ParallelHashClone: A Parallel Implementation of HashClone Suite for Clonality Assessment from NGS Data

Abstract

In the last years, B/T cell clonality assessment and Minimal Residual Disease (MRD) monitoring acquired a strong prediction value in the therapy response evaluation of haematologic B disorders, improving patients outcome prediction. Polymerase Chain Reaction (PCR) based methods are the most standardized and widely used techniques, allowing a risk stratification in a variable proportion of patients, depending on the analyzed disease. Since its recently introduction, Next Generation Sequencing (NGS) technology could increase the number of patients with a traceable disease during the clinical course. This issue is strictly associated with an appropriate computational analysis of the huge volume of complex data obtained by NGS. In this context, recently, we presented an innovative bioinformatics approach, called HashClone, an easy-to-use and reliable bioinformatics tool that simultane- ously provides clonality assessment and MRD detection over time in patients affected by Mantle Cell Lymphoma (MCL). Actually, HashClone original strategy is organized in three steps that provide the simultaneous analysis of a set of samples reads returning to the corresponding clonotypes list, in which each clone is featured by frequency reads and aligned target nomenclature notification with respect to the reference database [1]. HashClone is composed by four C++ applications combined to implement B-cells clonality assessment in patient's samples. Since its successful preliminary application, in this paper, we present ParallelHashClone, an improved version with a parallel implementation of HashClone suite. In detail, the parallelization of this two applications allows to analyze more efficiently the samples from the same patient in parallel. Moreover we integrated ParallelHashClone in a Docker container platform that allows to easily install and run the application since the Docker packages ParallelHashClone with all its dependencies and libraries. We tested ParallelHashClone version for four MCL-NGS data analysis, showing comparable performances with respect to the original HashClone version in B-lymphoprolipherative molecular clonality assessment.