Applications and Challenges of Real-time Mobile DNA Analysis

The DNA sequencing is the process of identifying the exact order of nucleotides within a given DNA molecule. The new portable and relatively inexpensive DNA sequencers, such as Oxford Nanopore MinION, have the potential to move DNA sequencing outside of laboratory, leading to faster and more accessible DNA-based diagnostics. However, portable DNA sequencing and analysis are challenging for mobile systems, owing to high data throughputs and computationally intensive processing performed in environments with unreliable connectivity and power. In this paper, we provide an analysis of the challenges that mobile systems and mobile computing must address to maximize the potential of portable DNA sequencing, and in situ DNA analysis. We explain the DNA sequencing process and highlight the main differences between traditional and portable DNA sequencing in the context of the actual and envisioned applications. We look at the identified challenges from the perspective of both algorithms and systems design, showing the need for careful co-design

Length-independent DNA packing into nanopore zero-mode waveguides for low-input DNA sequencing

Compared with conventional methods, single-molecule real-time (SMRT) DNA sequencing exhibits longer read lengths than conventional methods, less GC bias, and the ability to read DNA base modifications. However, reading DNA sequence from sub-nanogram quantities is impractical owing to inefficient delivery of DNA molecules into the confines of zero-mode waveguides-zeptolitre optical cavities in which DNA sequencing proceeds. Here, we show that the efficiency of voltage-induced DNA loading into waveguides equipped with nanopores at their floors is five orders of magnitude greater than existing methods. In addition, we find that DNA loading is nearly length-independent, unlike diffusive loading, which is biased towards shorter fragments. We demonstrate here loading and proof-of-principle four-colour sequence readout of a polymerase-bound 20,000-base-pair-long DNA template within seconds from a sub-nanogram input quantity, a step towards low-input DNA sequencing and mammalian epigenomic mapping of native DNA samples.R01 HG009186 - NHGRI NIH HHS; R21 HG006873 - NHGRI NIH HHSAccepted manuscrip

DNA Sequencing

The sequencing of the Human Reference Genome, with Human Genome Project announced ten years ago, provided a roadmap that is the foundation for modern biomedical research. Reference Genome represents digital database founded by scientists which contains representative examples of species genomes. The need for sequencing has never been greater than it is today. Sequencing has found its applications within diverse research sectors including comparative genomics and evolution, forensics, epidemiology, and applied medicine for diagnostics and therapeutics. Arguably, the strongest rationale for ongoing sequencing is the question for identification and interpretation of human sequence variation as it relates to health and disease. The paper gives review of current DNA sequencing algorithms and techniques as well as next-generation of DNA sequencing. Since the DNA sequencing field is changing rapidly the information in this paper represent a snapshot of this particular moment

Fast DNA Sequencing via Transverse Electronic Transport

A rapid and low-cost method to sequence DNA would usher in a revolution in medicine. We propose and theoretically show the feasibility of a protocol for sequencing based on the distributions of transverse electrical currents of single-stranded DNA while it translocates through a nanopore. Our estimates, based on the statistics of these distributions, reveal that sequencing of an entire human genome could be done with very high accuracy in a matter of hours without parallelization, e.g., orders of magnitude faster than present techniques. The practical implementation of our approach would represent a substantial advancement in our ability to study, predict and cure diseases from the perspective of the genetic makeup of each individual.Comment: 5 pages, 3 figure

DNA Sequencing

This book illustrates methods of DNA sequencing and its application in plant, animal and medical sciences. It has two distinct sections. The one includes 2 chapters devoted to the DNA sequencing methods and the second includes 6 chapters focusing on various applications of this technology. The content of the articles presented in the book is guided by the knowledge and experience of the contributing authors. This book is intended to serve as an important resource and review to the researchers in the field of DNA sequencing

Colloquium: Physical approaches to DNA sequencing and detection

With the continued improvement of sequencing technologies, the prospect of genome-based medicine is now at the forefront of scientific research. To realize this potential, however, a revolutionary sequencing method is needed for the cost-effective and rapid interrogation of individual genomes. This capability is likely to be provided by a physical approach to probing DNA at the single-nucleotide level. This is in sharp contrast to current techniques and instruments that probe (through chemical elongation, electrophoresis, and optical detection) length differences and terminating bases of strands of DNA. Several physical approaches to DNA detection have the potential to deliver fast and low-cost sequencing. Central to these approaches is the concept of nanochannels or nanopores, which allow for the spatial confinement of DNA molecules. In addition to their possible impact in medicine and biology, the methods offer ideal test beds to study open scientific issues and challenges in the relatively unexplored area at the interface between solids, liquids, and biomolecules at the nanometer length scale. This Colloquium emphasizes the physics behind these methods and ideas, critically describes their advantages and drawbacks, and discusses future research opportunities in the field

Functionalized nanopore-embedded electrodes for rapid DNA sequencing

The determination of a patient's DNA sequence can, in principle, reveal an increased risk to fall ill with particular diseases [1,2] and help to design "personalized medicine" [3]. Moreover, statistical studies and comparison of genomes [4] of a large number of individuals are crucial for the analysis of mutations [5] and hereditary diseases, paving the way to preventive medicine [6]. DNA sequencing is, however, currently still a vastly time-consuming and very expensive task [4], consisting of pre-processing steps, the actual sequencing using the Sanger method, and post-processing in the form of data analysis [7]. Here we propose a new approach that relies on functionalized nanopore-embedded electrodes to achieve an unambiguous distinction of the four nucleic acid bases in the DNA sequencing process. This represents a significant improvement over previously studied designs [8,9] which cannot reliably distinguish all four bases of DNA. The transport properties of the setup investigated by us, employing state-of-the-art density functional theory together with the non-equilibrium Green's Function method, leads to current responses that differ by at least one order of magnitude for different bases and can thus provide a much more robust read-out of the base sequence. The implementation of our proposed setup could thus lead to a viable protocol for rapid DNA sequencing with significant consequences for the future of genome related research in particular and health care in general.Comment: 12 pages, 5 figure