Mercurial > repos > davidvanzessen > shm_csr

<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";}
a:link, span.MsoHyperlink
	{color:blue;
	text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
	{color:purple;
	text-decoration:underline;}
span.apple-converted-space
	{mso-style-name:apple-converted-space;}
.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 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>
author	davidvanzessen
date	Mon, 31 Aug 2020 11:20:08 -0400
parents	ba33b94637ca
children	6809c63d9161