AUTHOR=Rosenfeld Aaron M. , Meng Wenzhao , Chen Dora Y. , Zhang Bochao , Granot Tomer , Farber Donna L. , Hershberg Uri , Luning Prak Eline T. 

TITLE=Computational Evaluation of B-Cell Clone Sizes in Bulk Populations

JOURNAL=Frontiers in Immunology

VOLUME=Volume 9 - 2018

YEAR=2018

URL=https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2018.01472

DOI=10.3389/fimmu.2018.01472

ISSN=1664-3224

ABSTRACT=B cell clones expand and contract during adaptive immune responses and can persist or grow uncontrollably in lymphoproliferative disorders.  One way to monitor and track B cell clones is to perform large-scale sampling of bulk cell populations, amplifying and sequencing antibody gene rearrangements by next generation sequencing (NGS).  Here we describe a series of computational approaches for estimating B cell clone size in NGS immune repertoire profiling data of antibody heavy chain gene rearrangements.  We define three different measures of B cell clone size-- copy numbers, instances and unique sequences-- and show how these measures can be used to rank clones, analyze their diversity and study their distribution within and between individuals.  We provide a detailed, step-by-step procedure for performing these analyses using two different data sets of spleen samples from human organ donors.  In the first data set, 19 independently generated biological replicates from a single individual are analyzed for B cell clone size, diversity and sampling sufficiency for clonal overlap analysis.  In the second data set, B cell clones are compared in 8 different organ donors.  We comment upon frequently encountered pitfalls and offer practical advice with alternative approaches. Overall, we provide a series of pragmatic analytical approaches and show how different clone size measures can be used to study the clonal landscape in bulk B cell immune repertoire profiling data.