Normalization and baseline shift removal for NANO pore-sbs signals

Abstract

A method of using a sequencing cell (300) includes applying an alternating voltage (328) across the sequencing cell while sequencing a nucleic acid (332), acquiring a plurality of signal values (P(ti)) from the sequencing cell while a tag molecule (338) is threaded in a nano pore (316) of the sequencing cell, and acquiring a plurality of correlated signal values (X(ti)) that are correlated with respective values of the plurality of acquired signal values (P(ti)) thereby forming a plurality of two-dimensional data points (1201, 1203, 1205, 1207, 1209, 1303, 1305, 1307, 1309, 1311). The two-dimensional data points comprise a first dimension for the acquired signal values and a second dimension for the correlated signal values. The method further includes computing a plurality of transformedsignal values by applying a two-dimensional transformation to the two-dimensional data points.

Description

[0001] Cross References to Related Applications

[0002] This application claims the benefit of U.S. Provisional Patent Application No. 62 / 591,099, filed November 27, 2017, the contents of which are hereby incorporated by reference in their entirety. Background technique

[0003] Nanoporous membrane devices with a pore size of about one nanometer in inner diameter show promise for rapid nucleotide sequencing. When an electric potential is applied over a nanopore immersed in a conducting fluid, there may be a small ionic current due to conduction of ions over the nanopore. The magnitude of the current is sensitive to the pore size and which molecules are in the nanopore. The molecule may be a specific tag attached to a specific nucleotide, thereby allowing detection of the nucleotide at a specific position in the nucleic acid. The voltage in the circuit comprising the nanopore (eg, at the integrating capacitor) can be measured as a means of measuring molecular resistance, the...

Examples

Embodiment Construction

[0046] According to certain embodiments, the methods and systems disclosed herein relate to improvements in the processing of nanopore sequencing signals, such as voltage signals as measured by ADCs connected to nanopore cells. More specifically, the methods and systems disclosed herein correct for both gain drift and baseline shift in nanopore sequencing signals.

[0047] The baseline shift phenomenon in the nanopore sequencing signal can be related to the charge imbalance that occurs during the measurement process and builds up on certain inherently capacitive elements in the system (e.g., the working electrode of the cell) during charge and discharge cycles related. Gain shifts in the signal can be caused by relatively slow (hundreds or thousands of seconds) changes in membrane capacitance where the membrane (eg, bilayer) covers the pores. Such membrane capacitance may change in a deterministic manner, for example in response to physical changes in the bilayer.

[0001] Cross References to Related Applications

[0002] This application claims the benefit of U.S. Provisional Patent Application No. 62 / 591,099, filed November 27, 2017, the contents of which are hereby incorporated by reference in their entirety. Background technique

[0003] Nanoporous membrane devices with a pore size of about one nanometer in inner diameter show promise for rapid nucleotide sequencing. When an electric potential is applied over a nanopore immersed in a conducting fluid, there may be a small ionic current due to conduction of ions over the nanopore. The magnitude of the current is sensitive to the pore size and which molecules are in the nanopore. The molecule may be a specific tag attached to a specific nucleotide, thereby allowing detection of the nucleotide at a specific position in the nucleic acid. The voltage in the circuit comprising the nanopore (eg, at the integrating capacitor) can be measured as a means of measuring molecular resistance, the...

Examples

Embodiment Construction

[0046] According to certain embodiments, the methods and systems disclosed herein relate to improvements in the processing of nanopore sequencing signals, such as voltage signals as measured by ADCs connected to nanopore cells. More specifically, the methods and systems disclosed herein correct for both gain drift and baseline shift in nanopore sequencing signals.

[0047] The baseline shift phenomenon in the nanopore sequencing signal can be related to the charge imbalance that occurs during the measurement process and builds up on certain inherently capacitive elements in the system (e.g., the working electrode of the cell) during charge and discharge cycles related. Gain shifts in the signal can be caused by relatively slow (hundreds or thousands of seconds) changes in membrane capacitance where the membrane (eg, bilayer) covers the pores. Such membrane capacitance may change in a deterministic manner, for example in response to physical changes in the bilayer.

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