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2018 | OriginalPaper | Chapter

Identification of Factors that Affect Reproducibility of Mutation Calling Methods in Data Originating from the Next-Generation Sequencing

Authors : Roman Jaksik, Krzysztof Psiuk-Maksymowicz, Andrzej Swierniak

Published in: Computer and Information Sciences

Publisher: Springer International Publishing

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Abstract

Identification of somatic mutations, based on data from next-generation sequencing of the DNA, has become one of the fundamental research strategies in oncology, with the goal to seek mechanisms underlying the process of carcinogenesis and resistance to commonly used therapies. Despite significant advances in the development of sequencing methods and data processing algorithms, the reproducibility of experiments is relatively low and depending significantly on the methods used to identify changes in the structure of the DNA. This is mainly due to the influence of three factors: (1) high heterogeneity of tumors due to which some mutations are characteristic for a small number of cells, (2) bias associated with the process of exome isolation and (3) specificity of data pre-processing strategies.

The aim of the work was to determine the impact of these factors on the identification of somatic mutations, allowing to determine the reasons for low reproducibility in such studies.

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Luo, J., Wu, M., Gopukumar, D., Zhao, Y.: Big data application in biomedical research and health care: a literature review. Biomed. Inf. Insights 8, 1–10 (2016)

Bensz, W., et al.: Integrated System supporting research on environment related cancers. In: Król, D., Madeyski, L., Nguyen, N.T. (eds.) Recent Developments in Intelligent Information and Database Systems. SCI, vol. 642, pp. 399–409. Springer, Cham (2016). https://doi.org/10.1007/978-3-319-31277-4_35CrossRef

Psiuk-Maksymowicz, K., et al.: A holistic approach to testing biomedical hypotheses and analysis of biomedical data. In: Kozielski, S., Mrozek, D., Kasprowski, P., Małysiak-Mrozek, B., Kostrzewa, D. (eds.) BDAS 2015-2016. CCIS, vol. 613, pp. 449–462. Springer, Cham (2016). https://doi.org/10.1007/978-3-319-34099-9_34CrossRef

Afgan, E., Baker, D., van den Beek, M., Blankenberg, D., Bouvier, D., Cech, M., Chilton, J.: The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Res. 44(W1), W3–W10 (2016)CrossRef

Psiuk-Maksymowicz, K., Mrozek, D., Jaksik, R., Borys, D., Fujarewicz, K., Swierniak, A.: Scalability of a genomic data analysis in the biotest platform. In: Nguyen, N.T., Tojo, S., Nguyen, L.M., Trawiński, B. (eds.) ACIIDS 2017. LNCS (LNAI), vol. 10192, pp. 741–752. Springer, Cham (2017). https://doi.org/10.1007/978-3-319-54430-4_71CrossRef

Gruca, A., Jaksik, R., Psiuk-Maksymowicz, K.: Functional interpretation of gene sets: semantic-based clustering of gene ontology terms on the biotest platform. In: Gruca, A., Czachórski, T., Harezlak, K., Kozielski, S., Piotrowska, A. (eds.) ICMMI 2017. AISC, vol. 659, pp. 125–136. Springer, Cham (2018). https://doi.org/10.1007/978-3-319-67792-7_13CrossRef

Gerlinger, M., Rowan, A.J., Horswell, S., Larkin, J., Endesfelder, D., Gronroos, E., Martinez, P., Matthews, N.: Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N. Engl. J. Med. 366, 883–892 (2012)CrossRef

Shi, W., Ng, C.K.Y., Lim, R.S., Jiang, T., Kumar, S., Li, X., Wali, V.B., Piscuoglio, S., Gerstein, M.B., Chagpar, A.B., Weigelt, B., Pusztai, L., Reis-Filho, J.S., Hatzis, C.: Reliability of whole-exome sequencing for assessing intratumor genetic heterogeneity. bioRxiv (2018)

Derryberry, D.Z., Cowperthwaite, M.C., Wilke, C.O.: Reproducibility of SNV-calling in multiple sequencing runs from single tumors. PeerJ 4, e1508 (2016)CrossRef

10.

Qi, Y., Liu, X., Liu, C., Wang, B., Hess, K.R., Symmans, W.F., Shi, W., Pusztai, L.: Reproducibility of variant calls in replicate next generation sequencing experiments. PLoS One 7, e0119230 (2015)CrossRef

11.

Meynert, A.M., Ansari, M., FitzPatrick, D.R., Taylor, M.S.: Variant detection sensitivity and biases in whole genome and exome sequencing. BMC Bioinform. 15, 247 (2014)CrossRef

12.

Li, H.: Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv.org p. arXiv:1303.3997 (2013)

13.

Cibulskis, C., Lawrence, M.S., Carter, S.L., Sivachenko, A., Jaffe, D., Sougnez, C., Gabriel, S., Meyerson, M., Lander, E.S., Getz, G.: Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat. Biotechnol. 31, 213–219 (2013)CrossRef

14.

Metzker, M.L.: Sequencing technologies – the next generation. Nat. Rev. Genet. 11(1), 31–46 (2010)CrossRef

15.

McLaren, W., Gil, L., Hunt, S.E., Riat, H.S., Ritchie, G.R., Thormann, A., Flicek, P., Cunningham, F.: The ensembl variant effect predictor. Genome Biol 17(1), 122 (2016)CrossRef

16.

Jaksik, R., Marczyk, M., Polanska, J., Rzeszowska-Wolny, J.: Sources of high variance between probe signals in affymetrix short oligonucleotide microarrays. Sensors 14, 532–548 (2014)CrossRef

17.

Vissers, L., van Nimwegen, K., Schieving, J., Kamsteeg, E., Kleefstra, T., Yntema, H., Pfundt, R., van der Wilt, G.J., Krabbenborg, L., Brunner, H., van der Burg, S., Grutters, J., Veltman, J., Willemsen, M.: A clinical utility study of exome sequencing versus conventional genetic testing in pediatric neurology. Genet. Med. 19, 1055–1063 (2017)CrossRef

18.

Bamshad, M.J., Ng, S.B., Bigham, A.W., Tabor, H.K., Emond, M.J., Nickerson, D.A., Shendure, J.: Exome sequencing as a tool for Mendelian disease gene discovery. Nat. Rev. Genet. 12, 745–755 (2011)CrossRef

Title: Identification of Factors that Affect Reproducibility of Mutation Calling Methods in Data Originating from the Next-Generation Sequencing
Authors: Roman Jaksik
Krzysztof Psiuk-Maksymowicz
Andrzej Swierniak
Publisher: Springer International Publishing
Book: Computer and Information Sciences
Print ISBN: 978-3-030-00839-0

Electronic ISBN: 978-3-030-00840-6

Copyright Year: 2018
DOI: https://doi.org/10.1007/978-3-030-00840-6_29

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