Applied Biosystems, LLC

Applera Corporation

The Perkin-elmer Corporation

The Perkin-emer Corporation

Pe Corporation

Muhammad A Sharaf

Timothy M Woudenberg

Khairuzzaman Bashar Mullah

Maria C Roque-Biewer

Kenneth J Livak

Jens J Hyldig-Nielsen

Michael Ybarra Lucero

Dar Bahatt

Charles R Connell

Timothy Z Liu

Serguei Ermakov

The present disclosure relates to methods of identifying target nucleic acids by using coded molecules and its analysis by translocation through a nanopore. Generally, coded molecules are subject to a target polynucleotide dependent modification. The modified coded molecule is detected by isolating the modified coded molecules from the unmodified coded molecules prior to analysis through the nanopore or by detecting a change in the signal pattern of the coded molecule when analyzed through the nanopore.

Methods of detecting target nucleic acids

The present invention generally relates to the detection of analytes, particularly biomolecules in samples. The invention also relates to compositions, methods, and kits for detecting the presence of analytes, typically in multiplex detection formats. The invention also relates to methods for determining the presence of at least one analyte in a sample, the methods employing employ single molecule detection techniques to individually detect at least one molecular complex or at least part of a molecular complex.

Multiplex detection compositions, methods, and kits

The invention relates to methods, compositions, and systems for calibrating a fluorescent polynucleotide separation apparatus. One aspect of the invention is multiple color calibration standards and their use. A multiple color calibration standard is a mixture of at least two polynucleotides of different length, wherein each of the polynucleotides is labeled with a spectrally distinct fluorescent dye. Another aspect of the invention is to produce total emission temporal profiles of multiple color calibration standards for use in calibrating fluorescent polynucleotide separation apparatus. The peaks corresponding to the fluorescently labeled polynucleotides in the total emission temporal profile may be detected using a peak detector that is driven by changes in the slopes of the total emission temporal profile. Calibration of fluorescent polynucleotide separation apparatus, with various embodiments of the methods of the invention, includes the step of identification of the labeled polynucleotides of the multiple color calibration standards. The process of spectral calibration of a fluorescent polynucleotide separation apparatus using a multiple color calibration standard may include the step of the estimating (extracting) of the dyes' reference spectra, using information from the peak detection process performed on the total emission temporal profile. Other aspects of the invention include systems for separating and detecting fluorescently labeled polynucleotides, wherein the system is designed for spectral calibration in accordance with the subject calibration methods employing multiple color calibration standards. Another aspect of the invention is methods and compositions for detecting the flow of electrical current through a separation channel of a fluorescent polynucleotide separation apparatus. These methods and compositions employ monitoring dyes. Monitoring dyes are fluorescent dyes that are spectrally distinct from the dye on the polynucleotide intended to convey genetic information, e.g., fluorescent polynucleotide sequencing reaction products.

Spectral calibration of fluorescent polynucleotide separation apparatus

The invention relates to improved methods of detecting and characterizing polynucleotide sequences and variations in polynucleotide sequences. The invention further relates to a device that can be used to detect and characterize polynucleotide sequences and variations in polynucleotide sequences.

Invasion assay

A signal processing method in a processor is provided for performing a multicomponent analysis of a signal resulting from a spectral response of a mixture comprising a plurality of spectrally resolvable molecular species. The method provides both a determination of a concentration estimate and a statistical confidence interval for each species. In the method, a data vector d is received from a multichannel detector, data vector d having a length n.sub.c, n.sub.c being the number of detector channels being monitored. A calibration matrix K having n.sub.c rows and n.sub.p columns is provided wherein n.sub.c is larger than n.sub.p, n.sub.p being the number of spectrally resolvable molecular species. Next, a concentration estimate vector c having length n.sub.p is determined. Finally, a confidence interval CI.sub.i for each of the elements of the concentration estimate vector is determined according to the expression

Multicomponent analysis method including the determination of a

Methods for assigning a quantitative score to the relatedness of aligned polymorphic biopolymer sequences such that small differences between otherwise identical sequences are highlighted are disclosed, including computer systems and program storage devices for carrying out the methods on a computer. Specifically, the methods of the invention comprise the steps of providing a test sequence and a basis set of sequences such that the test sequence and the basis set of sequences are aligned; determining the identity of a monomer unit at a position m in the test sequence; assigning a value of 1 to a local matching probability x.sub.m if the monomer unit at position m in the test sequence matches any members of the basis set at position m, or, assigning a value of between 0 and 1 to a local matching probability x.sub.m if the monomer unit at position m in the test sequence does not match any members of the basis set at position m. In a preferred embodiment, the above method is performed at a plurality of sequence locations and the local matching probabilities are multiplied together to provide a global matching probability.

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Oakland, CA, United States of America

Muhammad A Sharaf