System, method, computer-accessible medium and apparatus for DNA mapping

Abstract

Exemplary embodiments of the present disclosure can include, for example, an atomic force microscopy (AFM) system, including a cantilever(s), an optical pickup unit(s) (OPU(s)) including a laser positioned over the cantilever(s), and a power source providing noise with a noise level that is below 300 Picometers. The noise level of the power source can be below 200 Picometers. A digitizing arrangement can be included which can be associated with the OPU. The digitizing arrangement(s) can have a bandwidth of about 2 MHZ. The OPU(s) can have a detection bandwidth of at least 80 MHZ. The exemplary apparatus can be combined with a chemical protocol and statistical signal processing and image analysis procedures to map DNA at high speed and accuracy.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS[0001]This application claims benefit of U.S. provisional patent applications 62 / 442,672, filed Jan. 5, 2017 and 62 / 443,325 filed Jan. 6, 2017, the complete contents of which is hereby incorporated by reference.FIELD OF THE DISCLOSURE[0002]The present disclosure relates generally to deoxyribonucleic acid (“DNA”) mapping, and more specifically, to exemplary embodiments of an exemplary system, method, computer-accessible medium and apparatus for DNA mapping.BACKGROUND INFORMATION[0003]Progress in whole genome sequencing using short read technologies (e.g., less than 150 base pairs (“bp”)) has reinvigorated interest in high resolution physical mapping to fill technical gaps not well addressed by sequencing. For example, combining short range sequencing with long range maps to produce haplotypically correct whole genome sequences, and to provide an easy method to detect structural variants larger than the size of the sequence reads. Such a procedur...

AI Technical Summary

Benefits of technology

The present patent describes an atomic force microscopy (AFM) system that includes a cantilever and a scanning probe arrangement. The system is designed to generate low noise levels and has a tilt angle of the cantilever with respect to the scanning probe arrangement of less than 10 degrees. The system also includes a power source that generates displacement noise of less than 300 Picometers. The system can include a transparent sample plate and a light emitting arrangement positioned below the sample plate. The system can be used to generate information about a DNA sample, such as the distance between markers on the sample. The system can also include a camera positioned above the scanning probe arrangement. The AFM system can be used to analyze DNA samples of various sizes, such as tens to millions of base pairs.

Problems solved by technology

Despite recent progress, these technologies remain expensive, incomplete, computationally intense, or all of the above.

Nano-channel augmented (see, e.g., Reference 8) and super-resolution optical mapping (see, e.g., References 9 and 10) are more precise (e.g., down to + / −100 bp), but the experimental protocols to achieve this are still lengthy and complex, and utilize sophisticated Bayesian procedures involving multiple hyper-parameters (see, e.g., Reference 11).

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