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Table 3 Clonality comparison of the most abundant clonotypes based on CDR3 amino acid sequences in IMEX

From: ImmunExplorer (IMEX): a software framework for diversity and clonality analyses of immunoglobulins and T cell receptors on the basis of IMGT/HighV-QUEST preprocessed NGS data

CDR3 sequences

TRB Primer Set 2: CD4-/CD8+ T3

TRB Primer Set 2: CD4+/CD8- T3

MNC TRB Primer Set 2 T3

ASSMGQNNEQF

14.29447899

0.049037396

6.779536212

ASSVSGEGSDEQF

12.25748767

0.113766759

5.087625888

ASSGFGEVAPTMSS

5.681129492

0.002942244

1.856173462

FNPASGNIQY

2.506490689

0.003922992

1.020130731

ASLPGKLVRDPV

1.426455074

0.00245187

0.522809919

ASSLSSGFASYNEQF

1.366224477

0.00245187

0.570389587

ASSLGQNNEQF

1.048236852

0.002942244

0.481460922

AWSALAGDYNEQF

0.724263578

0.005394114

0.457671089

ASSLYNEQF

0.525988942

0.028932064

0.32286203

ASSLRYNEQF

0.414880324

0.002942244

0.233366941

SVGFLAGSTDTQY

0.062101113

0.860115924

0.549998301

SASGGLDETQY

0.003366928

0.398674029

0.240164037

ASSDD*RGGTDTQY

0.078187545

0.24273511

0.150102523

SVEVILDAGEQF

0.028431835

0.201543697

0.138207606

  1. We compared the top 20 clonotypes of the unsorted (mononuclear) and the sorted (CD4-/CD8+ and CD4+/CD8-) sample of the TRB primer set 2 timepoint 3. By using this method we could identify that the most expanded T cells in the proband p78690 belong to the T cell subtype CD4-/CD8+ (surface marker for cytotoxic T cells)
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BMC Bioinformatics

ISSN: 1471-2105

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