diff shm_overview.htm @ 81:b6f9a640e098 draft

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author davidvanzessen
date Fri, 19 Feb 2021 15:10:54 +0000
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+<body lang=EN-US>
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+<div class=WordSection1>
+
+<p class=MsoNormalCxSpFirst style='text-align:justify'><b><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Info
+table</span></b></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>This
+table contains information on different characteristics of SHM. For all
+characteristics information can be found for all sequences or only sequences of
+a certain (sub)class. All results are based on the sequences that passed the filter
+settings chosen on the start page of the SHM &amp; CSR pipeline and only
+include details on the analysed region as determined by the setting of the
+sequence starts at filter. All data in this table can be downloaded via the
+“downloads” tab.</span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Mutation
+frequency:</span></u></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><a name="OLE_LINK83"></a><a
+name="OLE_LINK82"></a><a name="OLE_LINK81"><span lang=EN-GB style='font-size:
+12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>These values
+give information on the level of SHM. </span></a><a name="OLE_LINK22"></a><a
+name="OLE_LINK21"></a><a name="OLE_LINK20"><span lang=EN-GB style='font-size:
+12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>More information
+on the values found in healthy individuals of different ages can be found in </span></a><a
+name="OLE_LINK15"></a><a name="OLE_LINK14"></a><a name="OLE_LINK13"><span
+lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>IJspeert
+and van Schouwenburg et al, PMID: 27799928</span></a></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><i><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Number
+of mutations:</span></i><span lang=EN-GB style='font-size:12.0pt;line-height:
+115%;font-family:"Times New Roman","serif"'> Shows the number of total
+mutations / the number of sequenced bases (the % of mutated bases).</span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><i><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Median
+number of mutations:</span></i><span lang=EN-GB style='font-size:12.0pt;
+line-height:115%;font-family:"Times New Roman","serif"'> Shows the median % of
+SHM of all sequences.</span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Patterns
+of SHM:</span></u></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><a name="OLE_LINK72"></a><a
+name="OLE_LINK71"></a><a name="OLE_LINK70"><span lang=EN-GB style='font-size:
+12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>These values
+give insights into the targeting and patterns of SHM. These values can give
+insight into the repair pathways used to repair the U:G mismatches introduced
+by AID. </span></a><a name="OLE_LINK40"></a><a name="OLE_LINK39"></a><a
+name="OLE_LINK38"></a><a name="OLE_LINK60"><span lang=EN-GB style='font-size:
+12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>More information
+on the values found in healthy individuals of different ages can be found in
+IJspeert and van Schouwenburg et al, PMID: 27799928</span></a></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><i><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Transitions:</span></i><span
+lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
+Shows the number of transition mutations / the number of total mutations (the
+percentage of mutations that are transitions). Transition mutations are C&gt;T,
+T&gt;C, A&gt;G, G&gt;A. </span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><i><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Transversions:</span></i><span
+lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
+Shows the number of transversion mutations / the number of total mutations (the
+percentage of mutations that are transitions). Transversion mutations are
+C&gt;A, C&gt;G, T&gt;A, T&gt;G, A&gt;T, A&gt;C, G&gt;T, G&gt;C.</span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><i><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Transitions
+at GC:</span></i><span lang=EN-GB style='font-size:12.0pt;line-height:115%;
+font-family:"Times New Roman","serif"'> <a name="OLE_LINK2"></a><a
+name="OLE_LINK1">Shows the number of transitions at GC locations (C&gt;T,
+G&gt;A) / the total number of mutations at GC locations (the percentage of
+mutations at GC locations that are transitions).</a></span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><i><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Targeting
+of GC:</span></i><span lang=EN-GB style='font-size:12.0pt;line-height:115%;
+font-family:"Times New Roman","serif"'> <a name="OLE_LINK7"></a><a
+name="OLE_LINK6"></a><a name="OLE_LINK3">Shows the number of mutations at GC
+locations / the total number of mutations (the percentage of total mutations
+that are at GC locations).</a> </span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><i><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Transitions
+at AT:</span></i><span lang=EN-GB style='font-size:12.0pt;line-height:115%;
+font-family:"Times New Roman","serif"'> Shows the number of transitions at AT
+locations (T&gt;C, A&gt;G) / the total number of mutations at AT locations (the
+percentage of mutations at AT locations that are transitions).</span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><i><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Targeting
+of AT:</span></i><span lang=EN-GB style='font-size:12.0pt;line-height:115%;
+font-family:"Times New Roman","serif"'> Shows the number of mutations at AT
+locations / the total number of mutations (the percentage of total mutations
+that are at AT locations).</span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><i><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>RGYW:</span></i><span
+lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
+<a name="OLE_LINK28"></a><a name="OLE_LINK27"></a><a name="OLE_LINK26">Shows
+the number of mutations that are in a RGYW motive / The number of total mutations
+(the percentage of mutations that are in a RGYW motive). </a><a
+name="OLE_LINK62"></a><a name="OLE_LINK61">RGYW motives are known to be
+preferentially targeted by AID </a></span><span lang=EN-GB style='font-size:
+12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>(R=Purine,
+Y=pyrimidine, W = A or T).</span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><i><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>WRCY:</span></i><span
+lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
+<a name="OLE_LINK34"></a><a name="OLE_LINK33">Shows the number of mutations
+that are in a </a><a name="OLE_LINK32"></a><a name="OLE_LINK31"></a><a
+name="OLE_LINK30"></a><a name="OLE_LINK29">WRCY</a> motive / The number of
+total mutations (the percentage of mutations that are in a WRCY motive). WRCY
+motives are known to be preferentially targeted by AID </span><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>(R=Purine,
+Y=pyrimidine, W = A or T).</span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><i><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>WA:</span></i><span
+lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
+<a name="OLE_LINK37"></a><a name="OLE_LINK36"></a><a name="OLE_LINK35">Shows
+the number of mutations that are in a WA motive / The number of total mutations
+(the percentage of mutations that are in a WA motive). It is described that
+polymerase eta preferentially makes errors at WA motives </a></span><span
+lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>(W
+= A or T).</span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><i><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>TW:</span></i><span
+lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
+Shows the number of mutations that are in a TW motive / The number of total mutations
+(the percentage of mutations that are in a TW motive). It is described that
+polymerase eta preferentially makes errors at TW motives </span><span
+lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>(W
+= A or T).</span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Antigen
+selection:</span></u></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>These
+values give insight into antigen selection. It has been described that during
+antigen selection, there is selection against replacement mutations in the FR
+regions as these can cause instability of the B-cell receptor. In contrast
+replacement mutations in the CDR regions are important for changing the
+affinity of the B-cell receptor and therefore there is selection for this type
+of mutations. Silent mutations do not alter the amino acid sequence and
+therefore do not play a role in selection. More information on the values found
+in healthy individuals of different ages can be found in IJspeert and van
+Schouwenburg et al, PMID: 27799928</span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><i><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>FR
+R/S:</span></i><span lang=EN-GB style='font-size:12.0pt;line-height:115%;
+font-family:"Times New Roman","serif"'> <a name="OLE_LINK43"></a><a
+name="OLE_LINK42"></a><a name="OLE_LINK41">Shows the number of replacement
+mutations in the FR regions / The number of silent mutations in the FR regions
+(the number of replacement mutations in the FR regions divided by the number of
+silent mutations in the FR regions)</a></span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><i><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>CDR
+R/S:</span></i><span lang=EN-GB style='font-size:12.0pt;line-height:115%;
+font-family:"Times New Roman","serif"'> Shows the number of replacement
+mutations in the CDR regions / The number of silent mutations in the CDR
+regions (the number of replacement mutations in the CDR regions divided by the
+number of silent mutations in the CDR regions)</span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Number
+of sequences nucleotides:</span></u></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>These
+values give information on the number of sequenced nucleotides.</span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><i><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Nt
+in FR:</span></i><span lang=EN-GB style='font-size:12.0pt;line-height:115%;
+font-family:"Times New Roman","serif"'> <a name="OLE_LINK46"></a><a
+name="OLE_LINK45"></a><a name="OLE_LINK44">Shows the number of sequences bases
+that are located in the FR regions / The total number of sequenced bases (the
+percentage of sequenced bases that are present in the FR regions).</a></span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><i><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Nt
+in CDR:</span></i><span lang=EN-GB style='font-size:12.0pt;line-height:115%;
+font-family:"Times New Roman","serif"'> Shows the number of sequenced bases
+that are located in the CDR regions / <a name="OLE_LINK48"></a><a
+name="OLE_LINK47">The total number of sequenced bases (the percentage of
+sequenced bases that are present in the CDR regions).</a></span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><i><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>A:
+</span></i><a name="OLE_LINK51"></a><a name="OLE_LINK50"></a><a
+name="OLE_LINK49"><span lang=EN-GB style='font-size:12.0pt;line-height:115%;
+font-family:"Times New Roman","serif"'>Shows the total number of sequenced
+adenines / The total number of sequenced bases (the percentage of sequenced
+bases that were adenines).</span></a></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><i><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>C:
+</span></i><a name="OLE_LINK53"></a><a name="OLE_LINK52"><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Shows
+the total number of sequenced cytosines / The total number of sequenced bases
+(the percentage of sequenced bases that were cytosines).</span></a></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><i><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>T:
+</span></i><a name="OLE_LINK57"></a><a name="OLE_LINK56"><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Shows
+the total number of sequenced </span></a><a name="OLE_LINK55"></a><a
+name="OLE_LINK54"><span lang=EN-GB style='font-size:12.0pt;line-height:115%;
+font-family:"Times New Roman","serif"'>thymines</span></a><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
+/ The total number of sequenced bases (the percentage of sequenced bases that
+were thymines).</span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><i><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>G:
+</span></i><span lang=EN-GB style='font-size:12.0pt;line-height:115%;
+font-family:"Times New Roman","serif"'>Shows the total number of sequenced <a
+name="OLE_LINK59"></a><a name="OLE_LINK58">guanine</a>s / The total number of
+sequenced bases (the percentage of sequenced bases that were guanines).</span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><a name="OLE_LINK69"><b><span
+lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Graphs</span></b></a></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><a name="OLE_LINK75"></a><a
+name="OLE_LINK74"></a><a name="OLE_LINK73"><span lang=EN-GB style='font-size:
+12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>These graphs visualize
+information on the patterns and targeting of SHM and thereby give information
+into the repair pathways used to repair the U:G mismatches introduced by AID. The
+data represented in these graphs can be downloaded in the download tab. More
+information on the values found in healthy individuals of different ages can be
+found in IJspeert and van Schouwenburg et al, PMID: 27799928</span></a><span
+lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>.
+<a name="OLE_LINK85"></a><a name="OLE_LINK84"></a></span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Percentage
+of mutations in AID and pol eta motives</span></u></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Visualizes
+<a name="OLE_LINK80"></a><a name="OLE_LINK79"></a><a name="OLE_LINK78">for each
+(sub)class </a>the percentage of mutations that are present in AID (RGYW or
+WRCY) or polymerase eta motives (WA or TW) in the different subclasses </span><span
+lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>(R=Purine,
+Y=pyrimidine, W = A or T).</span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=NL
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Relative
+mutation patterns</span></u></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Visualizes
+for each (sub)class the distribution of mutations between mutations at AT
+locations and transitions or transversions at GC locations. </span></p>
+
+<p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=NL
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Absolute
+mutation patterns</span></u></p>
+
+<p class=MsoNormalCxSpLast style='text-align:justify'><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Visualized
+for each (sub)class the percentage of sequenced AT and GC bases that are
+mutated. The mutations at GC bases are divided into transition and transversion
+mutations<a name="OLE_LINK77"></a><a name="OLE_LINK76">. </a></span></p>
+
+<p class=MsoNormal><span lang=NL style='font-size:12.0pt;line-height:115%;
+font-family:"Times New Roman","serif"'>Hanna IJspeert, Pauline A. van
+Schouwenburg, David van Zessen, Ingrid Pico-Knijnenburg, Gertjan J. Driessen,
+Andrew P. Stubbs, and Mirjam van der Burg (2016). </span><span
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Evaluation
+of the Antigen-Experienced B-Cell Receptor Repertoire in Healthy Children and
+Adults. In <i>Frontiers in Immunolog, 7, pp. e410-410. </i>[<a
+href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5066086/"><span
+style='color:windowtext'>doi:10.3389/fimmu.2016.00410</span></a>][<a
+href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5066086/"><span
+style='color:windowtext'>Link</span></a>]</span></p>
+
+</div>
+
+</body>
+
+</html>