Finalised melanoma lecture.

2df3988c · Laros · 82bc1c6f · 2df3988c · 2df3988c · 2df3988c
Commit 2df3988c authored Dec 02, 2015 by Laros
--- a/lectures/melanoma/cnv.png
+++ b/lectures/melanoma/cnv.png
+../../submodules/presentation-pics/pics/cnv.png
\ No newline at end of file
--- a/lectures/melanoma/exome_genome.jpg
+++ b/lectures/melanoma/exome_genome.jpg
+../../submodules/presentation-pics/pics/exome_genome.jpg
\ No newline at end of file
--- a/lectures/melanoma/melanoma.tex
+++ b/lectures/melanoma/melanoma.tex
 \documentclass[slidestop]{beamer}

 \author{Jeroen F.J. Laros}
-\title{Whole genome sequencing in Dutch melanoma families}
+\title{Whole genome sequencing of Dutch melanoma families}
 \providecommand{\mySubTitle}{Experiences and challenges}
-\providecommand{\myConference}{MTG work discussion}
+\providecommand{\myConference}{MTG meeting}
 \providecommand{\myDate}{3-dec-2015}
 \providecommand{\myGroup}{Leiden Genome Technology Center}
 \providecommand{\myDepartment}{Department of Human Genetics}
@@ -21,21 +21,55 @@

 % First page of the presentation.
 \section{Introduction}
-\subsection{Samples}
+\subsection{Full genome sequencing}
 \begin{pframe}
-  X families, about Y members per family.
+  In contrast to \emph{exome sequencing}, where we only the \emph{coding
+  regions} are sequenced, we sequence everything.
+  \bigskip
+  \pause
+
+  Advantages of \emph{full genome sequencing}:
  \begin{itemize}
-    \item Full genome.
-    \item $z\times$ coverage.
+    \item Introns.
+    \begin{itemize}
+      \item Branch points.
+      \item Intronic splicing enhancers.
+    \end{itemize}
+    \item Promoters.
+    \item Transcription factor binding sites, insulators, etc.
+    \item Consistent coverage.
+    \begin{itemize}
+      \item Copy number variation.
+    \end{itemize}
  \end{itemize}
 \end{pframe}

+\begin{pframe}
+  \begin{figure}[]
+    \begin{center}
+      \includegraphics[trim=0.3cm 1.5cm 0 3.4cm, clip, width=\textwidth]
+        {exome_genome}
+    \end{center}
+    \caption{Exome- versus genome sequencing.}
+  \end{figure}
+\end{pframe}
+
+\subsection{Copy number variation}
+\begin{pframe}
+  \begin{figure}[]
+    \begin{center}
+      \includegraphics[trim=0 8.4cm 0 2.2cm, clip, width=\textwidth]{cnv}
+    \end{center}
+    \caption{Coverage pattern over a whole chromosome.}
+  \end{figure}
+\end{pframe}
+
 \section{Data generation}
 \subsection{Sequencing}
 \begin{pframe}
  \begin{minipage}[t]{0.47\textwidth}
    \begin{figure}
-      \includegraphics[width=\textwidth]{hiseq_2000}
+      \includegraphics[trim=0 1cm 0 0.5cm, clip, width=\textwidth]{hiseq_2000}
      \caption{HiSeq 2500.}
    \end{figure}
  \end{minipage}
@@ -53,8 +87,18 @@
 \end{pframe}

 \begin{pframe}
-  Sequencing was one at the Sanger institute.
-  % 938528037 mapped reads
+  \begin{figure}[]
+    \begin{center}
+      \includegraphics[trim=0 1cm 0 23cm, clip, width=\textwidth]
+        {single_paired_end}
+    \end{center}
+    \caption{Paired end sequencing.}
+  \end{figure}
+\end{pframe}
+
+\begin{pframe}
+  Sequencing was done at the Sanger institute.
+  % 938,528,037 mapped reads
  % 1672174 unmapped reads

  \begin{itemize}
@@ -62,11 +106,13 @@
    \item $1,\!000,\!000,\!000$ reads.
    \item $100,\!000,\!000,\!000$ nucleotides.
    \item $150$GB of data per sample (compressed).
+    \item $35 \times$ coverage.
  \end{itemize}
  \bigskip
+  \pause

-  A grand total of $4.5$TB was used, which completely filled up the storage at
-  Sanger.
+  A grand total of $4.5$TB was generated, which completely filled up the
+  storage at Sanger.

  \vfill
  \permfoot{\url{http://www.sanger.ac.uk/}}
@@ -75,13 +121,25 @@
 \subsection{Data transfer}
 \begin{pframe}
  We need to make sure the data is transfered in a \emph{secure} way.
+  \bigskip

-  Sending disks?
+  Data carrier:
+  \begin{itemize}
+    \item Disks.
+    \item Network.
+  \end{itemize}
+  \bigskip
+  \pause

  Public server, GPG encryption.
+  \begin{itemize}
+    \item Encrypted with my \emph{public key}.
+    \item The encrypted data is public.
+    \item Can only be decrypted with my \emph{private key}.
+  \end{itemize}
 \end{pframe}

-
+\section{Data analysis}
 \subsection{Pipelines}
 \begin{pframe}
  \begin{figure}[]
@@ -116,7 +174,7 @@
 \end{pframe}

 \begin{frame}
-  \frametitle{Principle of variant calling}
+  \frametitle{Variant calling}

  \begin{figure}[]
    \begin{center}
@@ -151,46 +209,6 @@
  \end{itemize}
 \end{pframe}

-\section{Annotation}
-\subsection{Effect prediction}
-\begin{pframe}
-  In most cases we are still left with a lot of variants.
-  \bigskip
-
-  Variant annotation.
-  \begin{itemize}
-    \item Frequency within a population.
-    \item Location of the variant.
-    \begin{itemize}
-      \item Gene panels.
-      \item Location within a gene.
-    \end{itemize}
-    \item Conservation.
-  \end{itemize}
-\end{pframe}
-
-\subsection{Variant Effect Predictor}
-\begin{pframe}
-  A selection of VEP annotation:
-  \begin{itemize}
-    \item Affected genes and transcripts.
-    \item Location of the variant.
-    \begin{itemize}
-      \item Upstream of a transcript, in coding sequence, in non-coding RNA,
-        in regulatory region.
-    \end{itemize}
-    \item Consequence on the protein sequence.
-    \begin{itemize}
-      \item Stop gained, missense, stop lost, frameshift.
-    \end{itemize}
-    \item Minor allele frequencies from the 1000 Genomes Project.
-    \item SIFT and PolyPhen scores for changes to protein sequence.
-  \end{itemize}
-
-  \vfill
-  \permfoot{\url{http://www.ensembl.org/info/docs/tools/vep/index.html}}
-\end{pframe}
-
 \subsection{Databases}
 \begin{pframe}
  In most cases we are not interested in common variants.
@@ -201,7 +219,7 @@
  \end{itemize}
  \medskip

-  A cut-off of $1\%$ is usually fine.
+  A cut-off of $1$\% is usually fine.
  \bigskip
  \pause

@@ -220,26 +238,39 @@
  \bs{\url{http://www.hgmd.cf.ac.uk/}}
 \end{pframe}

+\subsection{Inheritance based filtering}
 \begin{pframe}
  % iets moet in alle familieleden voorkomen, maar mag niet in een deel van een
  % andere familie voorkomen maar wel in de gehele familie
+  We used the following intersection method.
+  \bigskip
+
+  {\it ``A variant should be present in all affected members of a family, but
+  it may not occur in part of the affected members of an other family.''}

  \begin{table}[]
    \begin{center}
      \begin{tabular}{ccl}
        Family one & Family two & Filter result \\
        \hline
-        $5/5$      & $4/4$      & Passed \\
-        $0/5$      & $4/4$      & Passed \\
+        $5/5$      & $4/4$      & Pass \\
+        $0/5$      & $4/4$      & Pass \\
        $3/5$      & $4/4$      & Filtered \\
        $3/5$      & $3/4$      & Filtered \\
      \end{tabular}
    \end{center}
-    \caption{The advanced intersection.}
+    \caption{Advanced intersection.}
  \end{table}
+
+  \vfill
+  \bs{P.J. van 't Hof}
 \end{pframe}

+\subsection{Filters}
 \begin{pframe}
+  We first did some general filtering based on allele frequencies found in
+  databases and inheritance patterns.
+
  \begin{table}[]
    \begin{center}
      \begin{tabular}{lr}
@@ -258,6 +289,8 @@
 \end{pframe}

 \begin{pframe}
+  By combining filters, we are left with a reasonable amount of variants.
+
  \begin{table}[]
    \begin{center}
      \begin{tabular}{lr}
@@ -274,7 +307,48 @@
    \caption{Combining filters.}
  \end{table}

-(25.127 in all families)
+  Note: $25,\!127$ variants are present in every individual.
+\end{pframe}
+
+\section{Annotation}
+\subsection{Effect prediction}
+\begin{pframe}
+  We are still left with a lot of variants.
+  \bigskip
+
+  Variant annotation.
+  \begin{itemize}
+    \item Frequency within a population.
+    \item Location of the variant.
+    \begin{itemize}
+      \item Gene panels.
+      \item Location within a gene.
+      \item Regulatory regions.
+    \end{itemize}
+    \item Conservation.
+  \end{itemize}
+\end{pframe}
+
+\subsection{Variant Effect Predictor}
+\begin{pframe}
+  A selection of VEP annotation:
+  \begin{itemize}
+    \item Affected genes and transcripts.
+    \item Location of the variant.
+    \begin{itemize}
+      \item Upstream of a transcript, in coding sequence, in non-coding RNA,
+        in regulatory region.
+    \end{itemize}
+    \item Consequence on the protein sequence.
+    \begin{itemize}
+      \item Stop gained, missense, stop lost, frameshift.
+    \end{itemize}
+    \item Minor allele frequencies from the 1000 Genomes Project.
+    \item SIFT and PolyPhen scores for changes to protein sequence.
+  \end{itemize}
+
+  \vfill
+  \permfoot{\url{http://www.ensembl.org/info/docs/tools/vep/index.html}}
 \end{pframe}

 \subsection{Conservation}
@@ -295,11 +369,15 @@
 % Make the acknowledgements slide.
 \makeAcknowledgementsSlide{
  \begin{tabular}{lll}
-    \bf Dermatology      & \bf SASC             & \bf Sanger \\
-    Mijke Visser         & Peter van 't Hof     & Thomas Keane \\
-    Nelleke Gruis        & Sander van der Zeeuw & Kim Wong \\
-    Nienke van der Stoep & Leon Mei             & Daniela Espinoza \\
-    Remco van Doorn      &                      & David Adams \\
+    \bf Dermatology       & \bf SASC               & \bf Sanger \\
+    Mijke Visser          & Peter van 't Hof       & Thomas Keane \\
+    Nelleke Gruis         & Sander van der Zeeuw   & Kim Wong \\
+    Remco van Doorn       & Leon Mei               & Daniela Espinoza \\
+    Remco van Doorn       &                        & David Adams \\
+    \\
+    \bf Clinical Genetics & \bf Medical Statistics \\
+    Nienke van der Stoep  & Ramin Monajemi \\
+                          & Jeanine Houwing \\
  \end{tabular}
 }


--- a/lectures/melanoma/single_paired_end.png
+++ b/lectures/melanoma/single_paired_end.png
+../../submodules/presentation-pics/pics/single_paired_end.png
\ No newline at end of file
--- a/presentation @ ed45c13b
+++ b/presentation @ ed45c13b
-Subproject commit 63b5792d877b40e3ffeca84ece106e63159439cb
+Subproject commit ed45c13b1e4237f49053420d0e47c1ca3fe545f2
--- a/presentation-pics @ 42ef031c
+++ b/presentation-pics @ 42ef031c
-Subproject commit 57047ad1fa7d5f013e2af50c306329e4abca9db7
+Subproject commit 42ef031c5797a73435d9c4eda433f54bc47e26f3