Diversity Complexity Index (DCI) for Spectratype/Immunoscope Analysis of the Expressed TCR Repertoire

• Activity Number: 391
• Type: Contributed
• Date/Time: Tuesday, August 5, 2014 : 2:00 PM to 3:50 PM
• Sponsor: Biometrics Section
• Author(s): Byung Park*+ and Partha Samadder and Janko Nikolich-Zugich and Afam Okoye and Motomi Mori
• Companies: Oregon Health & Science University and University of Arizona and University of Arizona College of Medicine and Oregon National Primate Research Center and Knight Cancer Institute
• Keywords: Spectratyping ; Shannon-Jensen divergence ; Kullback-Leibler divergence ; TCR repertoire diversity ; Immune reconstitution ; Diversity complexity index

Abstract

Spectratyping measures TCR repertoire diversity based on variation in the lengths of RT-PCR products generated from the CDR3 region in each TCR V? family. This technique has been used successfully on samples from humans such as in vitro activated T cells, peripheral blood, peripheral lymphoid tissues, extralymphoid sites of inflammation, and malignant tissue. General goal of quantitative analysis of spectratype data is to access the therapeutic benefits of treatment and its ability to maintain or even improve spectratype diversity. Most of analyzing spectratype profile methods is to measuring how objective spectratyping profile is diverted from the Gaussian pattern of spectratyping in CDR3 region. Many times, we are more interested in answering the question if a certain intervention is improving/loosing the repertoire diversity in CDR3 region. However, due to the absence of standardized methods of analyzing and reporting the data, the interpretation of the data generated has remained an issue. We are proposing a diversity complexity index (DCI) that can evaluate not only degree of divergence between two spectratype profiles but also the driection of the spectratype profile changes.