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GLIPH (Grouping of Lymphocyte Interactions by Paratope Hotspots) Analysis

HA Hussein A. Abbas
PR Patrick K. Reville
XJ Xianli Jiang
HY Hui Yang
AR Alexandre Reuben
JI Jin Seon Im
LL Latasha Little
JS Jefferson C. Sinson
KC Ken Chen
AF Andrew Futreal
GG Guillermo Garcia-Manero
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To identify T-cell specificity groups, GLIPH2 (24, 25) was used to cluster CDR3 β-chain sequences. Briefly, we ran the analysis for unique CDR3 sequences from only significantly changed clonotypes and 780 of them meet analysis criteria. Parameters were set as: simulation_depth=1000, kmer_min_depth=3. Clonotypes with missing or short (n<5) beta- CDR3 sequence were excluded from the clustering analysis. The output of GLIPH2 analyses was visualized with the iGraph package in R software. Clonotypes that belong to same cluster were connected by edges and clonotypes that have no shared clones were shown as single nodes.

Copyright and License information:  ©2021 Abbas, Reville, Jiang, Yang, Reuben, Im, Little, Sinson, Chen, Futreal and Garcia-Manero
This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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