From 2a5642334e983ac17b71d223d8049ecdd295b39a Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Wed, 18 Apr 2012 16:05:23 +0000
Subject: [PATCH] NBIC poster in progress
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@513 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
---
.../poster.bbl | 12 +--
.../poster.tex | 91 +++++++------------
2 files changed, 41 insertions(+), 62 deletions(-)
diff --git a/doc/Poster_24_25-04-12_NBIC_Mutalyzer2/poster.bbl b/doc/Poster_24_25-04-12_NBIC_Mutalyzer2/poster.bbl
index ff5e2d4c..56ee1b89 100644
--- a/doc/Poster_24_25-04-12_NBIC_Mutalyzer2/poster.bbl
+++ b/doc/Poster_24_25-04-12_NBIC_Mutalyzer2/poster.bbl
@@ -4,12 +4,6 @@
{Human Genome Variation Society}.
\newblock \begin{small}\texttt{http://www.hgvs.org/}\end{small}.
-\bibitem{LOVD}
-I.F.A.C Fokkema, J.T. {den}~Dunnen, and P.E.M. Taschner.
-\newblock {LOVD}: easy creation of a locus-specific sequence variation database
- using an ``{LSDB-in-a-Box}'' approach.
-\newblock {\em Human Mutation}, 26(2):63--68, 2005.
-
\bibitem{LRG}
R.~Dalgleish and et~al.
\newblock {Locus Reference Genomic} sequences: an improved basis for describing
@@ -17,4 +11,10 @@ R.~Dalgleish and et~al.
\newblock {\em Genome Med}, 2:24, 2010.
\newblock See also {\small\texttt{http://www.lrg-sequence.org/}}.
+\bibitem{LOVD}
+I.F.A.C Fokkema, J.T. {den}~Dunnen, and P.E.M. Taschner.
+\newblock {LOVD}: easy creation of a locus-specific sequence variation database
+ using an ``{LSDB-in-a-Box}'' approach.
+\newblock {\em Human Mutation}, 26(2):63--68, 2005.
+
\end{thebibliography}
diff --git a/doc/Poster_24_25-04-12_NBIC_Mutalyzer2/poster.tex b/doc/Poster_24_25-04-12_NBIC_Mutalyzer2/poster.tex
index 56ea8a51..879ca376 100644
--- a/doc/Poster_24_25-04-12_NBIC_Mutalyzer2/poster.tex
+++ b/doc/Poster_24_25-04-12_NBIC_Mutalyzer2/poster.tex
@@ -1,7 +1,7 @@
\documentclass[final, slidestop]{beamer}
\title{Generating variant descriptions based on sequence comparison}
-\author{Jeroen F.J. Laros, Martijn Vermaat Johan T. den Dunnen,
+\author{Jeroen F.J. Laros, Martijn Vermaat, Johan T. den Dunnen,
Peter E.M. Taschner}
\institute{Center for Human and Clinical Genetics, Leiden University Medical
Center, Leiden, The Netherlands}
@@ -22,48 +22,20 @@
\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
+ importance for DNA diagnostics. Descriptions can be checked and corrected
+ with the {\em Mutalyzer sequence variation nomenclature checker}
+ (Fig.~\ref{figure:namecheck}) (\color{red}\bt{http://www.mutalyzer.nl/}\color{LUMCBlue})
following the Human Genome Variation Society (HGVS) sequence variant
nomenclature recommendations~\cite{HGVS}.
- \begin{figure}
- \vspace{2cm}
- \setlength{\unitlength}{0.12cm}
- \input{positionpicture}
- \caption{Gene-centred key positions in HGVS numbering scheme.}
- \label{fig:positions}
- \end{figure}
+ \vspace{1cm}
- \begin{table}
- \caption{HGVS positions in genomic (g.), non-coding (n.) and coding DNA
- (c.) notations.}
- \colorbox{white}{
- {\small
- \begin{tabular}{l|r|r|r}
- Key position & \bt{g.} & \bt{n.} & \bt{c.} \\
- \hline
- Genomic start & \bt{1} & \bt{1-u470} & \bt{-29-u470} \\
- Transcription start & \bt{471} & \bt{1} & \bt{-29} \\
- CDS start & \bt{501} & \bt{30} & \bt{1} \\
- Intron 1 start & \bt{513} & \bt{41+1} & \bt{12+1} \\
- Intron 1 end & \bt{612} & \bt{42-1} & \bt{13-1} \\
- CDS stop & \bt{1830} & \bt{359} & \bt{330} \\
- Transcription end & \bt{2050} & \bt{579} & \bt{*220} \\
- Genomic end & \bt{2670} & \bt{579+d620} & \bt{*220+d620} \\
- \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}.
+ Initial construction of variant descriptions, however, requires comparison
+ of the reference sequence and the variant sequence and basic knowledge of
+ the HGVS recommendations. With the arrival of long read sequencers (e.g.
+ PacBio) and the rise of sophisticated variant callers, the chance of
+ finding a complex variant increases and so does the need to describe these
+ variants.
}
\colorBlock{SalmonBg}{Description Extraction}{1}{
The description extractor can be used to construct variant descriptions
@@ -108,6 +80,23 @@
}
\end{table}
}
+ \colorBlock{GreenBg}{Mutalyzer 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).$^*$ \\
+ SNP Converter & Convert a dbSNP rsId to HGVS notation.$^*$ \\
+ Name Generator & Contruct a HGVS notation. \\
+ Description Extractor & Extract HGVS notation from sequences. \\
+ GenBank Uploader & Upload custom GenBank files. \\
+ Webservices & Programmatic (SOAP) interface. \\
+ \end{tabular}
+ \bigskip
+
+ $^*$ {\small Also available as a batch interface.}
+ }
\colorBlock{YellowBg}{Acknowledgements}{1}{
{\small
Funded by the European Community's Seventh Framework Programme
@@ -126,23 +115,13 @@
\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).$^*$ \\
- SNP Converter & Convert a dbSNP rsId to HGVS notation.$^*$ \\
- Name Generator & Contruct a HGVS notation. \\
- Description Extractor & Extract HGVS notation from sequences. \\
- Reference File Loader & Upload custom GenBank files. \\
- Webservices & Programmatic (SOAP) interface. \\
- \end{tabular}
- \bigskip
-
- $^*$ {\small Also available as a batch interface.}
+ \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{Background}{References}{1}{
{\small
--
GitLab