Overcoming the limitations posed by TCRβ repertoire modeling through a GPU-based in-silico DNA recombination algorithm

Gregory Striemer; Harsha Krovi; Ali Akoglu; Benjamin Vincent; Ben Hopson; Jeffrey A Frelinger; Adam Buntzman

doi:10.1109/IPDPS.2014.34

Overcoming the limitations posed by TCRβ repertoire modeling through a GPU-based in-silico DNA recombination algorithm

Gregory Striemer, Harsha Krovi, Ali Akoglu, Benjamin Vincent, Ben Hopson, Jeffrey A Frelinger, Adam Buntzman

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

2 Scopus citations

Abstract

The DNA recombination process known as V(D)J recombination is the central mechanism for generating diversity among antigen receptors such as T-cell receptors (TCRs). This diversity is crucial for the development of the adaptive immune system. However, modeling of all the alpha beta TCR sequences is encumbered by the enormity of the potential repertoire, which has been predicted to exceed 10 15 sequences. Prior modeling efforts have, therefore, been limited to extrapolations based on the analysis of minor subsets of the overall TCRbeta repertoire. In this study, we map the recombination process completely onto the graphics processing unit (GPU) hardware architecture using the CUDA programming environment to circumvent prior limitations. For the first time, we present a model of the mouse TCRbeta repertoire to an extent which enabled us to evaluate the Convergent Recombination Hypothesis (CRH) comprehensively at peta-scale level on a single GPU.

Original language	English (US)
Title of host publication	Proceedings - IEEE 28th International Parallel and Distributed Processing Symposium, IPDPS 2014
Publisher	IEEE Computer Society
Pages	231-240
Number of pages	10
ISBN (Print)	9780769552071
DOIs	https://doi.org/10.1109/IPDPS.2014.34
State	Published - 2014
Event	28th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2014 - Phoenix, AZ, United States Duration: May 19 2014 → May 23 2014

Publication series

Name	Proceedings of the International Parallel and Distributed Processing Symposium, IPDPS
ISSN (Print)	1530-2075
ISSN (Electronic)	2332-1237

Other

Other	28th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2014
Country/Territory	United States
City	Phoenix, AZ
Period	5/19/14 → 5/23/14

Keywords

cuda
dna
gpu
recombination
t-cell receptors

ASJC Scopus subject areas

Computational Theory and Mathematics
Computer Networks and Communications
Hardware and Architecture
Software

Access to Document

10.1109/IPDPS.2014.34

Cite this

Striemer, G., Krovi, H., Akoglu, A., Vincent, B., Hopson, B., Frelinger, J. A., & Buntzman, A. (2014). Overcoming the limitations posed by TCRβ repertoire modeling through a GPU-based in-silico DNA recombination algorithm. In Proceedings - IEEE 28th International Parallel and Distributed Processing Symposium, IPDPS 2014 (pp. 231-240). Article 6877258 (Proceedings of the International Parallel and Distributed Processing Symposium, IPDPS). IEEE Computer Society. https://doi.org/10.1109/IPDPS.2014.34

Overcoming the limitations posed by TCRβ repertoire modeling through a GPU-based in-silico DNA recombination algorithm. / Striemer, Gregory; Krovi, Harsha; Akoglu, Ali et al.
Proceedings - IEEE 28th International Parallel and Distributed Processing Symposium, IPDPS 2014. IEEE Computer Society, 2014. p. 231-240 6877258 (Proceedings of the International Parallel and Distributed Processing Symposium, IPDPS).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Striemer, G, Krovi, H, Akoglu, A, Vincent, B, Hopson, B, Frelinger, JA & Buntzman, A 2014, Overcoming the limitations posed by TCRβ repertoire modeling through a GPU-based in-silico DNA recombination algorithm. in Proceedings - IEEE 28th International Parallel and Distributed Processing Symposium, IPDPS 2014., 6877258, Proceedings of the International Parallel and Distributed Processing Symposium, IPDPS, IEEE Computer Society, pp. 231-240, 28th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2014, Phoenix, AZ, United States, 5/19/14. https://doi.org/10.1109/IPDPS.2014.34

Striemer G, Krovi H, Akoglu A, Vincent B, Hopson B, Frelinger JA et al. Overcoming the limitations posed by TCRβ repertoire modeling through a GPU-based in-silico DNA recombination algorithm. In Proceedings - IEEE 28th International Parallel and Distributed Processing Symposium, IPDPS 2014. IEEE Computer Society. 2014. p. 231-240. 6877258. (Proceedings of the International Parallel and Distributed Processing Symposium, IPDPS). doi: 10.1109/IPDPS.2014.34

Striemer, Gregory ; Krovi, Harsha ; Akoglu, Ali et al. / Overcoming the limitations posed by TCRβ repertoire modeling through a GPU-based in-silico DNA recombination algorithm. Proceedings - IEEE 28th International Parallel and Distributed Processing Symposium, IPDPS 2014. IEEE Computer Society, 2014. pp. 231-240 (Proceedings of the International Parallel and Distributed Processing Symposium, IPDPS).

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abstract = "The DNA recombination process known as V(D)J recombination is the central mechanism for generating diversity among antigen receptors such as T-cell receptors (TCRs). This diversity is crucial for the development of the adaptive immune system. However, modeling of all the alpha beta TCR sequences is encumbered by the enormity of the potential repertoire, which has been predicted to exceed 10 15 sequences. Prior modeling efforts have, therefore, been limited to extrapolations based on the analysis of minor subsets of the overall TCRbeta repertoire. In this study, we map the recombination process completely onto the graphics processing unit (GPU) hardware architecture using the CUDA programming environment to circumvent prior limitations. For the first time, we present a model of the mouse TCRbeta repertoire to an extent which enabled us to evaluate the Convergent Recombination Hypothesis (CRH) comprehensively at peta-scale level on a single GPU.",

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author = "Gregory Striemer and Harsha Krovi and Ali Akoglu and Benjamin Vincent and Ben Hopson and Frelinger, {Jeffrey A} and Adam Buntzman",

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AU - Frelinger, Jeffrey A

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AB - The DNA recombination process known as V(D)J recombination is the central mechanism for generating diversity among antigen receptors such as T-cell receptors (TCRs). This diversity is crucial for the development of the adaptive immune system. However, modeling of all the alpha beta TCR sequences is encumbered by the enormity of the potential repertoire, which has been predicted to exceed 10 15 sequences. Prior modeling efforts have, therefore, been limited to extrapolations based on the analysis of minor subsets of the overall TCRbeta repertoire. In this study, we map the recombination process completely onto the graphics processing unit (GPU) hardware architecture using the CUDA programming environment to circumvent prior limitations. For the first time, we present a model of the mouse TCRbeta repertoire to an extent which enabled us to evaluate the Convergent Recombination Hypothesis (CRH) comprehensively at peta-scale level on a single GPU.

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Overcoming the limitations posed by TCRβ repertoire modeling through a GPU-based in-silico DNA recombination algorithm

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