Mercurial > repos > davidvanzessen > shm_csr
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author | davidvanzessen |
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date | Wed, 06 Dec 2017 08:04:52 -0500 |
parents | a24f8c93583a |
children | ba33b94637ca |
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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; 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, Cα, Cγ and Cε 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"'>Cα and Cγ 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>