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      Massively parallel sequencing techniques for forensics: A review

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          Abstract

          DNA sequencing, starting with Sanger's chain termination method in 1977 and evolving into the next generation sequencing (NGS) techniques of today that employ massively parallel sequencing (MPS), has become essential in application areas such as biotechnology, virology, and medical diagnostics. Reflected by the growing number of articles published over the last 2–3 years, these techniques have also gained attention in the forensic field. This review contains a brief description of first, second, and third generation sequencing techniques, and focuses on the recent developments in human DNA analysis applicable in the forensic field. Relevance to the forensic analysis is that besides generation of standard STR‐profiles, DNA repeats can also be sequenced to look for polymorphisms. Furthermore, additional SNPs can be sequenced to acquire information on ancestry, paternity or phenotype. The current MPS systems are also very helpful in cases where only a limited amount of DNA or highly degraded DNA has been secured from a crime scene. If enough autosomal DNA is not present, mitochondrial DNA can be sequenced for maternal lineage analysis. These developments clearly demonstrate that the use of NGS will grow into an indispensable tool for forensic science.

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          Comparison of Next-Generation Sequencing Systems

          With fast development and wide applications of next-generation sequencing (NGS) technologies, genomic sequence information is within reach to aid the achievement of goals to decode life mysteries, make better crops, detect pathogens, and improve life qualities. NGS systems are typically represented by SOLiD/Ion Torrent PGM from Life Sciences, Genome Analyzer/HiSeq 2000/MiSeq from Illumina, and GS FLX Titanium/GS Junior from Roche. Beijing Genomics Institute (BGI), which possesses the world's biggest sequencing capacity, has multiple NGS systems including 137 HiSeq 2000, 27 SOLiD, one Ion Torrent PGM, one MiSeq, and one 454 sequencer. We have accumulated extensive experience in sample handling, sequencing, and bioinformatics analysis. In this paper, technologies of these systems are reviewed, and first-hand data from extensive experience is summarized and analyzed to discuss the advantages and specifics associated with each sequencing system. At last, applications of NGS are summarized.
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            Accurate multiplex polony sequencing of an evolved bacterial genome.

            We describe a DNA sequencing technology in which a commonly available, inexpensive epifluorescence microscope is converted to rapid nonelectrophoretic DNA sequencing automation. We apply this technology to resequence an evolved strain of Escherichia coli at less than one error per million consensus bases. A cell-free, mate-paired library provided single DNA molecules that were amplified in parallel to 1-micrometer beads by emulsion polymerase chain reaction. Millions of beads were immobilized in a polyacrylamide gel and subjected to automated cycles of sequencing by ligation and four-color imaging. Cost per base was roughly one-ninth as much as that of conventional sequencing. Our protocols were implemented with off-the-shelf instrumentation and reagents.
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              The development and impact of 454 sequencing.

              The 454 Sequencer has dramatically increased the volume of sequencing conducted by the scientific community and expanded the range of problems that can be addressed by the direct readouts of DNA sequence. Key breakthroughs in the development of the 454 sequencing platform included higher throughput, simplified all in vitro sample preparation and the miniaturization of sequencing chemistries, enabling massively parallel sequencing reactions to be carried out at a scale and cost not previously possible. Together with other recently released next-generation technologies, the 454 platform has started to democratize sequencing, providing individual laboratories with access to capacities that rival those previously found only at a handful of large sequencing centers. Over the past 18 months, 454 sequencing has led to a better understanding of the structure of the human genome, allowed the first non-Sanger sequence of an individual human and opened up new approaches to identify small RNAs. To make next-generation technologies more widely accessible, they must become easier to use and less costly. In the longer term, the principles established by 454 sequencing might reduce cost further, potentially enabling personalized genomics.
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                Author and article information

                Contributors
                b.b.bruijns@utwente.nl
                Journal
                Electrophoresis
                Electrophoresis
                10.1002/(ISSN)1522-2683
                ELPS
                Electrophoresis
                John Wiley and Sons Inc. (Hoboken )
                0173-0835
                1522-2683
                22 August 2018
                November 2018
                : 39
                : 21 , Novel Applications of Massively Parallel Sequencing (MPS) in Forensic Analysis ( doiID: 10.1002/elps.v39.21 )
                : 2642-2654
                Affiliations
                [ 1 ] Mesoscale Chemical Systems, MESA + Institute for Nanotechnology University of Twente Enschede The Netherlands
                [ 2 ] Life Science Engineering & Design Saxion University of Applied Sciences Enschede The Netherlands
                [ 3 ] NanoLab cleanroom, MESA + Institute for Nanotechnology University of Twente Enschede The Netherlands
                Author notes
                [*] [* ] Correspondence: Brigitte Bruijns, Mesoscale Chemical Systems, MESA + Institute for Nanotechnology, University of Twente, Enschede, The Netherlands

                E‐mail: b.b.bruijns@ 123456utwente.nl

                Author information
                http://orcid.org/0000-0001-8536-3609
                http://orcid.org/0000-0003-0581-2668
                Article
                ELPS6707
                10.1002/elps.201800082
                6282972
                30101986
                4cfff719-6dd2-4f42-847b-60dc37f22a6c
                © 2018 The Authors. Electrophoresis Published by Wiley-VCH Verlag GmbH & Co. KGaA

                This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc-nd/4.0/ License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made.

                History
                : 14 February 2018
                : 07 July 2018
                : 23 July 2018
                Page count
                Figures: 3, Tables: 4, Pages: 13, Words: 9057
                Categories
                Review
                Part I. Reviews and Applications of STR Technologies Using Massively Parallel Sequencing (MPS)
                Custom metadata
                2.0
                elps6707
                November 2018
                Converter:WILEY_ML3GV2_TO_NLMPMC version:version=5.5.3 mode:remove_FC converted:06.12.2018

                Analytical chemistry
                dna analysis,forensics,massively parallel sequencing,short tandem repeat,single nucleotide polymorphism

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