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diff shm_csr.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_csr.htm	Fri Feb 19 15:10:54 2021 +0000
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+<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;
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+ /* Style Definitions */
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+</style>
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+</head>
+
+<body lang=EN-US link=blue vlink=purple>
+
+<div class=WordSection1>
+
+<p class=MsoNormalCxSpFirst style='text-align:justify'><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>The
+graphs in this tab give insight into the subclass distribution of IGG and IGA
+transcripts. </span><span lang=EN-GB style='font-size:12.0pt;line-height:115%;
+font-family:"Times New Roman","serif"'>Human Cµ, C&#945;, C&#947; and C&#949;
+constant genes are assigned using a </span><span lang=EN-GB style='font-size:
+12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>custom script
+specifically designed for human (sub)class assignment in repertoire data as
+described in van Schouwenburg and IJspeert et al, submitted for publication. In
+this script the reference sequences for the subclasses are divided in 8
+nucleotide chunks which overlap by 4 nucleotides. These overlapping chunks are
+then individually aligned in the right order to each input sequence. The
+percentage of the chunks identified in each rearrangement is calculated in the
+‘chunk hit percentage’. </span><span lang=EN-GB style='font-size:12.0pt;
+line-height:115%;font-family:"Times New Roman","serif"'>C&#945; and C&#947;
+subclasses are very homologous and only differ in a few nucleotides. To assign
+subclasses the </span><span lang=EN-GB style='font-size:12.0pt;line-height:
+115%;font-family:"Times New Roman","serif"'>‘nt hit percentage’ is calculated.
+This percentage indicates how well the chunks covering the subclass specific
+nucleotide match with the different subclasses. </span><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Information
+on normal distribution of subclasses 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'><a name="OLE_LINK100"></a><a
+name="OLE_LINK99"></a><a name="OLE_LINK25"><u><span lang=EN-GB
+style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>IGA
+subclass distribution</span></u></a></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"'>Pie
+chart showing the relative distribution of IGA1 and IGA2 transcripts in the
+sample.</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"'>IGG
+subclass distribution</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"'>Pie
+chart showing the relative distribution of IGG1, IGG2, IGG3 and IGG4
+transcripts in the sample.</span></p>
+
+</div>
+
+</body>
+
+</html>