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Genomics Inform > Volume 16(4); 2018 > Article
DOI: https://doi.org/10.5808/GI.2018.16.4.e29    Published online December 28, 2018.
A Universal Analysis Pipeline of Hybrid Capture-Based Targeted Sequencing Data with Unique Molecular Indexes (UMIs)
Min-Jung Kim1, Si-Cho Kim2, Young-Joon Kim1,2
1Department of Integrated Omics and Biomedical Science, Yonsei University, Seoul 03722, Korea
2Department of Biochemistry, Yonsei University 03722, Seoul, Korea
Corresponding author:  Young-Joon Kim
Tel: +82-2-2123-7699   Email: yjkim@yonsei.ac.kr
Received: December 4, 2018   Revised: December 18, 2018   Accepted: December 18, 2018
Abstract
Hybrid capture-based targeted sequencing is increasingly used for genomic variants profiling in tumor patients. Unique molecular index (UMI) technology has recently been developed and helps to increase the accuracy of variant calling by minimizing PCR biases and sequencing errors. However, UMI-adopted targeted sequencing data analysis is slightly different from the methods for other types of omics data, and its pipeline for variant calling is still being optimized in various studying groups for their own purpose. Due to this provincial usage range of tools, our group built an analysis pipeline for global application to many studies of targeted sequencing generated with different methods. First, we generated hybrid capture-based data using genomic DNA extracted from tumor tissues of colorectal cancer patients. Sequencing libraries were prepared, pooled together and an 8-plexed capture library was processed to the enrichment step before 150bp paired-end (PE) sequencing with Illumina Hiseq series. For the analysis, we evaluated several different tools published. We mainly focused on the compatibility of input and output of each tool. Finally, our laboratory built an analysis pipeline specialized for UMI-adopted data. Through this pipeline, we were able to estimate the even on-target rates and filtered consensus reads for more accurate variant calling. These results suggest the potential of our analysis pipeline in the precise examination of quality and efficiency of conducted experiments.
Keywords: Hybrid capture, precision medicine, targeted sequencing, UMI, variant calling
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