An integrated on-chip system and methods for real-time molecular sequencing. The system has a semiconductor chip and a laser. The semiconductor chip has integrated therein a main waveguide, a plurality of branch waveguides optically connected to the main waveguide, a plurality of nanochannels each having a fluid inlet and a fluid outlet, a plurality of molecule traps, a molecule trap at an intersection of a branch waveguide and a nanochannel, and a plurality of photodetectors operably connected to the plurality of molecule traps, one photodetector for a molecule trap, the photodetector to detect a spectral signature from a molecule in the molecule trap. The laser is optically connected to the main waveguide.

An integrated on-chip system and methods for real-time molecular sequencing. The system has a semiconductor chip and a laser. The semiconductor chip has integrated therein a main waveguide, a plurality of branch waveguides optically connected to the main waveguide, a plurality of nanochannels each having a fluid inlet and a fluid outlet, a plurality of molecule traps, a molecule trap at an intersection of a branch waveguide and a nanochannel, and a plurality of photodetectors operably connected to the plurality of molecule traps, one photodetector for a molecule trap, the photodetector to detect a spectral signature from a molecule in the molecule trap. The laser is optically connected to the main waveguide.

Provided herein are optimized methods for performing multiplexed detection of a plurality of sequence variations. Also provided are methods for performing multiplexed amplification of target nucleic acid.

Provided herein are optimized methods for performing multiplexed detection of a plurality of sequence variations. Also provided are methods for performing multiplexed amplification of target nucleic acid.

The invention provides methods of identifying a subject having cancer, such as lung cancer, by analyzing expression levels of one or more NRF2 splice variants or NRF2 target genes. The invention also provides methods of treating cancer in a subject with a NRF2 pathway antagonist, wherein the subject expresses one or more NRF2 splice variants or overexpresses one or more NRF2 target genes.

The invention provides methods of identifying a subject having cancer, such as lung cancer, by analyzing expression levels of one or more NRF2 splice variants or NRF2 target genes. The invention also provides methods of treating cancer in a subject with a NRF2 pathway antagonist, wherein the subject expresses one or more NRF2 splice variants or overexpresses one or more NRF2 target genes.

A method for identifying any of the presence, location and phasing of modified cytosines (C) in long stretches of nucleic acids is provided. In some embodiments, the method may comprise (a) reacting a first portion of a nucleic acid sample containing at least one C and/or at least one modified C with a DNA glucosyltransferase and a cytidine deaminase to produce a first product and/or reacting a second portion of the sample with a dioxygenase, optionally a DNA glucosyltransferase and a cytidine deaminase to produce a second product and; (b) comparing the sequences from the first and optionally the second product obtained in (a), or amplification products thereof, with each other and/or an untreated reference sequence to determine which Cs in the initial nucleic acid fragment are modified. A modified TET methylcytosine dioxygenase with improved efficiency compared to unmodified TET2 at converting methylcytosine to carboxymethylcytosine is also provided.

A method for identifying any of the presence, location and phasing of modified cytosines (C) in long stretches of nucleic acids is provided. In some embodiments, the method may comprise (a) reacting a first portion of a nucleic acid sample containing at least one C and/or at least one modified C with a DNA glucosyltransferase and a cytidine deaminase to produce a first product and/or reacting a second portion of the sample with a dioxygenase, optionally a DNA glucosyltransferase and a cytidine deaminase to produce a second product and; (b) comparing the sequences from the first and optionally the second product obtained in (a), or amplification products thereof, with each other and/or an untreated reference sequence to determine which Cs in the initial nucleic acid fragment are modified. A modified TET methylcytosine dioxygenase with improved efficiency compared to unmodified TET2 at converting methylcytosine to carboxymethylcytosine is also provided.

Methods are provided for detecting the amount of one or more CAH panel analytes (i.e., pregnenolone, 17-OH pregnenolone, progesterone, 17-OH progesterone, dehydroepiandrosterone (DHEA), androstenedione, testosterone, deoxycorticosterone, 11-deoxycortisol, and cortisol) in a sample by mass spectrometry. The methods generally involve ionizing one or more CAH panel analytes in a sample and quantifying the generated ions to determine the amount of one or more CAH panel analytes in the sample. In methods where amounts of multiple CAH panel analytes are detected, the amounts of multiple analytes are detected in the same sample injection.

The present invention relates to a method and a composition for detecting a target nucleic acid sequence using a cleaved complementary tag fragment. Specifically, the present invention relates to a method for linking a complementary tag sequence to a PCR primer so that a tagging can be produced by a restriction enzyme during a PCR reaction, diversifying the complementary tag sequence to be linked to each primer by utilizing factors such as length and nucleic acid combination, etc., and distinguishing the target sequence using the same. According to the present invention, a cleaved complementary tag fragment (CCTF) under stringent conditions is a complementary sequence to any sequence at the 5′ end linked to the primer and cannot be formed unless a PCR reaction and a restriction enzyme reaction occur, and the cleaved single strand is formed only when hybridization to the target sequence occurs and a primer extension product complementary to the target sequence is formed, so as to have a higher degree of accuracy secured by reading the cleaved single strand. In addition, the CCTF can be used to identify a plurality of target nucleic acid sequences by selecting various analytical techniques and analysis equipment according to a user's intention. For example, a result can be confirmed rapidly and accurately in genetic testing, identification of organisms in a sample, diagnosis of microbial or viral infection, etc.