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A Survey of Methods and Tools for Large-Scale DNA Mixture Profiling

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Smart Infrastructure and Applications

Part of the book series: EAI/Springer Innovations in Communication and Computing ((EAISICC))

Abstract

DNA typing or profiling is being widely used for criminal identification, paternity tests, and diagnosis of genetic diseases. DNA typing is considered one of the hardest problems in the forensic science domain, and it is an active area of research. The computational complexity of DNA typing increases significantly with the number of unknowns in the mixture and has been the major deterring factor holding its advancements and applications. In this chapter, we provide an extended review of DNA profiling methods and tools with a particular focus on their computational performance and accuracy. The process of DNA profiling within the broader context of forensic science and genetics is explained. The various classes of DNA profiling methods including general methods, and those based on maximum likelihood estimators, are reviewed. The reviewed DNA profiling tools include LRmix Studio, TrueAllele, DNAMIX V.3, Euroformix, CeesIt, NOCIt, DNAMixture, Kongoh, LikeLTD, LabRetriever, and STRmix. A review of high-performance computing literature in bioinformatics and HPC frameworks is also given. Faster interpretations of DNA mixtures with a large number of unknowns and higher accuracies are expected to open up new frontiers for this area.

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Acknowledgments

The work carried out in this chapter is supported by the HPC Center at the King Abdulaziz University.

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Authors and Affiliations

  1. Department of Computer Science, Faculty of Computing and Information Technology (FCIT), King Abdulaziz University, Jeddah, Saudi Arabia

    Emad Alamoudi & Aiiad Albeshri

  2. High Performance Computing Center, King Abdulaziz University, Jeddah, Saudi Arabia

    Rashid Mehmood

  3. Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia

    Takashi Gojobori

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  1. Emad Alamoudi
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  2. Rashid Mehmood
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  3. Aiiad Albeshri
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  4. Takashi Gojobori
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Correspondence to Emad Alamoudi .

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Editors and Affiliations

  1. High Performance Computing Center, King Abdulaziz University, Jeddah, Saudi Arabia

    Rashid Mehmood

  2. Nvidia AI Technology Center, Singapore, Singapore

    Simon See

  3. Faculty of Computing and Information Technology (FCIT), King Abdulaziz University, Jeddah, Saudi Arabia

    Iyad Katib

  4. European Alliance for Innovation, Gent, Belgium

    Imrich Chlamtac

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Alamoudi, E., Mehmood, R., Albeshri, A., Gojobori, T. (2020). A Survey of Methods and Tools for Large-Scale DNA Mixture Profiling. In: Mehmood, R., See, S., Katib, I., Chlamtac, I. (eds) Smart Infrastructure and Applications. EAI/Springer Innovations in Communication and Computing. Springer, Cham. https://doi.org/10.1007/978-3-030-13705-2_9

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  • DOI: https://doi.org/10.1007/978-3-030-13705-2_9

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