Strategies for identification of somatic variants using the Ion Torrent deep targeted sequencing platform.

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Abstract

'Next-generation' (NGS) sequencing has wide application in medical genetics, including the detection of somatic variation in cancer. The Ion Torrent-based (IONT) platform is among NGS technologies employed in clinical, research and diagnostic settings. However, identifying mutations from IONT deep sequencing with high confidence has remained a challenge. We compared various computational variant-calling methods to derive a variant identification pipeline that may improve the molecular diagnostic and research utility of IONT.

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An integrated semiconductor device enabling non-optical genome sequencing.

Jonathan Rothberg, Wolfgang Hinz, Todd M. Rearick … (2011)

The seminal importance of DNA sequencing to the life sciences, biotechnology and medicine has driven the search for more scalable and lower-cost solutions. Here we describe a DNA sequencing technology in which scalable, low-cost semiconductor manufacturing techniques are used to make an integrated circuit able to directly perform non-optical DNA sequencing of genomes. Sequence data are obtained by directly sensing the ions produced by template-directed DNA polymerase synthesis using all-natural nucleotides on this massively parallel semiconductor-sensing device or ion chip. The ion chip contains ion-sensitive, field-effect transistor-based sensors in perfect register with 1.2 million wells, which provide confinement and allow parallel, simultaneous detection of independent sequencing reactions. Use of the most widely used technology for constructing integrated circuits, the complementary metal-oxide semiconductor (CMOS) process, allows for low-cost, large-scale production and scaling of the device to higher densities and larger array sizes. We show the performance of the system by sequencing three bacterial genomes, its robustness and scalability by producing ion chips with up to 10 times as many sensors and sequencing a human genome.

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High-throughput sequencing technologies.

Jason A. Reuter, Damek Spacek, Michael Snyder (2015)

The human genome sequence has profoundly altered our understanding of biology, human diversity, and disease. The path from the first draft sequence to our nascent era of personal genomes and genomic medicine has been made possible only because of the extraordinary advancements in DNA sequencing technologies over the past 10 years. Here, we discuss commonly used high-throughput sequencing platforms, the growing array of sequencing assays developed around them, as well as the challenges facing current sequencing platforms and their clinical application. Copyright © 2015 Elsevier Inc. All rights reserved.

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Is Open Access

Comparison of Next-Generation Sequencing Systems

Lin Liu, Yinhu Li, Siliang Li … (2012)

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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PubMed ID:: 29301485

PMC ID:: 5753459

DOI:: 10.1186/s12859-017-1991-3

Keywords: MuTect,Variant calling strategies,Ion Reporter,Varscan2,Ion torrent,Next-generation sequencing

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Keywords: MuTect, Variant calling strategies, Ion Reporter, Varscan2, Ion torrent, Next-generation sequencing

Strategies for identification of somatic variants using the Ion Torrent deep targeted sequencing platform.

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Most cited references 15

An integrated semiconductor device enabling non-optical genome sequencing.

High-throughput sequencing technologies.

Comparison of Next-Generation Sequencing Systems

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