Mercurial > repos > davidvanzessen > shm_csr
diff shm_overview.htm @ 81:b6f9a640e098 draft
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| author | davidvanzessen |
|---|---|
| date | Fri, 19 Feb 2021 15:10:54 +0000 |
| parents | a24f8c93583a |
| children | ba33b94637ca |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/shm_overview.htm Fri Feb 19 15:10:54 2021 +0000 @@ -0,0 +1,332 @@ +<html> + +<head> +<meta http-equiv=Content-Type content="text/html; charset=windows-1252"> +<meta name=Generator content="Microsoft Word 14 (filtered)"> +<style> +<!-- + /* Font Definitions */ + @font-face + {font-family:Calibri; + panose-1:2 15 5 2 2 2 4 3 2 4;} + /* Style Definitions */ + p.MsoNormal, li.MsoNormal, div.MsoNormal + {margin-top:0in; + margin-right:0in; + margin-bottom:10.0pt; + margin-left:0in; + line-height:115%; + font-size:11.0pt; + font-family:"Calibri","sans-serif";} +.MsoChpDefault + {font-family:"Calibri","sans-serif";} +.MsoPapDefault + {margin-bottom:10.0pt; + line-height:115%;} +@page WordSection1 + {size:8.5in 11.0in; + margin:1.0in 1.0in 1.0in 1.0in;} +div.WordSection1 + {page:WordSection1;} +--> +</style> + +</head> + +<body lang=EN-US> + +<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 & 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>T, +T>C, A>G, G>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>A, C>G, T>A, T>G, A>T, A>C, G>T, G>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>T, +G>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>C, A>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>