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comparison shm_csr.htm @ 39:a24f8c93583a draft

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author davidvanzessen
date Thu, 22 Dec 2016 09:39:27 -0500
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38:05c62efdc393 39:a24f8c93583a
1 <html>
2
3 <head>
4 <meta http-equiv=Content-Type content="text/html; charset=windows-1252">
5 <meta name=Generator content="Microsoft Word 14 (filtered)">
6 <style>
7 <!--
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40 </style>
41
42 </head>
43
44 <body lang=EN-US link=blue vlink=purple>
45
46 <div class=WordSection1>
47
48 <p class=MsoNormalCxSpFirst style='text-align:justify'><span lang=EN-GB
49 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
50 graphs in this tab give insight into the subclass distribution of IGG and IGA
51 transcripts. </span><span lang=EN-GB style='font-size:12.0pt;line-height:115%;
52 font-family:"Times New Roman","serif"'>Human Cµ, C&#945;, C&#947; and C&#949;
53 constant genes are assigned using a </span><span lang=EN-GB style='font-size:
54 12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>custom script
55 specifically designed for human (sub)class assignment in repertoire data as
56 described in van Schouwenburg and IJspeert et al, submitted for publication. In
57 this script the reference sequences for the subclasses are divided in 8
58 nucleotide chunks which overlap by 4 nucleotides. These overlapping chunks are
59 then individually aligned in the right order to each input sequence. The
60 percentage of the chunks identified in each rearrangement is calculated in the
61 ‘chunk hit percentage’. </span><span lang=EN-GB style='font-size:12.0pt;
62 line-height:115%;font-family:"Times New Roman","serif"'>C&#945; and C&#947;
63 subclasses are very homologous and only differ in a few nucleotides. To assign
64 subclasses the </span><span lang=EN-GB style='font-size:12.0pt;line-height:
65 115%;font-family:"Times New Roman","serif"'>‘nt hit percentage’ is calculated.
66 This percentage indicates how well the chunks covering the subclass specific
67 nucleotide match with the different subclasses. </span><span lang=EN-GB
68 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Information
69 on normal distribution of subclasses in healthy individuals of different ages
70 can be found in IJspeert and van Schouwenburg et al, PMID: 27799928.</span></p>
71
72 <p class=MsoNormalCxSpMiddle style='text-align:justify'><a name="OLE_LINK100"></a><a
73 name="OLE_LINK99"></a><a name="OLE_LINK25"><u><span lang=EN-GB
74 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>IGA
75 subclass distribution</span></u></a></p>
76
77 <p class=MsoNormalCxSpMiddle style='text-align:justify'><span lang=EN-GB
78 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Pie
79 chart showing the relative distribution of IGA1 and IGA2 transcripts in the
80 sample.</span></p>
81
82 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB
83 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>IGG
84 subclass distribution</span></u></p>
85
86 <p class=MsoNormalCxSpLast style='text-align:justify'><span lang=EN-GB
87 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Pie
88 chart showing the relative distribution of IGG1, IGG2, IGG3 and IGG4
89 transcripts in the sample.</span></p>
90
91 </div>
92
93 </body>
94
95 </html>