black}ATGGAA\\
ATGGCTCCTGCC \color{red}C \color{black}ATGGAA\\
}%
\vspace{1cm}
\begin{tabular}{l}
\onslide<1->{NM\_002001.2:c.9\_10delinsTGC}\\
\onslide<2->{NM\_002001.2:c.10\_11insC}\\
\onslide<3->{NM\_002001.2:c.12\_13insC}\\
\onslide<4->{NM\_002001.2:c.12dup}
\end{tabular}
}}
\caption{}
\end{figure}
\end{pframe}
% Issues with sharing interpretations:
% - ...
......
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