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Laros
lectures
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f9eb7abb
Commit
f9eb7abb
authored
Sep 26, 2016
by
Laros
Browse files
Finished most figures.
parent
d9b2388c
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lectures/data_sharing/data_sharing.tex
View file @
f9eb7abb
...
...
@@ -25,11 +25,17 @@
\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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