presentation.tex

% LUMC presentation template by J. F. J. Laros.
% Last alteration on 20-02-2011.
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% The packages texlive-latex-recommended, texlive-latex-base and
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% Alter these four lines for a new presentation.
\providecommand{\me}{Jeroen F. J. Laros}
\providecommand{\myTitle}{Mutalyzer 2.0}
\providecommand{\myConference}{Work discussion}
\providecommand{\myDate}{Thursday, 24 February 2011}

% Now go to %%% BEGIN PRESENTATION %%%

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  {\bf\Large{\myTitle}}\\
  \vfill
  \textcolor{Blue}{
    {\bf
      \small{\me}\\
      \small{Leiden Genome Technology Center}\\
      \small{Department of Human Genetics}\\
      \small{Center for Human and Clinical Genetics}
    }
  }
  \vspace{1.1cm}
  \end{center}
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\providecommand{\positionshiftexampleheader}{
  We observe a change from \bt{GG\underline{ATCATC}G} to 
  \bt{GG\underline{ATCATCATC}G}.

}

\providecommand{\positionshiftexamplebody}{
  \bt{\,123456789}
  \vspace{-0.3cm}

  \bt{GGATCATCG}

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\providecommand{\inversionexampleheader}{
  We observe a change from \bt{GCT\underline{TTAATT}AGG} to 
  \bt{GCT\underline{AATTAA}AGG}.

}

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\begin{slide}
  \slideheading{Introduction}
  
  A curational tool for \emph{Locus Specific Mutation Databases} (LSDBs).
  
  \bigskip
  \begin{itemize}
    \item Variant nomenclature checker applying \emph{Human Genome Variation
          Society} (HGVS) guidelines.
    \begin{itemize}
      \item Is the syntax of the variant description valid?
      \item Does the reference sequence exist?
      \item Is the variant possible on this reference sequence?
      \item Is this variant description the recommended one?
    \end{itemize}
    \item Basic effect prediction.
    \begin{itemize}
      \item Is the description of the transcript product as expected?
      \item Is the predicted protein as expected?
    \end{itemize}
  \end{itemize}
  \vfill
\end{slide}

\begin{slide}
  \slideheading{HGVS nomenclature}

    Genomic orientated positions:
    \begin{center}
      \bt{AL449423.14:g.[65449\_65463del;65564\yellow T\white >\yellow C\white]}
    \end{center}
    \bigskip
    Coding sequence orientated positions:
    \begin{center}
      \bt{AL449423.14(CDKN2A\_v001):c.[5\yellow A\white >\yellow G\white
        ;106\_120del]}
    \end{center}
    \bigskip
    \begin{itemize}
      \item \bt{AL449423.14} -- reference sequence.
      \item \bt{CDKN2A\_v001}$\;$ -- transcript variant \bt{1} of gene CDKN2A.
      \item \bt{c.[5\yellow A\white >\yellow G\white ;106\_120del]} 
      \begin{itemize}
        \item A \emph{substitution} at position \bt{5} counting from the start
          codon.
        \item A \emph{deletion} from position \bt{106} to position \bt{120}.
      \end{itemize}
    \end{itemize}
  
  \vfill
\end{slide}

\begin{slide}
  \slideheading{HGVS nomenclature: positions}

  \positionpicture

  This gene is on the reverse strand.

  \bigskip
  \begin{tabular}{l|l|l}
    Name       &         & Description\\
    \hline
    Genomic    & \bt{g.} & From {\scriptsize Genomic start} to
                           {\scriptsize Genomic end}. \\
    Transcript & \bt{n.} & From {\scriptsize Transcription start} to 
                           {\scriptsize Transcription end}, skip introns.\\
    Coding     & \bt{c.} & From {\scriptsize CDS start} to 
                           {\scriptsize CDS stop}, skip introns.
  \end{tabular}
  \vfill
\end{slide}

\begin{slide}
  \slideheading{HGVS nomenclature: positions}

  \positionpicture

  \bt{c.} positions:
  \begin{itemize}
    \item Positions in introns are relative to the nearest exonic position.
    \item Positions before the CDS are indicated with a \bt{-} sign.
    \item Positions after the CDS are indicated with a \bt{*} sign.
  \end{itemize}

  Position \bt{-1} and \bt{1} are adjacent.

  If \bt{60} is the last position of the CDS, then \bt{60} and \bt{*1} are
  adjacent.
  \vfill
\end{slide}

\begin{slide}
  \slideheading{HGVS nomenclature: positions}

  \positionpicture

  \renewcommand{\arraystretch}{1}
  \begin{center}
    \begin{tabular}{l|r|r|r}
      Name                              & \bt{g.}  & \bt{n.}      & \bt{c.} \\
      \hline
      {\scriptsize Genomic start}       & \bt{1}   & \bt{100+d70} & 
        \bt{*10+d70} \\
      {\scriptsize Genomic end}         & \bt{300} & \bt{1-u50}   & 
        \bt{-30-u50} \\
      {\scriptsize Transcription start} & \bt{250} & \bt{1}       & \bt{-30} \\
      {\scriptsize Transcription end}   & \bt{70}  & \bt{100}     & \bt{*10} \\
      {\scriptsize CDS start}           & \bt{220} & \bt{30}      & \bt{1} \\
      {\scriptsize CDS stop}            & \bt{80}  & \bt{90}      & \bt{60} \\
    \end{tabular}
  \end{center}
  \vfill
\end{slide}

\begin{slide}
  \slideheading{HGVS nomenclature: positions}

  \positionpicture

  \renewcommand{\arraystretch}{1}
  \begin{center}
    \begin{tabular}{l|r|r|r}
      Name                    & \bt{g.}  & \bt{n.}    & \bt{c.} \\
      \hline
      {\scriptsize Variant A} & \bt{185} & \bt{50+15} & \bt{20+15} \\
      {\scriptsize Variant B} & \bt{140} & \bt{60}    & \bt{30} \\
    \end{tabular}
  \end{center}

  \bigskip
  \bt{NG\_001234.1:g.185\yellow A\white >\yellow C\white} 

  \bt{NG\_001234.1(GEN\_v001):n.50+15\yellow T\white >\yellow G\white } 

  \bt{NG\_001234.1(GEN\_v001):c.20+15\yellow T\white >\yellow G\white }
  \vfill
\end{slide}

\begin{slide}
  \slideheading{HGVS nomenclature: the position shift rule}
  
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  Which can be described as an insertion of \bt{ATC} at three places:
  \begin{itemize}
    \item \bt{g.2\_3ins\yellow ATC\white}
    \item \bt{g.5\_6ins\yellow ATC\white}% \ \ or \ \ \bt{g.3\_5dup}
    \item \bt{g.8\_9ins\yellow ATC\white}% \ \ or \ \ \bt{g.6\_8dup}
  \end{itemize}
  \vfill
\end{slide}

\begin{slide}
  \slideheading{HGVS nomenclature: the position shift rule}
  
  \positionshiftexampleheader
  \begin{center}
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  \ldots or an insertion of \bt{TCA} at two places:
  \begin{itemize}
    \item \bt{g.3\_4ins\yellow TCA\white}
    \item \bt{g.6\_7ins\yellow TCA\white}% \ \ or \ \ \bt{g.4\_6dup}
  \end{itemize}
  \vfill
\end{slide}

\begin{slide}
  \slideheading{HGVS nomenclature: the position shift rule}
  
  \positionshiftexampleheader
  \begin{center}
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  \ldots or an insertion of \bt{CAT} at two places:
  \begin{itemize}
    \item \bt{g.4\_5ins\yellow CAT\white}
    \item \bt{g.7\_8ins\yellow CAT\white}% \ \ or \ \ \bt{g.5\_7dup}
  \end{itemize}
  \vfill
\end{slide}

\begin{slide}
  \slideheading{HGVS nomenclature: the position shift rule}
  
  \positionshiftexampleheader
  \begin{center}
    \positionshiftexamplebody
    \begin{picture}(0, 0)(0, 0)
      % \put(-15.6, 5){\vector(0, 1){10}}
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      \put(21.4, 5){\vector(0, 1){10}}
    \end{picture}
  \end{center}

  The only correct one is the insertion on the 3' end.
  \begin{itemize}
    \item \bt{g.8\_9ins\yellow ATC}
  \end{itemize}

  However, this can also be described as a \emph{duplication}, which has
  precedence over the \emph{insertion}.

  The final description therefore is:
  \begin{itemize}
    \item \bt{g.6\_8dup}
  \end{itemize}
  \vfill
\end{slide}

\begin{slide}
  \slideheading{HGVS nomenclature: the position shift rule}
  
  However, the \bt{c.} notation of a gene on the reverse strand:

  \begin{minipage}{0.4\textwidth}
    \begin{center}
      Genomic

      \bt{\,123456789}
      \vspace{-0.15cm}

      \bt{GGATC\green\underline{\white ATC}\white G}
    \end{center}
  \end{minipage}
  \begin{minipage}{0.4\textwidth}
    \begin{center}
      Coding

      \bt{\,123456789}
      \vspace{-0.15cm}

      \bt{C\green\underline{\white GAT}\yellow\underline{\white GAT}\white CC}
    \end{center}
  \end{minipage}
  \bigskip

  \begin{itemize}
    \item \bt{g.6\_8dup}
    \item \bt{c.\yellow 5\white \_\yellow 7\white dup}\white \ \ \ and not \ \ 
      \bt{c.\green 2\white \_\green 4\white dup}
  \end{itemize}

  A substitution on position \bt{g.8}, \emph{would} be converted to \bt{c.2}.

  \begin{itemize}
    \item \bt{g.8\yellow C\white >\yellow A\white}
    \item \bt{c.2\yellow G\white >\yellow T\white}
  \end{itemize}
  \vfill
\end{slide}

\begin{slide}
  \slideheading{HGVS nomenclature: disambiguation}
  
  \inversionexampleheader
  \begin{center}
    \bt{\,\ \ \ \ \ \ \ \ \ 111}
    \vspace{-0.3cm}

    \bt{\,\,123456789012}
    \vspace{-0.3cm}

    \bt{G\underline{CTTTAATTAG}G}
  \end{center}

  We can describe it as follows:
  \begin{itemize}
    \item \bt{g.2\_11inv}
  \end{itemize}
  \begin{center}
    \bt{\,\ \ \ \ \ \ \ \ \ 111}
    \vspace{-0.3cm}

    \bt{\,\,123456789012}
    \vspace{-0.3cm}

    \bt{GCT\underline{TTAATT}AGG}
  \end{center}
  \begin{itemize}
    \item \bt{g.4\_9delins\yellow AATTAA\white}
  \end{itemize}

  But the correct way is:
  \begin{itemize}
    \item \bt{g.4\_9inv}
  \end{itemize}
  \vfill
\end{slide}

\begin{slide}
  \slideheading{HGVS nomenclature: disambiguation}

  Other pitfalls:
  \begin{itemize}
    \item A deletion-insertion can actually be:
    \begin{tabular}{llll}
      --\, An inversion & \bt{2\_3del\yellow AC\white ins\yellow GT\white}
        & $\Rightarrow$ & \bt{2\_3inv}\\
      --\, An insertion & \bt{2del\yellow T\white ins\yellow TAA\white}
        & $\Rightarrow$ & \bt{2\_3ins\yellow AA\white}\\
      --\, A substitution & \bt{2del\yellow A\white ins\yellow T\white} 
        & $\Rightarrow$ & \bt{2\yellow A\white >\yellow T\white}\\
      --\, A deletion & \bt{2\_3del\yellow TA\white ins\yellow A\white}
        & $\Rightarrow$ & \bt{2del}\\
    \end{tabular}
    \item An inversion can actually be a substitution 
      (\bt{2\_4inv\yellow ACT\white}).
    \item An insertion can actually be a duplication.
    \item A variant can have no effect (\bt{2\_5inv\yellow ACGT\white},
          \bt{2\yellow A\white >\yellow A\white}, etc.).
  \end{itemize}
  \vfill
\end{slide}

\begin{slide}
  \slideheading{Mutalyzer 2.0: name checker}

  \begin{center}
    \bt{NM\_002001.2:c.[12\_14del;102\yellow G\white >\yellow T\white]}
  \end{center}
  \begin{enumerate}
    \item Parse the variant description.
    \begin{itemize}
      \item Reference sequence e.g., \bt{NM\_002001.2}.
      \item Position system (\bt{c.}, \bt{g.}, \bt{n.}, \ldots).
      \item List of variants (\bt{12\_14del}, 
            \bt{102\yellow G\white >\yellow T\white}).
    \end{itemize}
    \item Download the reference sequence.
    \item Check the variants to the reference sequence.
    \begin{itemize}
      \item Is there a \bt{\yellow G\white } at position \bt{c.102}?
    \end{itemize}
    \item Mutate the reference sequence.
    \item Predict the variant protein when applicable.
    \item \ldots
  \end{enumerate}
  \vfill
\end{slide}
  
\begin{slide}
  \slideheading{Mutalyzer 2.0: name checker}

  \bigskip
  \bigskip
  \bigskip
  \bigskip
  \bigskip
  \begin{center}
    \bt{AL449423.14(CDKN2A\_v001):c.247\_250delins\yellow CTTT\white}

    \bigskip
    \bt{http://www.mutalyzer.nl/2.0/check}
  \end{center}
  \vfill
\end{slide}
  
\begin{slide}
  \slideheading{Mutalyzer 2.0: name checker}

  After a description is checked, other useful information is returned.
  \begin{itemize}
    \item Overview of the change on DNA level.
    \item A genomic description.
    \item A description on all affected transcripts.
    \item Description of affected proteins.
    \item Sequence of the original and affected protein with changes 
      highlighted.
    \item Exon and CDS start / stop information.
    \item Effects on restriction sites.
  \end{itemize}

  \vfill
\end{slide}

\begin{slide}
  \slideheading{Mutalyzer 2.0: design}

  This version was built from scratch.
  \begin{itemize}
    \item Modular design allows for partial functionality or other combinations.
    \begin{itemize}
      \item Convert positions.
      \item Check the syntax of a variant only.
      \item Get information about a gene.
      \item \ldots
    \end{itemize}
    \item Strict separation of functionality and interface.
    \begin{itemize}
      \item Web interface.
      \item Batch interface.
      \item Command line interface.
      \item Programmatic access (for LOVD and other programs).
    \end{itemize}
  \end{itemize}

  \vfill
\end{slide}

\begin{slide}
  \slideheading{Mutalyzer 2.0: position converter}

  Next Generation Sequencing uses chromosomal positions.

  LSDB's usually use transcripts.

  The position converter:
  \begin{itemize}
    \item Works on both hg18 (NCBI Build 36.1) and hg19 (GRCh37).
    \item Works in both ways:
    \begin{itemize}
      \item \bt{NM\_003002.2:c.274\yellow G\white >\yellow T\white} to
            \bt{NC\_000011.9:g.111959695\yellow G\white >\yellow T\white}.
      \item \bt{chr11:g.111959695\yellow G\white >\yellow T\white} to 
            \bt{NM\_003002.2:c.274\yellow G\white >\yellow T\white}.
    \end{itemize}
    \item Can be used to \emph{lift over} from hg18 to hg19 and vice versa.
  \end{itemize}

  \vfill
\end{slide}
  
\begin{slide}
  \slideheading{Mutalyzer 2.0: other functionalities}
  
  Other functionalities of Mutalyzer 2.0 include:
  \begin{itemize}
    \item SNP conversion (from dbSNP rsId to HGVS notation).
    \item Name generator (to help people that don't use the HGVS notation that
          often).
    \item GenBank uploader (to make your own reference sequences).
    \begin{itemize}
      \item Automatically uses the correct strand when a HGNC gene symbol is
            used.
    \end{itemize}
    \item Recently added functionality for the LRG (Locus Reference Genomic)
          reference files.
    \begin{itemize}
      \item Other formats can easily be added.
    \end{itemize}
  \end{itemize}
  \vfill
\end{slide}

\begin{slide}
  \slideheading{Mutalyzer 2.0: other functionalities}

  For a large number of checks, there are other interfaces.
  \begin{itemize}
    \item Batch interfaces (upload a table, receive the result by mail):
    \begin{itemize}
      \item Name checker.
      \item Syntax checker.
      \item Position converter.
    \end{itemize}
    \item Programmatic access (use from your own scripts).
    \begin{itemize}
      \item Currently $18$ functions available.
      \begin{itemize}
        \item Position conversion.
        \item Mutate a reference sequence.
        \item Retrieve all transcripts in a range of a chromosome.
        \item Give extensive information of transcripts.
        \item \ldots
      \end{itemize}
    \end{itemize}
  \end{itemize}
  \vfill
\end{slide}

\begin{slide}
  \slideheading{LOVD}

  LOVD, the \emph{Leiden Open Variation Database} is a \emph{locus specific
  database} (LSDB).

  \begin{itemize}
    \item Gene centred.
    \item Variants are supposed to be stored in HGVS format.
    \begin{itemize}
      \item Mutalyzer name checker.
    \end{itemize}
    \item Variants are described on one \emph{transcript}.
    \begin{itemize}
      \item Mutalyzer name checker gives descriptions for all annotated
        transcripts.
    \end{itemize}
    \item Variants must be mapped to the genome.
    \begin{itemize}
      \item Mutalyzer position converter.
    \end{itemize}
  \end{itemize}
  
  \begin{center}
    \bt{http://www.lovd.nl}
  \end{center}
  \vfill
\end{slide}

\begin{slide}
  \slideheading{LOVD: Mutalyzer 2.0 dependencies}

  Creating a database:
  \begin{itemize}
    \item The curator knows the accession number of a transcript.
    \begin{itemize}
      \item Find the gene.
      \item Find a genomic reference sequence.
      \item Use the accession number of the genomic and transcript reference to
        make a HGVS reference notation.
      \begin{itemize}
        \item \bt{NG\_007109.1} \ \  and \ \ \bt{NM\_000249.3} $\Rightarrow$ 
          \bt{NG\_007109.1(MLH1\_v001)}.
      \end{itemize}
    \end{itemize}
    \item The curator knows the gene name.
    \begin{itemize}
      \item Find a genomic reference sequence.
      \item Retrieve a list of transcripts.
      \item Show product information of each transcript.
    \end{itemize}
  \end{itemize}

  \vfill
\end{slide}

\begin{slide}
  \slideheading{LOVD: Mutalyzer 2.0 dependencies}

  Adding a variant:
  \begin{itemize}
    \item Verify the validity.
    \item Convert to genomic (chromosomal) positions.
    \begin{itemize}
      \item Used for visualisation in the UCSC genome browser.
      \item Enables all LOVD installations to be searched.
    \end{itemize}
    \item Convert variant descriptions to other transcripts.
    \item Provide a sortable \bt{c.}-like position.
  \end{itemize}

  \vfill
\end{slide}

\begin{slide}
  \slideheading{Conclusions and further research}

  Short term:
  \begin{itemize}
    \item Using protein reference sequences.
    \item Connection to SVEP.
    \begin{itemize}
      \item Splice prediction.
      \item Alternative start.
      \item Branch sites.
      \item Transcription factors binding sites.
      \item Protein effect prediction.
      \item \ldots
    \end{itemize}
  \end{itemize}
  \vfill
\end{slide}
  
\begin{slide}
  \rput(11.4,0.6){\includegraphics[scale=0.1]{Gen2Phen}}
  \slideheading{Questions?}
  \begin{center}
    Acknowledgements
    \bigskip
    \bigskip
    
    Gerben Stouten\\
    Martijn Vermaat\\
    Gerard Schaafsma\\
    Ivo Fokkema\\
    Jacopo Celli\\
    Johan den Dunnen\\
    Peter Taschner
    \bigskip
    
    \bt{http://www.mutalyzer.nl/}
  \end{center}
  \vfill
  \label{LastPage}
\end{slide}

\end{document}