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Commit c37509b0 authored by Laros's avatar Laros
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Added a picture in one of the presentations, added a poster presentation. 


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@270 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
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doc/Poster_19_20-04-11_NBIC_Mutalyzer2/Makefile 0 → 120000
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\vspace{-0.5cm}
\begin{center}
\colorbox{white}{
\begin{picture}(300, 60)(0, 0)
\put(0, 30){\line(1, 0){300}} % Genomic sequence.
\linethickness{4pt}
\put(50, 30){\line(1, 0){30}} % Non-coding parts of the exons.
\put(220, 30){\line(1, 0){10}}
\linethickness{12pt}
\put(80, 30){\line(1, 0){20}} % Coding parts of the exons.
\put(150, 30){\line(1, 0){20}}
\put(200, 30){\line(1, 0){20}}
\linethickness{0.5pt}
\put(20, 50){\scriptsize{Transcription start}}
\put(50, 45){\vector(0, -1){10}}
\put(200, 50){\scriptsize{Transcription end}}
\put(230, 45){\vector(0, -1){10}}
\put(70, 0){\scriptsize{CDS start}}
\put(80, 10){\vector(0, 1){10}}
\put(210, 0){\scriptsize{CDS stop}}
\put(220, 10){\vector(0, 1){10}}
\put(0, 0){\scriptsize{Genomic end}}
\put(0, 10){\vector(0, 1){10}}
\put(270, 0){\scriptsize{Genomic start}}
\put(300, 10){\vector(0, 1){10}}
\put(95, 50){\color{red}\scriptsize{Variant A}\color{black}}
\put(115, 45){\color{red}\vector(0, -1){10}\color{black}}
\put(140, 50){\color{red}\scriptsize{Variant B}\color{black}}
\put(160, 45){\color{red}\vector(0, -1){10}\color{black}}
\end{picture}
}
\end{center}
\bigskip
doc/Poster_19_20-04-11_NBIC_Mutalyzer2/poster.bbl 0 → 100644
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\begin{thebibliography}{1}
\bibitem{HGVS}
{Human Genome Variation Society}.
\newblock \begin{small}\texttt{http://www.hgvs.org/}\end{small}.
\bibitem{LOVD}
I.~Fokkema, J.~{den}~Dunnen, and P.~Taschner, ``{LOVD}: easy creation of a
locus-specific sequence variation database using an ``{LSDB-in-a-Box}''
approach.,'' {\em Human Mutation}, vol.~26, no.~2, pp.~63--68, 2005.
\bibitem{LRG}
R.~e.~a. Dalgleish, ``Locus reference genomic,'' {\em Genome Med}, vol.~2,
p.~24, 2010.
\newblock See also {\small\texttt{http://www.lrg-sequence.org/}}.
\end{thebibliography}
doc/Poster_19_20-04-11_NBIC_Mutalyzer2/poster.tex 0 → 100644
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\documentclass[final, slidestop]{beamer}
\title{Mutalyzer 2.0: Improved sequence variant descriptions from next
generation sequencing data and gene variant databases}
\author{Jeroen F. J. Laros, Martijn Vermaat, Gerben Stouten, \\
Johan T. den Dunnen, Peter E. M. Taschner}
\institute{Center for Human and Clinical Genetics, Leiden University Medical
Center, Leiden, The Netherlands}
\providecommand{\centerLogo}{
\includegraphics[height = 3cm]{gen2phen_logo}
}
\providecommand{\rightLogo}{
\includegraphics[height = 3cm]{nbic_logo}
}
\providecommand{\colOneWidth}{0.48}
\providecommand{\colTwoWidth}{0.48}
\usetheme{lumc}
\begin{document}
\begin{frame}{}
\begin{myPoster}
\colorBlock{Background}{Introduction}{1}{
Unambiguous and correct sequence variant descriptions are of utmost
importance for DNA diagnostics. The free Mutalyzer sequence variation
nomenclature checker
(\color{red}\bt{http://www.mutalyzer.nl/}\color{LUMCBlue}) names variants
following the Human Genome Variation Society (HGVS) sequence variant
nomenclature recommendations~\cite{HGVS}.
\begin{figure}
\vspace{2cm}
\setlength{\unitlength}{0.12cm}
\input{positionpicture}
\caption{Key positions in HGVS numbering scheme.}
\label{fig:positions}
\end{figure}
\begin{table}
\caption{Positions from Fig.~\ref{fig:positions} in HGVS genomic (g.),
non-coding (n.) and coding DNA (c.) notations.}
\colorbox{white}{
\begin{tabular}{l|r|r|r}
Key position & \bt{g.} & \bt{n.} & \bt{c.} \\
\hline
Genomic end & \bt{300} & \bt{1-u50} & \bt{-30-u50} \\
Transcription start & \bt{250} & \bt{1} & \bt{-30} \\
CDS start & \bt{220} & \bt{30} & \bt{1} \\
CDS stop & \bt{80} & \bt{90} & \bt{60} \\
Transcription end & \bt{70} & \bt{100} & \bt{*10} \\
Genomic start & \bt{1} & \bt{100+d70} & \bt{*10+d70} \\
\end{tabular}
}
\end{table}
}
\colorBlock{WhiteBg}{Conclusions}{1}{
Variants at intergenic, exonic, intronic, CDS and UTR positions can be
easily distinguished based on their gene-centered HGVS descriptions.
Mutalyzer facilitates batch-wise conversion from dbSNP rsIDs or
chromosomal position numbering of next generation sequencing data to
transcript position numbering, as well as sequence variant checking of
locus-specific sequence variant databases (LSDBs)~\cite{LOVD}.
}
\colorBlock{SalmonBg}{Position Conversion}{1}{
The position converter in batch mode is especially suited for NGS
applications. It can handle large numbers of genomic variant descriptions
and converts them to transcript-oriented positions. Following a semantic
check with the batch Name Checker, variant descriptions can be used for
annotation. CDS, exon and intron positions can be easily distinguished
from the HGVS descriptions and used to query LSDBs.
\begin{figure}
{
\includegraphics[width = 0.85\textwidth, height = 18cm]{mutalyzerPositionConvert}
}
\caption{Mutalyzer 2.0 Position Converter.}
\label{figure:positionconvert}
\end{figure}
}
\colorBlock{YellowBg}{Acknowledgements}{1}{
{\small
Funded by the European Community's Seventh Framework Programme
(FP7/2007-2013) under grant agreement no. 200754 - the GEN2PHEN project.
}
}
\nextColumn
\colorBlock{BlueBg}{Name Checking}{1}{
\begin{figure}
{
\includegraphics[width = 0.95\textwidth, height = 57cm]{mutalyzerNameCheck}
}
\caption{Mutalyzer 2.0 Name Checker using a LRG reference
sequence~\cite{LRG}}
\label{figure:namecheck}
\end{figure}
}
\colorBlock{GreenBg}{Interfaces}{1}{
\begin{tabular}{l@{\ \ --\ \ }p{25cm}}
Name Checker & Syntactic and semantic checks.
Fig.~\ref{figure:namecheck} $^*$ \\
Syntax Checker & Syntactic checks only. $^*$ \\
Position Converter & Convert chromosomal positions to gene-centered
notation (no semantic check)
Fig.~\ref{figure:positionconvert} $^*$ \\
SNP Converter & Convert a dbSNP rsId to HGVS notation. $^*$ \\
Name Generator & Contruct a HGVS notation. \\
GenBank Uploader & Upload custom GenBank files. \\
Webservices & Programmatic (SOAP) interface. \\
\end{tabular}
$^*$ Also available as a batch interface.
}
\colorBlock{Background}{References}{1}{
{\small
\bibliography{$HOME/projects/bibliography}{}
}
}
\end{myPoster}
\end{frame}
\end{document}
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\providecommand{\positionpicture}{
\vspace{-0.5cm}
\begin{center}
\fbox{
\begin{picture}(300, 60)(0, 0)
\put(0, 30){\line(1, 0){300}} % Genomic sequence.
\linethickness{4pt}
\put(50, 30){\line(1, 0){30}} % Non-coding parts of the exons.
\put(220, 30){\line(1, 0){10}}
\linethickness{12pt}
\put(80, 30){\line(1, 0){20}} % Coding parts of the exons.
\put(150, 30){\line(1, 0){20}}
\put(200, 30){\line(1, 0){20}}
\linethickness{0.5pt}
\put(20, 50){\scriptsize{Transcription start}}
\put(50, 45){\vector(0, -1){10}}
\put(200, 50){\scriptsize{Transcription end}}
\put(230, 45){\vector(0, -1){10}}
\put(70, 0){\scriptsize{CDS start}}
\put(80, 10){\vector(0, 1){10}}
\put(210, 0){\scriptsize{CDS stop}}
\put(220, 10){\vector(0, 1){10}}
\put(0, 0){\scriptsize{Genomic end}}
\put(0, 10){\vector(0, 1){10}}
\put(255, 0){\scriptsize{Genomic start}}
\put(300, 10){\vector(0, 1){10}}
\put(95, 50){\color{yellow}\scriptsize{Variant A}\color{white}}
\put(115, 45){\color{yellow}\vector(0, -1){10}\color{white}}
\put(140, 50){\color{yellow}\scriptsize{Variant B}\color{white}}
\put(160, 45){\color{yellow}\vector(0, -1){10}\color{white}}
\end{picture}
}
\end{center}
\bigskip
}
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