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Nietsch R, Haas J, Lai A, Oehler D, Mester S, Frese KS, Sedaghat-Hamedani F, Kayvanpour E, Keller A, Meder B. The Role of Quality Control in Targeted Next-generation Sequencing Library Preparation. GENOMICS PROTEOMICS & BIOINFORMATICS 2016; 14:200-6. [PMID: 27475404 PMCID: PMC4996852 DOI: 10.1016/j.gpb.2016.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 03/31/2016] [Accepted: 04/05/2016] [Indexed: 11/05/2022]
Abstract
Next-generation sequencing (NGS) is getting routinely used in the diagnosis of hereditary diseases, such as human cardiomyopathies. Hence, it is of utter importance to secure high quality sequencing data, enabling the identification of disease-relevant mutations or the conclusion of negative test results. During the process of sample preparation, each protocol for target enrichment library preparation has its own requirements for quality control (QC); however, there is little evidence on the actual impact of these guidelines on resulting data quality. In this study, we analyzed the impact of QC during the diverse library preparation steps of Agilent SureSelect XT target enrichment and Illumina sequencing. We quantified the parameters for a cohort of around 600 samples, which include starting amount of DNA, amount of sheared DNA, smallest and largest fragment size of the starting DNA; amount of DNA after the pre-PCR, and smallest and largest fragment size of the resulting DNA; as well as the amount of the final library, the corresponding smallest and largest fragment size, and the number of detected variants. Intriguingly, there is a high tolerance for variations in all QC steps, meaning that within the boundaries proposed in the current study, a considerable variance at each step of QC can be well tolerated without compromising NGS quality.
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Affiliation(s)
- Rouven Nietsch
- Institute for Cardiomyopathies, Department of Internal Medicine III, University of Heidelberg, 69120 Heidelberg, Germany
| | - Jan Haas
- Institute for Cardiomyopathies, Department of Internal Medicine III, University of Heidelberg, 69120 Heidelberg, Germany; German Centre for Cardiovascular Research (DZHK), Heidelberg/Mannheim, Germany
| | - Alan Lai
- Institute for Cardiomyopathies, Department of Internal Medicine III, University of Heidelberg, 69120 Heidelberg, Germany
| | - Daniel Oehler
- Institute for Cardiomyopathies, Department of Internal Medicine III, University of Heidelberg, 69120 Heidelberg, Germany; German Centre for Cardiovascular Research (DZHK), Heidelberg/Mannheim, Germany
| | - Stefan Mester
- Institute for Cardiomyopathies, Department of Internal Medicine III, University of Heidelberg, 69120 Heidelberg, Germany; German Centre for Cardiovascular Research (DZHK), Heidelberg/Mannheim, Germany
| | - Karen S Frese
- Institute for Cardiomyopathies, Department of Internal Medicine III, University of Heidelberg, 69120 Heidelberg, Germany; German Centre for Cardiovascular Research (DZHK), Heidelberg/Mannheim, Germany
| | - Farbod Sedaghat-Hamedani
- Institute for Cardiomyopathies, Department of Internal Medicine III, University of Heidelberg, 69120 Heidelberg, Germany; German Centre for Cardiovascular Research (DZHK), Heidelberg/Mannheim, Germany
| | - Elham Kayvanpour
- Institute for Cardiomyopathies, Department of Internal Medicine III, University of Heidelberg, 69120 Heidelberg, Germany; German Centre for Cardiovascular Research (DZHK), Heidelberg/Mannheim, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Medical Faculty, Saarland University, 66123 Saarbrücken, Germany
| | - Benjamin Meder
- Institute for Cardiomyopathies, Department of Internal Medicine III, University of Heidelberg, 69120 Heidelberg, Germany; German Centre for Cardiovascular Research (DZHK), Heidelberg/Mannheim, Germany.
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