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author davidvanzessen
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3 <head>
4 <meta http-equiv=Content-Type content="text/html; charset=windows-1252">
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34 </head>
35
36 <body lang=EN-US>
37
38 <div class=WordSection1>
39
40 <p class=MsoNormalCxSpFirst style='text-align:justify'><b><span lang=EN-GB
41 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Info
42 table</span></b></p>
43
44 <p class=MsoNormalCxSpMiddle style='text-align:justify'><span lang=EN-GB
45 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>This
46 table contains information on different characteristics of SHM. For all
47 characteristics information can be found for all sequences or only sequences of
48 a certain (sub)class. All results are based on the sequences that passed the filter
49 settings chosen on the start page of the SHM &amp; CSR pipeline and only
50 include details on the analysed region as determined by the setting of the
51 sequence starts at filter. All data in this table can be downloaded via the
52 “downloads” tab.</span></p>
53
54 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB
55 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Mutation
56 frequency:</span></u></p>
57
58 <p class=MsoNormalCxSpMiddle style='text-align:justify'><a name="OLE_LINK83"></a><a
59 name="OLE_LINK82"></a><a name="OLE_LINK81"><span lang=EN-GB style='font-size:
60 12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>These values
61 give information on the level of SHM. </span></a><a name="OLE_LINK22"></a><a
62 name="OLE_LINK21"></a><a name="OLE_LINK20"><span lang=EN-GB style='font-size:
63 12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>More information
64 on the values found in healthy individuals of different ages can be found in </span></a><a
65 name="OLE_LINK15"></a><a name="OLE_LINK14"></a><a name="OLE_LINK13"><span
66 lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>IJspeert
67 and van Schouwenburg et al, PMID: 27799928</span></a></p>
68
69 <p class=MsoNormalCxSpMiddle style='text-align:justify'><i><span lang=EN-GB
70 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Number
71 of mutations:</span></i><span lang=EN-GB style='font-size:12.0pt;line-height:
72 115%;font-family:"Times New Roman","serif"'> Shows the number of total
73 mutations / the number of sequenced bases (the % of mutated bases).</span></p>
74
75 <p class=MsoNormalCxSpMiddle style='text-align:justify'><i><span lang=EN-GB
76 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Median
77 number of mutations:</span></i><span lang=EN-GB style='font-size:12.0pt;
78 line-height:115%;font-family:"Times New Roman","serif"'> Shows the median % of
79 SHM of all sequences.</span></p>
80
81 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB
82 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Patterns
83 of SHM:</span></u></p>
84
85 <p class=MsoNormalCxSpMiddle style='text-align:justify'><a name="OLE_LINK72"></a><a
86 name="OLE_LINK71"></a><a name="OLE_LINK70"><span lang=EN-GB style='font-size:
87 12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>These values
88 give insights into the targeting and patterns of SHM. These values can give
89 insight into the repair pathways used to repair the U:G mismatches introduced
90 by AID. </span></a><a name="OLE_LINK40"></a><a name="OLE_LINK39"></a><a
91 name="OLE_LINK38"></a><a name="OLE_LINK60"><span lang=EN-GB style='font-size:
92 12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>More information
93 on the values found in healthy individuals of different ages can be found in
94 IJspeert and van Schouwenburg et al, PMID: 27799928</span></a></p>
95
96 <p class=MsoNormalCxSpMiddle style='text-align:justify'><i><span lang=EN-GB
97 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Transitions:</span></i><span
98 lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
99 Shows the number of transition mutations / the number of total mutations (the
100 percentage of mutations that are transitions). Transition mutations are C&gt;T,
101 T&gt;C, A&gt;G, G&gt;A. </span></p>
102
103 <p class=MsoNormalCxSpMiddle style='text-align:justify'><i><span lang=EN-GB
104 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Transversions:</span></i><span
105 lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
106 Shows the number of transversion mutations / the number of total mutations (the
107 percentage of mutations that are transitions). Transversion mutations are
108 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>
109
110 <p class=MsoNormalCxSpMiddle style='text-align:justify'><i><span lang=EN-GB
111 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Transitions
112 at GC:</span></i><span lang=EN-GB style='font-size:12.0pt;line-height:115%;
113 font-family:"Times New Roman","serif"'> <a name="OLE_LINK2"></a><a
114 name="OLE_LINK1">Shows the number of transitions at GC locations (C&gt;T,
115 G&gt;A) / the total number of mutations at GC locations (the percentage of
116 mutations at GC locations that are transitions).</a></span></p>
117
118 <p class=MsoNormalCxSpMiddle style='text-align:justify'><i><span lang=EN-GB
119 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Targeting
120 of GC:</span></i><span lang=EN-GB style='font-size:12.0pt;line-height:115%;
121 font-family:"Times New Roman","serif"'> <a name="OLE_LINK7"></a><a
122 name="OLE_LINK6"></a><a name="OLE_LINK3">Shows the number of mutations at GC
123 locations / the total number of mutations (the percentage of total mutations
124 that are at GC locations).</a> </span></p>
125
126 <p class=MsoNormalCxSpMiddle style='text-align:justify'><i><span lang=EN-GB
127 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Transitions
128 at AT:</span></i><span lang=EN-GB style='font-size:12.0pt;line-height:115%;
129 font-family:"Times New Roman","serif"'> Shows the number of transitions at AT
130 locations (T&gt;C, A&gt;G) / the total number of mutations at AT locations (the
131 percentage of mutations at AT locations that are transitions).</span></p>
132
133 <p class=MsoNormalCxSpMiddle style='text-align:justify'><i><span lang=EN-GB
134 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Targeting
135 of AT:</span></i><span lang=EN-GB style='font-size:12.0pt;line-height:115%;
136 font-family:"Times New Roman","serif"'> Shows the number of mutations at AT
137 locations / the total number of mutations (the percentage of total mutations
138 that are at AT locations).</span></p>
139
140 <p class=MsoNormalCxSpMiddle style='text-align:justify'><i><span lang=EN-GB
141 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>RGYW:</span></i><span
142 lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
143 <a name="OLE_LINK28"></a><a name="OLE_LINK27"></a><a name="OLE_LINK26">Shows
144 the number of mutations that are in a RGYW motive / The number of total mutations
145 (the percentage of mutations that are in a RGYW motive). </a><a
146 name="OLE_LINK62"></a><a name="OLE_LINK61">RGYW motives are known to be
147 preferentially targeted by AID </a></span><span lang=EN-GB style='font-size:
148 12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>(R=Purine,
149 Y=pyrimidine, W = A or T).</span></p>
150
151 <p class=MsoNormalCxSpMiddle style='text-align:justify'><i><span lang=EN-GB
152 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>WRCY:</span></i><span
153 lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
154 <a name="OLE_LINK34"></a><a name="OLE_LINK33">Shows the number of mutations
155 that are in a </a><a name="OLE_LINK32"></a><a name="OLE_LINK31"></a><a
156 name="OLE_LINK30"></a><a name="OLE_LINK29">WRCY</a> motive / The number of
157 total mutations (the percentage of mutations that are in a WRCY motive). WRCY
158 motives are known to be preferentially targeted by AID </span><span lang=EN-GB
159 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>(R=Purine,
160 Y=pyrimidine, W = A or T).</span></p>
161
162 <p class=MsoNormalCxSpMiddle style='text-align:justify'><i><span lang=EN-GB
163 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>WA:</span></i><span
164 lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
165 <a name="OLE_LINK37"></a><a name="OLE_LINK36"></a><a name="OLE_LINK35">Shows
166 the number of mutations that are in a WA motive / The number of total mutations
167 (the percentage of mutations that are in a WA motive). It is described that
168 polymerase eta preferentially makes errors at WA motives </a></span><span
169 lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>(W
170 = A or T).</span></p>
171
172 <p class=MsoNormalCxSpMiddle style='text-align:justify'><i><span lang=EN-GB
173 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>TW:</span></i><span
174 lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
175 Shows the number of mutations that are in a TW motive / The number of total mutations
176 (the percentage of mutations that are in a TW motive). It is described that
177 polymerase eta preferentially makes errors at TW motives </span><span
178 lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>(W
179 = A or T).</span></p>
180
181 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB
182 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Antigen
183 selection:</span></u></p>
184
185 <p class=MsoNormalCxSpMiddle style='text-align:justify'><span lang=EN-GB
186 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>These
187 values give insight into antigen selection. It has been described that during
188 antigen selection, there is selection against replacement mutations in the FR
189 regions as these can cause instability of the B-cell receptor. In contrast
190 replacement mutations in the CDR regions are important for changing the
191 affinity of the B-cell receptor and therefore there is selection for this type
192 of mutations. Silent mutations do not alter the amino acid sequence and
193 therefore do not play a role in selection. More information on the values found
194 in healthy individuals of different ages can be found in IJspeert and van
195 Schouwenburg et al, PMID: 27799928</span></p>
196
197 <p class=MsoNormalCxSpMiddle style='text-align:justify'><i><span lang=EN-GB
198 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>FR
199 R/S:</span></i><span lang=EN-GB style='font-size:12.0pt;line-height:115%;
200 font-family:"Times New Roman","serif"'> <a name="OLE_LINK43"></a><a
201 name="OLE_LINK42"></a><a name="OLE_LINK41">Shows the number of replacement
202 mutations in the FR regions / The number of silent mutations in the FR regions
203 (the number of replacement mutations in the FR regions divided by the number of
204 silent mutations in the FR regions)</a></span></p>
205
206 <p class=MsoNormalCxSpMiddle style='text-align:justify'><i><span lang=EN-GB
207 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>CDR
208 R/S:</span></i><span lang=EN-GB style='font-size:12.0pt;line-height:115%;
209 font-family:"Times New Roman","serif"'> Shows the number of replacement
210 mutations in the CDR regions / The number of silent mutations in the CDR
211 regions (the number of replacement mutations in the CDR regions divided by the
212 number of silent mutations in the CDR regions)</span></p>
213
214 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB
215 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Number
216 of sequences nucleotides:</span></u></p>
217
218 <p class=MsoNormalCxSpMiddle style='text-align:justify'><span lang=EN-GB
219 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>These
220 values give information on the number of sequenced nucleotides.</span></p>
221
222 <p class=MsoNormalCxSpMiddle style='text-align:justify'><i><span lang=EN-GB
223 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Nt
224 in FR:</span></i><span lang=EN-GB style='font-size:12.0pt;line-height:115%;
225 font-family:"Times New Roman","serif"'> <a name="OLE_LINK46"></a><a
226 name="OLE_LINK45"></a><a name="OLE_LINK44">Shows the number of sequences bases
227 that are located in the FR regions / The total number of sequenced bases (the
228 percentage of sequenced bases that are present in the FR regions).</a></span></p>
229
230 <p class=MsoNormalCxSpMiddle style='text-align:justify'><i><span lang=EN-GB
231 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Nt
232 in CDR:</span></i><span lang=EN-GB style='font-size:12.0pt;line-height:115%;
233 font-family:"Times New Roman","serif"'> Shows the number of sequenced bases
234 that are located in the CDR regions / <a name="OLE_LINK48"></a><a
235 name="OLE_LINK47">The total number of sequenced bases (the percentage of
236 sequenced bases that are present in the CDR regions).</a></span></p>
237
238 <p class=MsoNormalCxSpMiddle style='text-align:justify'><i><span lang=EN-GB
239 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>A:
240 </span></i><a name="OLE_LINK51"></a><a name="OLE_LINK50"></a><a
241 name="OLE_LINK49"><span lang=EN-GB style='font-size:12.0pt;line-height:115%;
242 font-family:"Times New Roman","serif"'>Shows the total number of sequenced
243 adenines / The total number of sequenced bases (the percentage of sequenced
244 bases that were adenines).</span></a></p>
245
246 <p class=MsoNormalCxSpMiddle style='text-align:justify'><i><span lang=EN-GB
247 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>C:
248 </span></i><a name="OLE_LINK53"></a><a name="OLE_LINK52"><span lang=EN-GB
249 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Shows
250 the total number of sequenced cytosines / The total number of sequenced bases
251 (the percentage of sequenced bases that were cytosines).</span></a></p>
252
253 <p class=MsoNormalCxSpMiddle style='text-align:justify'><i><span lang=EN-GB
254 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>T:
255 </span></i><a name="OLE_LINK57"></a><a name="OLE_LINK56"><span lang=EN-GB
256 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Shows
257 the total number of sequenced </span></a><a name="OLE_LINK55"></a><a
258 name="OLE_LINK54"><span lang=EN-GB style='font-size:12.0pt;line-height:115%;
259 font-family:"Times New Roman","serif"'>thymines</span></a><span lang=EN-GB
260 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>
261 / The total number of sequenced bases (the percentage of sequenced bases that
262 were thymines).</span></p>
263
264 <p class=MsoNormalCxSpMiddle style='text-align:justify'><i><span lang=EN-GB
265 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>G:
266 </span></i><span lang=EN-GB style='font-size:12.0pt;line-height:115%;
267 font-family:"Times New Roman","serif"'>Shows the total number of sequenced <a
268 name="OLE_LINK59"></a><a name="OLE_LINK58">guanine</a>s / The total number of
269 sequenced bases (the percentage of sequenced bases that were guanines).</span></p>
270
271 <p class=MsoNormalCxSpMiddle style='text-align:justify'><a name="OLE_LINK69"><b><span
272 lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Graphs</span></b></a></p>
273
274 <p class=MsoNormalCxSpMiddle style='text-align:justify'><a name="OLE_LINK75"></a><a
275 name="OLE_LINK74"></a><a name="OLE_LINK73"><span lang=EN-GB style='font-size:
276 12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>These graphs visualize
277 information on the patterns and targeting of SHM and thereby give information
278 into the repair pathways used to repair the U:G mismatches introduced by AID. The
279 data represented in these graphs can be downloaded in the download tab. More
280 information on the values found in healthy individuals of different ages can be
281 found in IJspeert and van Schouwenburg et al, PMID: 27799928</span></a><span
282 lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>.
283 <a name="OLE_LINK85"></a><a name="OLE_LINK84"></a></span></p>
284
285 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB
286 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Percentage
287 of mutations in AID and pol eta motives</span></u></p>
288
289 <p class=MsoNormalCxSpMiddle style='text-align:justify'><span lang=EN-GB
290 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Visualizes
291 <a name="OLE_LINK80"></a><a name="OLE_LINK79"></a><a name="OLE_LINK78">for each
292 (sub)class </a>the percentage of mutations that are present in AID (RGYW or
293 WRCY) or polymerase eta motives (WA or TW) in the different subclasses </span><span
294 lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>(R=Purine,
295 Y=pyrimidine, W = A or T).</span></p>
296
297 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=NL
298 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Relative
299 mutation patterns</span></u></p>
300
301 <p class=MsoNormalCxSpMiddle style='text-align:justify'><span lang=EN-GB
302 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Visualizes
303 for each (sub)class the distribution of mutations between mutations at AT
304 locations and transitions or transversions at GC locations. </span></p>
305
306 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=NL
307 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Absolute
308 mutation patterns</span></u></p>
309
310 <p class=MsoNormalCxSpLast style='text-align:justify'><span lang=EN-GB
311 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Visualized
312 for each (sub)class the percentage of sequenced AT and GC bases that are
313 mutated. The mutations at GC bases are divided into transition and transversion
314 mutations<a name="OLE_LINK77"></a><a name="OLE_LINK76">. </a></span></p>
315
316 <p class=MsoNormal><span lang=NL style='font-size:12.0pt;line-height:115%;
317 font-family:"Times New Roman","serif"'>Hanna IJspeert, Pauline A. van
318 Schouwenburg, David van Zessen, Ingrid Pico-Knijnenburg, Gertjan J. Driessen,
319 Andrew P. Stubbs, and Mirjam van der Burg (2016). </span><span
320 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Evaluation
321 of the Antigen-Experienced B-Cell Receptor Repertoire in Healthy Children and
322 Adults. In <i>Frontiers in Immunolog, 7, pp. e410-410. </i>[<a
323 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5066086/"><span
324 style='color:windowtext'>doi:10.3389/fimmu.2016.00410</span></a>][<a
325 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5066086/"><span
326 style='color:windowtext'>Link</span></a>]</span></p>
327
328 </div>
329
330 </body>
331
332 </html>