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author | davidvanzessen |
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date | Tue, 05 Dec 2017 10:57:13 -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;} @font-face {font-family:UICTFontTextStyleBody;} /* 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'><b><span lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>References</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"; color:black'>Yaari, G. and Uduman, M. and Kleinstein, S. H. (2012). Quantifying selection in high-throughput Immunoglobulin sequencing data sets. In<span class=apple-converted-space> </span><em>Nucleic Acids Research, 40 (17), pp. e134–e134.</em><span class=apple-converted-space><i> </i></span>[</span><span lang=EN-GB><a href="http://dx.doi.org/10.1093/nar/gks457" target="_blank"><span style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"; color:#303030'>doi:10.1093/nar/gks457</span></a></span><span lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"; color:black'>][</span><span lang=EN-GB><a href="http://dx.doi.org/10.1093/nar/gks457" target="_blank"><span style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"; color:#303030'>Link</span></a></span><span lang=EN-GB style='font-size:12.0pt; line-height:115%;font-family:"Times New Roman","serif";color:black'>]</span></p> <p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Graphs</span></b></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"'>AA mutation frequency</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"'>For each class, the frequency of replacement mutations at each amino acid position is shown, which is calculated by dividing the number of replacement mutations at a particular amino acid position/the number sequences that have an amino acid at that particular position. Since the length of the CDR1 and CDR2 region is not the same for every VH gene, some amino acids positions are absent. Therefore we calculate the frequency using the number of amino acids present at that that particular location. </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 (BASELINe)</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"'>Shows the results of the analysis of antigen selection as performed using BASELINe. Details on the analysis performed by BASELINe can be found in Yaari et al, PMID: 22641856. The settings used for the analysis are</span><span lang=EN-GB style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>: focused, SHM targeting model: human Tri-nucleotide, custom bounderies. The custom boundries are dependent on the ‘sequence starts at filter’. </span></p> <p class=MsoNormalCxSpMiddle style='line-height:normal'><span lang=NL style='font-family:UICTFontTextStyleBody;color:black'>Leader: 1:26:38:55:65:104:-</span></p> <p class=MsoNormalCxSpMiddle style='line-height:normal'><span lang=NL style='font-family:UICTFontTextStyleBody;color:black'>FR1: 27:27:38:55:65:104:-</span></p> <p class=MsoNormalCxSpMiddle style='line-height:normal'><span lang=NL style='font-family:UICTFontTextStyleBody;color:black'>CDR1: 27:27:38:55:65:104:-</span></p> <p class=MsoNormalCxSpLast style='line-height:normal'><span lang=NL style='font-family:UICTFontTextStyleBody;color:black'>FR2: 27:27:38:55:65:104:-</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>