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author davidvanzessen
date Fri, 19 Feb 2021 15:10:54 +0000
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50 <p class=MsoNormalCxSpFirst style='text-align:justify'><b><span lang=EN-GB
51 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>References</span></b></p>
52
53 <p class=MsoNormalCxSpMiddle style='text-align:justify'><span lang=EN-GB
54 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif";
55 color:black'>Yaari, G. and Uduman, M. and Kleinstein, S. H. (2012). Quantifying
56 selection in high-throughput Immunoglobulin sequencing data sets. In<span
57 class=apple-converted-space>&nbsp;</span><em>Nucleic Acids Research, 40 (17),
58 pp. e134–e134.</em><span class=apple-converted-space><i>&nbsp;</i></span>[</span><span
59 lang=EN-GB><a href="http://dx.doi.org/10.1093/nar/gks457" target="_blank"><span
60 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif";
61 color:#303030'>doi:10.1093/nar/gks457</span></a></span><span lang=EN-GB
62 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif";
63 color:black'>][</span><span lang=EN-GB><a
64 href="http://dx.doi.org/10.1093/nar/gks457" target="_blank"><span
65 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif";
66 color:#303030'>Link</span></a></span><span lang=EN-GB style='font-size:12.0pt;
67 line-height:115%;font-family:"Times New Roman","serif";color:black'>]</span></p>
68
69 <p class=MsoNormalCxSpMiddle style='text-align:justify'><b><span lang=EN-GB
70 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Graphs</span></b></p>
71
72 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB
73 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>AA
74 mutation frequency</span></u></p>
75
76 <p class=MsoNormalCxSpMiddle style='text-align:justify'><span lang=EN-GB
77 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>For
78 each class, the frequency of replacement mutations at each amino acid position
79 is shown, which is calculated by dividing the number of replacement mutations
80 at a particular amino acid position/the number sequences that have an amino
81 acid at that particular position. Since the length of the CDR1 and CDR2 region
82 is not the same for every VH gene, some amino acids positions are absent.
83 Therefore we calculate the frequency using the number of amino acids present at
84 that that particular location. </span></p>
85
86 <p class=MsoNormalCxSpMiddle style='text-align:justify'><u><span lang=EN-GB
87 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Antigen
88 selection (BASELINe)</span></u></p>
89
90 <p class=MsoNormalCxSpMiddle style='text-align:justify'><span lang=EN-GB
91 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Shows
92 the results of the analysis of antigen selection as performed using BASELINe.
93 Details on the analysis performed by BASELINe can be found in Yaari et al,
94 PMID: 22641856. The settings used for the analysis are</span><span lang=EN-GB
95 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>:
96 focused, SHM targeting model: human Tri-nucleotide, custom bounderies. The
97 custom boundries are dependent on the ‘sequence starts at filter’. </span></p>
98
99 <p class=MsoNormalCxSpMiddle style='line-height:normal'><span lang=NL
100 style='font-family:UICTFontTextStyleBody;color:black'>Leader:
101 1:26:38:55:65:104:-</span></p>
102
103 <p class=MsoNormalCxSpMiddle style='line-height:normal'><span lang=NL
104 style='font-family:UICTFontTextStyleBody;color:black'>FR1: 27:27:38:55:65:104:-</span></p>
105
106 <p class=MsoNormalCxSpMiddle style='line-height:normal'><span lang=NL
107 style='font-family:UICTFontTextStyleBody;color:black'>CDR1:&nbsp;27:27:38:55:65:104:-</span></p>
108
109 <p class=MsoNormalCxSpLast style='line-height:normal'><span lang=NL
110 style='font-family:UICTFontTextStyleBody;color:black'>FR2:&nbsp;27:27:38:55:65:104:-</span></p>
111
112 <p class=MsoNormal><span lang=NL style='font-size:12.0pt;line-height:115%;
113 font-family:"Times New Roman","serif"'>Hanna IJspeert, Pauline A. van
114 Schouwenburg, David van Zessen, Ingrid Pico-Knijnenburg, Gertjan J. Driessen,
115 Andrew P. Stubbs, and Mirjam van der Burg (2016). </span><span
116 style='font-size:12.0pt;line-height:115%;font-family:"Times New Roman","serif"'>Evaluation
117 of the Antigen-Experienced B-Cell Receptor Repertoire in Healthy Children and
118 Adults. In <i>Frontiers in Immunolog, 7, pp. e410-410. </i>[<a
119 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5066086/"><span
120 style='color:windowtext'>doi:10.3389/fimmu.2016.00410</span></a>][<a
121 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5066086/"><span
122 style='color:windowtext'>Link</span></a>]</span></p>
123
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